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Volumn 108, Issue 19, 2011, Pages 7787-7792

Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins

Author keywords

Kinetic cooperativity; Pathway diversity; Protein denaturation; Self organized polymer model

Indexed keywords

AMINO ACID; GLOBULAR PROTEIN; GUANIDINE; PEPTIDE; POLYPEPTIDE; PROTEIN SH3; SOLVENT;

EID: 79956370148     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1019500108     Document Type: Article
Times cited : (66)

References (62)
  • 1
    • 39149087014 scopus 로고    scopus 로고
    • Protein folding studied by single-molecule FRET
    • Schuler B, Eaton WA (2008) Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 18:16-26.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 16-26
    • Schuler, B.1    Eaton, W.A.2
  • 2
    • 77956208339 scopus 로고    scopus 로고
    • What lessons can be learned from studying the folding of homologous proteins?
    • Nickson AA, Clarke J (2010) What lessons can be learned from studying the folding of homologous proteins? Methods 52:38-50.
    • (2010) Methods , vol.52 , pp. 38-50
    • Nickson, A.A.1    Clarke, J.2
  • 4
    • 66849106554 scopus 로고    scopus 로고
    • An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms
    • Bartlett AI, Radford SE (2009) An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Nat Struct Mol Biol 16:582-588.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 582-588
    • Bartlett, A.I.1    Radford, S.E.2
  • 5
    • 77953231020 scopus 로고    scopus 로고
    • The folding cooperativity of a protein is controlled by its chain topology
    • Shank EA, Cecconi C, Dill JW, Marqusee S, Bustamante C (2010) The folding cooperativity of a protein is controlled by its chain topology. Nature 465:637-640.
    • (2010) Nature , vol.465 , pp. 637-640
    • Shank, E.A.1    Cecconi, C.2    Dill, J.W.3    Marqusee, S.4    Bustamante, C.5
  • 6
    • 76649093956 scopus 로고    scopus 로고
    • Full distance-resolved folding energy landscape of one single protein molecule
    • Gebhardt JCM, Bornschloegla T, Rief M (2010) Full distance-resolved folding energy landscape of one single protein molecule. Proc Natl Acad Sci USA 107:2013-2018.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 2013-2018
    • Gebhardt, J.C.M.1    Bornschloegla, T.2    Rief, M.3
  • 8
    • 16344371778 scopus 로고    scopus 로고
    • RNA and protein folding: Common themes and variations
    • DOI 10.1021/bi047314+
    • Thirumalai D, Hyeon C (2005) RNA and protein folding: Common themes and variations. Biochemistry 44:4957-4970. (Pubitemid 40471212)
    • (2005) Biochemistry , vol.44 , Issue.13 , pp. 4957-4970
    • Thirumalai, D.1    Hyeon, C.2
  • 9
    • 33646931471 scopus 로고    scopus 로고
    • Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
    • Shakhnovich E (2006) Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet. Chem Rev 106:1559-1588.
    • (2006) Chem Rev , vol.106 , pp. 1559-1588
    • Shakhnovich, E.1
  • 12
    • 57449106823 scopus 로고    scopus 로고
    • Chemical, physical, and theoretical kinetics of an ultrafast folding protein
    • Kubelka J, Henry E, Cellmer T, Hofrichter J, Eaton W (2008) Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc Natl Acad Sci USA 105:18655-18662.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 18655-18662
    • Kubelka, J.1    Henry, E.2    Cellmer, T.3    Hofrichter, J.4    Eaton, W.5
  • 15
    • 63449135082 scopus 로고    scopus 로고
    • An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields
    • Whitford PC, et al. (2009) An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields. Proteins 75:430-441.
