Artificial proteins and compositions and methods thereof

This application is a U.S. National Stage Patent Application of International Application No. PCT/US2016/060677, filed Nov. 4, 2016, which claims the benefit of priority to U.S. Provisional Application No. 62/250,812, filed Nov. 4, 2015, and U.S. Provisional Application No. 62/251,171, filed Nov. 5, 2015, all of which are incorporated herein by reference in their entireties.

The invention relates generally to artificial, de novo protein-based sensors that may be expressed in eurkaryotic cells and may be configured to bind one or more cofactors to thereby exhibit variable and tunable characteristics.

De novo proteins of human-made and computational designs are powerful tools for exploring principles and limits of protein folding, protein-protein interaction, and biochemical function without the distributed structure-function constraints imposed by natural scaffolds as starting points for protein engineering. However, despite their biomedical promise, completely non-natural proteins have not been functionally expressed in eukaryotic systems.

The invention described herein meets the needs in the field by providing artificial, de novo proteins as sensing agents that may be expressed in eukaryotic cells.

In an embodiment, the invention includes an artificial protein configured to bind one or more cofactors, wherein the artificial protein may be expressed in eurkaryotic cells. In some embodiments, the artificial protein may be expressed in mammalian cells. In some embodiments, the artificial protein of the invention may be amphiphilic. In some embodiments, the artificial protein of the invention may have a cytosolic portion, a transmembrane portion, and an extracellular portion. In some embodiments, the artificial proteins of the invention may be artificial transmembrane proteins.

In some embodiments, the invention includes an artificial protein may include an amino acid sequence selected to provide at least four helices (e.g., α-helices), wherein the artificial protein may be expressible in eukaryotic cells. In some embodiments, the artificial protein may be expressible in mammalian cells. In some embodiments, such amino acid sequences of the invention may be selected to provide an amphiphilic artificial protein.

In some embodiments, the artificial protein of the invention may have a net surface charge (i.e., Z net ) of about −12 to about +8. In some embodiments, the artificial protein of the invention may have a net surface charge that is negative.

In certain embodiments, the amino acid sequence of the artificial protein may include one or more of:

−XX+XX−−XX0+X−−XX00X−−XX0L  (Generic Sequence A);

−X+0+X−−XX++X−−XX++X−−X+0+  (Generic Sequence B);

+XX+XX−−XX0+X−−XX00X−−X+0L  (Generic Sequence C); and

−XX+0+−−XX++X−−XX++X−−XX0+  (Generic Sequence D),

wherein (+) represents a positively charged amino acid, (−) represents a negatively charged amino acid, (O) represents an amino acid having an amide side-chain, and (X) represents any amino acid.

In certain embodiments, the amino acid sequence of the artificial protein may include one or more of: SEQ ID No: 1, SEQ ID No: 2, SEQ ID No: 3, SEQ ID No: 4, SEQ ID No: 5, SEQ ID No: 6, SEQ ID No: 7, SEQ ID No: 8, SEQ ID No: 9, SEQ ID No: 10, SEQ ID No: 11, SEQ ID No: 12, SEQ ID No: 13, SEQ ID No: 14, SEQ ID No: 15, and SEQ ID No: 16, or a variant thereof.

In certain embodiments, the amino acid sequence of the artificial protein may include one or more LOOPs selected from the group consisting of GGSGKGSGG (SEQ ID No. 17), GGCG (SEQ ID No: 18), GACG (SEQ ID No: 19), and GGSG (SEQ ID No. 20), or a variant thereof.

In certain embodiments, the amino acid sequence of the artificial protein may include SEQ ID NO: 25, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 51, SEQ ID NO: 54, SEQ ID NO: 63, SEQ ID NO: 64, or SEQ ID NO: 69, or a variant thereof.

In certain embodiments, the amino acid sequence of the artificial protein may include SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 141, SEQ ID NO: 142, or SEQ ID NO: 147, or a variant thereof.

In some embodiments, the invention includes a composition comprising a peptide comprising one or more amino acid sequences of a formula selected from the group consisting of:

−XX+XX−−XX0+X−−XX00X−−XX0L  (Generic Sequence A);

−X+0+X−−XX++X−−XX++X−−X+0+  (Generic Sequence B);

+XX+XX−−XX0+X−−XX00X−−X+0L   (Generic Sequence C); and

−XX+0+−−XX++X−−XX++X−−XX0+  (Generic Sequence D), or a variant thereof,

wherein (+) represents a positively charged amino acid, (−) represents a negatively charged amino acid, (O) represents an amino acid having an amide side-chain, and (X) represents any amino acid.

In some embodiments, the invention includes a composition comprising a peptide comprising one or more amino acid sequences selected from the group consisting of SEQ ID No: 1, SEQ ID No: 2, SEQ ID No: 3, SEQ ID No: 4, SEQ ID No: 5, SEQ ID No: 6, SEQ ID No: 7, SEQ ID No: 8, SEQ ID No: 9, SEQ ID No: 10, SEQ ID No: 11, SEQ ID No: 12, SEQ ID No: 13, SEQ ID No: 14, SEQ ID No: 15, and SEQ ID No: 16, or a variant thereof.

In some embodiments, the invention includes a composition comprising a peptide comprising an amino acid sequence selected from the group consisting of SEQ ID Nos. 25, 30, 31, 51, 54, 63, 66, and 69, or a variant thereof.

In some embodiments, the invention includes a composition comprising a peptide comprising an amino acid sequence selected from Table 2, or a variant thereof.

In some embodiments, the invention includes a composition comprising a peptide comprising an amino acid sequence selected from Table 3, or a variant thereof.

In some embodiments, the invention includes a composition comprising a peptide comprising an amino acid sequence selected from Table 4, or a variant thereof.

The following detailed description of embodiments will be better understood when read in conjunction with the appended drawings. However, the invention is not limited to the precise arrangements and instrumentalities of the embodiments depicted in the drawings.

In the drawings:

FIG. 1 is a chart showing timescales of optical voltage indicators. Stark cofactor absorbance and fluorescence effects take place at ultrafast timescales with respect to action potentials, while electron transfer mediated transmembrane field enhancement takes place on ns-to-μs timescales. Sensors based on such biophysics are intrinsically faster than state-of-the-art GEVIs that require structural rearrangements that reduce fluorescence.

FIG. 2 is an illustration of an artificial protein according to an embodiment of the invention that allows modular assembly of functional cofactors for field sensing. Example designs for rapid Stark cofactor field sensing in the depolarized state (hence shown as positive charge on cytoplasmic side) (Panel A) and enhanced field sensing through field stimulated electron transfer (Panel B), field stimulated redox quenching (Panel C). (Top) Scheme, (Bottom) Structural model. Systems are directional so that signal increases upon depolarization to avoid false positives from bleaching.

FIG. 3 is an illustration of various views of an artificial protein according to an embodiment of the invention. (Panel A) Transmembrane 4-helix bundle maquette with polar (cyan) and nonpolar regions (gray) using Cys (yellow) to anchor a field sensing biliverdin fluorophore (red). The stability and sequence tolerance of maquette first principles design permits systematic adjustment of the Cys bilin anchoring position to optimize field sensitivity. (Panel B) Sequences are based on heptad repeats (of SEQ ID No. 148) that place polar groups on one face of the helix (binary patterning) so that hydrophobic forces drive 4-helix bundle assembly. Heptads are modified to be predominantly nonpolar in membrane spanning regions. Cofactors such as biliverdin, flavin, heme, and retinal are anchored with Cys, His, Thr and Lys residues at design specified sites for electron transfer and fluorescence function.

FIG. 4 is an illustration of x-ray crystal structures of an artificial protein according to an embodiment of the invention, confirming the assembly expected from simple first principles.

FIG. 5 shows the results of multi-chromophore binding in a single membrane artificial protein according to an embodiment of the invention. (Panel A) Local electric fields from the artificial protein environment typically change pigment color upon binding, a type of Stark effect. Here Ni bacteriochlorophyll changes from pink to blue upon binding to a transmembrane maquette. (Panel B) Maquettes bind multiple different cofactors types site-specifically within a single frame (three pigment complex: bilin and chlorin and a bacteriopheophytins).

FIG. 6 shows the results of the Stark effect in flavin-binding maquettes. Electric field sensitive transition dipoles to S1 and S2 excited states (left, red and blue) are oriented nearly along the long axis of the flavin cofactor—thus the long flavin axis should be oriented parallel to field changes for maximum sensitivity. The Stark electric field induced absorption changes of flavomaquettes (right) follows the second derivative of the oxidized absorption spectrum (left) as expected.

FIG. 7 shows the stark effect of bilins in natural proteins (left), which correlates with emission that are comparable to the Stark effects that have been previously measured in tetrapyrrole cofactors, the bacteriochlorophylls and bacteriopheophytins in transmembrane photosynthetic reaction centers (right). Depending on the orientation of the transition dipoles of the pigments with respect to the applied field (right, red), Stark Effects can be enhanced or depressed (right, relative amplitude of red vs blue peaks and troughs).

FIG. 8 shows the results of a model of high-fidelity optical recording of action potentials. Left: The action potential transmembrane field (red) moves the electron from the distal heme (green) to the proximal heme (blue) in microseconds. Proximal heme reduction is 2.2% at resting potential and 65% at peak depolarization. The charge on the reduced proximal heme creates a strong Stark field over the fluorescent bilin (red sticks). Right: A typical Stark field change of 5 MV/cm acting on the ˜5 Debye bilin difference dipole leads to a 20 nm red shift, comparable to the absorbance difference of iRFP702 (red) and iRFP720 (blue) (75). The field coupled redox change generates increased excitation absorbance at 660 nm and increased emission at 680 nm, and leads to a large ΔF/F of 350% per 100 mV.

FIG. 9 shows control of heme redox potential in electron transfer chain. Equilibrium redox titrations sequentially oxidize and reduced 3 hemes with 3 different midpoint potentials in a membrane embedded maquette.

FIG. 10 shows the Stark effect measurements of purified GEVIs. Maquettes oriented at an air/water interface L-B deposited as a multilayer film on transparent ITO electrode. Linear dichroism of pigments (left) reveals pigment/protein orientation (upper right) in the final thin layer capacitor (lower right) for applied fields and Stark measurements.

FIG. 11 shows trafficking of artificial protein variants according to embodiments of the invention. All show even cytosolic expression and HEK 293t cells (Panel A) and rat hippocampal neurons (Panel B). The artificial proteins of the invention described in FIG. 11 include 1083 (SEQ ID NO: 21), 1137 (SEQ ID NO: 22), 1138 (SEQ ID NO: 23), 1139 (SEQ ID NO: 24), 1196 (SEQ ID NO: 25), 1198 (SEQ ID NO: 27), and 1200 (SEQ ID NO:29).

