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Protein & Peptide Letters

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ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

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Mini-Review Article

Understanding Protein Functions in the Biological Context

Author(s): Wei Zhang and Tianwen Wang*

Volume 30, Issue 6, 2023

Published on: 16 May, 2023

Page: [449 - 458] Pages: 10

DOI: 10.2174/0929866530666230507212638

Price: $65

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Abstract

Proteins are essential biomacromolecules in all living systems because they are the prominent ultimate executives of the genetic information stored in DNA. Thus, studying protein is one of the central tasks in biological sciences. The complexity, diversity, and dynamics of a protein's structure, function, and structure-function relationship, the inherent structural fragility and thus the requirements on handling proteins to maintain protein's structural and functional orderliness make it a rather tricky task to work with protein. The approach to understanding the functions of a protein has been progressing steadily. In this paper, we reviewed the progress on the approach to the functional study of proteins that tremendously contributed to understanding their biological significance. Emphasis was put on the advances in the age in which high-throughput DNA sequencing and bioinformatics analysis are revolutionizing biological study.

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[1]
Lu, H.P.; Xun, L.; Xie, X.S. Single-molecule enzymatic dynamics. Science, 1998, 282(5395), 1877-1882.
[http://dx.doi.org/10.1126/science.282.5395.1877] [PMID: 9836635]
[2]
White, H.E.; Ignatiou, A.; Clare, D.K.; Orlova, E.V. Structural study of heterogeneous biological samples by cryoelectron microscopy and image processing. BioMed Res. Int., 2017, 2017, 1032432.
[http://dx.doi.org/10.1155/2017/1032432] [PMID: 28191458]
[3]
Bhattacharya, S.; Margheritis, E.G.; Takahashi, K.; Kulesha, A.; D’Souza, A.; Kim, I.; Yoon, J.H.; Tame, J.R.H.; Volkov, A.N.; Makhlynets, O.V.; Korendovych, I.V. NMR-guided directed evolution. Nature, 2022, 610(7931), 389-393.
[http://dx.doi.org/10.1038/s41586-022-05278-9] [PMID: 36198791]
[4]
Tsai, C.J.; Maizel, J.V., Jr; Nussinov, R. Anatomy of protein structures: Visualizing how a one-dimensional protein chain folds into a three-dimensional shape. Proc. Natl. Acad. Sci. USA, 2000, 97(22), 12038-12043.
[http://dx.doi.org/10.1073/pnas.97.22.12038] [PMID: 11050234]
[5]
Rivoire, O.; Reynolds, K.A.; Ranganathan, R. Evolution-based functional decomposition of proteins. PLOS Comput. Biol., 2016, 12(6), e1004817.
[http://dx.doi.org/10.1371/journal.pcbi.1004817] [PMID: 27254668]
[6]
Romero, P.A.; Tran, T.M.; Abate, A.R. Dissecting enzyme function with microfluidic-based deep mutational scanning. Proc. Natl. Acad. Sci. USA, 2015, 112(23), 7159-7164.
[http://dx.doi.org/10.1073/pnas.1422285112] [PMID: 26040002]
[7]
Morrison, K.L.; Weiss, G.A. Combinatorial alanine-scanning. Curr. Opin. Chem. Biol., 2001, 5(3), 302-307.
[http://dx.doi.org/10.1016/S1367-5931(00)00206-4] [PMID: 11479122]
[8]
Kokoszka, M.E.; Kay, B.K. Mapping protein-protein interactions with phage-displayed combinatorial peptide libraries and alanine scanning. Methods Mol. Biol., 2015, 1248, 173-188.
[http://dx.doi.org/10.1007/978-1-4939-2020-4_12] [PMID: 25616333]
[9]
Halabi, N.; Rivoire, O.; Leibler, S.; Ranganathan, R. Protein sectors: Evolutionary units of three-dimensional structure. Cell, 2009, 138(4), 774-786.
[http://dx.doi.org/10.1016/j.cell.2009.07.038] [PMID: 19703402]
[10]
Scott, L.H.; Mathews, J.C.; Filipovska, A.; Rackham, O. Building artificial genetic circuits to understand protein function. Methods Enzymol., 2020, 633, 231-250.
[http://dx.doi.org/10.1016/bs.mie.2019.11.003] [PMID: 32046848]
[11]
Scott, L.H.; Mathews, J.C.; Flematti, G.R.; Filipovska, A.; Rackham, O. An artificial yeast genetic circuit enables deep mutational scanning of an antimicrobial resistance protein. ACS Synth. Biol., 2018, 7(8), 1907-1917.
