Abstract:Conformation dynamics attributes to the biological functions of active proteins and conformation ensembles. The conformation ensembles include protein stable states (PSS) that can be measured by conventional structural biology approaches and the invisible protein states (IPS) that cannot be measured by conventional structural biology ones. The conformational exchange between IPS and PSS plays an important role in the biological functions of proteins. In this review, we briefly describe the basic properties of IPS and discuss its contribution to the development of the classical molecular recognition mechanism of “key-lock hypothesis” and "induced fit hypothesis" into "conformational selection hypothesis". Furthermore, this review compares the advantages and disadvantages of the current structural biology approaches for investigating the conformational properties of IPS. Because of advanced NMR technology, the exploration of the conformational properties of IPS in experimental manner has become feasible. It is expected that the study of IPS and its function will not only help clarify the molecule recognition mechanism of proteins, but also provide a basis for guiding the design of targeted drugs.
成细瑶, 李刚, 苏正定. 蛋白质隐态构象[J]. 中国生物化学与分子生物学报, 2021, 37(8): 1010-1016.
CHENG Xi-Yao, LI Gang, SU Zheng-Ding. Invisible Protein State. Chinese Journal of Biochemistry and Molecular Biol, 2021, 37(8): 1010-1016.
[1] Alderson TR, Kay LE. Unveiling invisible protein states with NMR spectroscopy[J]. Current Opinion in Structural Biology, 2020, 60: 39-49 [2] Auer R, Neudecker P, Muhandiram DR, et al. Measuring the signs of 1H(alpha) chemical shift differences between ground and excited protein states by off-resonance spin-lock R(1rho) NMR spectroscopy[J]. J Am Chem Soc, 2009, 131(31): 10832-10833 [3] Boehr DD, Mcelheny D, Dyson HJ, et al. The dynamic energy landscape of dihydrofolate reductase catalysis[J]. Science, 2006, 313(5793): 1638-1642 [4] Varela AE, England KA, Cavagnero S. Kinetic trapping in protein folding[J]. Protein Eng Des Sel, 2019, 32(2): 103-108 [5] Waudby CA, Dobson CM, Christodoulou J. Nature and Regulation of Protein Folding on the Ribosome[J]. Trends Biochem Sci, 2019, 44(11): 914-926 [6] Balchin D, Hayer-Hartl M, Hartl FU. Recent advances in understanding catalysis of protein folding by molecular chaperones[J]. FEBS Lett, 2020, 594(17): 2770-2781 [7] Su ZD, Arooz MT, Chen HM, et al. Least activation path for protein folding: investigation of staphylococcal nuclease folding by stopped-flow circular dichroism[J]. Proc Natl Acad Sci U S A, 1996, 93(6): 2539-2544 [8] Fersht AR, Matouschek A, Sancho J, et al. Pathway of protein folding[J]. Faraday Discuss, 1992,93: 183-193 [9] Creighton TE. Protein folding. Up the kinetic pathway[J]. Nature, 1992, 356(6366): 194-195 [10] Ghosh DK, Ranjan A. The metastable states of proteins[J]. Protein Sci, 2020, 29(7): 1559-1568 [11] Bowman GR, Geissler PL. Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites[J]. Proc Natl Acad Sci U S A, 2012, 109(29): 11681-11686 [12] Fersht AR. Characterizing transition states in protein folding: an essential step in the puzzle[J]. Curr Opin Struct Biol, 1995, 5(1): 79-84 [13] Long D, Bouvignies G, Kay LE. Measuring hydrogen exchange rates in invisible protein excited states[J]. Proc Natl Acad Sci U S A, 2014, 111(24): 8820-8825 [14] Hansen AL, Kay LE. Measurement of histidine pKa values and tautomer populations in invisible protein states[J]. Proc Natl Acad Sci U S A, 2014, 111(17): E1705-1712 [15] Hansen AL, Lundstrom P, Velyvis A, et al. Quantifying millisecond exchange dynamics in proteins by CPMG relaxation dispersion NMR using side-chain 1H