FIG. 12 shows trafficking of various scaffolds according to embodiments of the invention at 20×. GL (neutral surface), POS (positive surface, +12), and BT6 (negative surface, −14). GL both trafficks well and shows even cytosolic expression. Both BT6 and POS express less effectively and show some blebbing in ER/Golgi indicating cellular stress.

FIG. 13 shows heptad patterning of a 4-helix bundle (Panel a) and common sequence (Panel b) and generalized sequence (Panel c).

FIG. 14 shows sequence listings of five sequences comprising four helices each, according to various embodiments of the invention, of increasingly greater generalization. Each helix is labeled with its appropriate SEQ ID No. (SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No. 14, SEQ ID No. 15, and SEQ ID No. 16 are shown).

FIG. 15 shows possible Stark sensors from minimal requirements (left), to BV-based model and electron-amplified BV-based model (middle), and an artificial-protein based BV-sensor according to an embodiment of the invention (right).

FIG. 16 shows HEK293t cells expressing a transmembrane artificial protein in accordance with an embodiment of the invention (1083 (SEQ ID NO: 21)) as a GFP fusion at 63x.

FIG. 17 shows (Panel A) Fluorescence excitation (solid) and emission (dashed) spectra normalized to absorbance at excitation wavelength 600 nm of maquette series with (Panel B) varying cysteine positions (yellow bubbles) and (Panel B) stabilizing amino acid combinations that result in (Panel C) differing quantum yields and amount of biliverdin bound in vitro.

FIG. 18 shows (Panel A) Fluorescence excitation (solid) and emission (dashed) spectra normalized to absorbance at excitation wavelength 600 nm of maquette series with (Panel B) varying cytsteine positions (yellow bubbles) and (Panel B) stabilizing histidine positions (green pentagons) that result in (Panel C) differing quantum yields and amount of biliverdin bound in vitro.

FIG. 19 illustrates the directed evolution of de novo fluorescent proteins and physiological reporters. Similar strategies apply for cytosolic dFPs or membrane proteins. Beginning with a well-placed cysteine for ligation, candidate mutation sites are identified by modeling to stabilize the propionates of BV with arginines, and to lock the bilin in its fluorescent conformer. The library is created in a single step using wildcards during chemical synthesis. Ring scanning with His/Phe stabilizes the pyrroles and adds hydrophobic core bulk to augment fluorescence. Brighter variants are candidates for experiments and subsequent rounds of computational design-guided directed evolution to stabilize the A-ring and add core bulk. Fluorescence Micrograph and Spectrum: Amphiphilic membrane protein expressed in live-cell yeast (λem>660 nm, λexc=630±10 nm).

FIG. 20 illustrates single-domain IR fluorescent calcium indicators. Two modular binding sites are defined by different heptad repeats: a calcium binding sensor and a biliverdin-binding fluorescent transducer. Calcium binding rigidifies an intentionally dynamic and less fluorescent dFP (left: blurry to indicate motion), which increases fluorescence quantum yield by rigidification of the scaffold and binding pocket.

FIG. 21 illustrates de novo design of genetically encoded voltage indicator (GEVI) based on the ultrafast optical Stark Effect. (Panel A) First-generation MASTER design, which positions a field-sensing biliverdin co-factor across the plasma membrane parallel to the electric field, is composed of hydrophilic (gray) and lipophilic regions (purple). (Panels B-C) HEK293 cell line stably expressing GFPtagged MASTER created by lentiviral mediated transduction (scale=20 um, B: GFP, C: far-red, λem>660 nm). Fluorescence decreases by ˜10-15% ΔF/F per 100 mV. (Panel D) Emission spectrum shifts upon high-K+ depolarization of transducing HEK293 as measured by spectral imaging. (Panel E) Spectral imaging apparatus on a Leica SP8 confocal STED microscope, in which excitation and emitted light is passed through dispersive optics for wavelength selection.

FIG. 22 illustrates de novo contrast agents for molecular fMRT. (Panel a) A hemoglobin-like pentacoordinated heme is paramagnetic and alters the T1 and T2 relaxation of local water molecules. (Panel b) Absorbance spectrum of purified 3M shows an intense Soret band and missing Q-band (arrow), indicative of paramagnetic iron porphyrins. (Panel c) T2-weighted contrast is evident by darkening in a protein concentration dependent manner (taken on a 9.4 T gradient coil H1-NMR). (Panel d) Molecular fMRI strategy by ligand-induced paramagnetic switching Ligand binding, here shown as calcium, rotates a Phe residue into the axial site of a fully coordinated diamagnetic heme, displacing water in the process. The now high-spin iron accelerates water T2 relaxation for MR contrast.

FIG. 23 illustrates the engineering of de novo protein maquettes to functionally express in mammalian cells. (Panel a) Maquettes are self-assembling single-chain tetrahelical bundles created by binary patterning of hydrophobic and hydrophobic residues of high propensity for a-helix formation as described by the helical wheel. (Panel b) Strategy for creating a far-red de novo fluorescent protein by covalent attachment and stabilization of biliverdin in a fluorescent conformer within the core of mammalian cell-expressible maquettes (see Panels b-d). (Panel c) Fluorescence micrographs of HEK293 cells transducing maquettes of various net surface charges (Znet from −15 to +11), imaged by C-terminal GFP fusion tags (FOV=832 μm). (Panel d) Pymol-generated exterior electrostatic maps (APBS, Adaptive Poisson-Boltzmann Solver) of the tested tetrahelical bundles (red=negative side chains, blue=positive side chains). Surface potentials are pronounced for visualization clarity. (Panel e) Relative GFP fluorescence by image analysis (box=median+/−quartile; whisker=range; N=4 coverslips, 3 FOV each).

FIG. 24 illustrates the iterative engineering of a human-designed de novo fluorescent protein. (Panel a) Homology-based contact schematic for biliverdin (BV) stabilization within the core (black=side-chains, green=BV). (Panel b) Excitation (dashed line, λ em >715 nm) and emission spectra (solid line, λ ex =600 nm) of the iterative construction of dFP1.0. (Panel c) Photophysical summary of the dFP build series and IFP1.4 reference. Holoprotein was formed by either in vitro bilin attachment or in cellulo in HO-1 bacterial co-transformants plus levulinic acid. Brightness is a calculated parameter of quantum yield×BV attachment efficiency (ε=extinction coefficient, QY=relative quantum yield vs. Cy5). (Panel d) Excitation and emission spectra of the nature-derived IFP1.4 and first principles-derived dFP1.0 redshift from far-red to the near infrared by in cellulo holoprotein formation (red arrow for emission shift).

FIG. 25 illustrates the functional expression and cell-specific spectral properties of de novo fluorescent proteins in mammalian cells. Unless noted specifically, holoprotein was formed without the addition of any exogenous cofactor or biosynthetic enzymes and data is from transfected HEK cells. Fluorescence micrographs include (Panel a) lentiviral-transduced rat hippocampal neurons and (Panel b) HEK293 cells expressing dFP1.0; (Panel c) HEK293 expressing the integral membrane protein, human melanopsin with a N-terminal dFP1.0, and (Panel d) dFP1.0 with a C-terminal SV-40 nuclear localization tag (left: fluorescence, right: bright-field; arrow=nucleus). (a-d: λ ex =631/28 nm, λ em >665 nm, Scale=15 μm) (e) Total cellular brightness (bottom) and normalized by expression level (bottom) of dFP1.0 and IFP1.4 control (mean+/−stdev, trans=transfected, stable=clonal stably expressing cell line). (Panel f) Summary of mammalian-specific spectral peaks from HEK cell lysate from panels g-h. (Panel g) Mammalian-specific spectra of dFP1.0 from HEK cell lysate (dashed line=excitation (λ em >715 nm), solid line=emission spectra (λ ex =600 nm)) and live-cell spectral imaging (dots: emission stack λ ex =635 nm). (Panel h) Mammalian specific spectra of IFP1.4 as described for in panel g.

FIG. 26 illustrates a net surface charge scanning library. (Panel a) Helical wheel summarizing the relative positions of hydrophobic and hydrophilic residue placement. (Panel b) Schematic of four helical wheels to denote helix locations in the bundle. (Panel c) Protein sequences (SEQ ID No. 149, SEQ ID No. 150, SEQ ID No. 122, SEQ ID No. 151, SEQ. ID No. 152, SEQ ID No. 153, and SEQ ID No. 154) for the net surface charge scanning library (Red=negative side chains, Blue=positive side chains).

FIG. 27 illustrates a cysteine scanning for biliverdin (BV) attachment efficiency in vitro. (Panel a) Relative levels of BV attachment, fluorescence, and brightness of cysteine scanning library (mean±s.e.). BV attachment was quantified from the absorbance spectrum Soret band after FPLC purification. Fluorescence was measured at fixed holoprotein concentrations, estimated by bound BV levels (λ ex =600 nm), and brightness was a calculated parameter of absorbance multiplied by fluorescence. (Panel b) Pymol model of scaffold, with candidate cysteine mutation sites denoted. (Panel c) Summary of values including absorbance spectrum Soret- and Q-band peak wavelengths.

FIG. 28 illustrates protein sequences for iterative build of dFP1.0. Mutated residues from the initial scaffold that likely contribute to bilverdin stabilization are highlighted in yellow. The final iterative construct is untagged dFP1.0. The E66R mutation was introduced with S64C based on a consensus “CXR” motif found in bilin attachment sites of natural proteins, but does not contribute to stabilization. SEQ ID No, 155, SEQ ID No. 114, SEQ ID No. 156, and SEQ ID No. 25 are shown.

FIG. 29 illustrates spectral evidence for bilin rigidification. Absorbance spectra of fluorescent bili-maquettes before and after D-ring stabilization. Addition of core histidines in dFP1.0 resulted in an increase and sharpening of the Soret and Q-bands (λ=350-400 nm and 600-700 nm, respectively), which are hallmarks linear tetrapyrrole rigidification.

FIG. 30 illustrates covalent attachment of biliverdin to a maquette. Zinc-binding gel assays confirming covalent cofactor attachment in dFP1.0 holoprotein formed in vitro. His-tagged biliverdin-bound protein appears as a monomer at MW=17.4 kD.