[http://dx.doi.org/10.1021/acssynbio.8b00121] [PMID: 29979580]
[12]
Zhang, S.; Tao, F.; Qing, R.; Tang, H.; Skuhersky, M.; Corin, K.; Tegler, L.; Wassie, A.; Wassie, B.; Kwon, Y.; Suter, B.; Entzian, C.; Schubert, T.; Yang, G.; Labahn, J.; Kubicek, J.; Maertens, B. QTY code enables design of detergent-free chemokine receptors that retain ligand-binding activities. Proc. Natl. Acad. Sci., 2018, 115(37), E8652-E8659.
[http://dx.doi.org/10.1073/pnas.1811031115] [PMID: 30154163]
[13]
Qing, R.; Han, Q.; Skuhersky, M.; Chung, H.; Badr, M.; Schubert, T.; Zhang, S. QTY code designed thermostable and water-soluble chimeric chemokine receptors with tunable ligand affinity. Proc. Natl. Acad. Sci., 2019, 116(51), 25668-25676.
[http://dx.doi.org/10.1073/pnas.1909026116] [PMID: 31776256]
[14]
Burns, B.P.; Mendz, G.L.; Hazell, S.L. Methods for the measurement of a bacterial enzyme activity in cell lysates and extracts. Biol. Proced. Online, 1998, 1(1), 17-26.
[http://dx.doi.org/10.1251/bpo5] [PMID: 12734591]
[15]
Miranda, H.V.; Ferreira, A.E.N.; Quintas, A.; Cordeiro, C.; Freire, A.P. Measuring intracellular enzyme concentrations. Biochem. Mol. Biol. Educ., 2008, 36(2), 135-138.
[http://dx.doi.org/10.1002/bmb.20166] [PMID: 21591178]
[16]
Zhou, H.X.; Rivas, G.; Minton, A.P. Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences. Annu. Rev. Biophys., 2008, 37(1), 375-397.
[http://dx.doi.org/10.1146/annurev.biophys.37.032807.125817] [PMID: 18573087]
[17]
Pastore, A.; Temussi, P.A. Crowding revisited: Open questions and future perspectives. Trends Biochem. Sci., 2022, 47(12), 1048-1058.
[http://dx.doi.org/10.1016/j.tibs.2022.05.007] [PMID: 35691783]
[18]
Chhabra, A.; Rani, V. Cell in situ zymography: Imaging enzyme-substrate interactions. Methods Mol. Biol., 2017, 1626, 133-143.
[http://dx.doi.org/10.1007/978-1-4939-7111-4_12] [PMID: 28608206]
[19]
Emery, A.E. Recombinant DNA technology. Lancet, 1981, 2(8260-61), 1406-1409.
[http://dx.doi.org/10.1016/S0140-6736(81)92814-2]
[20]
Georgiou, G. Recombinant DNA technology. Trends Biotechnol., 1995, 13(3), 79-80.
[http://dx.doi.org/10.1016/S0167-7799(00)88909-X] [PMID: 7766219]
[21]
Liu, X.; Yang, Y.; Zhang, W.; Sun, Y.; Peng, F.; Jeffrey, L.; Harvey, L.; McNeil, B.; Bai, Z. Expression of recombinant protein using Corynebacterium glutamicum: Progress, challenges and applications. Crit. Rev. Biotechnol., 2016, 36(4), 652-664.
[http://dx.doi.org/10.3109/07388551.2015.1004519] [PMID: 25714007]
[22]
Reece-Hoyes, J.S.; Walhout, A.J.M. Gateway recombinational cloning. Cold Spring Harb. Protoc., 2018, 2018(1), pdb.top094912.
[http://dx.doi.org/10.1101/pdb.top094912] [PMID: 29295908]
[23]
Kosobokova, E.N.; Skrypnik, K.A.; Kosorukov, V.S. Overview of fusion tags for recombinant proteins. Biochemistry, 2016, 81(3), 187-200.
[http://dx.doi.org/10.1134/S0006297916030019] [PMID: 27262188]
[24]
Wingfield, P.T. Overview of the purification of recombinant proteins. Curr. Protoc. Protein Sci., 2015, 80, 6.1.1-6.1.35.
[http://dx.doi.org/10.1002/0471140864.ps0601s80]
[25]
Baslé, E.; Joubert, N.; Pucheault, M. Protein chemical modification on endogenous amino acids. Chem. Biol., 2010, 17(3), 213-227.