    • (2009) Proteins , vol.75 , pp. 430-441
    • Whitford, P.C.1
  • 16
    • 77649264931 scopus 로고    scopus 로고
    • Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins
    • Zhang Z, Chan HS (2010) Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins. Proc Natl Acad Sci USA 107:2920-2925.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 2920-2925
    • Zhang, Z.1    Chan, H.S.2
  • 22
    • 67749147584 scopus 로고    scopus 로고
    • Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories
    • Chung HS, Louis JM, Eaton WA (2009) Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories. Proc Natl Acad Sci USA 106:11837-11844.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 11837-11844
    • Chung, H.S.1    Louis, J.M.2    Eaton, W.A.3
  • 23
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • Jackson S (1998) How do small single-domain proteins fold? Fold Des 3:R81-R91.
    • (1998) Fold des , vol.3
    • Jackson, S.1
  • 24
    • 79955470885 scopus 로고    scopus 로고
    • Coarse-grained models of protein folding: Toy models or predictive tools?
    • Clementi C (2007) Coarse-grained models of protein folding: Toy models or predictive tools? Curr Opin Struct Biol 17:1-6.
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 1-6
    • Clementi, C.1
  • 25
    • 0036785556 scopus 로고    scopus 로고
    • The origins of asymmetry in the folding transition states of protein L and protein G
    • Karanicolas J, Brooks CL, III (2002) The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci 11:2351-2361.
    • (2002) Protein Sci , vol.11 , pp. 2351-2361
    • Karanicolas, J.1    Brooks III, C.L.2
  • 26
    • 33747592347 scopus 로고    scopus 로고
    • The experimental survey of protein-folding energy landscapes
    • DOI 10.1017/S0033583506004185, PII S0033583506004185
    • Oliveberg M, Wolynes PG (2005) The experimental survey of protein-folding energy landscapes. Q Rev Biophys 38:245-288. (Pubitemid 44268537)
    • (2005) Quarterly Reviews of Biophysics , vol.38 , Issue.3 , pp. 245-288
    • Oliveberg, M.1    Wolynes, P.G.2
  • 27
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
    • Clementi C, Nymeyer H, Onuchic J (2000) Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 298:937-953.
    • (2000) J Mol Biol , vol.298 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.3
  • 29
    • 51649087154 scopus 로고    scopus 로고
    • Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model
    • O'Brien EP, Ziv G, Haran G, Brooks BR, Thirumalai D (2008) Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model. Proc Natl Acad Sci USA 105:13403-13408.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 13403-13408
    • O'Brien, E.P.1    Ziv, G.2    Haran, G.3    Brooks, B.R.4    Thirumalai, D.5
  • 30
    • 66049114131 scopus 로고    scopus 로고
    • Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins
    • O'Brien EP, Brooks BR, Thirumalai D (2009) Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins. Biochemistry 48:3743-3754.
    • (2009) Biochemistry , vol.48 , pp. 3743-3754
    • O'Brien, E.P.1    Brooks, B.R.2    Thirumalai, D.3
  • 31
    • 63649163700 scopus 로고    scopus 로고
    • How accurate are polymer models in the analysis of Forster resonance energy transfer experiments on proteins?
    • O'Brien EP, Morrison G, Brooks BR, Thirumalai D (2009) How accurate are polymer models in the analysis of Forster resonance energy transfer experiments on proteins? J Chem Phys 130:124903.
    • (2009) J Chem Phys , vol.130 , pp. 124903
    • O'Brien, E.P.1    Morrison, G.2    Brooks, B.R.3    Thirumalai, D.4
  • 34
    • 0031444104 scopus 로고    scopus 로고
    • Folding dynamics of the src SH3 domain
    • DOI 10.1021/bi971786p
    • Grantcharova VP, Baker D (1997) Folding dynamics of the src SH3 domain. Biochemistry 36:15685-15692. (Pubitemid 28027367)
    • (1997) Biochemistry , vol.36 , Issue.50 , pp. 15685-15692
    • Grantcharova, V.P.1    Baker, D.2
  • 35
    • 0032750509 scopus 로고    scopus 로고
    • The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
    • Martinez J, Serrano L (1999) The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat Struct Biol 6:1010-1016.