probes[J]. J Am Chem Soc, 2012, 134(6): 3178-3189 [16] Bouvignies G, Kay LE. A 2D (1)(3)C-CEST experiment for studying slowly exchanging protein systems using methyl probes: an application to protein folding[J]. J Biomol NMR, 2012, 53(4): 303-310 [17] Tsai CJ, Kumar S, Ma B, et al. Folding funnels, binding funnels, and protein function[J]. Protein Sci, 1999, 8(6): 1181-1190 [18] Charlier C, Bouvignies G, Pelupessy P, et al. Structure and Dynamics of an Intrinsically Disordered Protein Region That Partially Folds upon Binding by Chemical-Exchange NMR[J]. J Am Chem Soc, 2017, 139(35): 12219-12227 [19] Barnes CA, Mishra P, Baber JL, et al. Conformational Heterogeneity in the Activation Mechanism of Bax[J]. Structure, 2017, 25(8): 1310-1316 e1313 [20] Walker AS, Rablen PR, Schepartz A. Rotamer-Restricted Fluorogenicity of the Bis-Arsenical ReAsH[J]. J Am Chem Soc, 2016, 138(22): 7143-7150 [21] Vallurupalli P, Bouvignies G, Kay LE. Studying "invisible" excited protein states in slow exchange with a major state conformation[J]. J Am Chem Soc, 2012, 134(19): 8148-8161 [22] Gopalan AB, Vallurupalli P. Measuring the signs of the methyl (1)H chemical shift differences between major and ‘invisible' minor protein conformational states using methyl (1)H multi-quantum spectroscopy[J]. J Biomol NMR, 2018, 70(3): 187-202 [23] Torrens-Fontanals M, Stepniewski TM, Aranda-Garcia D, et al. How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs[J]. Int J Mol Sci, 2020, 21(16): 5933 [24] Kappel K, Miao Y, Mccammon JA. Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor[J]. Q Rev Biophys, 2015, 48(4): 479-487 [25] Stank A, Kokh DB, Fuller JC, et al. Protein Binding Pocket Dynamics[J]. Acc Chem Res, 2016, 49(5): 809-815 [26] Martin SF, Clements JH. Correlating structure and energetics in protein-ligand interactions: paradigms and paradoxes[J]. Annu Rev Biochem, 2013, 82: 267-293 [27] Vishwanath S, Sukhwal A, Sowdhamini R, et al. Specificity and stability of transient protein-protein interactions[J]. Curr Opin Struct Biol, 2017, 44: 77-86 [28] Acuner Ozbabacan SE, Engin HB, Gursoy A, et al. Transient protein-protein interactions[J]. Protein Eng Des Sel, 2011, 24(9): 635-648 [29] Thielges MC, Zimmermann J, Yu W, et al. Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition[J]. Biochemistry, 2008, 47(27): 7237-7247 [30] Popowicz G, Czarna A, Holak T. Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain[J]. Cell Cycle, 2008, 7(15): 2441-2443 [31] Agarwal PK, Doucet N, Chennubhotla C, et al. Conformational Sub-states and Populations in Enzyme Catalysis[J]. Methods Enzymol, 2016, 578: 273-297 [32] Warshel A, Bora RP. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis[J]. J Chem Phys, 2016, 144(18): 180901 [33] Kovermann M, Aden J, Grundstrom C, et al. Structural basis for catalytically restrictive dynamics of a high-energy enzyme state[J]. Nat Commun, 2015, 6: 7644 [34] Takahashi S, Kamagata K, Oikawa H. Where the complex things are: single molecule and ensemble spectroscopic investigations of protein folding dynamics[J]. Curr Opin Struct Biol, 2016, 36: 1-9 [35] Ahmad B, Borana MS, Chaudhary AP. Understanding curcumin-induced modulation of protein aggregation[J]. Int J Biol Macromol, 2017, 100: 89-96 [36] Mothi N, Muthu SA, Kale A, et al. Curcumin promotes fibril formation in F isomer of human serum albumin via amorphous aggregation[J]. Biophys Chem, 2015, 207: 30-39 [37] Spyrakis F, Bidonchanal A, Barril X, et al. Protein flexibility and ligand recognition: challenges for molecular modeling[J]. Curr Top Med Chem, 2011, 11(2): 192-210 [38] Mittag T, Kay LE, Forman-Kay JD. Protein dynamics and conformational disorder in molecular recognition[J]. J