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Volumn 18, Issue 1, 2009, Pages 58-68

Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape

Author keywords

Energy landscape; Folding kinetics; Protein folding; Repeat protein

Indexed keywords

ANKYRIN; NOTCH RECEPTOR;

EID: 58149464544     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.9     Document Type: Article
Times cited : (15)

References (49)
  • 1
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins fold?
    • Jackson SE (1998) How do small single-domain proteins fold? Fold Des 3:R81-R91.
    • (1998) Fold Des , vol.3
    • Jackson, S.E.1
  • 2
    • 0034687123 scopus 로고    scopus 로고
    • Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics
    • Plaxco KW, Simons KT, Ruczinski I, Baker D (2000) Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry 39:11177-11183.
    • (2000) Biochemistry , vol.39 , pp. 11177-11183
    • Plaxco, K.W.1    Simons, K.T.2    Ruczinski, I.3    Baker, D.4
  • 3
    • 1942473645 scopus 로고    scopus 로고
    • Critical nucleation size in the folding of small apparently two-state proteins
    • Bai Y, Zhou H, Zhou Y (2004) Critical nucleation size in the folding of small apparently two-state proteins. Prot Sci 13:1173-1181.
    • (2004) Prot Sci , vol.13 , pp. 1173-1181
    • Bai, Y.1    Zhou, H.2    Zhou, Y.3
  • 4
    • 0024358426 scopus 로고
    • Mapping the transition state and pathway of protein folding by protein engineering
    • Matouschek A, Kellis JT, Jr, Serrano L, Fersht AR (1989) Mapping the transition state and pathway of protein folding by protein engineering. Nature 340:122-126.
    • (1989) Nature , vol.340 , pp. 122-126
    • Matouschek, A.1    Kellis Jr, J.T.2    Serrano, L.3    Fersht, A.R.4
  • 5
    • 33846901901 scopus 로고    scopus 로고
    • Intermediates: Ubiquitous species on folding energy landscapes?
    • Brockwell DJ, Radford SE (2007) Intermediates: ubiquitous species on folding energy landscapes? Curr Opin Struct Biol 17:30-37.
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 30-37
    • Brockwell, D.J.1    Radford, S.E.2
  • 6
    • 42449151176 scopus 로고    scopus 로고
    • Protein folding and misfolding: Mechanism and principles
    • Englander SW, Mayne L, Krishna MM (2007) Protein folding and misfolding: mechanism and principles. Q Rev Biophys 40:287-326.
    • (2007) Q Rev Biophys , vol.40 , pp. 287-326
    • Englander, S.W.1    Mayne, L.2    Krishna, M.M.3
  • 7
    • 0029010695 scopus 로고
    • Kinetics of protein folding: Nucleation mechanism, time scales, and pathways
    • Guo Z, Thirumalai D (1995) Kinetics of protein folding: nucleation mechanism, time scales, and pathways. Biopolymers 36:83-102.
    • (1995) Biopolymers , vol.36 , pp. 83-102
    • Guo, Z.1    Thirumalai, D.2
  • 8
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21:167-195.
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 9
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill KA, Chan HS (1997) From Levinthal to pathways to funnels. Nat Struct Biol 4:10-19.
    • (1997) Nat Struct Biol , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 10
    • 33747592347 scopus 로고    scopus 로고
    • The experimental survey of protein-folding energy landscapes
    • Oliveberg M, Wolynes PG (2005) The experimental survey of protein-folding energy landscapes. Q Rev Biophys 38:245-288.
    • (2005) Q Rev Biophys , vol.38 , pp. 245-288
    • Oliveberg, M.1    Wolynes, P.G.2
  • 11
    • 0024963569 scopus 로고
    • Residual structure in large fragments of staphylococcal nuclease: Effects of amino acid substitutions
    • Shortle D, Meeker AK (1989) Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitutions. Biochemistry 28:936-944.
    • (1989) Biochemistry , vol.28 , pp. 936-944
    • Shortle, D.1    Meeker, A.K.2
  • 12
    • 0038131090 scopus 로고    scopus 로고
