WO2024015362A1 - Protéines fluorescentes chimiquement stables pour microscopie avancée - Google Patents

Protéines fluorescentes chimiquement stables pour microscopie avancée Download PDF

Info

Publication number
WO2024015362A1
WO2024015362A1 PCT/US2023/027373 US2023027373W WO2024015362A1 WO 2024015362 A1 WO2024015362 A1 WO 2024015362A1 US 2023027373 W US2023027373 W US 2023027373W WO 2024015362 A1 WO2024015362 A1 WO 2024015362A1
Authority
WO
WIPO (PCT)
Prior art keywords
protein
hfyfp
fluorescent protein
fluorescence
fps
Prior art date
Application number
PCT/US2023/027373
Other languages
English (en)
Inventor
Benjamin C. CAMPBELL
Gregory A. Petsko
Original Assignee
Cornell University
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Cornell University filed Critical Cornell University
Publication of WO2024015362A1 publication Critical patent/WO2024015362A1/fr

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/60—Fusion polypeptide containing spectroscopic/fluorescent detection, e.g. green fluorescent protein [GFP]

Definitions

  • the fluorescent protein comprises the amino acid sequence of any one of SEQ ID NOs: 1, 3, 5, 7-10, and 12. In some embodiments, the fluorescent protein is chloride insensitive.
  • the disclosure also encompasses a fusion protein comprising the fluorescent protein disclosed herein. In some embodiments, the fluorescent protein is linked to a polypeptide.
  • the disclosure also encompasses a nucleic acid molecule encoding the fluorescent protein disclosed herein.
  • the disclosure also encompasses a nucleic acid molecule encoding the fusion protein disclosed herein.
  • the disclosure also encompasses a nucleic acid molecule comprising the nucleotide sequence selected from SEQ ID NOs: 2, 4, and 6. In some embodiments, the nucleic acid molecule is a cDNA.
  • the disclosure also encompasses a vector comprising the nucleic acid molecule disclosed herein.
  • the disclosure also encompasses a host cell comprising the nucleic acid molecule disclosed herein.
  • the disclosure also encompasses a host cell comprising the vector disclosed herein.
  • the disclosure also encompasses a host cell comprising the fluorescent protein disclosed herein.
  • the disclosure also encompasses a host cell comprising the fusion protein disclosed herein.
  • the host cell is a mammalian host cell.
  • the disclosure also encompasses a method of detecting the expression of a protein of interest in a cell.
  • the method comprises introducing into a cell a nucleic acid molecule comprising a nucleotide sequence encoding a protein of interest fused to a nucleotide sequence encoding the fluorescent protein disclosed herein.
  • the method may further comprise culturing the cell under conditions suitable for the expression of said protein of interest.
  • the method may further comprise detecting the expression of said protein of interest by measuring the fluorescence of said cell.
  • said nucleic acid molecule being operatively linked and under the control of a suitable expression control sequence.
  • the fluorescence is measured by optical means.
  • the optical means is fluorescent microscopy, flow cytometry, spectroscopy, laser-scanning confocal microscope, confocal microscope, correlative light and electron microscopy, or protein-retention expansion microscopy.
  • the disclosure also encompasses a method of purifying a protein of interest.
  • the method comprises introducing into a cell a nucleic acid molecule comprising a nucleotide sequence encoding a protein of interest fused to a nucleotide sequence encoding the fluorescent protein disclosed herein.
  • the method may further comprise culturing the cell under conditions suitable for the expression of said protein of interest.
  • the method may further comprise lysing the cell.
  • the method may further comprise purifying the protein of interest by purifying the fluorescent protein.
  • Figures 1A-1M shows biochemical characterization of hyperfolder YFP and its performance in cells.
  • Figure 1A shows excitation and emission spectrum of hfYFP.
  • Figure 1B shows absorbance spectrum at pH 7.5. Arrow indicates the non-excitable 390-405 nm band present in eYFP and absent in hfYFP and mhYFP. The latter two spectra overlap.
  • Figure 1D shows fluorescence of FP-expressing bacteria after overnight growth at 37 °C.
  • Figure 1F shows pH titration of hfYFP and eYFP.
  • Figures 1H-1M show live HeLa cells imaged after overnight transfection using plasmids encoding: Figure 1H shows LifeAct-7aahfYFP; actin. Figure 1I shows hfYFP-6aa-tubulin; tubulin. Figure 1J shows hfYFP-15aa-clathrin; clathrin. Figure 1K shows pCytERM-hfYFP; endoplasmic reticulum.
  • Figure 1I shows COX8A[x4]-4aa- hfYFP; mitochondria, here shown in BE(2)-M17 cells.
  • Figure 1M shows H2B-6aa-hfYFP; nucleus, in HeLa cells. Scale bars: 10 um
  • Figures 2A-2H show stability of purified fluorescent proteins in chaotropic conditions.
  • Figure 2A shows kinetic unfolding in 6.3 M buffered guanidinium HCI (GdnHCI) solution, pH 7.5. Inset figure: first 10 min of the same data set.
  • FIG. 1 fluorescence of 1 uM purified superfolder GFP (sfGFP) and hyperfolder YFP (hfYFP) protein after 3 months in 6.3 M GdnHCI solution at room temperature (RT), protected from light.
  • Figure 2B shows kinetic unfolding in 3.6 M buffered guanidinium thiocyanate (GdnSCN), pH 7.5.
  • Inset first 60 s. Every individual data point in Figures 2A-2B is normalized to native protein run in parallel under identical conditions in the same buffer without Gdn.
  • Figure 2C shows equilibrium unfolding in GdnHCI and Figure 2D shows in GdnSCN, at 24 hr.
  • Fluorescence is normalized to the intensity value for each FP at 0 M Gdn; mean ⁇ s.d.
  • Figure 2E shows fluorescence intensity during isothermal melting at 87 °C, relative to time zero, with normalization as described in Figures 2A-2B shows. Inset: first 8 min data set.
  • Figure 2G shows fluorescence during a 0.3 °C/min temperature ramp from 25-100 °C, with temperature range 60-100 °C displayed. Data are normalized to the intensity values at 25 °C for the individual FPs.
  • Figure 2H shows intensity versus H 2 O 2 concentration in buffered solution after exactly 15 min incubation at RT.
  • Figures 3A-3E show fluorescence retained by transfected human cells after expansion microscopy and fixation.
  • Figure 3A shows Fluorescence retained by HEK293T cells after fixation using room temperature 4% PFA in PBS, pH 7.4, or b, 4% PFA + 5% Glut in PBS, pH 7.4. Cytosolic expression, n > 227 cells for each condition per FP.
  • Figure 3C shows representative images of HEK293T cells captured on a widefield microscope using the same acquisition settings before and after fixation as in Figure 3B. Retained fluorescence (%) is indicated below the fixed images in gray. Scale bars, 20 pm. Cytosolic expression.
  • Figure 3DA shows HeLa cells transfected with LifeAct-mhYFP were imaged on a confocal microscope before proExM (left); after partial expansion of the hydrogelenmeshed sample using PBS (middle); and after full expansion using dd- H20 (right). All images were acquired at 63x magnification.
  • Figure 3E shows fluorescence retained by H2B-FP transfected HeLa cells in hypertonic "shrinking solution” after full expansion in proExM, relative to the same live cells (Methods).
  • Complete statistics for Figures 3A, B, and E are available in Figure 24.
  • proExM protein-retention expansion microscopy
  • PFA paraformaldehyde
  • Glut glutaraldehyde
  • PBS phosphate buffered saline
  • mNG mNeonGreen
  • mClo3, mClover3 mGL, mGreenLantern
  • hfYFP hyperfolder YFP
  • Figures 4A-4H show resilience of hfYFP during electron microscopy preservation.
  • Figure 4A shows Osmium tetroxide (OsO 4 ) dose-response curve using purified FPs after 1 hr incubation at RT.
  • n 3 replicate experiments, mean ⁇ s.e.m.
  • Figure 4C shows workflow for evaluating the performance of FPs in electron microscopy (EM). FPs were expressed in the cytoplasm using adeno-associated virus (AAV) transduction and imaged using confocal microscopy. Cultures were then post-fixed with EM fixative (4% paraformaldehyde and 0.2% glutaraldehyde), harvested in bovine serum albumin (BSA), and embedded in agarose. The cryosectioning. Images of mounted cryosections were collected using the same settings as for live imaging, to evaluate fluorescence retention.
  • EM fixative 4% paraformaldehyde and 0.2% glutaraldehyde
  • BSA bovine serum albumin
  • Figure 4D shows HEK293T cells imaged using confocal microscopy and 488 nm laser excitation after AAV transduction of cytosolic eGFP, mGL, or hfYFP. Magnification, 10x. Imaging parameters are identical between FPs.
  • Figure 4E shows representative images of cultures viewed at 63x magnification with DAPI staining. Imaging parameters are identical between FPs and are different than those used in Figure 4E.
  • Figure 4F shows background-subtracted mean fluorescence intensity units (MIU) of live and osmicated-and- OCT-embedded cultures, averaged from 10 ROIs per FP, per condition. These raw intensity values should not be used for brightness comparison because different settings were used for each FP.
  • MIU mean fluorescence intensity units
  • Figure 4G shows cellular fluorescence retention after OsO 4 incubation and OCT embedding, expressed as a percentage relative to the same live cells.
  • Figure 4H left shows Toluidine Blue staining was used to verify the presence of cells before preparation. Cells were fixed in EM aldehyde fixative, followed by high-pressure freezing and freeze substitution, 1% OsO 4 incubation, dehydration with 100% acetone, HM20 resin infiltration, and UV polymerization.
  • Figure 4H right shows laser scanning confocal images show 100 nm thick sections of fluorescent HEK293 cells expressing eGFP (top), mGL (middle), and hfYFP (bottom). Scale bars, 20 pm, unless otherwise indicated.
  • FIGS. 5A-5H show structure-guided engineering of large Stokes shift GFPs.
  • Figures 5A- 5B show hfYFP crystal structure. Residues on 13-strands 10 (cyan) 11 (magenta) that were targeted to generate the LSS-FP libraries are indicated. Dashes: hydrogen bonds.
  • c Excitation spectra of mGL, LSSmGFP, and LSSA12. The latter two FP spectra overlap.
  • Figure 5D shows excitation spectra of mT-Sapphire and eGFP. Arrows indicate wavelength ranges where cross-excitation would be expected from typical 405 nm or 470-491 nm excitation sources.
  • Figure 5E shows live HeLa cells transfected with LifeAct-eGFP and H2B-mT-Sapphire or LifeAct-mGL and H2B- LSSmGFP. Excitation at 470 nm co-excites mT-Sapphire and eGFP (white arrow) whereas LSSmGFP is not excited by 470 nm. Scale bars: 25 um.
  • Figure 5F shows benchtop fluorescence- assisted purification of SAV from E.
  • eGFP coli inclusion bodies using eGFP, hfYFP, or LSSmGFP fusions as depicted in Figure 5G.