[http://dx.doi.org/10.1016/j.chembiol.2010.02.008] [PMID: 20338513]
[26]
Boutureira, O.; Bernardes, G.J.L. Advances in chemical protein modification. Chem. Rev., 2015, 115(5), 2174-2195.
[http://dx.doi.org/10.1021/cr500399p] [PMID: 25700113]
[27]
Chalker, J.M.; Bernardes, G.J.L.; Lin, Y.A.; Davis, B.G. Chemical modification of proteins at cysteine: Opportunities in chemistry and biology. Chem. Asian J., 2009, 4(5), 630-640.
[http://dx.doi.org/10.1002/asia.200800427] [PMID: 19235822]
[28]
Gunnoo, S.B.; Madder, A. Chemical protein modification through cysteine. ChemBioChem, 2016, 17(7), 529-553.
[http://dx.doi.org/10.1002/cbic.201500667] [PMID: 26789551]
[29]
Rosen, C.B.; Francis, M.B. Targeting the N terminus for site-selective protein modification. Nat. Chem. Biol., 2017, 13(7), 697-705.
[http://dx.doi.org/10.1038/nchembio.2416] [PMID: 28632705]
[30]
Wu, Y.W.; Goody, R.S. Probing protein function by chemical modification. J. Pept. Sci., 2010, 16(10), 514-523.
[http://dx.doi.org/10.1002/psc.1287] [PMID: 20814888]
[31]
Ravasco, J.M.J.M.; Faustino, H.; Trindade, A.; Gois, P.M.P. Bioconjugation with maleimides: A useful tool for chemical biology. Chemistry, 2019, 25(1), 43-59.
[http://dx.doi.org/10.1002/chem.201803174] [PMID: 30095185]
[32]
Jones, C.M.; Venkatesh, Y.; Petersson, E.J. Protein labeling for FRET with methoxycoumarin and acridonylalanine. Methods Enzymol., 2020, 639, 37-69.
[http://dx.doi.org/10.1016/bs.mie.2020.04.008] [PMID: 32475410]
[33]
Jaiswal, R.; Panda, D. Cysteine 155 plays an important role in the assembly of Mycobacterium tuberculosis FtsZ. Protein Sci., 2008, 17(5), 846-854.
[http://dx.doi.org/10.1110/ps.083452008] [PMID: 18436955]
[34]
Sigrist, H.; Kempf, C.; Zahler, P. Interaction of phenylisothiocyanate with human erythrocyte band 3 protein I. Covalent modification and inhibition of phosphate transport. Biochim. Biophys. Acta Biomembr., 1980, 597(1), 137-144.
[http://dx.doi.org/10.1016/0005-2736(80)90157-1] [PMID: 7370239]
[35]
Deshpande, M.; Sathe, S.K. Interactions with 8-anilinonaphthalene-1-sulfonic acid (ANS) and surface hydrophobicity of black gram (Vigna mungo) phaseolin. J. Food Sci., 2018, 83(7), 1847-1855.
[http://dx.doi.org/10.1111/1750-3841.14204] [PMID: 29928765]
[36]
Kameel, N.I.; Shuib, A.; Tayyab, S. Acid-induced unfolding of champedak galactose-binding lectin. Protein Pept. Lett., 2016, 23(12), 1111-1117.
[http://dx.doi.org/10.2174/0929866523666161019152250] [PMID: 27774894]
[37]
Barros, A.E.B.; Carvalho, F.A.O.; Alves, F.R.; Carvalho, J.W.P.; Tabak, M. Denaturant effects on HbGp hemoglobin as monitored by 8-anilino-1-naphtalene-sulfonic acid (ANS) probe. Int. J. Biol. Macromol., 2015, 74, 327-336.
[http://dx.doi.org/10.1016/j.ijbiomac.2014.12.035] [PMID: 25546245]
[38]
Benner, S.A. Expanding the genetic lexicon: Incorporating non-standard amino acids into proteins by ribosome-based synthesis. Trends Biotechnol., 1994, 12(5), 158-163.
[http://dx.doi.org/10.1016/0167-7799(94)90076-0] [PMID: 7764897]
[39]
Chin, J.W. Expanding and reprogramming the genetic code of cells and animals. Annu. Rev. Biochem., 2014, 83(1), 379-408.
[http://dx.doi.org/10.1146/annurev-biochem-060713-035737] [PMID: 24555827]
[40]
Chin, J.W. Expanding and reprogramming the genetic code. Nature, 2017, 550(7674), 53-60.