Mol Recognit, 2010, 23(2): 105-116 [39] Smith-Gill SJ. Protein-protein interactions: structural motifs and molecular recognition[J]. Curr Opin Biotechnol, 1991, 2(4): 568-575 [40] Yuwen T, Kay LE, Bouvignies G. Dramatic Decrease in CEST Measurement Times Using Multi-Site Excitation[J]. Chemphyschem, 2018, 19(14): 1707-1710 [41] Yuwen T, Sekhar A, Kay LE. Separating Dipolar and Chemical Exchange Magnetization Transfer Processes in (1) H-CEST[J]. Angew Chem Int Ed Engl, 2017, 56(22): 6122-6125 [42] Xiong J, Gao M, Zhou J, et al. The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding-binding process during target recognition[J]. Proteins, 2019, 87(4): 265-275 [43] Hansen DF, Neudecker P, Kay LE. Determination of isoleucine side-chain conformations in ground and excited states of proteins from chemical shifts[J]. J Am Chem Soc, 2010, 132(22): 7589-7591 [44] Su Z, Osborne MJ, Xu P, et al. A bivalent dissectional analysis of the high-affinity interactions between Cdc42 and the Cdc42/Rac interactive binding domains of signaling kinases in Candida albicans[J]. Biochemistry, 2005, 44(50): 16461-16474 [45] Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition[J]. Nature Chemical Biology, 2009, 5(11): 789-796 [46] Jagtap PKA, Asami S, Sippel C, et al. Selective Inhibitors of FKBP51 Employ Conformational Selection of Dynamic Invisible States[J]. Angew Chem Int Ed Engl, 2019, 58(28): 9429-9433 [47] Olsen GL, Bardaro MF, Jr., Echodu DC, et al. Intermediate rate atomic trajectories of RNA by solid-state NMR spectroscopy[J]. J Am Chem Soc, 2010, 132(1): 303-308 [48] Liu G, Prabhakar A, Aucoin D, et al. Mechanistic studies of peptide self-assembly: transient alpha-helices to stable beta-sheets[J]. J Am Chem Soc, 2010, 132(51): 18223-18232 [49] Korzhnev DM, Religa TL, Banachewicz W, et al. A transient and low-populated protein-folding intermediate at atomic resolution[J]. Science, 2010, 329(5997): 1312-1316 [50] Nieslanik BS, Dietze EC, Atkins WM, et al. The locally denatured state of glutathione S-transferase A1-1: transition state analysis of ligand-dependent formation of the C-terminal helix[J]. Pac Symp Biocomput, 1999, 554-565 [51] Kuznetsova IM, Turoverov KK, Uversky VN. Use of the phase diagram method to analyze the protein unfolding-refolding reactions: fishing out the "invisible" intermediates[J]. J Proteome Res, 2004, 3(3): 485-494 [52] Chizmadzhev YA. The mechanisms of lipid-protein rearrangements during viral infection[J]. Bioelectrochemistry, 2004, 63(1-2): 129-136 [53] Spoerner M, Herrmann C, Vetter IR, et al. Dynamic properties of the Ras switch I region and its importance for binding to effectors[J]. Proc Natl Acad Sci U S A, 2001, 98(9): 4944-4949 [54] Diederix RE, Ubbink M, Canters GW. Peroxidase activity as a tool for studying the folding of c-type cytochromes[J]. Biochemistry, 2002, 41(43): 13067-13077 [55] Korzhnev DM, Kay LE. Probing invisible, low-populated States of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding[J]. Acc Chem Res, 2008, 41(3): 442-451 [56] Kleckner IR, Foster MP. An introduction to NMR-based approaches for measuring protein dynamics[J]. Biochim Biophys Acta, 2011, 1814(8): 942-968 [57] Shih O, Yeh Y Q, Liao KF, et al. Oligomerization process of Bcl-2 associated X protein revealed from intermediate structures in solution[J]. 