FIG. 31 illustrates spectral properties of in vitro refolded bili-proteins. Relative fluorescence (mean±s.e.) of dFP1.0 and iFP1.4 at λ em =661 nm and 715 nm (λ ex =600 nm and 640 nm, respectively) are not dramatically impacted when in vitro refolded with covalently attached cofactor, over a wide range of pH and in the presence of oxidizing/reducing agents at pH7 (DTT=dithiothreiotol, GSH=oxidized and reduced glutathione).

FIG. 32 illustrates dFP 1.0 transduction stability in mammalian cell lines. Stable HEK293 cell lines were produced by lentivirus-mediated infection and clonal selection. Expression of the de novo protein quantified by fluorescence is robust and uniform over 30 cell passages or the typical useful lifetime of immortalized mammalian cell lines (box=median±quartile, whisker=range).

FIG. 33 illustrates isolated structure-function between the dFP hydrophobic core (photophysical determinants) and scaffold exterior (expression determinants). (Panel a) Sequences used for dFP transposition analysis (red=exposed negative side-chain, blue=exposed positive-side chain, pink=core leucine) include SEQ ID No. 25, SEQ ID No. 157, and SEQ ID No. 120. Supercharged dFP[Z.sub.net=−15] is a transposition of the hydrophobic bilin-binding core of dFP1.0 into the Z.sub.net=−15 scaffold. “Leu-Core” has leucine substituted for all hydrophobic core residues of dFP1.0. (Panel b) Schematized dFP[Z.sub.net=−15] design. (Panel c) Relative protein expression levels in transfected HEK cells assessed by fluorescence imaging of C-terminal GFP tags, including iFP1.4 control (box=mean.+−.s.d., whisker=range). Leu-Core has an identical exterior and similar expression level to dFP1.0, whereas dFP[Z.sub.net=−15] lacks viable mammalian expression. (Panel d) Excitation (.lamda.sub.em>715 nm) and emission (.lamda.sub.exc=600 nm) spectrum of dFP1.0 and dFP[Z.sub.net=−15]. (e) Summary of spectral properties for SEQ ID No. 25, SEQ ID No. 157, and SEQ ID No. 120. dFP absorbance and fluorescence properties governed by the hydrophobic core are preserved during core transposition despite loss of mammalian viability from the change in exterior (QY=relative quantum yield, 6=extinction coefficient).

FIG. 34 illustrates that mammalian-specific spectra of dFP1.0 and IFP1.4 do not shift over long protein maturation periods. (Panel a) Spectra of dFP1.0 in rat hippocampal neurons obtained by live-cell spectral imaging (excitation stack λ em =680-800 nm; emission stack λ em =635 nm). The Stokes shift observed by spectral imaging is consistent with that of cell lysate obtained by spectroscopy. (Panel b) Emission spectra for dFP1.0 and IFP1.4 do not shift depending on heme oxygenase co-expression (HO1). Only single-cell spectral imaging is shown because chronic expression of HO1 was overall toxic to cells in our hands, thus hindering cell lysate measurements from pooled cells.

FIG. 35 illustrates spectral properties of fluorescent bili-proteins in yeast. Live-cell spectrum acquired by spectroscopy (lines) and spectral imaging (dots) of dFP1.0 and iFP1.4 expressed in engineered S. cerevisiae . Both the natural and de novo bili-proteins exhibit red-shifted spectra from mammalian live-cell spectra (Lysate: excitation λ em >735 nm, and emission λ em =640 nm; Live cell spectral imaging: excitation stack λ em =680-800 nm, and emission stack λ em =635 nm with 15 nm bandpass on emission).

FIG. 36 illustrates a maquette protease susceptibility study comparing the GL/BT maquette scaffolds, and MM scaffold with myoglobin.

FIG. 37 illustrates the results of a depolarization study for three maquette probes where fluorescence was measured before and after depolarization. In FIG. 37 , the artificial proteins listed include 1321 (i.e., AM-528-C4 (SEQ ID NO. 63)), 1323 (i.e., AM-1196, SEQ ID NO. 66), and 1329 (i.e., AM-528 (SEQ ID NO. 69).

FIG. 38 illustrates potential means of sensing by modifying reporter function.

FIG. 39 illustrates T2 and MRI image slices of maquettes on a Bruker Avance III 400, 9.4 T. (Panel A) T2 decay graphs of BT6 CysAla, MM3, and MM3 FC maquettes with T2s of 629 ms, 678 ms, and 275 ms, respectively. These correspond to relaxivities of 111, 7.5, and 3.4 for T2. (Panel B) T2-weighted image using CPMG pulse sequence with TE=100 ms (250 ms effective) a TR=10 s, slice width of 0.5 mm on bundle of 0.5 mm tubes from 1 o'clock clockwise of 640 μM, 320 μM, 160 μM, 80 μM, 40 μM, and 1 μM bound heme concentration in PBS center tube.

FIG. 40 illustrates GFP expression levels at 2 days post-transfection for an MZH3 variant (SEQ ID NO. 147), fused to eGFP, and transfected into HEK293T cells.

FIG. 41 illustrates the spectral characteristics for dFP, mini dFP, and nano dFP in E. coli BL21 cell lysate after 20 hours of co-expression with heme oxygenase.

FIG. 42 illustrates an immunocytochemical analysis of the GFP fusion effect on mammalian maquette expression. HEK293 cells expressing 6×-His-tagged variants ([Znet=−3] with or without the GFP fusion) were paraformaldehyde-fixed 48 hours post-transfection, and then stained with DyLight650-conjugated 6×-His antibody (box=median+/−quartile, whisker=range). No difference in expression level is observed.

In some embodiments, the invention includes artificial, de novo proteins that may function as sensors, and which may be expressed in eukaryotic cells. In some embodiments, the artificial proteins of the invention may be expressed in mammalian cells.

In some embodiments, the artificial proteins described herein may be soluble proteins and may or may not be amphiphilic. Indeed, in certain selected embodiments of the invention, the artificial proteins described herein may include (1) soluble de novo fluorescent proteins (i.e., proteins that may include a fluorophore), and/or (2) de novo fluorescent amphiphiles that may form integral membrane proteins in which the amphiphile may be a chimeric structure that includes the soluble proteins.

In some embodiments, the artificial proteins of the invention may be transmembrane proteins having a transmembrane portion, an intracellular or cytosolic portion, and an extracellular portion. For example, in some embodiments, the transmembrane portion of the artificial proteins described herein may include leucine rich sequences having a ratio of at least about of at least about 1:1 Leu to Ala, or at least about 2:1 Leu to Ala, or at least about 3:1 Leu to Ala, or at least about 4:1 Leu to Ala, or at least about 5:1 Leu to Ala. In certain embodiments, the transmembrane portion of the artificial proteins described herein may include leucine rich sequences having a ratio of about 4:1 Leu to Ala. In some embodiments, the transmembrane portion of the artificial proteins described herein may include aromatic residues providing lower insertion energies for placement at the cell membrane interface.

In some embodiments, the artificial proteins of the invention may be configured to traffic through a eukaryotic (e.g., mammalian) cell's endoplasmic reticulum and Golgi apparatus. In some methods of the invention that include the preparation of one or more of the artificial proteins described herein, such methods may include trafficking the artificial protein through a eukaryotic (e.g., mammalian) cell's endoplasmic reticulum and Golgi apparatus.

In some embodiments, the artificial protein of the invention may have a net surface charge (i.e., Z net ) of about −12 to about +8. The net surface charge of the artificial proteins of the invention may be varied or modified by adjusting the amino acid sequence of the artificial proteins described herein. In some embodiments, those artificial proteins of the invention having a net surface charge of about −12 to about +8 may be expressed in eurkaryotic (e.g., mammalian) cells. In some embodiments, the net surface charge may be greater than about −12, or greater than about −11, or greater than about −10, or greater than about −9, or greater than about −8, or greater than about −7, or greater than about −6, or greater than about −5, or greater than about −4, or greater than about −3, or greater than about −2, or greater than about −1, or greater than about 0, or greater than about +1, or greater than about +2, or greater than about +3, or greater than about +4, or greater than about +5, or greater than about +6, or greater than about +7. In some embodiments, the net surface charge may be less than about +8, or less than about +7, or less than about +6, or less than about +5, or less than about +4, or less than about +3, or less than about +2, or less than about +1, or less than about 0, or less than about −1, or less than about −2, or less than about −3, or less than about −4, or less than about −5, or less than about −6, or less than about −7, or less than about −8, or less than about −9, or less than about −10, or less than about −11. In some embodiments, the artificial protein of the invention may have a net surface charge that is negative.

In some embodiments, the artificial proteins of the invention may be modified as described herein to provide a range of functions when associated with a fluorophore and/or a cofactor. For example, the artificial proteins of the invention may be modified to function as voltage sensors, MRI contrast agents, metal binding reporters, and/or cellular probes.

In some embodiments, artificial proteins described herein are artificially designed and may be rigid 2, 3, 4, 5, 6, or more-helix bundle proteins that serve as custom scaffolds for 1, 2, 3, 4, 5, 6, or more types of biological co-factors (e.g. fluorophores or redox sensors) that can each be arbitrarily or purposefully positioned within an artificial protein of the invention. In certain embodiments, the artificial proteins of the invention include 4 helical protein bundles (i.e., α-helical protein bundles).

In some embodiments, artificial proteins of the invention are compact 4-TM helix proteins that are completely modular with respect to structure and mechanism. This compactness can be advantageous in viral transgene delivery with limited genetic payloads such as with adeno-associated virus (AAV, by comparison, opsins and mFP-based systems are ˜2-3 larger genes). In some embodiments, the fluorescence signal positively correlates and increases upon depolarization to avoid false positives from bleaching, and the exposed amino acid side chains in the TM region may be uncharged/non-polar, to avoid membrane capacitance alterations. In some embodiments, the artificial proteins of the invention may provide sensors with microsecond (μs)-resolution or log orders faster resolution than current state-of-the-art protein-based sensing techniques.

By employing fundamental rules for alpha helical protein folding and association between alpha helices, in some embodiments, artificial proteins according to the invention are stable and robust from the start. Furthermore, the simplicity and modularity of first principles design keeps the re-engineering options open and allows unprecedented adaptability to be maintained in both the number and type of cofactors that can be anchored in the artificial protein frame ( FIG. 3 ). In natural proteins complex interdependence between structural parts accumulates during repeated cycles of mutation and natural selection; such complexity impedes or even halts re-engineering for desired function due to fragility. In contrast, the role of individual residues in structure/function relationships of artificial proteins according to some embodiments of the invention is usually isolated and identifiable. This allows for, in some embodiments, manipulation of local electric fields around cofactors or rates of electron tunneling between redox centers, in the scaffold of an artificial protein.