[http://dx.doi.org/10.1038/nature24031] [PMID: 28980641]
[41]
Wang, L.; Schultz, P.G. Expanding the genetic code. Angew. Chem. Int. Ed., 2005, 44(1), 34-66.
[http://dx.doi.org/10.1002/anie.200460627] [PMID: 15599909]
[42]
Wang, T.; Liang, C.; Xu, H.; An, Y.; Xiao, S.; Zheng, M.; Liu, L.; Nie, L. Incorporation of nonstandard amino acids into proteins: Principles and applications. World J. Microbiol. Biotechnol., 2020, 36(4), 60.
[http://dx.doi.org/10.1007/s11274-020-02837-y] [PMID: 32266578]
[43]
Fredens, J.; Wang, K.; de la Torre, D.; Funke, L.F.H.; Robertson, W.E.; Christova, Y.; Chia, T.; Schmied, W.H.; Dunkelmann, D.L.; Beránek, V.; Uttamapinant, C.; Llamazares, A.G.; Elliott, T.S.; Chin, J.W. Total synthesis of Escherichia coli with a recoded genome. Nature, 2019, 569(7757), 514-518.
[http://dx.doi.org/10.1038/s41586-019-1192-5] [PMID: 31092918]
[44]
Robertson, W.E.; Funke, L.F.H.; de la Torre, D.; Fredens, J.; Elliott, T.S.; Spinck, M.; Christova, Y.; Cervettini, D.; Böge, F.L.; Liu, K.C.; Buse, S.; Maslen, S.; Salmond, G.P.C.; Chin, J.W. Sense codon reassignment enables viral resistance and encoded polymer synthesis. Science, 2021, 372(6546), 1057-1062.
[http://dx.doi.org/10.1126/science.abg3029] [PMID: 34083482]
[45]
Smits, A.H.; Borrmann, A.; Roosjen, M.; van Hest, J.C.M.; Vermeulen, M. Click-MS: Tagless protein enrichment using bioorthogonal chemistry for quantitative proteomics. ACS Chem. Biol., 2016, 11(12), 3245-3250.
[http://dx.doi.org/10.1021/acschembio.6b00520] [PMID: 27643597]
[46]
Laxman, P.; Ansari, S.; Gaus, K.; Goyette, J. The benefits of unnatural amino acid incorporation as protein labels for single molecule localization microscopy. Front Chem., 2021, 9, 641355.
[http://dx.doi.org/10.3389/fchem.2021.641355] [PMID: 33842432]
[47]
Liu, C.C.; Schultz, P.G. Adding new chemistries to the genetic code. Annu. Rev. Biochem., 2010, 79(1), 413-444.
[http://dx.doi.org/10.1146/annurev.biochem.052308.105824] [PMID: 20307192]
[48]
Roy, S.; Ghosh, P.; Ahmed, I.; Chakraborty, M.; Naiya, G.; Ghosh, B. Constrained alpha-helical peptides as inhibitors of protein-protein and protein-DNA Interactions. Biomedicines, 2018, 6(4), 118.
[http://dx.doi.org/10.3390/biomedicines6040118] [PMID: 30567318]
[49]
Davis, L.; Chin, J.W. Designer proteins: Applications of genetic code expansion in cell biology. Nat. Rev. Mol. Cell Biol., 2012, 13(3), 168-182.
[http://dx.doi.org/10.1038/nrm3286] [PMID: 22334143]
[50]
Virdee, S.; Ye, Y.; Nguyen, D.P.; Komander, D.; Chin, J.W. Engineered diubiquitin synthesis reveals Lys29-isopeptide specificity of an OTU deubiquitinase. Nat. Chem. Biol., 2010, 6(10), 750-757.
[http://dx.doi.org/10.1038/nchembio.426] [PMID: 20802491]
[51]
Yang, Y.; Song, H.; He, D.; Zhang, S.; Dai, S.; Lin, S.; Meng, R.; Wang, C.; Chen, P.R. Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label. Nat. Commun., 2016, 7(1), 12299.
[http://dx.doi.org/10.1038/ncomms12299] [PMID: 27460181]
[52]
Mohibullah, N.; Hahn, S. Site-specific cross-linking of TBP in vivo and in vitro reveals a direct functional interaction with the SAGA subunit Spt3. Genes Dev., 2008, 22(21), 2994-3006.
[http://dx.doi.org/10.1101/gad.1724408] [PMID: 18981477]
[53]
Staus, D.P.; Wingler, L.M.; Choi, M.; Pani, B.; Manglik, A.; Kruse, A.C.; Lefkowitz, R.J. Sortase ligation enables homogeneous GPCR phosphorylation to reveal diversity in β-arrestin coupling. Proc. Natl. Acad. Sci., 2018, 115(15), 3834-3839.