2017, 19(11): 7947-7954 [58] Alderson TR, Kay LE. Unveiling invisible protein states with NMR spectroscopy[J]. Curr Opin Struct Biol, 2020, 60: 39-49 [59] Ertekin A, Massi F. Understanding therole of conformational dynamics in protein–ligand interactions using NMR relaxation methods [M]. eMagRes. John Wiley & Sons, Ltd. 2007, 3: 266-266 [60] Kay LE. NMR studies of protein structure and dynamics - a look backwards and forwards[J]. J Magn Reson, 2011, 213(2): 492-494 [61] Liu X, Speckhard DC, Shepherd T R, et al. Distinctroles for conformational dynamics in protein-ligand interactions[J]. Structure, 2016, 24(12): 2053-2066 [62] Orts J, Walti MA, Marsh M, et al. NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment[J]. J Am Chem Soc, 2016, 138(13): 4393-4400 [63] Walti MA, Riek R, Orts J. Fast NMR-based determination of the 3D structure of the binding site of protein-ligand complexes with weak affinity binders[J]. Angew Chem Int Ed Engl, 2017, 56(19): 5208-5211 [64] Liao M, Cao E, Julius D, et al. Structure of the TRPV1 ion channel determined by electron cryo-microscopy[J]. Nature, 2013, 504(7478): 107-112 [65] Pena A, Sweeney A, Cook AD, et al. Structure of microtubule-trapped human kinesin-5 and its mechanism of inhibition revealed using cryoelectron microscopy[J]. Structure, 2020, 28(4): 450-457.e5 [66] Murata K, Wolf M. Cryo-electron microscopy for structural analysis of dynamic biological macromolecules[J]. Biochim Biophys Acta, 2018, 1862(2): 324-334 [67] Barnes CA, Robertson AJ, Louis JM, et al. Observation of beta-amyloid peptide oligomerization by pressure-jump NMR spectroscopy[J]. J Am Chem Soc, 2019, 141(35): 13762-13766 [68] Giegé R. A historical perspective on protein crystallization from 1840 to the present day[J]. Febs Journal, 2013, 280(24): 6456-6497 [69] Blackburn BJ, Li S, Roznowski AP, et al. Coatprotein mutations that alter the flux of morphogenetic intermediates through theØX174 early assembly pathway[J]. J Virol, 2017, 91(24): [70] Chapman HN, Fromme P, Barty A, et al. Femtosecond X-ray protein nanocrystallography[J]. Nature, 2011, 470(7332): 73-77 [71] Ghosh DK, Kumar A, Ranjan A. Metastable states of HYPK-UBA domain's seeds drive the dynamics of its own aggregation[J]. Biochim Biophys Acta Gen Subj, 2018, 1862(12): 2846-2861 [72] Pirchi M, Ziv G, Riven I, et al. Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein[J]. Nat Commun, 2011, 2: 493 [73] Yang J, Dear AJ, Michaels TCT, et al. Directobservation of oligomerization by single molecule fluorescence reveals a multistep aggregation mechanism for the yeast prion protein Ure2[J]. J Am Chem Soc, 2018, 140(7): 2493-2503 [74] Fazeli A, Shojaosadati SA, Fazeli MR, et al. The role of trehalose for metastable state and functional form of recombinant interferon beta-1b[J]. J Biotechnol, 2013, 163(3): 318-324 [75] Stocks BB, Sarkar A, Wintrode PL, et al. Early hydrophobic collapse of alpha(1)-antitrypsin facilitates formation of a metastable state: insights from oxidative labeling and mass spectrometry[J]. J Mol Biol, 2012, 423(5): 789-799 [76] Zheng X, Wintrode PL, Chance MR. Complementary structural mass spectrometry techniques reveal local dynamics in functionally important regions of a metastable serpin[J]. Structure, 2008, 16(1): 38-51 [77] Scholl ZN, Li Q, Yang W, et al. Single-molecule force spectroscopy reveals the calcium dependence of the alternative conformations in the native state of a betagamma-crystallin protein[J]. J Biol Chem, 2016, 291(35): 18263-18275 [78] Auer R, Hansen DF, Neudecker P, et al. Measurement of signs of chemical shift differences between ground and excited protein states: a comparison between H(S/M)QC and R1rho methods[J]. J Biomol NMR, 2010, 46(3): 205-216 [79] Bouvignies G, Korzhnev DM, Neudecker P, et al. A simple method for measuring signs of (1)H (N) chemical shift differences between ground and excited protein states[J]. J Biomol NMR, 2010, 47(2): 135-141 [80] Cheng L, Zhu J, Hui WH, et al. Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics[J]. J Mol Biol, 2010, 397(3): 852-863