    • Chain length dependence of apomyoglobin folding: Structural evolution from misfolded sheets to native helices
    • Chow CC, Chow C, Raghunathan V, Huppert TJ, Kimball EB, Cavagnero S (2003) Chain length dependence of apomyoglobin folding: structural evolution from misfolded sheets to native helices. Biochemistry 42:7090-7099.
    • (2003) Biochemistry , vol.42 , pp. 7090-7099
    • Chow, C.C.1    Chow, C.2    Raghunathan, V.3    Huppert, T.J.4    Kimball, E.B.5    Cavagnero, S.6
  • 13
    • 36749050344 scopus 로고    scopus 로고
    • Repeat-protein folding: New insights into origins of cooperativity, stability, and topology
    • Kloss E, Courtemanche N, Barrick D (2008) Repeat-protein folding: new insights into origins of cooperativity, stability, and topology. Arch Biochem Biophys 469:83-99.
    • (2008) Arch Biochem Biophys , vol.469 , pp. 83-99
    • Kloss, E.1    Courtemanche, N.2    Barrick, D.3
  • 14
    • 4644306518 scopus 로고    scopus 로고
    • An experimentally determined protein folding energy landscape
    • Mello CC, Barrick D (2004) An experimentally determined protein folding energy landscape. Proc Natl Acad Sci USA 101:14102-14107.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 14102-14107
    • Mello, C.C.1    Barrick, D.2
  • 15
    • 17644425688 scopus 로고    scopus 로고
    • Local and long-range stability in tandemly arrayed tetratricopeptide repeats
    • Main ER, Stott K, Jackson SE, Regan L (2005) Local and long-range stability in tandemly arrayed tetratricopeptide repeats. Proc Natl Acad Sci USA 102:5721-5726.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 5721-5726
    • Main, E.R.1    Stott, K.2    Jackson, S.E.3    Regan, L.4
  • 17
    • 34848827883 scopus 로고    scopus 로고
    • Dissection of protein-protein interaction and CDK4 inhibition in the oncogenic versus tumor suppressing functions of gankyrin and P16
    • Mahajan A, Guo Y, Yuan C, Weghorst CM, Tsai MD, Li J (2007) Dissection of protein-protein interaction and CDK4 inhibition in the oncogenic versus tumor suppressing functions of gankyrin and P16. J Mol Biol 373:990-1005.
    • (2007) J Mol Biol , vol.373 , pp. 990-1005
    • Mahajan, A.1    Guo, Y.2    Yuan, C.3    Weghorst, C.M.4    Tsai, M.D.5    Li, J.6
  • 18
    • 45849140515 scopus 로고    scopus 로고
    • Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex
    • Sue SC, Cervantes C, Komives EA, Dyson HJ (2008) Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex. J Mol Biol 380:917-931.
    • (2008) J Mol Biol , vol.380 , pp. 917-931
    • Sue, S.C.1    Cervantes, C.2    Komives, E.A.3    Dyson, H.J.4
  • 19
    • 38049063892 scopus 로고    scopus 로고
    • Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins
    • Wetzel SK, Settanni G, Kenig M, Binz HK, Pluckthun A (2008) Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins. J Mol Biol 376:241-257.
    • (2008) J Mol Biol , vol.376 , pp. 241-257
    • Wetzel, S.K.1    Settanni, G.2    Kenig, M.3    Binz, H.K.4    Pluckthun, A.5
  • 20
    • 0142210110 scopus 로고    scopus 로고
    • Structure and stability of the ankyrin domain of the Drosophila notch receptor
    • Zweifel ME, Leahy DJ, Hughson FM, Barrick D (2003) Structure and stability of the ankyrin domain of the Drosophila notch receptor. Protein Sci 12:2622-2632.
    • (2003) Protein Sci , vol.12 , pp. 2622-2632
    • Zweifel, M.E.1    Leahy, D.J.2    Hughson, F.M.3    Barrick, D.4
  • 22
    • 33746841062 scopus 로고    scopus 로고
    • The notch ankyrin domain folds via a discrete, centralized pathway
    • Bradley CM, Barrick D (2006) The notch ankyrin domain folds via a discrete, centralized pathway. Structure 14:1303-1312.
    • (2006) Structure , vol.14 , pp. 1303-1312
    • Bradley, C.M.1    Barrick, D.2
  • 23
    • 0036438808 scopus 로고    scopus 로고
    • Limits of cooperativity in a structurally modular protein: Response of the notch ankyrin domain to analogous alanine substitutions in each repeat