  • eGFP is immediately denatured during inclusion body solubilization with 6 M GdnHCI (arrow) and never regains fluorescence.
  • hfYFP is illuminated using a 470 nm LED and photographed through a long-pass filter; LSSmGFP: 405 nm LED excitation without emission filter.
  • Figure 5G shows the fusion construct used for purification contains an N-terminal hexahistidine (His6)-tagged hfYFP (or eGFP or LSSmGFP for the example in Figure 5F) and Cterminal Protein of Interest (POI) separated by a flexible linker containing a TEV cleavage site. After cleavage, His6-TEV and His6- hfYFP are adsorbed to Ni-NTA resin and the flow-through is collected to obtain the POI.
  • Figure 5H shows fluorescence of biotin-4-fluorescein is quenched upon SAV binding (see Kada et al., Biochimica et Biophysica Acta, 1999).
  • Figures 6A-6B show protein quantified from expression of fusion constructs in E. coll.
  • Figure 6A shows coomassie gels of soluble protein, insoluble protein, and protein from the media of the same cultures (without cells). Equal quantity of protein was run in each lane as determined by BCA assay, except for the media condition, where equal volume was used without adjustment.
  • the molecular weight (MW) predicted by ExPASy for the FP fusions with mScarlet-1 (mSca), Bacillus circulans xylanase (Bcx), and streptavidin (SAV) are approximately 57 kDa, 51 kDa, and 44 kDa, respectively.
  • the MW of an avFP is —27 kDa.
  • Figures 7A-7E show characterization of cysteine-free mutants.
  • Figure 7A shows crystal structure of Clover (PDB ID: 5WJ2), with cysteines indicated. In all avFPs, C48 and C70 are situated -24 A apart (dotted line) and cannot form a disulfide bond under native conditions in properly folded protein.
  • Figure 7D shows data from Figure 7C plotted as the negative first derivative of the cells.
  • Figures 9A-9D show screening of fluorescent protein libraries.
  • Figure 9A shows melting curves for a subset of C48S/C7OV and
  • Figure 9B shows yellow fluorescent mutants compared to eGFP and eYFP.
  • Figure 9C shows cellular brightness for each FP in three mammalian cell lines (Methods).
  • n 3 replicate experiments, each averaging 4 independent transfections, mean ⁇ s.e.m. mF6-HL and mfoxYY were not tested in BE(2)-M17 cells.
  • Clover-cc signifies the C48S/C7OV mutations to distinguish it from unmodified Clover in this figure.
  • Figures 10A-10B show effect of cysteine residues on refolding.
  • Figure 10A shows refolding of FPs after denaturation, relative to untreated native samples.
  • Figure 11A shows coomassie gel of soluble protein extracted from E. coli lysate after overnight expression. Black arrowhead indicates the fluorescent protein band. The same quantity of protein was run in each lane, so the band intensity at -27 kDa indicates soluble FP yield.
  • Figures 12A-12C show determination of FP oligomeric state.
  • Figure 12A shows gel filtration chromatography using 10 uM purified fluorescent protein in a Superdex S200 Increase 10/300 GL sizing column with elution monitored at 280 nm. The monomer fraction elutes at -17.0 mL and the dimer -15.5 mL. Data are normalized to the maximum A280 value for each FP.
  • Figure 12B shows representative HeLa cells imaged 16 hr after chemical transfection with CytERM-FP plasmids. The organized smooth endoplasmic reticulum assay (OSER) is a cellular FP aggregation protocol.
  • OSER smooth endoplasmic reticulum assay
  • OSER Cells with large, bright aggregates, like those in tdTomato, are scored as "OSER.” Normal cells have healthy reticular ER structure, nuclei, and no OSER structures (see Methods; refer to definitions by Costantini et al., Traffic, 2012). Scale bars, 25 pm. mGL: mGreenLantern. hfYFP: hyperfolder YFP. hfYFP-K: hfYFP-V206K. mhYFP: monomeric hyperfolder YFP. tdTomato: tandem dimer Tomato. Figures 13 shows isothermal melting of fluorescent proteins. FPs were rapidly heated to the target temperatures in individual wells using the gradient function of a real-time PCR machine.
  • hfYFP hyperfolder YFP.
  • Figures 14A-14K show Behavior of FPs in sodium hydroxide solution.
  • Figure 14A Clover and Figure 14B sfGFP show absorbance scans of the native and alkalinedenatured protein.
  • Figures 14D-14K show time-dependent FP denaturation in 1 M NaOH (Methods). Absorbance at 447 nm (brown) and 505 nm (green) was measured every 10 s, promptly after mixing 2 M NaOH into a cuvette containing the same volume of FP solution (A505 c 1.0.3-0.9) in phosphate buffered saline (PBS) for a final concentration of 1 M NaOH.
  • PBS phosphate buffered saline
  • Figure 15 shows kinetic unfolding of V206 and K206 mutants in GdnHCI. Fluorescent proteins were unfolded in 6.3 M GdnHCI, pH 7.5. Asterisks indicate the final mutants, i.e., mGreenLantern, mF4Y-SR, hfYFP, and mhYFP, whose properties are reported in Table 2 and elsewhere.
  • Figures 16A-16H show rational engineering and characterization of fluorescent proteins using only 18 of the 20 naturally occurring amino acids.
  • Figure 16A shows location of Trp57 in a high-resolution eGFP crystal structure (PDB ID: 4EUL), with interactions of particular interest indicated by dashed lines. Showing: vdW interactions, including weakly polar interactions from C48; sulfur-aromatic interactions at approximately 5.5 A distance to the ring centroid; hydrogen bonds.
  • Figure 16B shows absorbance spectra of W57F mutants and parental templates.
  • Figure 16C shows isothermal melting of W57F mutants at 80 °C.
  • Figure 16E shows melting curves of W57F mutants compared to the original proteins.
  • Figure 16F shows whole-cell fluorescence intensity of E. coli cultures grown overnight before extraction of soluble protein. One experiment is shown.
  • Figure 16H shows spectroscopic characterization table of W57F mutants.
  • mF4P-W57F and hfYFP-W57F contain no cysteine or tryptophan residues.
  • Molecular brightness x 0103.
  • E. coli brightness fluorescence data from f with experimental samples normalized to eGFP.
  • Figures 17A-17D show proton wires of hyperfolder YFPs and FOLD6.
  • Figure 17A shows hfYFP and mhYFP superposition.
  • mhYFP displays an atypical E222 conformation for a YFP in which E222 is hydrogen-bonded (H-bonded) to [N2] and 5205 instead of [N2] and wat 2 .
  • Figure 17B shows FOLD6 and Clover superposition.
  • FIG. 17C shows overhead view of hfYFP and Citrine crystal structures.
  • the chromophore phenolate points toward [3-strand 7 at the 12 o'clock position.
  • the polar and nonpolar cores of the protein are indicated at the 7 o'clock and 3 o'clock positions.
  • the F46L and F64L mutations in hfYFP, relative to Citrine, are located at the 3 o'clock position (bolded).
  • FIG. 17D shows FOLD6 cutaway side view of the protein's polar core, with the central a-helix visible, and the chromophore phenolate pointing toward B-strand 7.
  • H2O3 is stacked on top.
  • sfGFP side chains of H169 and 1167 are visible in grey line form for comparison.
  • Figures 18A-18D show chromophore conservation and proposed role of C48 and C70 in avFPs.
  • Figure 18A shows superposition of hfYFP, eYFP, Citrine, and Venus.
  • FIG. 18B shows structure of the hfYFP chromophore environment as seen from B-strand 8.
  • Y203 is pictured above the chromophore.
  • FIG. 18C shows the C48S mutation in hfYFP produces a tight 2.3 A H-bond between the S48 hydroxyl side chain and the G51 carbonyl.
  • L53 has rotated relative to its conformation in eGFP to stabilize W57 through vdW forces.
  • C48 of eGFP is just close enough to the electropositive edges of the F27 and W57 rings, with an average 5.5 A distance.
  • W57 No is Hbonded to D216 0 61 in every structure, but we have removed the foreground D216 side-chain in the images to improve visualization of residue 48.
  • Figure 18D shows the C70V mutation in hfYFP eliminates the lone- pair electrons of the C70 sulfur atom that in eYFP and other avFPs, can interact with the electropositive edges of the F8, F71, and Y92 ring to stabilize them (dashes: sulfuraromatic interactions). These sulfur-aromatic interactions likely provide greater support than vdW forces alone. Consequently, ring positions have shifted 0.3-0.5 A in hfYFP relative to Venus to adjust to new vdW distances from V70. 3.0 A.
  • Figure 19A shows eGFP displays an H-bond between E17 and S30 in addition to the E115- R122 salt bridge observed in each of the depicted structures.
  • Figure 19B shows sfGFP.
  • Figure 19C shows FOLD6, with multiple conformations observed for the critical R30 superfolder mutation that stabilizes several neighboring side-chains.
  • Figure 19D shows in hfYFP, R30 is found in a single conformation that secures it with four ionic bonds, one each to the E17 and D19 carboxylates, and two to main-chain carbonyls.
  • Figure 19E shows mhYFP shows a sfGFP-like salt bridge network with an additional R30 conformation observed.
  • Figures 20A-20F show library generation and screening of GFPs with a large Stokes shift.
  • Figure 20A shows excitation spectrum of hfYFP and hfYFP-KSI (hfYFP-V206K/G65S/Y2031).
  • FIG. 20B shows degenerate codon sets chosen to mutate hfYFP-KSI at residues shown in Fig.5a-b to produce an LSS FP without B-band excitation.
  • Figure 20C shows excitation spectra of 33 mutants from the library in Figure 20B that were selected from LB-agar plates based on high 410-nm and low 470-nm excitation by eye under LED illumination.
  • Light green LSSA12.
  • Inset zoom of the B-band excitation range.
  • Figure 20D shows kinetic unfolding of clarified lysate of 23 mutants from library Figure 20C in buffered 6.3 M GdnHCI.
  • Figure 20E shows kinetic unfolding of purified FPs.
  • Figure 20F shows excitation spectra of LSSA12 point mutants. The spectra of these mutants reinforce the importance of residues S65 and D222 for eliminating B-band excitation of LSSA12. Note that the excitation spectra of mT-Sapphire and LSSA12-S65G overlap, as do LSSA12 and LSSA12-E204D.
  • Figures 21A-21K show Additional characterization of LSSmGFP.
  • Figure 21A shows introducing the V68Q mutation into mT-Sapphire greatly diminished the 488 nm excitation band, suggesting generalizability of this LSSmGFP derived mutation for spectral tuning of LSS FPs.
  • Figure 21B shows melting curve derivative plots generated from the thermofluor assay. Here, SYPRO Orange is used instead of endogenous fluorescence. Tm values are reported in Table 5.
  • Figure 21C shows kinetic unfolding of purified FPs at 1 uM concentration in bufferednHCI 6.3 M solution, pH 7.4.
  • Figure 21D shows purified FP at 0.1 uM concentration incubated at RT in 16 different solutions of H 2 O 2 in Tris buffer, pH 7.4, for exactly 15 min.
  • Figure 21E shows representative images of LSS FPs in the OSER assay when expressed from pCytERM fusions. White wedge in quantitation but might represent an important effect. Scale bars, 25 pm.