[http://dx.doi.org/10.1073/pnas.1722336115] [PMID: 29581292]
[54]
Hartrampf, N.; Saebi, A.; Poskus, M.; Gates, Z.P.; Callahan, A.J.; Cowfer, A.E.; Hanna, S.; Antilla, S.; Schissel, C.K.; Quartararo, A.J.; Ye, X.; Mijalis, A.J.; Simon, M.D.; Loas, A.; Liu, S.; Jessen, C.; Nielsen, T.E.; Pentelute, B.L. Synthesis of proteins by automated flow chemistry. Science, 2020, 368(6494), 980-987.
[http://dx.doi.org/10.1126/science.abb2491] [PMID: 32467387]
[55]
Proulx, C. Catching up to nature’s ribosomes. Science, 2020, 368(6494), 941.
[http://dx.doi.org/10.1126/science.abb9711] [PMID: 32467378]
[56]
Tamura, K. The genetic code: Francis crick’s legacy and beyond. Life, 2016, 6(3), 36.
[http://dx.doi.org/10.3390/life6030036] [PMID: 27571106]
[57]
Mullis, K.; Faloona, F.; Scharf, S.; Saiki, R.; Horn, G.; Erlich, H. Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol., 1986, 51, 263-273.
[http://dx.doi.org/10.1101/SQB.1986.051.01.032] [PMID: 3472723]
[58]
O’Brien, E.P.; Ciryam, P.; Vendruscolo, M.; Dobson, C.M. Understanding the influence of codon translation rates on cotranslational protein folding. Acc. Chem. Res., 2014, 47(5), 1536-1544.
[http://dx.doi.org/10.1021/ar5000117] [PMID: 24784899]
[59]
Taylor, W.R. The classification of amino acid conservation. J. Theor. Biol., 1986, 119(2), 205-218.
[http://dx.doi.org/10.1016/S0022-5193(86)80075-3] [PMID: 3461222]
[60]
Hoshika, S.; Leal, N.A.; Kim, M.J.; Kim, M.S.; Karalkar, N.B.; Kim, H.J.; Bates, A.M.; Watkins, N.E., Jr; SantaLucia, H.A.; Meyer, A.J.; DasGupta, S.; Piccirilli, J.A.; Ellington, A.D.; SantaLucia, J., Jr; Georgiadis, M.M.; Benner, S.A. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science, 2019, 363(6429), 884-887.
[http://dx.doi.org/10.1126/science.aat0971] [PMID: 30792304]
[61]
Wang, T.W.; Zhu, H.; Ma, X.Y.; Zhang, T.; Ma, Y.S.; Wei, D.Z. Mutant library construction in directed molecular evolution: Casting a wider net. Mol. Biotechnol., 2006, 34(1), 55-68.
[http://dx.doi.org/10.1385/MB:34:1:55] [PMID: 16943572]
[62]
Rowlinson, B.; Crublet, E.; Kerfah, R.; Plevin, M.J. Specific isotopic labelling and reverse labelling for protein NMR spectroscopy: Using metabolic precursors in sample preparation. Biochem. Soc. Trans., 2022, 50(6), 1555-1567.
[http://dx.doi.org/10.1042/BST20210586] [PMID: 36382942]
[63]
Wright, P.E.; Dyson, H.J. Intrinsically disordered proteins in cellular signalling and regulation. Nat. Rev. Mol. Cell Biol., 2015, 16(1), 18-29.
[http://dx.doi.org/10.1038/nrm3920] [PMID: 25531225]
[64]
Tang, Y.J.; Pang, Y.H.; Liu, B. DeepIDP-2L: Protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network. Bioinformatics, 2022, 38(5), 1252-1260.
[http://dx.doi.org/10.1093/bioinformatics/btab810] [PMID: 34864847]
[65]
Mu, J.; Pan, Z.; Chen, H.F. Balanced solvent model for intrinsically disordered and ordered proteins. J. Chem. Inf. Model., 2021, 61(10), 5141-5151.
[http://dx.doi.org/10.1021/acs.jcim.1c00407] [PMID: 34546059]
[66]
Earl, L.A.; Falconieri, V.; Milne, J.L.S.; Subramaniam, S. Cryo-EM: Beyond the microscope. Curr. Opin. Struct. Biol., 2017, 46, 71-78.