In some embodiments, a stripped-down protein construct exploits relatively simple, repeating, binary patterning of amino acids to create α-helices that assemble into a 4-helix bundle. In some embodiments, for the hydrophilic region extending away from the membrane, the amino acid order is selected so that polar or charged residues (positively charged Lys or Arg, negatively charged Glu or Asp) lie on one face of the helix and non-polar residues (Ala, Phe) lie on the other. Hydrophobic forces may drive the nonpolar faces together into the four-helix bundle ( FIG. 3 ). For the lipophilic transmembrane region, one or more of the amino acids are nonpolar, with the exception of select polar amino acids that perform the task of binding cofactors between helices or making hydrogen bonds across the bundle interior from one helix to another. In some embodiments, Cys, His, and interior Lys anchor cofactors to specific locations in the helical frame.

In some embodiments, a wide variety of natural and synthetic cofactors can be anchored to the frame at many different positions along the helices and in the connecting loops, for example, hemes and other porphyrins, flavins, various bilins, quinones, iron-sulfur clusters, carotenoids, chlorins and bacterio-chlorins ( FIG. 5 , see also Farid, T. A. et al., “Elementary tetrahelical protein design for diverse oxidoreductase functions” Nature Chemical Biology, 9, 826-833 (2013), hereby incorporated by reference in its entirety). In some embodiments, local electric fields from the artificial protein environment can change pigment color upon binding, a type of Stark effect ( FIG. 5 ). X-ray crystallography up to 1.4 Å resolution and 2D-NMR can provide details of protein-cofactor interactions for iterative redesign to tune maquette physical chemical properties ( FIG. 4 ). Because of the strong driving forces for assembly of this first principles alpha helical frame and associated high tolerance to sequence manipulation, redesign and tuning of maquette functional properties can be as simple as moving the cofactor anchoring amino acid one helical turn to adjust cofactor position. FIG. 3 illustrates three examples of Cys scanning along a single helix to anchor a field reporting cofactor at different membrane depths to optimize for maximum sensitivity.

The definitions used in this application are for illustrative purposes and do not limit the scope used in the practice of the invention.

Unless defined otherwise, all technical and scientific terms used herein generally have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Generally, the nomenclature used herein and the laboratory procedures in cell culture, molecular genetics, organic chemistry, and nucleic acid chemistry and hybridization are those well known and commonly employed in the art.

As used herein, the articles “a” and “an” are used herein to refer to one or to more than one (i.e. to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.

As used herein, the term “about” will be understood by persons of ordinary skill in the art and will vary to some extent on the context in which it is used. As used herein, “about” when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20% or ±10%, more preferably ±5%, even more preferably ±1%, and still more preferably ±0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.

As used herein, the terms “peptide,” “polypeptide,” or “protein” are used interchangeably, and refer to a compound comprised of amino acid residues covalently linked by peptide bonds. A protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprise the sequence of a protein or peptide. Polypeptides include any peptide or protein comprising two or more amino acids joined to each other by peptide bonds. As used herein, the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types. “Polypeptides” include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs and fusion proteins, among others. The polypeptides include natural peptides, recombinant peptides, synthetic peptides or a combination thereof. A peptide that is not cyclic will have an N-terminus and a C-terminus. The N-terminus will have an amino group, which can be free (i.e., as a NH 2 group) or appropriately protected (for example, with a BOC or an Fmoc group). The C-terminus will have a carboxylic group, which can be free (i.e., as a COOH group) or appropriately protected (for example, as a benzyl or a methyl ester). A cyclic peptide does not necessarily have free N- or C-termini, since they are covalently bonded through an amide bond to form the cyclic structure.

As used herein, the term “(SEQ ID NO: X)-(SEQ ID NO: Y)” indicates that SEQ ID NO: X is covalently linked to SEQ ID NO: Y by an amide bond, involving the carboxylate group on the C-terminus of SEQ ID NO: X and the amino group on the N-terminus of SEQ ID NO: Y. Accordingly, the term “(SEQ ID NO: X)-LOOP-(SEQ ID NO: Y)” indicates that SEQ ID NO: X is covalently linked to LOOP by an amide bond, involving the carboxylate group on the C-terminus of SEQ ID NO: X and an amino group in LOOP, and LOOP is covalently linked to SEQ ID NO: Y by an amide bond, involving a carboxylate group in LOOP and the amino group in the N-terminus of SEQ ID NO: Y.

As used herein, the term “LOOP” refers to a chemical linker that connects two protein segments and is able to form a loop between the two protein segments. In one embodiment, LOOP is a peptide of 4 to 8 amino acid residues, 6 to 15 amino acid residues, a hydrocarbon chain of 18 to 30 carbons, or a chain consisting of —HN −1 (CH 2 CH 2 O)CH 2 C(O)—, wherein “n” is an integer of value between 5 and 10, the group —HN 1 forms an amide bond with the carboxylate group at the C-terminus of one protein segment and CH 2 C(O)— forms an amide bond with the amino group at the N-terminus of the other protein segment. In another embodiment, LOOP is a peptide consisting of from 3 to 15 amino acids. In another embodiment, LOOP is a peptide consisting of from 4 to 8 amino acids. In yet another embodiment, LOOP is a peptide formed by amino acids selected from the group of glycine, serine and cysteine. In yet another embodiment, LOOP is a peptide of amino acid sequence selected from the group consisting of GGSGKGSGG (SEQ ID No. 17), GGCG (SEQ ID No: 18), GACG (SEQ ID No: 19), GGSG (SEQ ID No. 20).

As used herein, amino acids are represented by the full name thereof, by the three-letter code, as well as the one-letter code corresponding thereto, as indicated in the following Table 1. Additionally, as used herein “+” represents a positively charged amino acid, “−” represents a negatively charged amino acid, and “0” represents an amino acid having an amide side-chain. In some embodiments, positively charged amino acids may include acidic side-chains and may be selected from the group consisting of lysine, arginine, and histidine. In some embodiments, negatively charged amino acids may include basic side chains and may be selected from the group consisting of aspartate and glutamate. In some embodiments, amide bearing amino acids, or amino acids having an amide side-chain, (e.g., those represented by a “0”) may include glutamine or asparagine. As shown in Table 1, below, “X” may represent any amino acid. The structure of amino acids and their abbreviations can also be found in the chemical literature, such as in Stryer, 1988, “Biochemistry”, 3.sup.rd Ed., W. H. Freeman and Co., New York.

As used herein the term “cofactor” refers to any naturally occurring or artificial chemical group or compound that may be bound to an artificial protein of the invention.

As used herein to refer to the association between a cofactor and the peptides of the invention, the term “bound” indicates that the cofactor is coordinated to residues of the peptide, forming a complex. The complex may be more or less labile, depending on the specific nature of the cofactor and the peptide in use. In one embodiment, the complex between the cofactor and the peptides is stable enough for the complex to be useful within the needs of the invention. In another embodiment, the cofactor is covalently bound to the peptides of the invention.

As used herein, the term “fluorophore” refers to a chemical group or compound that emits light, typically ranging from the visible to near infrared regions of the electromagnetic spectrum.

As used herein, the term “electrochromic” refers to a chemical group or compound that emits light in response to an electric charge.

As used herein with respect to the compounds of the invention, “biologically active” means that the compounds elicit a biological response in a mammal that can be monitored and characterized in comparison with an untreated mammal.

As used herein, the term “treating” means ameliorating the effects of, or delaying, halting or reversing the progress of a disease or disorder. The word encompasses reducing the severity of a symptom of a disease or disorder and/or the frequency of a symptom of a disease or disorder.

As used herein, the term “medical intervention” means a set of one or more medical procedures or treatments that are required for ameliorating the effects of, delaying, halting or reversing a disease or disorder of a subject. A medical intervention may involve surgical procedures or not, depending on the disease or disorder in question. A medical intervention may be wholly or partially performed by a medical specialist, or may be wholly or partially performed by the subject himself or herself, if capable, under the supervision of a medical specialist or according to literature or protocols provided by the medical specialist.

As used herein, a “subject” or a “mammal” includes a human or a non-human mammal Non-human mammals include, for example, livestock and pets, such as ovine, bovine, porcine, canine, feline and murine mammals. Preferably, the subject or mammal is canine, feline or human. Most preferably, the subject or mammal is human.

The terms “sequence identity,” “percent identity,” and “sequence percent identity” in the context of two or more nucleic acids or polypeptides, refer to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned (introducing gaps, if necessary) for maximum correspondence, not considering any conservative amino acid substitutions as part of the sequence identity. The percent identity can be measured using sequence comparison software or algorithms or by visual inspection. Various algorithms and software are known in the art that can be used to obtain alignments of amino acid or nucleotide sequences.

Certain embodiments of the present invention comprise a variant of a peptide or polypeptide or of a nucleotide or polynucleotide of the invention. As used herein, the term “variant” encompasses but is not limited to polypeptides (or peptides) or polynucleotides (or nucleotides) which comprise an amino acid or nucleotide sequence which differs from the amino acid or nucleotide sequence of a reference polypeptide (or peptide) or polynucleotide (or nucleotide) by way of one or more substitutions, deletions and/or additions at certain positions within or adjacent to the amino acid or nucleotide sequence of the reference polypeptide (or peptide) or polynucleotide (or nucleotide). The variant may comprise one or more conservative substitutions in its amino acid or nucleotide sequence as compared to the amino acid or nucleotide sequence of a reference polypeptide (or peptide) or polynucleotide (or nucleotide). Conservative substitutions may involve, e.g., the substitution of similarly charged or uncharged amino acids. The variant retains the ability to specifically bind to the antigen of the reference peptide or polypeptide. In certain embodiments, variants possess biological activities that are the same or similar to the sequences in question.

Artificial Proteins of the Invention

In some embodiments, artificial proteins according to the invention comprise 1, 2, 3, 4, 5, 6, or more synthetic peptides. In some embodiments, the invention includes a nucleotide sequence encoding a synthetic peptide. In an embodiment an artificial protein according to the invention comprises four (4) synthetic peptides. Each peptide may comprise an alpha helix. In some embodiments, the artificial protein has a maquette structure, i.e. comprises four (4) synthetic α-helical peptides. In some embodiments two peptides may be connected by a LOOP sequence of amino acids. In some embodiments an artificial protein comprises a first pair of peptides connected by a first LOOP sequence of amino acids and a second pair of peptides connected by a second LOOP sequence of amino acids, wherein the first and second LOOP sequences are connected by a third LOOP sequence. In some embodiments a first peptide is connected to a second peptide by a LOOP sequence, the second peptide is connected to a third peptide by a second LOOP sequence, and the third peptide is connected to a fourth peptide by a third LOOP sequence, e.g. to form a single chain artificial protein. In some embodiments, each LOOP sequence is an independently selected group of 3-15 or 4-8 amino acids.