  • Figure 21F shows OSER assay results analyzed using scoring criteria described in Figure 12.
  • Figures 21G-21K shows live HeLa cells imaged after overnight transfection using plasmids encoding: Figure 21G, LifeAct- 7aa-LSSmGFP; actin.
  • Figure 21H LSSmGFP-6aa-tubulin; tubulin.
  • Figure 21IG LSSmGFP- 15aa-clathrin; clathrin.
  • Figure 21J COX8A[x4]-4aa-LSSmGFP; mitochondria.
  • Figure 22 shows benchtop fluorescence-assisted protein purification workflow. As described in Methods, proteins were purified by Ni-NTA chromatography (immobilized metal affinity chromatography, or IMAC) under fully denaturing conditions with all buffers containing 6 M GdnHCI.
  • IMAC immobilized metal affinity chromatography
  • the experiment is completed once the fusion protein is dialyzed out of denaturing purification buffer. Otherwise, the fusion construct illustrated in Figure 5G is cleaved using TEV protease and the protein of interest (P01) is isolated using IMAC: His6-TEV and His6-hfYFP are adsorbed onto the resin while the untagged and cleaved POI elutes in native buffer of choice for collection.
  • the soluble fraction is purified by IMAC; fusion is cleaved using TEV protease in a dialysis cassette (or after dialysis); and the unbound, cleaved POI is obtained by Ni-NTA chromatography in the flow- through while His6-TEV and His6-hfYFP remain bound to the resin. All steps of purification can be visualized using 470 nm illumination for the hfYFP fusion or 405 nm illumination for the LSSmGFP fusion.
  • Isolated POI The final image (“Isolated POI") depicts successful isolation of mScarlet from the hfYFP-mScarlet fusion in phosphate buffered saline after cleavage.
  • * if the refolding buffer inhibits TEV protease activity, a separate dialysis step is recommended to improve activity.
  • the TEV protease buffer selected is incompatible with IMAC (e.g., if nontrivial amounts of DTT or EDTA are present), then a dialysis step should be performed after cleavage, before IMAC.
  • Figure 23 shows that mhYFP is compatible with commercially available antibodies designed for eGFP.
  • Antibody signal co-localized with HEK293T cells expressing cytosolic FPs is a hyperfolder mutant related to mGreenLantern.
  • mNeonGreen is derived from from B. lanceolatum rather than A. victoria and therefore serves as a negative control.
  • Antibody channel Alexa 555 conjugated Donkey secondary antibody.
  • Merged image features DAPI in the blue Figure 24 shows statistics for Figure 3 and Figure 21. Data were analyzed using one-way ANOVA with multiple comparisons. Full details of the experiment from Figure 3 and Figure 21 are available in Methods.
  • Figure 25 shows fluorescent protein amino acid sequence comparison to mGreenLantern (mGL). Mutations that are most important to the properties of the specific FP are highlighted.
  • Figures 26A-26B show protein quantified from expression of fusion constructs in E. coli.
  • Figure 26A shows coomassie gels of soluble protein, insoluble protein, and protein from the media of the same cultures (without cells). Equal quantity of protein was run in each lane as determined by BCA assay, except for the media condition where equal volume was used without adjustment.
  • the molecular weight (MW) predicted by ExPASy for the FP fusions to mScarlet-1 (mSca), Bacillus circulars xylanase (Bcx), and streptavidin (SAV) are approximately 57 kDa, 51 kDa, and 44 kDa, respectively.
  • the MW of an avFP is —27 kDa.
  • the disclosure provides fluorescent proteins comprising the amino acid sequence selected from SEQ ID NOs: 1, 3, 5, 7-10, and 12.
  • the disclosure provides the rational engineering of a remarkably stable yellow fluorescent protein, ‘hyperfolder YFP,’ (hfYFP) that withstands chaotropic conditions that denature most biological structures within seconds, including superfolder GFP.
  • hfYFP contains no cysteines, is chloride insensitive, and tolerates aldehyde and osmium tetroxide fixation better than common and correlative light and electron microscopy (CLEM).
  • CLEM common and correlative light and electron microscopy
  • hfYFP and LSSmGFP represent a new generation of robustly stable FPs developed for advanced biotechnological applications.
  • FPs particularly constitutively fluorescent ones like green fluorescent protein (GFP)— are required to expand the reach of such methods.
  • GFP green fluorescent protein
  • FPs should have favorable properties for routine use, including fast and complete folding and maturation, high brightness and photostability, and low oligomericity when used in fusions.
  • mGreenLantern a bright, monomeric green FP that is well suited for ExM and tissue clearing methods such as 3DISCO, thereby facilitating neuronal imaging experiments including the tracing of supraspinal projections in a cleared, fully intact brain, while bypassing the laborious and time-consuming antibody enhancement steps.
  • hfYFP yellow fluorescent protein
  • hfYFP is a versatile FP that overcomes most of eYFP’s limitations and can directly replace it in many applications.
  • hfYFP offers powerful cross- compatibility with proExM and CLEM, as well as applications traditionally served by sfGFP.
  • Our crystal structures offer launch points for engineering novel biosensors and may even provide simple, actionable solutions to folding problems of existing sensors. Hyperfolder YFP is ripe for biotechnological applications that have previously been unreachable.
  • hfYFP survived all steps of CLEM preparation and may find use in super-resolution imaging and other advanced microscopy methods, as well as numerous biotechnological applications that can benefit from a fluorophore whose melting temperature is only 6 °C below the boiling point of water.
  • hfYFP showed the greatest structural plasticity, implying that it will tolerate random mutagenesis and circular permutation at least as well as sfGFP. Indeed, hfYFP proved to be an excellent template for engineering two new LSS-FPs, LSSA12 and LSSmGFP. hfYFP performs well in fusions, and mhYFP offers a slightly more monomeric option at a very small cost to stability. Hyperfolder YFP’s stability (Table 3) is uncommon for any class of protein, and perhaps most notable is its peculiar stability in GdnHCl solutions of 7 M concentration (Figure 2C), practically indefinitely (Figure 2A).
  • hfYFP resilience was not an idiosyncratic response to guanidinium: apart from the GdnHCl and GdnSCN kinetic- and equilibrium-unfolding experiments, hfYFP retained more fluorescence than eGFP, sfGFP, mClover3, mNeonGreen, eYFP, and even mGL, at higher temperatures and for greater lengths of time (Figure 13), in the presence of hydrogen peroxide (H ⁇ O ⁇ ) (Figure 2H), after exposure to paraformaldehyde (PFA) (Figure 3D), PFA/glutaraldehyde ( Figures 3B-3C), and in a 3% glyoxal / 20% ethanol, pH 4.0 more organelles and other cellular environments without fear of artifacts.
  • H ⁇ O ⁇ hydrogen peroxide
  • PFA paraformaldehyde
  • Figures 3B-3C PFA/glutaraldehyde
  • mNeonGreen is by far the least stable FP we tested against temperature, guanidinium, H 2 O 2 , glutaraldehyde, and OsO 4 —this FP should be used in challenging applications with great caution. Even small gains in fluorescence retained after chemical fixation or other quenching processes can amplify cellular brightness differences, and vice versa.
  • mGreenLantern with its 6.0- fold greater fluorescence than eGFP in mammalian cells compared to 2.4-fold for hfYFP, may be best suited for proExM (Figure 3A), while hfYFP may be most advantageous for CLEM due to its tolerance of osmication that matches that of mEos4b ( Figure 4A-4B).
  • hfYFP has proven itself to be a versatile tool for routine imaging and shows promise in the tested super-resolution modalities.
  • the high-resolution crystal structures of hfYFP, mhYFP, and FOLD6 that we solved to 1.7 ⁇ , 1.6 ⁇ , and 1.2 ⁇ resolution, respectively, offer excellent templates for biosensor engineering, particularly when combined with our characterization data (Tables 1-3), library development approach for the GFPs/YFPs, LSS-FPs, and the structural interpretations.
  • the crystallographic data and our characterized mutants enable us to describe which mutations are critical to hfYFP’s function and should be preserved during engineering, which are expendable, which can be transferred into existing templates to enhance them, and how that may be accomplished.
  • the dense hydrophobic packing of the hfYFP chromophore environment in addition to surface mutations and interactions that stabilize the barrel structure, may help the protein resist core solvation effects that have been proposed as part of a two-stage mechanism for GdnHCl-induced protein denaturation, thereby extending the duration of fluorescence perhaps even while the protein is in a molten globule state.
  • Hyperfolder YFP and FOLD6 have potential to serve similar functions as sfGFP, such as multiple epitope tag insertion, extremophile research, reconstitution of split fragments, sensor stabilization, circular permutation, and random mutagenesis, while their stability improvements open doors to new applications that have not yet been realized for expression-enhanced biosensors, perhaps along with concomitant decreases in cytotoxicity due to the large improvements in protein folding and solubility.
  • hfYFP is a versatile protein that may find use in expansion microscopy (proExM), correlative light and electron microscopy (CLEM), and tissue clearing.
  • hfYFP and LSSmGFP enable fluorescence-assisted protein purification and may even act as visualizable solubility tags ( Figures 5F-5G).
  • LSSmGFP and LSSA12 performed well in assays in which hfYFP excelled, including protein purification, and they may find similar uses.
  • Biotechnological applications that were previously complicated or irresolvable due to superfolder GFP’s limitations, such as the presence of cysteines and susceptibility to chemical denaturation, may now be in reach. Definitions Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure is related.
  • the term “and/or” as used in a phrase such as “A and/or B” herein is intended to include “A and B,” “A or B,” “A” (alone), and “B” (alone).
  • the term “and/or” as used in a phrase such as "A, B, and/or C” is intended to encompass each of the following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).
  • fusion protein refers to a protein composed of two or more polypeptides that, although typically unjoined in their native state, are joined to form a single continuous polypeptide.
  • linkage or “linker” (L) is used herein to refer to an atom or a collection of atoms used to link, preferably by one or more covalent bonds, interconnecting moieties such as two polymer segments or a terminus of a polymer and a reactive functional group present on a bioactive agent, such as a polypeptide.