[http://dx.doi.org/10.1016/j.sbi.2017.06.002] [PMID: 28646653]
[67]
Shi, D.; Nannenga, B.L.; de la Cruz, M.J.; Liu, J.; Sawtelle, S.; Calero, G.; Reyes, F.E.; Hattne, J.; Gonen, T. The collection of MicroED data for macromolecular crystallography. Nat. Protoc., 2016, 11(5), 895-904.
[http://dx.doi.org/10.1038/nprot.2016.046] [PMID: 27077331]
[68]
Shi, D.; Nannenga, B.L.; Iadanza, M.G.; Gonen, T. Three-dimensional electron crystallography of protein microcrystals. eLife, 2013, 2, e01345.
[http://dx.doi.org/10.7554/eLife.01345] [PMID: 24252878]
[69]
Nannenga, B.L.; Shi, D.; Leslie, A.G.W.; Gonen, T. High-resolution structure determination by continuous-rotation data collection in MicroED. Nat. Methods, 2014, 11(9), 927-930.
[http://dx.doi.org/10.1038/nmeth.3043] [PMID: 25086503]
[70]
Buermans, H.P.J.; den Dunnen, J.T. Next generation sequencing technology: Advances and applications. Biochim. Biophys. Acta Mol. Basis Dis., 2014, 1842(10), 1932-1941.
[http://dx.doi.org/10.1016/j.bbadis.2014.06.015] [PMID: 24995601]
[71]
Neuwald, A.F. Gleaning structural and functional information from correlations in protein multiple sequence alignments. Curr. Opin. Struct. Biol., 2016, 38, 1-8.
[http://dx.doi.org/10.1016/j.sbi.2016.04.006] [PMID: 27179293]
[72]
Greene, L.H.; Chrysina, E.D.; Irons, L.I.; Papageorgiou, A.C.; Acharya, K.R.; Brew, K. Role of conserved residues in structure and stability: Tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily. Protein Sci., 2001, 10(11), 2301-2316.
[http://dx.doi.org/10.1110/ps.22901] [PMID: 11604536]
[73]
Suemori, A. Conserved and non-conserved residues and their role in the structure and function of p-hydroxybenzoate hydroxylase. Protein Eng. Des. Sel., 2013, 26(7), 479-488.
[http://dx.doi.org/10.1093/protein/gzt026] [PMID: 23766373]
[74]
Cocco, S.; Monasson, R.; Weigt, M. From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLOS Comput. Biol., 2013, 9(8), e1003176.
[http://dx.doi.org/10.1371/journal.pcbi.1003176] [PMID: 23990764]
[75]
Callaway, D.J.E.; Bu, Z. Visualizing the nanoscale: protein internal dynamics and neutron spin echo spectroscopy. Curr. Opin. Struct. Biol., 2017, 42, 1-5.
[http://dx.doi.org/10.1016/j.sbi.2016.10.001] [PMID: 27756047]
[76]
Salinas, V.H.; Ranganathan, R. Coevolution-based inference of amino acid interactions underlying protein function. eLife, 2018, 7, e34300.
[http://dx.doi.org/10.7554/eLife.34300] [PMID: 30024376]
[77]
Wang, T.; Liang, C.; Hou, Y.; Zheng, M.; Xu, H.; An, Y.; Xiao, S.; Liu, L.; Lian, S. Small design from big alignment: Engineering proteins with multiple sequence alignment as the starting point. Biotechnol. Lett., 2020, 42(8), 1305-1315.
[http://dx.doi.org/10.1007/s10529-020-02914-0] [PMID: 32430802]
[78]
Sutto, L.; Marsili, S.; Valencia, A.; Gervasio, F.L. From residue coevolution to protein conformational ensembles and functional dynamics. Proc. Natl. Acad. Sci., 2015, 112(44), 13567-13572.
[http://dx.doi.org/10.1073/pnas.1508584112] [PMID: 26487681]
[79]
Malinverni, D.; Marsili, S.; Barducci, A.; De Los Rios, P. Large-scale conformational transitions and dimerization are encoded in the amino-acid sequences of Hsp70 chaperones. PLOS Comput. Biol., 2015, 11(6), e1004262.
[http://dx.doi.org/10.1371/journal.pcbi.1004262] [PMID: 26046683]
[80]
Kamisetty, H.; Ovchinnikov, S.; Baker, D. Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era. Proc. Natl. Acad. Sci., 2013, 110(39), 15674-15679.
[http://dx.doi.org/10.1073/pnas.1314045110] [PMID: 24009338]
[81]
Neuwald, A.F.; Altschul, S.F. Inference of functionally-relevant n-acetyltransferase residues based on statistical correlations. PLOS Comput. Biol., 2016, 12(12), e1005294.