In some embodiments, an artificial protein includes a peptide comprising any one of the amino acid sequences set forth in SEQ ID NOS: 1-16, represented below:

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 2, represented below:

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 3, represented below:

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 4, represented below:

In some embodiments, an artificial protein includes a peptide comprising one or more of an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4. In some embodiments an artificial protein includes a peptide comprising two or more of amino acid sequences selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4, wherein the two or more amino acid sequences are connected by a LOOP. A LOOP structure may comprise 3 to 15 amino acids, or preferably, 4-8 amino acids. In some embodiments a LOOP structure comprises glycine and cysteine amino acids. In some embodiments, LOOP structures are independently selected from:

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 1)-LOOP-(SEQ ID NO: 2). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 2)-LOOP-(SEQ ID NO: 3). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 3)-LOOP-(SEQ ID NO: 4). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 1)-LOOP-(SEQ ID NO: 2)-LOOP-(SEQ ID NO: 3). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 2)-LOOP-(SEQ ID NO: 3)-LOOP-(SEQ ID NO: 4). In some embodiments, the an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 1)-LOOP-(SEQ ID NO: 2)-LOOP-(SEQ ID NO: 3)-LOOP-(SEQ ID NO: 4). In each embodiment the LOOP sequence may be as described herein.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO:5, represented below:

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 6, represented below:

SEQ ID NO: 6: EXKQRXEDXXRKXEEXXKRXEDXKQK.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 7, represented below:

SEQ ID NO. 7: RXXKXXEDXXQKXEEXXNQXEDXKQL.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 8, represented below:

SEQ ID NO. 8: EXKQRXEDXXRKXEEXXKRXEDXXQK.

In some embodiments, an artificial protein includes a peptide comprising one or more of an amino acid sequence selected from the group consisting of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8. In some embodiments, an artificial protein includes a peptide comprising two or more of amino acid sequences selected from the group consisting of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8, wherein the two or more amino acid sequences are connected by a LOOP. A LOOP structure may comprise 3 to 15 amino acids, or preferably, 4-8 amino acids. In some embodiments, a LOOP structure comprises glycine and cysteine amino acids. In some embodiments, LOOP structures are independently selected from: SEQ ID NO: 17: GGSGKGSGG, SEQ ID NO: 18: GGCG, SEQ ID NO: 19: GACG, and SEQ ID NO: 20: GGSG.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 5)-LOOP-(SEQ ID NO: 6). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 6)-LOOP-(SEQ ID NO: 7). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 7)-LOOP-(SEQ ID NO: 8). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 5)-LOOP-(SEQ ID NO: 6)-LOOP-(SEQ ID NO: 7). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 6)-LOOP-(SEQ ID NO: 7)-LOOP-(SEQ ID NO: 8). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 5)-LOOP-(SEQ ID NO: 6)-LOOP-(SEQ ID NO: 7)-LOOP-(SEQ ID NO: 8). In each embodiment the LOOP sequence may be as described herein.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 9, represented below:

SEQ ID NO. 9: EXXKXXEDXXQKXEEXXNQXEDXXQL.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 10, represented below:

SEQ ID NO: 10: EXKQRXEDXXRKXEEXXKRXEDXKQK.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 11, represented below:

SEQ ID NO. 11: RXXKXXEDXXQKXEEXXNQXEDXKQL.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 12, represented below:

SEQ ID NO. 12: EXKQRXEDXXRKXEEXXKRXEDXXQK.

In some embodiments, an artificial protein includes a peptide comprising one or more of an amino acid sequence selected from the group consisting of SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, and SEQ ID NO: 12. In some embodiments an artificial protein includes a peptide comprising two or more of amino acid sequences selected from the group consisting of SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, and SEQ ID NO: 12, wherein the two or more amino acid sequences are connected by a LOOP. A LOOP structure may comprise 3 to 15 amino acids, or preferably, 4-8 amino acids. In some embodiments a LOOP structure comprises glycine and cysteine amino acids. In some embodiments, LOOP structures are independently selected from:

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 9)-LOOP-(SEQ ID NO: 10). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 10)-LOOP-(SEQ ID NO: 11). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 11)-LOOP-(SEQ ID NO: 12). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 9)-LOOP-(SEQ ID NO: 10)-LOOP-(SEQ ID NO: 11). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 10)-LOOP-(SEQ ID NO: 11)-LOOP-(SEQ ID NO: 12). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 9)-LOOP-(SEQ ID NO: 10)-LOOP-(SEQ ID NO: 11)-LOOP-(SEQ ID NO: 12). In each embodiment the LOOP sequence may be as described herein.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 13, represented below:

SEQ ID NO. 13: EXXKXXEDXXQKXEEXXNQXEDXXQL.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 14, represented below:

SEQ ID NO: 14: EXKQRXEDXXRKXEEXXKRXEDXKQK.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 15, represented below:

SEQ ID NO. 15: RXXKXXEDXXQKXEEXXNQXEDXKQL.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of SEQ ID NO: 16, represented below:

SEQ ID NO. 16: EXKQRXEDXXRKXEEXXKRXEDXXQK.

In some embodiments, an artificial protein includes a peptide comprising one or more of an amino acid sequence selected from the group consisting of SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, and SEQ ID NO: 16. In some embodiments an artificial protein includes a peptide comprising two or more of amino acid sequences selected from the group consisting of SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, and SEQ ID NO: 16, wherein the two or more amino acid sequences are connected by a LOOP. A LOOP structure may comprise 3 to 15 amino acids, or preferably, 4-8 amino acids. In some embodiments a LOOP structure comprises glycine and cysteine amino acids. In some embodiments, LOOP structures are independently selected from: SEQ ID NO: 17: GGSGKGSGG, SEQ ID NO: 18: GGCG, SEQ ID NO: 19: GACG, and SEQ ID NO: 20: GGSG.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 13)-LOOP-(SEQ ID NO: 14). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 14)-LOOP-(SEQ ID NO: 15). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 15)-LOOP-(SEQ ID NO: 16). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 13)-LOOP-(SEQ ID NO: 14)-LOOP-(SEQ ID NO: 15). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 14)-LOOP-(SEQ ID NO: 15)-LOOP-(SEQ ID NO: 16). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (SEQ ID NO: 13)-LOOP-(SEQ ID NO: 14)-LOOP-(SEQ ID NO: 15)-LOOP-(SEQ ID NO: 16). In each embodiment the LOOP sequence may be as described herein.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of Generic Sequence A, represented below:

−XX+XX−−−XX0+X−−XX00X−−XX0L  Generic Sequence A:

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of Generic Sequence B, represented below:

−X+0+X−−XX++X−−XX++X−−X+0+  Generic Sequence B:

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of Generic Sequence C, represented below:

+XX+XX−−XX0+X−−XX00X−−X+0L  Generic Sequence C:

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of Generic Sequence D, represented below:

−XX+0+−−XX++X−−XX++X−−XX0+  Generic Sequence D:

In some embodiments, an artificial protein includes a peptide comprising one or more of an amino acid sequence selected from the group consisting of Generic Sequences A, B, C, and D. In some embodiments an artificial protein includes a peptide comprising two or more of amino acid sequences selected from the group consisting of Generic Sequences A, B, C, and D, wherein the two or more amino acid sequences are connected by a LOOP. A LOOP structure may comprise 3 to 15 amino acids, or preferably, 4-8 amino acids. In some embodiments a LOOP structure comprises glycine and cysteine amino acids. In some embodiments, LOOP structures are independently selected from: SEQ ID NO: 17: GGSGKGSGG, SEQ ID NO: 18: GGCG, SEQ ID NO: 19: GACG, and SEQ ID NO: 20: GGSG.

In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (Generic Sequence A)-LOOP-(Generic Sequence B). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (Generic Sequence B)-LOOP-(Generic Sequence C). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (Generic Sequence C)-LOOP-(Generic Sequence D). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (Generic Sequence A)-LOOP-(Generic Sequence B)-LOOP-(Generic Sequence C). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (Generic Sequence B)-LOOP-(Generic Sequence C)-LOOP-(Generic Sequence D). In some embodiments, an artificial protein includes a peptide comprising the amino acid sequence of (Generic Sequence A)-LOOP-(Generic Sequence B)-LOOP-(Generic Sequence C)-LOOP-(Generic Sequence D). In each embodiment the LOOP sequence may be as described herein.

In some embodiments, an artificial protein includes a peptide comprising an amino acid sequence selected from the group consisting of: SEQ ID NO: 21; SEQ ID NO: 22; SEQ ID NO: 23; SEQ ID NO: 24; SEQ ID NO: 25; SEQ ID NO: 26; SEQ ID NO: 27; SEQ ID NO: 28; SEQ ID NO: 29; SEQ ID NO: 30; SEQ ID NO: 31; SEQ ID NO: 32; SEQ ID NO: 33; SEQ ID NO: 34; SEQ ID NO: 35; SEQ ID NO: 36; SEQ ID NO: 37; SEQ ID NO: 38; SEQ ID NO: 39; SEQ ID NO: 40; SEQ ID NO: 41, SEQ ID NO: 42; SEQ ID NO: 43; and SEQ ID NO: 44, where SEQ ID NOS: 21-44 are as shown in Table 2.

In some embodiments, an artificial protein includes a peptide comprising an amino acid sequence as set forth in SEQ ID NO: 45, as shown in Table 2. Without being limited to any one theory of the invention, SEQ ID NO: 45 (i.e., dFP1.1) demonstrate an increase in fluorescence as compared to dFP because histidines in the 7 position of each helix, which may be due to the addition of core bulk and the ability to hydrogen bond, thereby rigidifying the core structure.

In some embodiments an artificial protein comprises one or more amino acid sequences as set forth in Table 3.

In some embodiments an artificial protein comprises one or more amino acid sequences as set forth in Table 4, or a variant thereof.

In some embodiments, the invention includes nucleotide sequences encoding any of the foregoing polypeptides. In some embodiments, the invention includes a nucleotide sequence set forth in Table 4 or a variant thereof, as would be understood by a person having ordinary skill in the art.