  • a protein, polynucleotide, vector, cell, or composition which is "isolated” is a protein (e.g., antibody), polynucleotide, vector, cell, or composition which is in a form not found in nature.
  • Isolated proteins, polynucleotides, vectors, cells or compositions include those which have been purified to a degree that they are no longer in a form in which they are found in nature.
  • a protein, polynucleotide, vector, cell, or composition which is isolated is substantially pure.
  • Isolated proteins and isolated nucleic acid will be free or substantially free of material with which they are naturally associated such as other polypeptides or nucleic acids with which they are found in their natural environment, or the environment in which they are prepared (e.g., cell culture) when such preparation is by recombinant DNA technology practiced in vitro or in vivo.
  • Proteins and nucleic acid may be formulated with diluents or adjuvants and still for practical purposes be isolated - for example the proteins will normally be mixed with gelatin or other carriers if used to coat microtitre plates for use in immunoassays, or will be mixed with pharmaceutically acceptable carriers or diluents when used in diagnosis or therapy.
  • polynucleotide and “nucleic acid” are used interchangeably and are intended plasmid DNA (pDNA).
  • a polynucleotide comprises a conventional phosphodiester bond or a non-conventional bond (e.g., an amide bond, such as found in peptide nucleic acids (PNA)).
  • PNA peptide nucleic acids
  • nucleic acid refers to any one or more nucleic acid segments, e.g., DNA, cDNA, or RNA fragments, present in a polynucleotide.
  • polypeptide polypeptide
  • peptide and “protein” are used interchangeably herein to refer to polymers of amino acids of any length.
  • the polymer can be linear or branched, it can comprise modified amino acids, and it can be interrupted by non-amino acids.
  • the terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component.
  • polypeptides containing one or more analogs of an amino acid including, for example, unnatural amino acids, etc.
  • a "recombinant" polypeptide, protein or antibody refers to polypeptide, protein or antibody produced via recombinant DNA technology.
  • polypeptides, proteins and antibodies expressed in host cells are considered isolated for the purpose of the present disclosure, as are native or recombinant polypeptides which have been separated, fractionated, or partially or substantially purified by any suitable technique.
  • percent sequence identity or “percent identity” between two polynucleotide or polypeptide sequences refers to the number of identical matched positions shared by the sequences over a comparison window, taking into account additions or deletions (i.e., gaps) that must be introduced for optimal alignment of the two sequences.
  • a matched position is any position where an identical nucleotide or amino acid is presented in both the target and reference sequence.
  • Gaps presented in the target sequence are not counted since gaps are not nucleotides or amino acids.
  • gaps presented in the reference sequence are not counted since target sequence nucleotides or amino acids are counted, not nucleotides or amino acids from the reference sequence.
  • the percentage of sequence identity is calculated by determining the number of positions at which the identical amino-acid residue or nucleic acid base occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage software programs are available from various sources, and for alignment of both protein and nucleotide sequences.
  • Bl2seq performs a comparison between two sequences using either the BLASTN or BLASTP algorithm.
  • BLASTN is used to compare nucleic acid sequences
  • BLASTP is used to compare amino acid sequences.
  • Other suitable programs are, e.g., Needle, Stretcher, Water, or Matcher, part of the EMBOSS suite of bioinformatics programs and also available from the European Bioinformatics Institute (EBI) at www.ebi.ac.uk/Tools/psa.
  • nucleotide sequence "encoding" a polypeptide means that the sequence, upon transcription and translation of mRNA, produces the polypeptide. This includes both the coding strand, whose nucleotide sequence is identical to mRNA and whose sequence is usually provided in the sequence listing, as well as its complementary strand, which is used as the template for transcription. As any person skilled in the art recognizes, this also includes all degenerate nucleotide sequences encoding the same amino acid sequence. Nucleotide sequences encoding a polypeptide include sequences containing introns. Fluorescent Proteins Hyperfolder YFP (hfYFP) withstands chaotropic conditions that denature most biological structures within seconds, including superfolder GFP.
  • hfYFP Fluorescent Proteins Hyperfolder YFP
  • hfYFP contains no cysteines, is chloride insensitive, and tolerates aldehyde and osmium tetroxide fixation better than common FPs, enabling its use in protein-retention expansion microscopy (proExM) and correlative light and electron microscopy (CLEM).
  • ProExM protein-retention expansion microscopy
  • CLEM correlative light and electron microscopy
  • hfYFP and LSSmGFP represent a new generation of robustly stable FPs developed for advanced biotechnological applications.
  • hyperfolder YFP The amino acid sequence of hyperfolder YFP (hfYFP) is as follows: 121 VNRIVLKGID FKEDGNILGH KLEYNFNSHN VYITADKQKN GIKANFKIRH NVEDGGVQLA 181 DHYQQNTPIG DGPVLLPDNH YLSYQSVLSK DPNEKRDHMV LKERVTAAGI THDMNELYK (SEQ ID NO: 1)
  • the nucleic acid sequence of hyperfolder YFP (hfYFP) is as follows: ATGGTGAGCA AGGGCGAGGA GCTGTTCACC GGGGTGGTGC CCATCCTGGT CGAGCTGGAC GGCGACGTAA ACGGCCACAA GTTCAGCGTC CGCGGCGAGG GCGAGGGCGA TGCCACCAAC 121 GGCAAGCTGA CCCTGAAGCT CATCTCCACC ACCGGCAAGC TGCCCGTGCC CTGGCCCACC 181 CTCGTGACC
  • eGFP-C48S/C70V was mostly nonfluorescent in human cells, while moxGFP (sfGFP-C48S/C70S) was slightly dimmer than eGFP and half as bright as sfGFP.
  • Clover-C48S/C70V was brighter than Clover in all three human cell lines tested, displaying 2.7-fold greater brightness than eGFP, compared to 2.2-fold for Clover relative to eGFP.
  • mF1Y and its double mutant were both 3.5-fold brighter than eGFP (Figure 7B).
  • Clover-C48S/C70V primary T m peak decreased by only 3 °C compared to the 7 °C drop seen between sfGFP and moxGFP.
  • the secondary peak ( Figure 7C, arrow) was visible as a distinctive phase that was absent in the other FPs ( Figure 7D).
  • the data suggest that a unique structural change occurs at high temperature in Clover-C48S/C70V that stabilizes the protein and/or shields the chromophore from quenching. There were no obvious differences in typical spectroscopic characteristics that could satisfactorily explain the cellular brightness and T m differences between the cysteine-replaced variants and their parents ( Figure 7E), indicating that folding and/or chromophore maturation processes might be hindered.
  • the foundational protein of our “hyperfolder” library was FOLD4, a C48S/C70V mutant that we constructed as a hybrid template containing the superfolder GFP (Pédelacq et al., 2006) and superfast GFP “P7” (Fisher and DeLisa, 2008) mutations in the Clover background (characterized by T65G/Q69A/T203H mutations relative to sfGFP) (Figure 8), along with several mutations from Emerald that improve E. coli colony brightness (Table 1).
  • V68L mutation is widespread in avFPs because it improves the chromophore oxidation rate of YFPs (GFP-T203Y variants) through structural rearrangements including H-bonding of the central ⁇ -helix main chain to structural water molecules involved in the proton wire. Moreover, for our purposes here, V68L was present in the superfast GFP library template that influenced our development of this series of proteins, perhaps indicating a beneficial role in folding and/or structural stability.
  • V68L did indeed slow chromophore maturation when introduced into F4P to produce FOLD6, doubling the latency to completed chromophore cyclization compared to mF4P, to 25 min. That rate, however, was still faster than the maturation rate of eGFP, sfGFP, moxGFP, mClover3, and eYFP, among others (Table 2).
  • the V68L mutation of FOLD6 also improved the rate of refolding to the half-maximal value relative to mGL, but with reduced slow-phase kinetics of its double-exponential curve (Figure 10B).
  • T-Sapphire a well-folded GFP with a large Stokes shift (LSS)
  • LLS Large Stokes shift
  • T203Y is the defining mutation that produces the bathochromic shift separating the GFP and YFP spectral classes.
  • the D234N mutation was later identified independently alongside G232D in one of the “superfast GFP” mutants, reinforcing our impression that the avFP C-terminus, which is usually unstructured in X-ray F46L/V68L/A69M/H203Y converted FOLD6 into foxY, which we then monomerized using L221K and F223R (to produce mfoxY), supposing that including both mutations would be advantageous in the more dimer-prone A206V background.
  • hfYFP is mGL- F46L/C48S/V68L/A69M/C70V/K101E/T105Y/K149N/T167I/H203Y/K206V/D234N.
  • Mechanisms for maturation enhancement by the I167T mutation Our mF4P and FOLD6 point mutants allow us to define structure-function relationships resulting from the I167T mutation and, more generally, suggest a potential tradeoff between solvent accessibility that accelerates the chromophore cyclization rate at some cost to stability of the final structure.
  • the I167T mutation has been known to diminish the 405 nm absorbance (A-band) that arises from the protonated chromophore species.
  • E222 remains protonated (and the chromophore deprotonated) because the FOLD6 H-bond network minimizes environmental changes to the proton wire that would alter the protonation status of either residue, with interactions resulting from the I167T mutation further conferring a low pKa ( Figure 17D).
  • I167T through the pKa-reducing effect that decreases the A-band—shifting the pH curve—while the hydrated channel from outside the protein into the chromophore environment accelerates chromophore maturation during folding.
  • a third water molecule in the chromophore proton wire The FOLD6 structure reveals an unusual water molecule, wat 3 , that is also found in roClover0.1 (structure solved to 1.3 ⁇ resolution), but only in the B-chain. It does not appear in Clover, perhaps due to limitations of the structure’s solved resolution (2.4 ⁇ ).
  • wat 3 is interesting because, to our knowledge, the only other structure that renders wat 3 is the 1.7 ⁇ resolution off-state of Dreiklang (Citrine-V61L/F64I/Y145H/N146D) where it is referred to as “wat c ”. It does not appear in the on-state (2.0 ⁇ resolution) or the equilibrium state structures.
  • PCR primers 21 nucleotides in length were designed using those sequences in the appropriate orientation to amplify the FP gene, or the entire host plasmid as a linearized empty vector. This primer design strategy maintains proper stop codon placement.