[http://dx.doi.org/10.1371/journal.pcbi.1005294] [PMID: 28002465]
[82]
Wang, L.Y. Covariation analysis of local amino acid sequences in recurrent protein local structures. J. Bioinform. Comput. Biol., 2005, 3(6), 1391-1409.
[http://dx.doi.org/10.1142/S0219720005001648] [PMID: 16374913]
[83]
Huang, Y.; Bonett, S.; Kloczkowski, A.; Jernigan, R.; Wu, Z. Statistical measures on residue-level protein structural properties. J. Struct. Funct. Genomics, 2011, 12(2), 119-136.
[http://dx.doi.org/10.1007/s10969-011-9104-4] [PMID: 21452025]
[84]
Wang, S.; Wei, W.; Zheng, Y.; Hou, J.; Dou, Y.; Zhang, S.; Luo, X.; Cai, X. The role of insulin C-peptide in the coevolution analyses of the insulin signaling pathway: A hint for its functions. PLoS One, 2012, 7(12), e52847.
[http://dx.doi.org/10.1371/journal.pone.0052847] [PMID: 23300796]
[85]
Sander, I.M.; Chaney, J.L.; Clark, P.L. Expanding Anfinsen’s principle: Contributions of synonymous codon selection to rational protein design. J. Am. Chem. Soc., 2014, 136(3), 858-861.
[http://dx.doi.org/10.1021/ja411302m] [PMID: 24392935]
[86]
Sarkar, A.; Panati, K.; Narala, V.R. Code inside the codon: The role of synonymous mutations in regulating splicing machinery and its impact on disease. Mutat. Res. Rev. Mutat. Res., 2022, 790, 108444.
[http://dx.doi.org/10.1016/j.mrrev.2022.108444] [PMID: 36307006]
[87]
Komar, A.A. A pause for thought along the co-translational folding pathway. Trends Biochem. Sci., 2009, 34(1), 16-24.
[http://dx.doi.org/10.1016/j.tibs.2008.10.002] [PMID: 18996013]
[88]
Hanson, G.; Coller, J. Codon optimality, bias and usage in translation and mRNA decay. Nat. Rev. Mol. Cell Biol., 2018, 19(1), 20-30.
[http://dx.doi.org/10.1038/nrm.2017.91] [PMID: 29018283]
[89]
Uddin, A.; Paul, N.; Chakraborty, S. The codon usage pattern of genes involved in ovarian cancer. Ann. N. Y. Acad. Sci., 2019, 1440(1), 67-78.
[http://dx.doi.org/10.1111/nyas.14019] [PMID: 30843242]
[90]
Brar, G.A. Beyond the triplet code: Context cues transform translation. Cell, 2016, 167(7), 1681-1692.
[http://dx.doi.org/10.1016/j.cell.2016.09.022] [PMID: 27984720]
[91]
Dinman, J.D. Translational recoding signals: Expanding the synthetic biology toolbox. J. Biol. Chem., 2019, 294(19), 7537-7545.
[http://dx.doi.org/10.1074/jbc.REV119.006348] [PMID: 30936208]
[92]
Hussain, S.; Rasool, S.T. Analysis of synonymous codon usage in Zika virus. Acta Trop., 2017, 173, 136-146.
[http://dx.doi.org/10.1016/j.actatropica.2017.06.006] [PMID: 28606821]
[93]
Jumper, J.; Evans, R.; Pritzel, A.; Green, T.; Figurnov, M.; Ronneberger, O.; Tunyasuvunakool, K.; Bates, R.; Žídek, A.; Potapenko, A.; Bridgland, A.; Meyer, C.; Kohl, S.A.A.; Ballard, A.J.; Cowie, A.; Romera-Paredes, B.; Nikolov, S.; Jain, R.; Adler, J.; Back, T.; Petersen, S.; Reiman, D.; Clancy, E.; Zielinski, M.; Steinegger, M.; Pacholska, M.; Berghammer, T.; Bodenstein, S.; Silver, D.; Vinyals, O.; Senior, A.W.; Kavukcuoglu, K.; Kohli, P.; Hassabis, D. Highly accurate protein structure prediction with AlphaFold. Nature, 2021, 596(7873), 583-589.