In some embodiments, the artificial protein of SEQ ID NO. 21 may be encoded by the nucleotide sequence of SEQ ID NO. 70 ( E. coli ) or SEQ ID NO. 71 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 25 may be encoded by the nucleotide sequence of SEQ ID NO. 46 ( E. coli ) or SEQ ID NO. 47 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 26 may be encoded by the nucleotide sequence of SEQ ID NO. 89 ( E. coli ) or SEQ ID NO. 90 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 27 may be encoded by the nucleotide sequence of SEQ ID NO. 92 ( E. coli ) or SEQ ID NO. 93 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 28 may be encoded by the nucleotide sequence of SEQ ID NO. 95 ( E. coli ) or SEQ ID NO. 96 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 29 may be encoded by the nucleotide sequence of SEQ ID NO. 98 ( E. coli ) or SEQ ID NO. 99 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 30 may be encoded by the nucleotide sequence of SEQ ID NO. 55 ( E. coli ) or SEQ ID NO. 56 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 31 may be encoded by the nucleotide sequence of SEQ ID NO. 58 ( E. coli ) or SEQ ID NO. 59 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 34 may be encoded by the nucleotide sequence of SEQ ID NO. 109 ( E. coli ) or SEQ ID NO. 110 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 35 may be encoded by the nucleotide sequence of SEQ ID NO. 137 ( E. coli ).

In some embodiments, the artificial protein of SEQ ID NO. 51 may be encoded by the nucleotide sequence of SEQ ID NO. 49 ( E. coli ) or SEQ ID NO. 50 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 54 may be encoded by the nucleotide sequence of SEQ ID NO. 52 ( E. coli ) or SEQ ID NO. 53 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 63 may be encoded by the nucleotide sequence of SEQ ID NO. 61 ( E. coli ) or SEQ ID NO. 62 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 66 may be encoded by the nucleotide sequence of SEQ ID NO. 64 ( E. coli ) or SEQ ID NO. 65 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 69 may be encoded by the nucleotide sequence of SEQ ID NO. 67 ( E. coli ) or SEQ ID NO. 68 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 103 may be encoded by the nucleotide sequence of SEQ ID NO. 101 ( E. coli ) or SEQ ID NO. 102 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 108 may be encoded by the nucleotide sequence of SEQ ID NO. 106 ( E. coli ) or SEQ ID NO. 107 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 117 may be encoded by the nucleotide sequence of SEQ ID NO. 115 ( E. coli ) or SEQ ID NO. 116 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 120 may be encoded by the nucleotide sequence of SEQ ID NO. 118 ( E. coli ) or SEQ ID NO. 119 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 127 may be encoded by the nucleotide sequence of SEQ ID NO. 125 ( E. coli ) or SEQ ID NO. 126 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 130 may be encoded by the nucleotide sequence of SEQ ID NO. 128 ( E. coli ) or SEQ ID NO. 129 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 133 may be encoded by the nucleotide sequence of SEQ ID NO. 131 ( E. coli ) or SEQ ID NO. 132 (FCK mammal).

In some embodiments, the artificial protein of SEQ ID NO. 136 may be encoded by the nucleotide sequence of SEQ ID NO. 134 ( E. coli ) or SEQ ID NO. 135 (FCK mammal).

In some embodiments, the invention includes a vector comprising a nucleotide sequence encoding any of the foregoing polypeptides.

In some aspects of the invention, substantially similar artificial protein amino acid sequences (e.g., polypeptide variants) may have at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or 100% identity to an amino acid sequence described herein. Similarly, a substantially similar nucleotide sequence of the invention (e.g., polynucleotide variants) may have at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or 100% identity to a nucleotide sequence described herein.

Compositions of the Invention

The invention includes compositions comprising an artificial protein as described herein and at least one cofactor. In some embodiments the cofactor may be naturally occurring, while in other embodiments, the cofactor may be artificial. In some embodiments, compositions of the invention comprise an artificial protein as described herein and two, three, four, or more different cofactors.

In some embodiments a cofactor may be a cofactor that exhibits an electrochromic effect. In some embodiments the cofactor may exhibit an electrochromic effect in the presence of 50-100 mV voltage. In some embodiments the cofactor may exhibit an electrochromic effect in the presence of 10-1000 mV, 25-500 mV, 50-75 mV, 60-80 mV, or 80-100 mV. In some embodiments, the cofactor may be a fluorophore. In some embodiments the fluorophore may be naturally occurring in a host cell. Suitable naturally occurring fluorophores include flavins, bilins (e.g. biliverdin or bilirubin), retinals, and carotenoids. In some embodiments an electrochromic material may be used as a fluorophore. The fluorophore may be bound to the peptide through covalent or non-covalent bonds. In an embodiment, the fluorophore (e.g. a flavin) is covalently bound to a threonine residue of the peptide. In an embodiment, the fluorophore (e.g. a retinal) is covalently bound to a lysine residue. In an embodiment, the fluorophore (e.g. a bilin) is covalently bound to a cysteine residue.

In some embodiments a cofactor may be a heme. As used herein, the term “heme” refers to a prosthetic group formed of an iron atom contained in the center of a large heterocyclic organic ring called a porphyrin. Non-limiting examples of hemes are heme A, heme B, heme C, heme O, mesohemes, deuterohemes, synthetic dicyano porphyrins and symmetrical porphyrins (such as, but not limited to, protoporphyrin III). In some embodiments the heme is naturally occurring in the host cell, e.g. in a mammal. The heme may be bound to the peptide through covalent or non-covalent bonds. In an embodiment, the heme is covalently bound to a histidine residue of the peptide. In an embodiment, the heme is covalently bound to a cysteine residue of the peptide.

In some embodiments a cofactor may be a metal ion or cluster of metal ions. Non-limiting examples of useful metal ions are Zn 2+ , Fe 2+ , Fe 3+ , Mn 2+ , Mg 2+ , Cu + , Cu 2+ , Co 2+ , Co 3+ , Ca 2+ , and K + .

In some embodiments a cofactor may be a tetrapyrrole, for example a heme or biliverdin, though in some embodiments a cofactor may be a tetrapyrrole other than a heme or other than biliverdin. In some embodiments a cofactor may be a messenger molecule such as cAMP, ATP, a neurotransmitter, a short peptide (e.g. neuropeptide). In some embodiments a cofactor may be water. In some embodiments a cofactor may be a gas, for example oxygen. In some embodiments a cofactor may be any amphipathic molecule sized to fit within the core of an artificial protein as described herein. Suitable cofactors are also described in Solomon, L. C., et al, “Engineering the Assembly of Heme Cofactors in Man-Made Proteins” J. Am. Chem. Soc., 136, 319203199 (2014), which is hereby incorporated by reference in its entirety.

The invention also includes a preparation comprising a vesicle. The vesicle comprises an amphiphilic material, an artificial protein as described herein, and at least one cofactor. In one aspect, an artificial protein of the invention is incorporated in the walls of the vesicle, whereby the outer residues of the peptide structure contact the molecules that comprises the vesicle wall.

The amphiphilic material used in the preparation of the vesicle may be a detergent, a phospholipid or a mixture thereof. The detergent useful within the invention may be an anionic detergent, a cationic detergent, a zwitterion ionic detergent and a non-ionic detergent. Non-limiting examples of ionic detergents are perfluorooctanoate, perfluorooctanesulfonate, sodium dodecyl sulfate (SDS), ammonium lauryl sulfate, and other alkyl sulfate salts, sodium laureth sulfate, also known as sodium lauryl ether sulfate (SLES), alkyl benzene sulfonate, soaps and fatty acid salts. Non-limiting examples of cationic detergents are cetyl trimethylammonium bromide (CTAB), also known as hexadecyl trimethyl ammonium bromide, and other alkyltrimethylammonium salts, cetylpyridinium chloride (CPC), polyethoxylated tallow amine (POEA), benzalkonium chloride (BAC), and benzethonium chloride (BZT). Non-limiting examples of zwitterionic (amphoteric) detergents are dodecyl betaine, cocamidopropyl betaine and coco ampho glycinate. Non-limiting examples of non-ionic detergents are alkyl poly(ethylene oxide), alkylphenol poly(ethylene oxide), copolymers of poly(ethylene oxide) and poly(propylene oxide) (commercially called Poloxamers or Poloxamines), alkyl polyglucosides (including octyl glucoside and decyl maltoside), fatty alcohols (including cetyl alcohol and oleyl alcohol), cocamide MEA, cocamide DEA, polysorbates (such as Tween 20, Tween 80 and dodecyl dimethylamine oxide).

The phospholipid useful within the invention may be a diacylglyceride, such as phosphatidic acid (phosphatidate), phosphatidylethanolamine (cephalin), phosphatidylcholine (lecithin), phosphatidylserine, sphingomyelin or phosphoinositides. Non-limiting examples of phosphoinositides are phosphatidylinositol, phosphatidylinositol phosphate, phosphatidylinositol bisphosphate and phosphatidylinositol triphosphate.

The invention also includes a viable host cell capable of expressing an artificial protein as described herein. In an embodiment the host cell is a eukaryotic (e.g., mammalian) host cell. In an embodiment, a viable host cell is capable of expressing an artificial protein, wherein the artificial protein comprises a 1, 2, 3, 4, 5, 6, or more peptides connected by one or more LOOP amino acid sequences. In an embodiment, a viable host cell comprises four (4) peptides connected by three (3) LOOP amino acid sequences.

The invention also includes a viable host cell capable of expressing a composition as described herein. In an embodiment the host cell is a eukaryotic (e.g., mammalian) host cell. In an embodiment, a viable host cell is capable of expressing a composition comprising an artificial protein as described herein and a cofactor as described herein. In an embodiment, a viable host cell is capable of expressing an artificial protein, wherein the artificial protein comprises a 1, 2, 3, 4, 5, 6, or more peptides connected by one or more LOOP amino acid sequences. In an embodiment, a viable host cell comprises four (4) peptides connected by three (3) LOOP amino acid sequences. In some embodiments a cofactor is a heme, a fluorophore, an electrochromic material, or a metal ion. In some embodiments a viable host cell is capable of expressing a composition comprising an artificial protein as described herein and one (1), two (2), three (3), four (4), or more independently selected cofactors.

In some embodiments a viable cell does not undergo cell death for a period of 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 12 hours, 18 hours, 24 hours, 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months, 3 months, or more. In some embodiments a viable cell line survives for greater than 10 passages, greater than 15 passages, greater than 20 passages, greater than 25 passages, greater than 30 passages, or more. In some embodiments a viable cell line survives for greater than 1 week, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months, 3 months, or more.