  • FP gene amplicons and linearized empty vectors ith th tibl t i i lifi d ifi d d lit t ll d th t using restriction site-independent isothermal “Gibson” assembly of the overlapping DNA fragments. This approach works well for simple plasmids like pBAD and pcDNA3.1 but should not be used for plasmids with repetitive elements or complex secondary structure, such as viral vectors.
  • cloning into the adeno-associated virus (AAV) expression vector pAAV- CAG-FLEX was performed using standard T4 ligation between the BamHI/EcoRI sites. Fusion constructs depicted in Figure 5F were cloned into a pET28a vector modified to remove the N-terminal thrombin cleavage site while preserving the N-terminal hexahistidine (His 6 ) tag. The full pET28a-hfYFP plasmid was amplified to linearize it between the 3’ end of hfYFP and vector backbone.
  • AAV adeno-associated virus
  • the oligonucleotides provided long overhangs coding for the first half of a linker at the 3’ end of the hfYFP sequence, while the fusion protein genes (mScarlet-I, Bacillus circulans xylanase, or streptavidin) were amplified using oligos to complete the linker (GSAGSAAGSGEFENLYFQGH) at the 5’ end of the gene and hybridize with the pET28a backbone on the 3’ end. The complete circular plasmid was generated from these two fragments using Gibson Assembly.
  • pEGFP-N1-moxGFP was obtained from Addgene (#68070).
  • pCytERM_mScarlet-i_N1 was obtained from Addgene (#85066).
  • the streptavidin core domain sequence constituting amino acids 13-140 of the native protein and responsible for its activity, was synthesized without further codon optimization.
  • Bacillus circulans xylanase (synonymous with Niallia circulans endo-1,4-beta-xylanase) was synthesized from UniProtKB/Swiss-Prot: P09850.1 amino acid sequence using a bacterial codon set (Eurofins Genomics).
  • Site-directed mutagenesis Site-directed mutagenesis was performed using the QuikChange (Stratagene) method with Pfu polymerase (Agilent), or using the QuikChange Lightning Multi Site-Directed Mutagenesis Kit (Agilent) as described (Campbell et al., 2020).
  • Non-phosphorylated mutagenic primers were designed to introduce the most abundant human codon for the target amino acid.
  • primers When modifying multiple adjacent codons (e.g., to mutate ⁇ -strands 10 and 11), primers were designed to amplify large sections of the FP gene with overhangs at junctions between the segments containing the standard or degenerate codons targeting those sites, followed at the 3’ end by a homology arm for the adjacent gene fragments amplified in separate reactions.
  • the gene fragments containing these degenerate codons at the junctions were stitched together by overlap-extension PCR (Heckman and Pease, 2007), gel purified, and cloned by isothermal assembly (Gibson, 2011) into a PCR-amplified linear pBAD vector for transformation and expression in E. coli.
  • Mutated FP genes were transformed into TOP10 competent cells and grown at 37 °C on LB agar plates supplemented with carbenicillin (100 ⁇ g/ ⁇ L) and 0.02% arabinose. The next day, colonies were screened by eye using alternating 405 nm and 470 nm LED strip illumination while fluorescence was observed through amber long-pass filter goggles (Invitrogen #S37103 or ThorLabs #LG10). Colonies that glowed brightest under 405 nm excitation while showing minimal fluorescence under 470 nm illumination were picked into sterile 96-well deep-well blocks containing 1 mL LB medium supplemented with ampicillin (100 ⁇ g/ ⁇ L) and 0.2% arabinose.
  • the culture blocks were sealed with a breathable adhesive (EasyApp Microporous Film, USA Scientific #2977-6202) to permit air and gas exchange while minimizing evaporation, and cultures were grown at 37 °C with 275 rpm shaking for 16-18 hr.
  • a breathable adhesive EsyApp Microporous Film, USA Scientific #2977-6202
  • 100 ⁇ L overnight culture was pipetted into black clear-bottom 96-well optical plates (Corning) for first-pass excitation scans, and the ratio of 405 nm to 488 nm excitation was scored. Soluble protein from cultures with the greatest 405/488 nm ratio scores were extracted using B-PER II reagent (Thermo Scientific), re- scanned for confirmation, and the same lysate was then used for kinetic unfolding screens.
  • Error-prone libraries were generated using the staggered extension process (StEP) (Zhao and Zha, 2006) with some modifications. Plasmid DNA from 12 mutants from the LSSA12 library was pooled and diluted 50% with hfYFP-V206K/G65S/Y203I plasmid. To increase error rate, the Taq polymerase-based PCR reaction containing 33 ng total template DNA and 30 pmol of forward annealing/extension steps at 55 °C for 5 s, repeated 100 times before the reaction was cooled to 4- 10 °C. The PCR product was digested for 5 min using DpnI to eliminate residual parental plasmid, and the reaction was PCR purified.
  • StEP staggered extension process
  • the StEP library was amplified using Phusion HS II polymerase (Thermo Fisher) with the same flanking primers, and the reaction product was cloned without further purification by isothermal assembly into PCR-amplified linear pBAD vector and expressed and screened as described.
  • Protein purification Fluorescent proteins were purified as described (Campbell et al., 2020) using Ni-NTA chromatography, without lysozyme or DNAse for the large scale 500 mL preparations.
  • TN buffer 50 mM Tris-HCl, 150 mM NaCl, pH 7.5
  • TNG buffer TN plus 10% glycerol
  • Protein for X-ray crystallography was prepared as described (Campbell et al., 2018) using pET28a-hfYFP, pET28a-mhYFP, and pET28a-FOLD6 vectors and purified by Ni-NTA chromatography.
  • the frozen pellets from 50 mL culture were thawed at RT and lysed in B-PER II reagent centrifuged at 20,000 x g for 10 min at 4 °C in a benchtop microcentrifuge.
  • the soluble fraction was collected.
  • the insoluble pellet was washed with PBS plus 1% Triton X-100, briefly sonicated, centrifuged, and the supernatant containing residual soluble protein was discarded. This inclusion body pellet was washed twice more as described using PBS without the Triton X-100.
  • the IBs were resuspended in Denaturing Purification Buffer (20 mM phosphate, 300 mM NaCl, 6 M GdnHCl, pH 7.4) containing 10 mM imidazole, rapidly and without trituration, and were immediately sonicated on ice until completely solubilized. Under these conditions, the IB pellets typically dissolved in ⁇ 10 s, producing a brightly fluorescent and homogeneous solution.
  • the fusion proteins were purified from solubilized IB solutions using HisPur Ni-NTA resin (Thermo Scientific, #88223).
  • hexahistidine (His 6 )-tagged AcTEV protease (Invitrogen, #12575023) was added for cleavage according to manufacturer instructions. IMAC-incompatible chemicals such as DTT and EDTA were omitted. Cleavage proceeded at 4 °C for at least 24 hr. The cleaved Protein of Interest was then isolated by Ni-NTA chromatography under native conditions in the mentioned Purification Buffer without GdnHCl. His 6 -TEV protease and His 6 - hfYFP or His 6 -LSSmGFP are adsorbed onto the Ni-NTA resin while the Protein of Interest remains in solution.
  • FP stocks were diluted 10-fold into TNG buffer, pH 7.5, with and without 7 M guanidinium hydrochloride (GdnHCl) (Fisher Scientific, #BP178-500), for final concentrations of 0.1 ⁇ M FP and 6.3 M GdnHCl (or 0 M GdnHCl for the native control samples).
  • Short-term and long-term unfolding curves were generated using 10 s or 1 min sampling interval for total experiment durations of 1 hr or 12 hr, respectively.
  • the fluorescence ratio of the unfolding protein to the same FP’s native control wells was plotted for each FP (“fraction folded”). Data points were fit to single- or double-exponential equations where indicated.
  • Preliminary screening of mutant libraries for generating the large Stokes shift constructs was performed using clarified lysate and then confirmed using purified protein for final data sets. For initial screening the LSS FPs, clarified lysate was used, and purified protein was used for confirmation.
  • Refolding Purified protein in TNG buffer 50 mM Tris-HCl, 150 mM NaCl, 10% glycerol, pH 7.5 was diluted into a solution of 7 M GdnHCl prepared in TNG buffer and supplemented with dithiothreitol (DTT), for final concentrations of 1 ⁇ M protein, 6.8 M GdnHCl, and 1 mM DTT.
  • DTT dithiothreitol
  • the samples in this solution were fully denatured by heating at 98 °C for 10 min, cooled to RT, and briefly checked under a 470 nm handheld LED to confirm loss of fluorescence. Native samples in the same buffer without GdnHCl were prepared in parallel.
  • hfYFP/mhYFP or any fast-folding FP—may wish to test several DNA concentrations beginning in the lower range for their specific transfection system to minimize cytosolic spillover, particularly for endoplasmic reticulum and mitochondrial targeting.
  • FP fusion localization images were acquired at 2048x2048 px resolution with 4 times averaging and represent a single Z-section at 1 Airy unit.
  • OSER assay images were tile scans (4x4) acquired at 1024x1024 px resolution with 4 times averaging using the 40X oil immersion objective. OSER images were stitched using ZEN software and analyzed using the established scoring criteria (Costantini et al., 2012). Cross-excitation assays were performed by culturing and transfecting HeLa cells on 35 mm MatTek plates as described with individual plasmids (0.5 ⁇ g DNA each) encoding LifeAct-eGFP and H2B-mT-Sapphire, or LifeAct-mGreenLantern and H2B-LSSmGFP.
  • HEK293T cells were cultured in Matrigel-coated black 96-well tissue plates and transfected with cytosolic expression plasmids using 0.11.4 DNA per well and Turbofect transfection reagent. Media was changed the following morning. After 48 hr total expression time, cells were washed twice using phenol red-free medium and imaged at 10x magnification on the mentioned widefield Keyence BZ-X700 plate reader microscope using a PlanFluor DL 10x 0.30/15.20mm Ph1 air objective, GFP filter cube for GFPs and YFPs, or the mentioned 405/525 nm filter cube for LSS FPs.
  • the live cell image was thresholded, cell regions of interest (ROIs) were applied to the post-fixation image by creating a mask, and the mean fluorescence intensity (MFI) of each cell before and after fixation was collected. Data were expressed as a ratio of the post- fixation MFI relative to the live cell MFI (percent "fluorescence retention") and analyzed for significance by one-way ANOVA with multiple comparisons. Fluorescence retention, proExM Protein-retention expansion microscopy (proExM) was performed in a similar manner as the FP screening method from (Tillberg et al., 2016), with stock reagents and buffers prepared as described.