[http://dx.doi.org/10.1038/s41586-021-03819-2] [PMID: 34265844]
[94]
Tunyasuvunakool, K.; Adler, J.; Wu, Z.; Green, T.; Zielinski, M.; Žídek, A.; Bridgland, A.; Cowie, A.; Meyer, C.; Laydon, A.; Velankar, S.; Kleywegt, G.J.; Bateman, A.; Evans, R.; Pritzel, A.; Figurnov, M.; Ronneberger, O.; Bates, R.; Kohl, S.A.A.; Potapenko, A.; Ballard, A.J.; Romera-Paredes, B.; Nikolov, S.; Jain, R.; Clancy, E.; Reiman, D.; Petersen, S.; Senior, A.W.; Kavukcuoglu, K.; Birney, E.; Kohli, P.; Jumper, J.; Hassabis, D. Highly accurate protein structure prediction for the human proteome. Nature, 2021, 596(7873), 590-596.
[http://dx.doi.org/10.1038/s41586-021-03828-1] [PMID: 34293799]
[95]
Terwilliger, T.C.; Poon, B.K.; Afonine, P.V.; Schlicksup, C.J.; Croll, T.I.; Millán, C.; Richardson, J.S.; Read, R.J.; Adams, P.D. Improved AlphaFold modeling with implicit experimental information. Nat. Methods, 2022, 19(11), 1376-1382.
[http://dx.doi.org/10.1038/s41592-022-01645-6] [PMID: 36266465]
[96]
Leman, J.K.; Weitzner, B.D.; Lewis, S.M.; Adolf-Bryfogle, J.; Alam, N.; Alford, R.F.; Aprahamian, M.; Baker, D.; Barlow, K.A.; Barth, P.; Basanta, B.; Bender, B.J.; Blacklock, K.; Bonet, J.; Boyken, S.E.; Bradley, P.; Bystroff, C.; Conway, P.; Cooper, S.; Correia, B.E.; Coventry, B.; Das, R.; De Jong, R.M.; DiMaio, F.; Dsilva, L.; Dunbrack, R.; Ford, A.S.; Frenz, B.; Fu, D.Y.; Geniesse, C.; Goldschmidt, L.; Gowthaman, R.; Gray, J.J.; Gront, D.; Guffy, S.; Horowitz, S.; Huang, P.S.; Huber, T.; Jacobs, T.M.; Jeliazkov, J.R.; Johnson, D.K.; Kappel, K.; Karanicolas, J.; Khakzad, H.; Khar, K.R.; Khare, S.D.; Khatib, F.; Khramushin, A.; King, I.C.; Kleffner, R.; Koepnick, B.; Kortemme, T.; Kuenze, G.; Kuhlman, B.; Kuroda, D.; Labonte, J.W.; Lai, J.K.; Lapidoth, G.; Leaver-Fay, A.; Lindert, S.; Linsky, T.; London, N.; Lubin, J.H.; Lyskov, S.; Maguire, J.; Malmström, L.; Marcos, E.; Marcu, O.; Marze, N.A.; Meiler, J.; Moretti, R.; Mulligan, V.K.; Nerli, S.; Norn, C.; Ó’Conchúir, S.; Ollikainen, N.; Ovchinnikov, S.; Pacella, M.S.; Pan, X.; Park, H.; Pavlovicz, R.E.; Pethe, M.; Pierce, B.G.; Pilla, K.B.; Raveh, B.; Renfrew, P.D.; Burman, S.S.R.; Rubenstein, A.; Sauer, M.F.; Scheck, A.; Schief, W.; Schueler-Furman, O.; Sedan, Y.; Sevy, A.M.; Sgourakis, N.G.; Shi, L.; Siegel, J.B.; Silva, D.A.; Smith, S.; Song, Y.; Stein, A.; Szegedy, M.; Teets, F.D.; Thyme, S.B.; Wang, R.Y.R.; Watkins, A.; Zimmerman, L.; Bonneau, R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat. Methods, 2020, 17(7), 665-680.
[http://dx.doi.org/10.1038/s41592-020-0848-2] [PMID: 32483333]
[97]
Dauparas, J.; Anishchenko, I.; Bennett, N.; Bai, H.; Ragotte, R.J.; Milles, L.F.; Wicky, B.I.M.; Courbet, A.; de Haas, R.J.; Bethel, N.; Leung, P.J.Y.; Huddy, T.F.; Pellock, S.; Tischer, D.; Chan, F.; Koepnick, B.; Nguyen, H.; Kang, A.; Sankaran, B.; Bera, A.K.; King, N.P.; Baker, D. Robust deep learning–based protein sequence design using ProteinMPNN. Science, 2022, 378(6615), 49-56.
[http://dx.doi.org/10.1126/science.add2187] [PMID: 36108050]

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