    • (1999) Nat Struct Biol , vol.6 , pp. 1010-1016
    • Martinez, J.1    Serrano, L.2
  • 36
    • 18844459862 scopus 로고    scopus 로고
    • Nucleation and the transition state of the SH3 domain
    • DOI 10.1016/j.jmb.2005.03.050, PII S002228360500330X
    • Hubner IA, Edmonds KA, Shakhnovich EI (2005) Nucleation and the transition state of the SH3 domain. J Mol Biol 349:424-434. (Pubitemid 40693760)
    • (2005) Journal of Molecular Biology , vol.349 , Issue.2 , pp. 424-434
    • Hubner, I.A.1    Edmonds, K.A.2    Shakhnovich, E.I.3
  • 37
    • 0036295960 scopus 로고    scopus 로고
    • Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains
    • DOI 10.1006/jmbi.2002.5453
    • Klimov D, Thirumalai D (2002) Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J Mol Biol 317:721-737. (Pubitemid 34722160)
    • (2002) Journal of Molecular Biology , vol.317 , Issue.5 , pp. 721-737
    • Klimov, D.K.1    Thirumalai, D.2
  • 38
    • 21744452297 scopus 로고    scopus 로고
    • Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations
    • DOI 10.1016/j.jmb.2005.05.017, PII S0022283605005486
    • Ding F, Guo WH, Dokholyan NV, Shakhnovich EI, Shea JE (2005) Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. J Mol Biol 350:1035-1050. (Pubitemid 40943460)
    • (2005) Journal of Molecular Biology , vol.350 , Issue.5 , pp. 1035-1050
    • Ding, F.1    Guo, W.2    Dokholyan, N.V.3    Shakhnovich, E.I.4    Shea, J.-E.5
  • 39
    • 0001504441 scopus 로고    scopus 로고
    • Cooperativity in protein folding: From lattice models with sidechains to real proteins
    • DOI 10.1016/S1359-0278(98)00018-2
    • Klimov D, Thirumalai D (1998) Cooperativity in protein folding: From lattice models with side chains to real proteins. Fold Des 3:127-139. (Pubitemid 28166184)
    • (1998) Folding and Design , vol.3 , Issue.2 , pp. 127-139
    • Klimov, D.K.1    Thirumalai, D.2
  • 40
    • 20544461199 scopus 로고    scopus 로고
    • Thermodynamics of protein interactions with urea and guanidinium hydrochloride
    • Makhatadze G (1999) Thermodynamics of protein interactions with urea and guanidinium hydrochloride. J Phys Chem B 103:4781-4785.
    • (1999) J Phys Chem B , vol.103 , pp. 4781-4785
    • Makhatadze, G.1
  • 41
    • 77957752175 scopus 로고    scopus 로고
    • Evidence for initial non-specific polypeptide chain collapse during the refolding of the SH3 domain of PI3 kinase
    • Dasgupta A, Udgaonkar J (2010) Evidence for initial non-specific polypeptide chain collapse during the refolding of the SH3 domain of PI3 kinase. J Mol Biol 403:430-445.
    • (2010) J Mol Biol , vol.403 , pp. 430-445
    • Dasgupta, A.1    Udgaonkar, J.2
  • 42
    • 77956361829 scopus 로고    scopus 로고
    • Extremely slow intramolecular diffusion in unfolded protein L
    • Waldauer S, Bakajin O, Lapidus L (2010) Extremely slow intramolecular diffusion in unfolded protein L. Proc Natl Acad Sci USA 107:13713-13717.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 13713-13717
    • Waldauer, S.1    Bakajin, O.2    Lapidus, L.3
  • 43
    • 0001510938 scopus 로고
    • Minimum energy compact structures of random sequences of heteropolymers
    • Camacho CJ, Thirumalai D (1993) Minimum energy compact structures of random sequences of heteropolymers. Phys Rev Lett 71:2505-2508.