  • the 16-chamber slide was then imaged using a Keyence BZ-X700 All-in-One Fluorescence Microscope equipped with a PlanFluor DL 4x 0.13/16.50mm PhL air objective, standard GFP filter cube, and computer- controlled motorized stage. After manually focusing each well, 5x5 tile scans of 640x480 px (3x3 binning) resolution were acquired in 8-bit TIFF format under imaging conditions specific to each FP to provide optimal exposure while minimizing oversaturation. The imaging settings for each well were recorded.
  • samples were treated with acryloyl-X (AcX) (Thermo Fisher, #A20770) in PBS, pH 7.4, overnight at RT while protected from light. The next day, AcX was removed using a micropipette, and samples were washed 3 times for 5 min each using PBS. Ideally, the same side of the well should be used for every pipetting step to minimize loss of cells.
  • the slide was placed on a clean benchtop, with the experimenter seated low, facing the 16-chamber slide at approximately eye level.
  • the plastic silo chambers that are adhered to the upper silicone spacer were separated from the lower silicone gasket (which itself is adhered to the coverslip surface), by looping dental floss carefully between the silicone spacer and silicone gasket from one end of the slide, all the way pressing the slide against the benchtop), can be helpful to reduce the risk of coverslip breakage. After the floss has been passed through, the two gaskets usually remain in their original positions while PBS has seeped between the narrow gaps opened by the dental floss to weaken the adhesive. This way, the chamber and silicone spacer together can be separated from the lower gasket carefully using fingertips or forceps to lift the plastic chamber/space gently, beginning from one end of the slide to the other, taking great care to avoid bending the brittle No.1 coverslip.
  • the lower silicone gasket must remain behind, attached to the coverslip on which the slides were grown. Since PBS will have leaked out, as mentioned, fresh PBS should be added swiftly to any empty wells to prevent them from drying out (a P20 micropipette set to 20 ⁇ L, with gentle pipetting against the side of the gasket reservoir, is useful for this).
  • Grace Bio-Labs offers a removal tool, but we have had far greater success using the dental floss.
  • the coverslip on which the cells are grown now has only the lower black silicone gasket attached to it. This slide was placed inside a clean, dry, 15 cm culture plate with a 1 ⁇ L drop of water beneath it to keep it in place by surface tension.
  • the black silicone gasket was very carefully and slowly peeled off using blunt forceps, taking the greatest care not to bend the coverslip to any degree.
  • the glass coverslip was then cut using a diamond scribe, with good practice and eye protection, to separate the coverslip into sections of individual gels, each still attached to a square of glass as described (Asano et al., 2018). Thoughtful planning is necessary for maintaining sample order when the slide is divided, or else the gels cannot be distinguished. Digestion buffer was prepared and supplemented with proteinase K (New England Biolabs, #P8107S), dispensed into 12-well plate, and the gels were immersed, with their cut glass fragment al., 2018).
  • Digestion buffer was removed using a P1000 micropipette or 5 mL serological pipette, taking care not to break the semi-transparent gels.
  • the gels were then washed 3-4 times, ⁇ 20 min per wash, using PBS to semi-expand them.
  • An orbital shaker on a slow setting is optional and can help facilitate diffusion.
  • Semi-expanded gels were then shrunk back (to ⁇ 1.5x original size) using the same wash step timing using shrinking solution (1 M NaCl and 60 mM MgCl ⁇ in water) instead of PBS.
  • shrinking solution (1 M NaCl and 60 mM MgCl ⁇ in water
  • Gels were imaged in a No.1 thickness empty glass-bottom 6-well plate or in a MatTek 35 mm glass-bottom plate with a few microliters of shrinking solution added to help adhere the gels by surface tension. Gels become very sticky when dry and should be kept moist. Alternatively, the gels may be fully submerged in shrinking buffer if they can remain flat against the plate. Gels were flipped so that the cell-side would face down against the glass (determined by focusing). A metal spatula bent at the end was useful for transferring the gels from the 12-well plate into the glass-bottom imaging vessel, with practice.
  • the pre- and post-expansion tile scan image sets for each FP were stitched using Keyence BZ-X Analyzer software to produce a 2428x1821 px (3x3 binning) 8-bit image.
  • Post-expansion images of the shrunken gels were registered by unwarping and aligning by hand in Adobe Photoshop to the pre-expansion image for each pair using the Screen layer blending option and transform tool until the images overlapped.
  • the unwarped post-expansion image was saved as a separate layer and exported as the same file type without compression or further modification. Image pairs were thresholded identically in ImageJ, and cells with measurable fluorescence and positive overlap in both the pre- and post-expansion images were further analyzed. Oversaturated cells were not used.
  • MFI mean fluorescence intensity
  • Antibody compatibility images were acquired as described (Campbell et al., 2020). Briefly, HEK293T cells were transfected with pcDNA3.1-FP for cytosolic expression and were fixed with room temperature (RT) 4% PFA before immunostaining using primary antibodies: Gt a GFP polyclonal, Abcam #ab6673; Gt a GFP polyclonal, Novus #NB1001770; Ms a GFP monoclonal, applied, followed by DAPI to label nuclei. Cells were imaged on a Nikon Eclipse 80i microscope after mounting on slides.
  • Laser power was measured at the objective with a Thorlabs PMD100 power meter equipped with S130VC photodetector (Thorlabs) and was initially set to the minimum power necessary to identify suitable regions of the live HeLa cell cultures for bleaching.
  • power was raised to 147 ⁇ W from the blue diode (LSS FPs), or 18.3 ⁇ W (GFPs) or 9.8 ⁇ W (YFPs) from the argon-ion laser.
  • Time series images were collected in the 490- to 650-nm emission range using ZEN acquisition software (Zeiss). Uniformly fluorescent nuclei were selected for analysis. Mitotic cells with bright and condensed/punctate nucleoli were excluded.
  • pellets were resuspended in PBS and lysed by freeze-thaw PBS, and this new supernatant containing residual soluble protein was discarded.
  • the washed insoluble pellet was resuspended in ice-cold PBS and homogenized by brief sonication to yield in the insoluble fraction.
  • Total protein concentration of the soluble and insoluble fractions was determined using the BCA Protein Assay (BCA) kit (Pierce) with BSA standard curve. Samples were adjusted to matching protein concentration and boiled for 10 min at 100 °C in the presence of SDS-containing loading dye supplemented with 0.2 M DTT.
  • BCA BCA Protein Assay
  • HEK293 cells (ATCC) were maintained in Eagle's Minimum Essential Medium (DMEM), containing 1 mM sodium pyruvate, 4 mM L-glutamine, 4.5 g/mL glucose, and 1.5 g/mL sodium bicarbonate. Complete growth medium was prepared by addition of fetal bovine serum to 10% (w/v) final concentration.
  • DMEM Eagle's Minimum Essential Medium
  • eGFP mGreenLantern
  • mhYFP cytosolic expression cells were co- transduced with adeno-associated virus (AAV) particles with FP expression under control of a Cre- fluorescence measurements, ⁇ 8 ⁇ 10 5 live HEK293 cells were seeded on 35mm glass-bottom dishes (MatTek).
  • AAV adeno-associated virus
  • Brightness quantitation of the live cells before and after aldehyde/OsO 4 processing were performed using a laser-scanning confocal microscope (Zeiss LSM 880) with the following settings: 488 nm laser (0.5% power); 10 ⁇ objective; emission range 495-560 nm; GaAsP detector gain of 715 V. Imaging settings for mhYFP used the 488 nm laser at 0.45% power; 10 ⁇ objective; emission range 400-700 nm detection, and 600 V detector voltage. Images were quantified using Fiji (ImageJ).
  • the mean fluorescence intensity of 10 fields of view (FOVs) containing non-fluorescent cells were subtracted from each of 10 regions of interest (ROIs) containing the live fluorescent cells to be quantified.
  • FOVs fields of view
  • ROIs regions of interest
  • cultures were fixed with CLEM fixative (4% (w/v) paraformaldehyde (PFA) + 0.2% (w/v) glutaraldehyde) (Electron Microscopy Sciences) in 100 mM phosphate buffer (PB) and then harvested in 10% bovine serum albumin (BSA) using a rubber spatula. Cells were then mixed with a 2% (w/v) agarose solution and pelleted.
  • the agarose solidified, it was cut using a scalpel into squares and submerged in a 1% (w/v) solution of OsO 4 for 1 hr at room temperature (RT). Osmicated pellets in agarose were then embedded in optimal cutting temperature (OCT) frozen tissue specimen medium (Fisher Scientific, #23-730-571). 8-10 mm sections of the osmicated pellets were cut on a cryotome (Leica), placed on a glass slide, and mounted with antifade mounting media (Invitrogen). Images of the mounted cells were then captured using the same imaging settings as described for the live cells.
  • OCT optimal cutting temperature
  • OsO 4 -resistant labels, high-pressure freezing, and freeze substitution Live fluorescent cells seeded in 35 mm tissue culture dishes were fixed in CLEM fixative, harvested with a 20% (w/v) BSA solution, and assembled into the high pressure freezing (HPF) specimen carrier (Type A, 0.1/0.2 mm; Type B, flat; TechnoTrade). The carrier assembly was then introduced into the sample holder and frozen in the HPF machine per manufacturer’s instructions (Wohlwend HPF Compact 01 High-pressure freezer; Techno Trade). Cell tissue was then freeze- substituted, osmicated with a 1% OsO 4 (w/v) solution, dehydrated in 100% (w/v) acetone, and embedded in Lowicryl HM20 resin (Electron Microscopy Sciences).
  • HPF high pressure freezing
  • PEG 3350 PEG 4000
  • PEG 8000 PEG 8000
  • the most effective salts were MgCl ⁇ , Li 2 SO 4 , and sodium acetate, in descending order. Screening primarily consisted of optimization around the mentioned conditions with 0.1 M Tris-HCl, pH 8.5, and 18 °C storage in the dark. hfYFP formed large, smooth, fluorescent yellow crystals after 1 wk in a solution of 0.1 M Tris-HCl pH 8.5, 25% PEG 3350, 0.2 M sodium acetate.
  • mhYFP formed crystals after 1 wk equilibration against reservoir solution consisting of 0.1 M Tris-HCl pH 8.5, 25% PEG 3350, 25 mM MgCl ⁇ . The solution was a good cryo-condition and did not require supplementation.
  • Clover- C48S/C70V, mF4P, and mF4Y-RKH appear at 88.9 °C, 96.7 °C, and 76.8 °C, respectively. See Fig. S1c-d and Fig. S3a-b for melt curves.