Delivery of proteins and/or compositions as described herein to a cell and/or expression of proteins and/or compositions as described herein in a cell can be done using delivery means known in the art.

In some embodiments of the invention an artificial protein and/or composition of the invention is included in a fusion protein. It is well known in the art how to prepare and utilize fusion proteins that comprise a polypeptide sequence. In certain embodiments of the invention, a fusion protein can be used to deliver a protein and/or composition of the invention to a cell and can also in some embodiments be used to target a protein and/or composition of the invention to specific cells or to specific cells, tissues, or regions in a subject. Targeting and suitable targeting sequences for delivery to a desired cell, tissue or region can be performed using art-known procedures.

It is an aspect of the invention to provide an artificial protein and/or composition of the invention that is non-toxic, or substantially non-toxic in cells in which it is expressed. In some embodiments, an artificial protein or composition of the invention does not significantly alter cell health or ongoing electrical activity in the cell in which it is expressed.

In some embodiments of the invention, an artificial protein and/or composition of the invention is genetically introduced into a cellular membrane, and reagents and methods are provided for genetically targeted expression of proteins and/or compositions of the invention. Genetic targeting can be used to deliver artificial proteins and/or compositions of the invention to specific cell types, to specific cell subtypes, to specific spatial regions within an organism, and to sub-cellular regions within a cell. Genetic targeting also relates to the control of the amount of artificial protein and/or compositions of the invention, and the timing of the expression.

Some embodiments of the invention include a reagent for genetically targeted expression of a deliver artificial proteins and/or compositions of the invention, wherein the reagent comprises a vector that contains the gene for the deliver artificial proteins and/or compositions of the invention.

As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting between different genetic environments another nucleic acid to which it has been operatively linked. The term “vector” also refers to a virus or organism that is capable of transporting the nucleic acid molecule. One type of vector is an episome, i.e., a nucleic acid molecule capable of extra-chromosomal replication. Some useful vectors are those capable of autonomous replication and/or expression of nucleic acids to which they are linked. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as “expression vectors”. Other useful vectors, include, but are not limited to viruses such as lentiviruses, retroviruses, adenoviruses, and phages. Vectors useful in some methods of the invention can genetically insert artificial proteins and/or compositions of the invention into dividing and non-dividing cells and can insert artificial proteins and/or compositions of the invention to cells that are in vivo, in vitro, or ex vivo cells.

Vectors useful in methods of the invention may include additional sequences including, but not limited to one or more signal sequences and/or promoter sequences, or a combination thereof. Expression vectors and methods of their use are well known in the art. Non-limiting examples of suitable expression vectors and methods for their use are provided herein.

In certain embodiments of the invention, a vector may be a lentivirus comprising a DNA sequence for a protein and/or composition of the invention, such as one or more sequences shown in the Appendix, or a derivative or variant thereof. A lentivirus is a non-limiting example of a vector that may be used to create stable cell line. The term “cell line” as used herein is an established cell culture that will continue to proliferate given the appropriate medium.

Promoters that may be used in methods and vectors of the invention include, but are not limited to, cell-specific promoters or general promoters. Methods for selecting and using cell-specific promoters and general promoters are well known in the art. A non-limiting example of a general purpose promoter that allows expression of a protein and/or composition of the invention in a wide variety of cell types—thus a promoter for a gene that is widely expressed in a variety of cell types, for example a “housekeeping gene” can be used to express a protein or composition of the invention in a variety of cell types. Non-limiting examples of general promoters are provided elsewhere herein and suitable alternative promoters are well known in the art. In some embodiments the promoter is CAMKII.

Specific Artificial Proteins as Cytosolic Fluorescence Reporters

In some embodiments, an artificial protein for cytosolic fluorescence reporting may include an amino acid sequence selected from the group consisting of SEQ ID NOS. 25, 30, 51, and 54.

In some embodiments, the artificial protein for cytosolic fluorescence reporting may include the amino acid sequence of SEQ ID NO. 25 (i.e., dFP1.0), and may be expressed in mammalian cells. Such an embodiment may fluoresce with a quantum yield (QY) of about 1.6% at an excitation wavelength (λ ex ) of 648 nm and emission wavelength (λ em ) of 662 nm. In some embodiments, the artificial protein for cytosolic fluorescence reporting, which includes the amino acid sequence of SEQ ID NO. 25, may include the cofactor biliverdin (BV). In certain embodiments, the biliverdin may bind in the b loop of the artificial protein that includes the amino acid sequence of SEQ ID NO. 25.

In some embodiments, the artificial protein for cytosolic fluorescence reporting may include the amino acid sequence of SEQ ID NO. 30 (i.e., 528-GL), and may be expressed in mammalian cells. Such an embodiment may fluoresce with a quantum yield (QY) of about 1.8% at an excitation wavelength (λ ex ) of 648 nm and emission wavelength (λ em ) of 662 nm. In some embodiments, the artificial protein for cytosolic fluorescence reporting, which includes the amino acid sequence of SEQ ID NO. 30, may include the cofactor biliverdin (BV). In certain embodiments, the biliverdin may bind in the core of the artificial protein that includes the amino acid sequence of SEQ ID NO. 30.

In some embodiments, the artificial protein for cytosolic fluorescence reporting may include the amino acid sequence of SEQ ID NO. 51 (i.e., minidfp), and may be expressed in mammalian cells. In some embodiments, the artificial protein that may include the amino acid sequence of SEQ ID NO. 51 may be one heptad smaller than the artificial protein for that may include SEQ ID NO. 30.

In some embodiments, the artificial protein for cytosolic fluorescence reporting may include the amino acid sequence of SEQ ID NO. 54 (i.e., nanodfp), and may be expressed in mammalian cells. In some embodiments, the artificial protein that may include the amino acid sequence of SEQ ID NO. 54 may be two heptads smaller than the artificial protein for that may include SEQ ID NO. 30.

Specific Artificial Proteins as T2 MRI Contrast Reporters

In some embodiments, an artificial protein of the invention may be a T2 MRI contrast agent and may include the amino acid sequence of SEQ ID NO. 31 (i.e., MM3 FC), and may be expressed in mammalian cells. Such an embodiment may display a T2 NMR contrast with an r2 of about 3.4 mM −1 s −1 . In some embodiments, the artificial protein may include a cofactor, such as Heme B.

Specific Artificial Proteins as Membrane Fluorescence Reporters

In some embodiments, an artificial protein for membrane fluorescence reporting may include an amino acid sequence selected from the group consisting of SEQ ID NOS. 63 and 66.

In some embodiments, the artificial protein for membrane fluorescence reporting may include the amino acid sequence of SEQ ID NO. 63 (i.e., AM-528-C4), and may be expressed in mammalian cells and trafficks to the membrane. In some embodiments, the artificial protein for membrane fluorescence reporting, which includes the amino acid sequence of SEQ ID NO. 63, may include the cofactor biliverdin (BV). In certain embodiments, the biliverdin may bind to the transmembrane region of the artificial protein and fluoresce.

In some embodiments the artificial protein for membrane fluorescence reporting may include the amino acid sequence of SEQ ID NO. 66 (i.e., AM-1196), and may be expressed in mammalian cells and trafficks to the membrane. In some embodiments, the artificial protein for membrane fluorescence reporting, which includes the amino acid sequence of SEQ ID NO. 66, may include the cofactor of biliverdin (BV). In certain embodiments, the biliverdin may bind to the HP region of the artificial protein and fluoresce.

Specific Artificial Proteins as Stark Effect Reporters

In some embodiments, an artificial protein for stark effect reporting may include an amino acid of SEQ ID NO. 69.

In some embodiments, the artificial protein for stark effect reporting may include the amino acid sequence of SEQ ID NO. 69 (i.e., AM-528), and may be expressed in mammalian cells and trafficks to the membrane. In some embodiments, the artificial protein for stark effect reporting, which includes the amino acid sequence of SEQ ID NO. 69, may include the cofactor biliverdin (BV). In certain embodiments, the biliverdin may bind to the transmembrane region of the artificial protein and fluoresce. Moreover, in certain embodiments, the artificial protein for stark effect reporting, which includes the amino acid sequence of SEQ ID NO. 69, may be sensitive to voltage and may demonstrate an electrochromic shift (i.e., a Stark effect).

Specific Artificial Proteins as Metal Binding Reporters

In some embodiments, an artificial protein for metal binding reporting may include an amino acid sequence selected from the group consisting of SEQ ID NOS. 35, 36, 37, 38, 39, 40, 41, 141, and 142.

In some embodiments, the artificial protein for metal binding reporting may bind a metal selected from the group consisting of Zn 2+ , Fe 2+ , Fe 3+ , Mn 2+ , Mg 2+ , Cu + , Cu 2+ , Co 2+ , Co 3+ , Ca 2+ , and K + . In some embodiments, the artificial protein for metal binding reporting may bind Ca 2+ .

In some embodiments, the artificial protein for metal binding reporting may include the amino acid sequence of SEQ ID NO. 35 (i.e., MZH3), and may be expressed in mammalian cells. Such an embodiment may bind a metal, such as Ca 2+ .

In some embodiments, the artificial protein for metal binding reporting may include the amino acid sequence of SEQ ID NO. 36 (i.e., MZH3 H138D), and may be expressed in mammalian cells. Such an embodiment may bind a metal, such as Ca 2+ .

In some embodiments, the artificial protein for metal binding reporting may include the amino acid sequence of SEQ ID NO. 37 (i.e., MZH3 H138N), and may be expressed in mammalian cells. Such an embodiment may bind a metal, such as Ca 2+ .

In some embodiments, the artificial protein for metal binding reporting may include the amino acid sequence of SEQ ID NO. 38 (i.e., MZH3 H67D, H138D), and may be expressed in mammalian cells. Such an embodiment may bind a metal, such as Ca 2+ .

In some embodiments, the artificial protein for metal binding reporting may include the amino acid sequence of SEQ ID NO. 39 (i.e., MZH3 H67D, H138N), and may be expressed in mammalian cells. Such an embodiment may bind a metal, such as Ca 2+ .

In some embodiments, the artificial protein for metal binding reporting may include the amino acid sequence of SEQ ID NO. 40 (i.e., MZH3 H67N, H138D), and may be expressed in mammalian cells. Such an embodiment may bind a metal, such as Ca 2+ .

In some embodiments, the artificial protein for metal binding reporting may include the amino acid sequence of SEQ ID NO. 41 (i.e., MZH3 H67N, H138N), and may be expressed in mammalian cells. Such an embodiment may bind a metal, such as Ca 2+ .