    • (1993) Phys Rev Lett , vol.71 , pp. 2505-2508
    • Camacho, C.J.1    Thirumalai, D.2
  • 44
    • 0035370662 scopus 로고    scopus 로고
    • Multiple protein folding nuclei and the transition state ensemble in two-state proteins
    • DOI 10.1002/prot.1058
    • Klimov D, Thirumalai D (2001) Multiple protein folding nuclei and the transition state ensemble in two state proteins. Proteins 43:465-475. (Pubitemid 32476441)
    • (2001) Proteins: Structure, Function and Genetics , vol.43 , Issue.4 , pp. 465-475
    • Klimov, D.K.1    Thirumalai, D.2
  • 45
    • 0031303354 scopus 로고    scopus 로고
    • The nucleation-collapse mechanism in protein folding: Evidence for the non-uniqueness of the folding nucleus
    • Guo Z, Thirumalai D (1997) The nucleation-collapse mechanism in protein folding: Evidence for the non-uniqueness of the folding nucleus. Fold Des 2:377-391. (Pubitemid 127740562)
    • (1997) Folding and Design , vol.2 , Issue.6 , pp. 377-391
    • Guo, Z.1    Thirumalai, D.2
  • 46
    • 0032544484 scopus 로고    scopus 로고
    • Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism
    • DOI 10.1006/jmbi.1998.1997
    • Klimov D, Thirumalai D (1998) Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J Mol Biol 282:471-492. (Pubitemid 28418797)
    • (1998) Journal of Molecular Biology , vol.282 , Issue.2 , pp. 471-492
    • Klimov, D.K.1    Thirumalai, D.2
  • 47
    • 0038648562 scopus 로고    scopus 로고
    • Folding specificity induced by loop stiffness
    • DOI 10.1110/ps.0302603
    • Spagnolo L, Ventura S, Serrano L (2003) Folding specificity induced by loop stiffness. Protein Sci 12:1473-1482. (Pubitemid 36759351)
    • (2003) Protein Science , vol.12 , Issue.7 , pp. 1473-1482
    • Spagnolo, L.1    Ventura, S.2    Serrano, L.3
  • 49
    • 1842857771 scopus 로고    scopus 로고
    • Asymmetry in the shapes of folded and denatured states of proteins
    • Dima R, Thirumalai D (2004) Asymmetry in the shapes of folded and denatured states of proteins. J Phys Chem B 108:6564-6570.
    • (2004) J Phys Chem B , vol.108 , pp. 6564-6570
    • Dima, R.1    Thirumalai, D.2
  • 50
    • 33947315248 scopus 로고    scopus 로고
    • Microsecond Hydrophobic Collapse in the Folding of Escherichia coli Dihydrofolate Reductase, an alpha/beta-Type Protein
    • DOI 10.1016/j.jmb.2007.01.085, PII S0022283607001635
    • Arai M, et al. (2007) Microsecond hydrophobic collapse in the folding of Escherichia coli Dihydrofolate reductase, an alpha/beta-type protein. J Mol Biol 368:219-229. (Pubitemid 46441220)
    • (2007) Journal of Molecular Biology , vol.368 , Issue.1 , pp. 219-229
    • Arai, M.1    Kondrashkina, E.2    Kayatekin, C.3    Matthews, C.R.4    Iwakura, M.5    Bilsel, O.6
  • 52
    • 0344407048 scopus 로고    scopus 로고
    • Kinetics of cytochrome C folding: Atomically detailed simulations
    • DOI 10.1002/prot.10349
    • Cardenas A, Elber R (2003) Kinetics of cytochrome C folding: Atomically detailed simulations. Proteins 51:245-257. (Pubitemid 36397757)
    • (2003) Proteins: Structure, Function and Genetics , vol.51 , Issue.2 , pp. 245-257
    • Cardenas, A.E.1    Elber, R.2
  • 53
    • 0000050196 scopus 로고
    • From minimal models to proteins: Time scales for protein folding kinetics
    • Thirumalai D (1995) From minimal models to proteins: Time scales for protein folding kinetics. J Phys I 5:1457-1467.