  • Crystallographic data collection, processing, and refinement Crystallographic diffraction data were collected at GM/CA CAT 23-IDD of the Advanced Photon Source at Argonne National Laboratory with monochromatic x-rays of 1.033 angstroms at 100 K on a Dectris Pilatus36M HPC detector (Dectris Ltd., Switzerland) and processed with XDS (Kabsch, 2010).
  • Structural homology model of each respective proteins was generated from the crystal structure of Clover (PDB: 5WJ2) (Campbell et al., 2018) using the online server Swiss- Model (Schwede et al., 2003).
  • hfYFP tolerated deleterious mutations that rendered eGFP and even sfGFP almost entirely nonfunctional, suggesting that it will be a good template for mutagenesis and sensor engineering.
  • hfYFP is compatible with antibodies designed for eGFP ( Figure 23), and cells transfected with nuclear localized hfYFP and mhYFP show healthy morphology. With photostability under laser- scanning confocal illumination approximately equal to mGL's (Campbell et al., 2020), hfYFP bleaches faster than Clover or eYFP, so care should be taken during intensive prolonged imaging.
  • Hyperfolder YFP localized properly upon fusion or targeting to common intracellular targets, including actin, tubulin, clathrin, endoplasmic reticulum, mitochondria, and nuclei ( Figures 1H-1M), indicating that it should perform well in difficult fusions that demand monomeric fluorescent proteins.
  • Monomeric hyperfolder YFP eluted as a pure monomer by gel filtration chromatography (Figure 12A) and scored as a monomer in the organized smooth endoplasmic reticulum (OSER) assay ( Figure 12B).
  • OSER smooth endoplasmic reticulum
  • hfYFP exhibited weak dimer properties in this assay, like Clover ( Figure 12C) and eGFP, both of which perform well in fusions.
  • mhYFP and hfYFP offer many advantages over eYFP that make them better choices for routine imaging.
  • Example 4. Chemical stability We subjected hfYFP to a barrage of denaturing challenges and compared it to widely used FPs (eGFP, sfGFP, mClover3, mNeonGreen, eYFP, and mGreenLantern) in each experiment.
  • b Monomeric hyperfolder YFP is hfYFP-S147P/L195M/V206K.
  • c Fluorescence at the highest GdnHCl concentration of 6.3 M was ⁇ 50% greater than the initial value in buffer without GdnHCl.
  • hfYFP- S147P/V206K/L195M behaved as a stronger monomer in the OSER assay than did hfYFP ( Figures 12B-12C); the L195M mutation originated de novo.
  • the V206K mutation (on ⁇ -strand 10) largely preserved GdnHCl stability in multiple mutants ( Figure 15).
  • mhYFP further demonstrates that peculiar performance features can be structurally engineered into FPs without perturbing spectral properties (Table 2, Figure 16). Example 5.
  • hfYFP retained 75% of its fluorescence after fixation with a 4% PFA+ 5% Glut solution compared to 65% for mGL and eGFP, and 29% for mNG ( Figures3B-3C) ( Figure 24).
  • mhYFP is compatible with protein-retention expansion microscopy (proExM) (Tillberg et al., 2016) ( Figure 3D) and retains 16% more fluorescence than eGFP at the end of the process ( Figure 3E).
  • ProExM protein-retention expansion microscopy
  • Figure 3E retains 16% more fluorescence than eGFP at the end of the process
  • mhYFP and mGL retained greater fluorescence after protein-retention expansion microscopy (proExM) compared to other FPs ( Figure 3A).
  • Cells were fixed with 4% paraformaldehyde (PFA) before confocal imaging; cellular fluorescence was compared after expanded hydrogels were shrunk back down using NaCl for post-imaging.
  • eYFP was almost totally quenched, but this effect was likely mediated by the 1 M NaCl concentration of the buffer used to consequence of eYFP’s chloride sensitivity that makes it unsuitable for many applications, in contrast to hfYFP, which unlike most YFPs, is chloride-insensitive ( Figure 1F).
  • hfYFP retained nearly 80% of its fluorescence in the 2% PFA / 2% Glut condition, a 360% improvement over eGFP and a 750% improvement over mNeonGreen (Figure 3B).
  • mGL was sensitive to glutaraldehyde ( Figures 3B-3C), but it retained 23%, 180%, and 300% greater fluorescence after 4% PFA fixation than eGFP, mClover3, and mNeonGreen, respectively ( Figure 3D).
  • eYFP was severely quenched by glyoxal.
  • HEK293 cells were transduced with adeno-associated virus (AAV) particles and live fluorescent cells were imaged by confocal microscopy at 10 ⁇ (Figure 4D) and 63 ⁇ magnification (Figure 4E) before and after processing, using the same settings.
  • the processed hfYFP cells retained ⁇ 35% of the initial live cell fluorescence ( Figure 4F), a 14- and 25-fold fluorescence retention improvement compared to mGL and eGFP, respectively ( Figure 4G).
  • hfYFP also retained fluorescence after acrylate-based resin embedding in a high-pressure freezing / freeze substitution protocol, with fluorescence levels well above background (Figure 4h).
  • Example 8 Example 8
  • Hyperfolder YFP (hfYFP), monomeric hyperfolder YFP (mhYFP), and FOLD6, crystallized with the symmetry of space groups C2221, C2221, and P64, diffracting to 1.7 ⁇ , 1.6 ⁇ , and 1.2 ⁇ , respectively.
  • Each FP crystallized as a monomer with no asymmetric unit. Structures were solved by molecular replacement using homology models generated from Clover (PDB: 5WJ2; (Campbell et al., 2018)) (Table 4).
  • hfYFP features a chromophore hydrogen bond (H-bond) network indistinguishable from that of eYFP, Citrine, or Venus, besides trivial H-bond distance variation ( ⁇ 0.1-0.3 ⁇ ).
  • E222 O ⁇ 2 is H-bonded to N2 of the chromophore (CRO) imidazolinone ring
  • E222 O ⁇ 1 is H-bonded to a structurally conserved water molecule, which we will refer to wat 2 .
  • Wat 2 is H-bonded to the backbone amide of L68 and, as we will discuss later, it also connects E222 O ⁇ 1 to the Y203 phenolic side chain ( Figure 17A).
  • the chromophore phenolate remains stabilized by H-bonds from wat 1 and H148, this new completed proton wire through E222 (Fig.17A) might further stabilize the structure while functionally decoupling the Y203 phenolate from the spectroscopically critical E222 side chain.
  • LSSA12 was more stable in GdnHCl than mT-Sapphire, mAmetrine, and eGFP (Figure 20E).
  • Site-directed mutagenesis confirmed the functional importance of the E222D and G65S mutations in LSSA12 ( Figure 20F). Since hfYFP can tolerate avFP knockout substitutions ( Figure 16), we produced a diversified LSSA12 library by purifying the 12 best plasmids from the LSSA12 screen, diluted the DNA with original template to back-cross the library, and recombined the genes in a high-error rate staggered extension process (StEP) reaction spiked with 0.5 mM MnCl ⁇ .
  • StEP staggered extension process
  • LSSmGFP which is hfYFP-T43S G65S/L68Q/H77N/K140N/Y203I/V206K. Both LSSA12 and LSSmGFP show no B-band excitation, in contrast to mT-Sapphire ( Figure 21A). LSSmGFP persisted longer in GdnHCl than LSSA12, mT-Sapphire, and mAmetrine ( Figure 21B).
  • LSSA12 and LSSmGFP behaved as monomers in cultured cells (Figure 21H-21I).
  • LSSmGFP localized properly to common intracellular targets (LSSA12 was not tested) ( Figure 21J-21N).
  • LSSmGFP and LSSA12 enjoy similar advantages as hfYFP including the absence of cysteine residues, low pKa, tolerance of fixatives, high chemical and thermal stability, and a single excitation band.
  • eGFP immediately denatured in GdnHCl during the inclusion body solubilization step (Figure 5F, arrow) while hfYFP and LSSmGFP remained fluorescent.
  • hfYFP and LSSmGFP appear to function as solubility tags that enhance expression of the C-terminal fusion protein.
  • hfYFP and LSSmGFP have potential to serve as solubility tags or at least as markers for fluorescence-assisted protein purification in addition to the numerous applications that we have described for proExM, CLEM, and protein engineering.
  • the FOLD6 chromophore is far more planar than hfYFP’s where, by contrast, the centrosymmetric ⁇ -stacking of Y66-Y203 leaves the Y66 ring noticeably rotated about the methylene bridge relative to the imidazolinone moiety to achieve greater coplanarity with the Y203 ring.
  • Deviations from planarity between the chromophore imidazolinone and phenolate moieties are well known to decrease quantum yield.
  • the highly off-center H203 orientation relative to Y66 considerably widens a separation between ⁇ -strands 7 and 8 in FOLD6 through steric effects on H203.
  • the H203 side chain has shifted 0.5 ⁇ away from E222 and toward V150, pushing the V150 side chain and local ⁇ -strand 7 backbone 1.0-1.3 ⁇ outward and away from H203.
  • This new V150 position forces the F165 side chain down 0.6 ⁇ toward H181 and the F165 C ⁇ carbon 1.0 ⁇ outward, while the neighboring N164 carbonyl rotates more than 25° away from the Y151 amide, severing the ⁇ - strand H-bond between the two (linear distances of 3.1 ⁇ in sfGFP and 5.1 ⁇ in FOLD6).
  • the F46L/F64L mutations eliminate the antiparallel ⁇ - ⁇ stacking interaction present in eGFP and the closely related structures, eYFP and Venus. Consequently, the smaller alkyl side- chains of L44, L42, and L220, among other residues that line the protein’s hydrophobic core (approximately bordered by N121), shift to occupy the space ( Figure 17C).
  • the Q69M mutation from Citrine substitutes a polar side chain with the hydrophobic yet weakly polar and larger methionine, which packs more efficiently into the chromophore cavity and is known to improve chromophore maturation.
  • M69 is situated directly between three aromatic residues, not including the chromophore’s ⁇ -conjugated system itself, and M69 shows notable orientational preference for the ⁇ + ring edge of F84, whose centroid is located approximately 5 ⁇ away with the ⁇ - M69 sulfur atom and a ⁇ -cloud presumably oriented 90° relative to the ring ( Figure 18B).
  • This configuration indicates a sulfur-aromatic interaction that should contribute stabilizing energy greater than the sum of the vdW forces.
  • Example 16 Salt bridges on the hyperfolder protein surfaces It has been shown that the S30R superfolder mutation enables salt bridges between several residues on the protein surface that contribute to its stability, and we observe extensive electrostatic interactions across ⁇ strands 1, 2, 5, and 6, in FOLD6, hfYFP, and mhYFP ( Figure 19).
  • hfYFP shows a single R30 conformation through which four different side-chains are stabilized (Figure 19D), whereas mhYFP shows two R30 conformations, shifting the equilibrium more toward stabilization of E32 than D19 ( Figure 19E).
  • R30 in FOLD6 also shows two conformations, but the rotamers allow R30 to stabilize E32 and D19 via salt bridges and to an H- bond to S28 ( Figure 19C). These electrostatic surface interactions may contribute to the stability of the hyperfolder FPs.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Medicinal Chemistry (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Toxicology (AREA)
  • Peptides Or Proteins (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