In some embodiments, the artificial protein for metal binding reporting may include the amino acid sequence of SEQ ID NO. 141 (i.e., MZH3 H67D), and may be expressed in mammalian cells. Such an embodiment may bind a metal, such as Ca 2+ .

In some embodiments, the artificial protein for metal binding reporting may include the amino acid sequence of SEQ ID NO. 142 (i.e., MZH3 H67N), and may be expressed in mammalian cells. Such an embodiment may bind a metal, such as Ca 2+ .

In some embodiments, the artificial protein for metal binding reporting may include the amino acid sequence of SEQ ID NO. 147 (i.e., MZH3 P3G H9A Q10D L12I A13R F16L T91R G92E L95G G100N P105T L106R R107L Q108E H110I A114G Q115R Q118R V182M Q183E L185C Q186G T188R G189A Q190M L192R W193N), and may be expressed in mammalian cells.

Methods of Use

Artificial proteins described herein are well suited for transporting a cofactor to a desired location of a cell. In an embodiment, an artificial protein described herein is used to transport a cofactor to the membrane of a cell, for example, from the nucleus of the cell to the membrane of the cell. In an embodiment, a composition described herein comprising an artificial protein and a cofactor is used to transport a cofactor to the membrane of a cell, for example, from the nucleus of the cell to the membrane of the cell. In an embodiment the cofactor is electrochromic.

In some embodiments, the compositions described herein comprising an artificial protein and a cofactor that is electrochromic are well suited for detecting electrical activity of a cell. In some embodiments, a host cell can be transfected to express a composition comprising an artificial protein as described herein and a cofactor, wherein the artificial protein is configured to traffic to the cell membrane. In some embodiments the cofactor is electrochromic. In some embodiments the cofactor is a fluorophore. In some embodiments the method further comprises detecting a change in an emission of light from the cofactor. In some embodiments the emitted light may be in the visible to near infrared (IR) region of the electromagnetic spectrum. The method may further comprise correlating the light emission to an electrical activity of the cell. For example, the method may comprise correlating wavelength of the emission of light or number of photons emitted per second to an electrical activity of the cell. In some embodiments a light emission is detected at a first time and a light emission is detected at a second time. In such embodiments the method may further comprise calculating a difference between the light emission at the first time and the light emission at the second time and correlating the difference to a change in electrical activity of the cell.

In some embodiments, the compositions described herein comprising an artificial protein and a cofactor that is fluorescent may be used as optical reporters of cell physiology. In some embodiments a composition described herein comprising an artificial protein and a cofactor that is fluorescent may be used to detect changes in the concentration of a chemical, such as a metal ion or proton. For example, in an embodiment binding of a metal ion to a composition of the invention may increase the fluorescence of the cofactor by increasing the rigidity of the artificial protein. In another embodiment, an artificial protein and a cofactor that is fluorescent may be used to detect a ligand binding event. In another embodiment, an artificial protein and a cofactor that is fluorescent may be used to detect a protein binding event and/or a protein interaction event. In another embodiment, an artificial protein and a cofactor that is fluorescent may be used to detect a change in oxidative state. In some embodiments, a host cell can be transfected to express a composition comprising an artificial protein as described herein and a cofactor. In some embodiments the cofactor is a fluorophore. In some embodiments the method further comprises detecting a change in an emission of light from the cofactor. In some embodiments the emitted light may be in the visible to near infrared (IR) region of the electromagnetic spectrum. The method may further comprise correlating the light emission to an aspect of the cell's physiology, such as concentration of a chemical, such as a metal ion or proton. For example, the method may comprise correlating wavelength of the emission of light or number of photons emitted per second to an aspect of the cell's physiology, such as concentration of a chemical, such as a metal ion or proton. In some embodiments a light emission is detected at a first time and a light emission is detected at a second time. In such embodiments the method may further comprise calculating a difference between the light emission at the first time and the light emission at the second time and correlating the difference to a change in an aspect of the cell's physiology, such as concentration of a chemical, such as a metal ion or proton.

In some embodiments, the compositions described herein comprising an artificial protein and a cofactor may be used to enhance contrast of proton nuclear magnetic resonance imaging. In some embodiments, suitable compositions include a cofactor that interacts with water. In some embodiments, suitable compositions include a cofactor that is a heme. In some embodiments, suitable compositions include a cofactor that is a metal ion. In some embodiments suitable compositions include a heme and a metal ion as cofactors. In some embodiments, compositions described herein may increase T2 contrast. In some embodiments a composition described herein may be used as a genetically encoded transcriptional reporter for protein expression detection by magnetic resonance imaging. In some embodiments a composition described herein may be used as a fusion tag for protein expression detection by magnetic resonance imaging.

It will be appreciated by persons skilled in the art that numerous variations and/or modifications may be made to the invention shown in the specific embodiments without departing from the spirit and scope of the invention as broadly described. Further, each and every reference cited above is hereby incorporated by reference as if fully set forth herein.

Artificial Proteins of the Invention as Voltage Sensors

Optical transmembrane voltage sensors are of particular importance because of the ability to resolve cellular and sub-cellular activities with commercial imaging equipment for ex vivo and in vivo brain analyses. Previously reported sensors were organically synthesized amphipathic voltage sensitive dyes (VSDs) that were embedded into the plasma membrane and reported activity as Stark Effect probes, in which transmembrane potential modulates optical absorbance efficiency, wavelength and resultant emission. More recently, genetically encoded protein-based probes—i.e. optogenetic sensors or genetically encoded voltage indicators (GEVIs)—have dominated technology development efforts for their ability to isolate the activity of genetically targeted cell types when heterologously expressed under cell-type specific promoters. Previously reported GEVIs present several problems: 1) inertial and structural reorganization of previously reported sensors results in a fundamental limit to the temporal resolution such sensors can achieve; 2) natural proteins broadly impose engineering constraints (e.g. dimness of sensor); and 3) signal directionality of monomeric fluorescent protein (FP)-voltage sensor domains of membrane proteins (mVSDs) allows for bleaching to be mistaken for increased reactivity (i.e. as a false positive). There is a need for improved optical voltage sensors.

High-performance in vivo optical recording of neuronal electrical activity with the temporal and fine-feature waveform resolution on par with whole-cell patch clamp electrophysiology would permit the physiology of individual cells and cell types to be correlated to (i) neural circuit-level activity, and (ii) to the resultant activity-dependent behaviors, cognitive states, and affective states observed in the normal and diseased brain. Optical transmembrane voltage sensors are of particular importance because of the ability to resolve cellular and sub-cellular activities with commercial imaging equipment for ex vivo and in vivo brain analyses. An ideal optical reporter of electrophysiological activities would be optimized along multiple parameters:

Temporal Resolution (for Maximal Information Content): Voltage indicator response kinetics should be sub-ms timescale to reliably resolve in vivo individual action potentials, particularly during periods of high activity such as evoked responses. Microsecond-scale responses that faithfully resolve the waveforms of spikes and sub-threshold “minis” maximize information content by revealing molecular scale phenomenon such as specific ion channel/receptor contributions to spike propagation and synaptic transmission.

Safety and Genetic Targeting (for Chronic Neural Circuit Analysis): Isolating physiological activity from targeted cell types facilitates neural circuit analyses in a way that electrical recording cannot. Toxicity and exogenous chromophore supplementation impede chronic in vivo applications. Excessive membrane charge or reporter loading alters cell capacitance, and consequently, spike timing and circuit dynamics.

Signal Amplitude and Responsiveness (for Maximal Measurement Reliability): Lesser voltage-sensitivity and/or brightness reduce signal amplitude and signal-to-noise ratio (SNR), thereby making it difficult to detect sub-threshold events and “minis” that are critical to synaptic scaling and homeostatic plasticity. Lesser signal quality also indirectly reduces temporal resolution due to the requirement for increased signal integration/averaging, and increase hardware cost due to the need for sensitivity. Negative signal direction (emission decreases with depolarization) confounds reporter bleaching as false positives for neural activity.

Moreover, it is also desirable that a reporter possess:

Tunable Structure and Mechanism (for Rational Optimization): Certainty over the biophysical mechanisms augment engineering capacity for enhanced function, particularly with known first principles and molecular structures. Chromophore redshift-tuning increases light penetration, reduces background noise from endogenous proteins (including hemoglobin), and reduces scattering for better spatial contrast.

Strategic positioning of a chromophore within a transmembrane (TM) artificial protein of the invention allows for voltage sensing by the optical Stark Effect ( FIG. 1 ), by which chromophores exhibit electric field-induced changes in absorbance on the ns timescale resulting in ultrafast changes in observed fluorescence for example, Stark-effect dyes may exhibit ˜2 μs-resolution in neurons. The voltage-dependent optical response can be molecularly amplified by introducing non-fluorescent heme co-factors to (i) tune the local electric field changes at a Stark fluorophore via electron transfer and (ii) shift the emission wavelength away from the fluorescence at neuronal resting state ( FIG. 2B ). In some embodiments, this combination of optical Stark Effect and local molecular amplification of field-sensitivity will be (i) ultrafast (μs resolution or ˜102 enhanced vs. existing GEVIs), (ii) ultrahigh voltage-sensitive (ΔF/F of 350% per 100 mV, or ˜20-fold enhanced vs. existing GEVIs).

In some embodiments, the artificial proteins of the invention that may be provided for voltage sensing and may function as Stark Effect reporters, may include an artificial protein or sequence of amino acids set forth in Table 2, or a variant thereof.

In some embodiments, the artificial proteins of the invention that may be provided for voltage sensing, and may function as Stark Effect reporters, may include an artificial protein comprising a sequence of amino acids described by one or more of Generic Sequence A, Generic Sequence B, Generic Sequence C, and Generic Sequence D.

In some embodiments, the artificial proteins of the invention that may be provided for voltage sensing, and may function as Stark Effect reporters, may include an artificial protein comprising a sequence of amino acids described by one or more of SEQ ID NOS. 1 to 16, or a variant thereof.

In some embodiments, the artificial proteins of the invention that may be provided for voltage sensing and may function as Stark Effect reporters may include an artificial protein described by one of SEQ ID NO. 21 (“GLSloop”), 22 (“PEB MUT B”), 23 (“PEB MUT C”), 24 (“PEB MUT D”), 25 (“dFP1.0”), 27 (“C41 Stab Map”), and 29 (“C41 Py Stab”), or a variant thereof.

The following examples describe the invention in further detail. These examples are provided for illustrative purposes only, and should in no way be considered as limiting the invention.