    • (1995) J Phys I , vol.5 , pp. 1457-1467
    • Thirumalai, D.1
  • 54
    • 33846193288 scopus 로고    scopus 로고
    • Pathways and Kinetic Barriers in Mechanical Unfolding and Refolding of RNA and Proteins
    • DOI 10.1016/j.str.2006.09.002, PII S0969212606003881
    • Hyeon C, Dima RI, Thirumalai D (2006) Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure 14:1633-1645. (Pubitemid 46107269)
    • (2006) Structure , vol.14 , Issue.11 , pp. 1633-1645
    • Hyeon, C.1    Dima, R.I.2    Thirumalai, D.3
  • 55
    • 0033005899 scopus 로고    scopus 로고
    • Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
    • Betancourt M, Thirumalai D (1999) Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 8:361-369. (Pubitemid 29072436)
    • (1999) Protein Science , vol.8 , Issue.2 , pp. 361-369
    • Betancourt, M.R.1    Thirumalai, D.2
  • 56
    • 0030601851 scopus 로고    scopus 로고
    • Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein
    • DOI 10.1006/jmbi.1996.0578
    • Guo Z, Thirumalai D (1996) Kinetics and thermodynamics of folding of a de novo designed four helix bundle. J Mol Biol 263:323-343. (Pubitemid 26363091)
    • (1996) Journal of Molecular Biology , vol.263 , Issue.2 , pp. 323-343
    • Guo, Z.1    Thirumalai, D.2
  • 57
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • Ermak D, McCammon J (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69:1352-1360.
    • (1978) J Chem Phys , vol.69 , pp. 1352-1360
    • Ermak, D.1    McCammon, J.2
  • 58
    • 0022555885 scopus 로고
    • Determination and analysis of urea and guanidine hydrochloride denaturation curves
    • Pace C (1986) Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol 131:266-280.
    • (1986) Methods Enzymol , vol.131 , pp. 266-280
    • Pace, C.1
  • 59
    • 79956343427 scopus 로고
    • Solubility of amino acids and related compounds in aqueous urea solutions
    • Nozaki Y, Tanford C (1963) Solubility of amino acids and related compounds in aqueous urea solutions. J Am Chem Soc 288:4074-4081.
    • (1963) J Am Chem Soc , vol.288 , pp. 4074-4081
    • Nozaki, Y.1    Tanford, C.2
  • 60
    • 0842304735 scopus 로고    scopus 로고
    • Additive Transfer Free Energies of the Peptide Backbone Unit That Are Independent of the Model Compound and the Choice of Concentration Scale
    • DOI 10.1021/bi035908r
    • Auton M, Bolen D (2004) Additive transfer free energies of the peptide backbone unit that are independent of the model compound and the choice of concentration scale. Biochemistry 43:1329-1342. (Pubitemid 38176532)
    • (2004) Biochemistry , vol.43 , Issue.5 , pp. 1329-1342
    • Auton, M.1    Bolen, D.W.2
  • 62
    • 14744271380 scopus 로고    scopus 로고
    • A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients
    • DOI 10.1002/jcc.20125
    • Hayryan S, Hu CK, Skrivanek J, Hayryan E, Pokorny I (2005) A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients. J Comput Chem 26:334-343. (Pubitemid 40325537)
    • (2005) Journal of Computational Chemistry , vol.26 , Issue.4 , pp. 334-343
    • Hayryan, S.1    Hu, C.-K.2    Skrivanek, J.3    Hayryan, E.4    Pokorny, I.5


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