La présente invention concerne des protéines fluorescentes résistant aux conditions chaotropiques qui dénaturent la plupart des structures biologiques en quelques secondes, y compris la GFP superfolder. Les protéines fluorescentes divulguées ne contiennent pas de cystéines, sont insensibles au chlorure et tolèrent mieux la fixation à l'aldéhyde et au tétroxyde d'osmium que les protéines fluorescentes courantes. Les protéines fluorescentes divulguées représentent une nouvelle génération de protéines fluorescentes robustes et stables développées pour des applications biotechnologiques avancées.
PCT/US2023/027373 2022-07-11 2023-07-11 Protéines fluorescentes chimiquement stables pour microscopie avancée WO2024015362A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202263388051P 2022-07-11 2022-07-11
US63/388,051 2022-07-11

Publications (1)

Publication Number Publication Date
WO2024015362A1 true WO2024015362A1 (fr) 2024-01-18

Family

ID=87556194

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2023/027373 WO2024015362A1 (fr) 2022-07-11 2023-07-11 Protéines fluorescentes chimiquement stables pour microscopie avancée

Country Status (1)

Country Link
WO (1) WO2024015362A1 (fr)

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20040137528A1 (en) * 1998-02-02 2004-07-15 Watson Michnick Stephen William Fragments of fluorescent proteins for protein fragment complementation assays
WO2021081404A1 (fr) * 2019-10-25 2021-04-29 Cercacor Laboratories, Inc. Composés indicateurs, dispositifs comprenant des composés indicateurs, et leurs procédés de fabrication et d'utilisation
WO2022010761A1 (fr) * 2020-07-06 2022-01-13 The Board Of Regents Of The University Of Texas System Lignées cellulaires de biocapteur tdp-43

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20040137528A1 (en) * 1998-02-02 2004-07-15 Watson Michnick Stephen William Fragments of fluorescent proteins for protein fragment complementation assays
WO2021081404A1 (fr) * 2019-10-25 2021-04-29 Cercacor Laboratories, Inc. Composés indicateurs, dispositifs comprenant des composés indicateurs, et leurs procédés de fabrication et d'utilisation
WO2022010761A1 (fr) * 2020-07-06 2022-01-13 The Board Of Regents Of The University Of Texas System Lignées cellulaires de biocapteur tdp-43

Non-Patent Citations (11)

* Cited by examiner, † Cited by third party
Title
"UniProtKB/Swiss-Prot", Database accession no. P09850.1
CAMPBELL BENJAMIN C. ET AL: "Chemically stable fluorescent proteins for advanced microscopy", NATURE METHODS, vol. 19, no. 12, 7 November 2022 (2022-11-07), New York, pages 1612 - 1621, XP093086736, ISSN: 1548-7091, Retrieved from the Internet <URL:https://www.nature.com/articles/s41592-022-01660-7> [retrieved on 20230929], DOI: 10.1038/s41592-022-01660-7 *
CAMPBELL BENJAMIN C. ET AL: "mGreenLantern: a bright monomeric fluorescent protein with rapid expression and cell filling properties for neuronal imaging", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, vol. 117, no. 48, 18 November 2020 (2020-11-18), pages 30710 - 30721, XP093086831, ISSN: 0027-8424, DOI: 10.1073/pnas.2000942117 *
CAMPBELL ET AL., PNAS, 2020
COSTANTINI ET AL., NAR. COMM., 2015
COSTANTINI ET AL., NAT. COMM., 2015
COSTANTINI ET AL., TRAFFIC., 2012
HIRANO MASAHIKO ET AL: "A highly photostable and bright green fluorescent protein", NATURE BIOTECHNOLOGY, NATURE PUBLISHING GROUP US, NEW YORK, vol. 40, no. 7, 25 April 2022 (2022-04-25), pages 1132 - 1142, XP037903041, ISSN: 1087-0156, [retrieved on 20220425], DOI: 10.1038/S41587-022-01278-2 *
KADA ET AL., BIOCHIMICA ET BIOPHYSICA ACTA, 1999
SHANER ET AL., MNEONGREEN, 2013
THONG ET AL., J. NEUROSCI. MET., 2019

Similar Documents

Publication Publication Date Title
Lim et al. Stable, high‐affinity streptavidin monomer for protein labeling and monovalent biotin detection
US7157566B2 (en) Monomeric and dimeric fluorescent protein variants and methods for making same
Mattila et al. A high-affinity interaction with ADP-actin monomers underlies the mechanism and in vivo function of Srv2/cyclase-associated protein
Povelones et al. Structure-function analysis of the Anopheles gambiae LRIM1/APL1C complex and its interaction with complement C3-like protein TEP1
US7329735B2 (en) Fluorescent protein variants and methods for making same
Campbell et al. Chemically stable fluorescent proteins for advanced microscopy
US20100227400A1 (en) Monomeric and dimeric fluorescent protein variants and methods for making same
Fujii et al. In planta comparative analysis of improved green fluorescent proteins with reference to fluorescence intensity and bimolecular fluorescence complementation ability
US8679749B2 (en) Red fluorescent proteins with enhanced bacterial expression, increased brightness and reduced aggregation
US8206978B2 (en) Green fluorescent protein optimized for expression with self-cleaving polypeptides
US10962528B2 (en) Blue fluorescent protein monomers and uses thereof
US20160229899A1 (en) LUCIGEN YELLOW (LucY), A YELLOW FLUORESCENT PROTEIN
WO2024015362A1 (fr) Protéines fluorescentes chimiquement stables pour microscopie avancée
WO2006024041A2 (fr) Variantes de proteines fluorescentes monomeriques et dimeriques et procedes de production desdites variantes
US9034599B2 (en) Polynucleotides encoding monomeric variants of the tetrameric eqFP611
JP5265491B2 (ja) モノマーおよびダイマー蛍光タンパク質変異体および上記変異体を作製する方法
US20210347833A1 (en) Blue fluorescent protein monomers and uses thereof
Campbell Structure-Guided Engineering of Chemically Stable Fluorescent Proteins for Super-Resolution Imaging
JPH10234382A (ja) 蛍光タンパク質
Pujari Crystallization of GSK3β with an inhibiting peptide of psychiatric risk factor DISC1
EP4392438A2 (fr) Capteur fluorescent pour la surveillance de la dynamique du calcium
Povelones et al. Structure-Function Analysis of the Anopheles gambiae LRIM1
WO2011043814A2 (fr) Protéines fluorescentes et utilisations de celles-ci

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 23751162

Country of ref document: EP

Kind code of ref document: A1