    • Bradley CM, Barrick D (2002) Limits of cooperativity in a structurally modular protein: response of the notch ankyrin domain to analogous alanine substitutions in each repeat. J Mol Biol 324:373-386.
    • (2002) J Mol Biol , vol.324 , pp. 373-386
    • Bradley, C.M.1    Barrick, D.2
  • 24
    • 23944525891 scopus 로고    scopus 로고
    • Effect of multiple prolyl isomerization reactions on the stability and folding kinetics of the notch ankyrin domain: Experiment and theory
    • Bradley CM, Barrick D (2005) Effect of multiple prolyl isomerization reactions on the stability and folding kinetics of the notch ankyrin domain: experiment and theory. J Mol Biol 352:253-265.
    • (2005) J Mol Biol , vol.352 , pp. 253-265
    • Bradley, C.M.1    Barrick, D.2
  • 25
    • 23944479773 scopus 로고    scopus 로고
    • Experimental characterization of the folding kinetics of the notch ankyrin domain
    • Mello CC, Bradley CM, Tripp KW, Barrick D (2005) Experimental characterization of the folding kinetics of the notch ankyrin domain. J Mol Biol 352:266-281.
    • (2005) J Mol Biol , vol.352 , pp. 266-281
    • Mello, C.C.1    Bradley, C.M.2    Tripp, K.W.3    Barrick, D.4
  • 26
    • 0016292941 scopus 로고
    • Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, alpha-chymotrypsin, and beta-lactoglobulin
    • Greene RF, Jr, Pace CN (1974) Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, alpha-chymotrypsin, and beta-lactoglobulin. J Biol Chem 249:5388-5393.
    • (1974) J Biol Chem , vol.249 , pp. 5388-5393
    • Greene Jr, R.F.1    Pace, C.N.2
  • 27
    • 0022555885 scopus 로고
    • Determination and analysis of urea and guanidine hydrochloride denaturation curves
    • Pace CN (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.N.1
  • 28
    • 0023697408 scopus 로고
    • Unfolding free energy changes determined by the linear extrapolation method, Part 1: Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants
    • Santoro MM, Bolen DW (1988) Unfolding free energy changes determined by the linear extrapolation method, Part 1: Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. Biochemistry 27:8063-8068.
    • (1988) Biochemistry , vol.27 , pp. 8063-8068
    • Santoro, M.M.1    Bolen, D.W.2
  • 29
    • 0033580679 scopus 로고    scopus 로고
    • Structural changes in the transition state of protein folding: Alternative interpretations of curved chevron plots
    • Otzen DE, Kristensen O, Proctor M, Oliveberg M (1999) Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots. Biochemistry 38:6499-6511.
    • (1999) Biochemistry , vol.38 , pp. 6499-6511
    • Otzen, D.E.1    Kristensen, O.2    Proctor, M.3    Oliveberg, M.4
  • 30
    • 0034718547 scopus 로고    scopus 로고
    • Absence of stable intermediates on the folding pathway of barnase
    • Takei J, Chu RA, Bai Y (2000) Absence of stable intermediates on the folding pathway of barnase. Proc Natl Acad Sci USA 97:10796-10801.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10796-10801
    • Takei, J.1    Chu, R.A.2    Bai, Y.3
  • 31
    • 0037438623 scopus 로고    scopus 로고
    • Non-linear rate-equilibrium free energy relationships and Hammond behavior in protein folding
    • Sanchez IE, Kiefhaber T (2003) Non-linear rate-equilibrium free energy relationships and Hammond behavior in protein folding. Biophys Chem 100:397-407.
    • (2003) Biophys Chem , vol.100 , pp. 397-407
    • Sanchez, I.E.1    Kiefhaber, T.2
  • 32
    • 33845796109 scopus 로고    scopus 로고
    • The folding pathway of T4 lysozyme: An on-pathway hidden folding intermediate
    • Kato H, Vu ND, Feng H, Zhou Z, Bai Y (2007) The folding pathway of T4 lysozyme: an on-pathway hidden folding intermediate. J Mol Biol 365:881-891.
    • (2007) J Mol Biol , vol.365 , pp. 881-891
    • Kato, H.1    Vu, N.D.2    Feng, H.3    Zhou, Z.4    Bai, Y.5
  • 33
    • 0023494191 scopus 로고
    • Structure and thermal stability of phage T4 lysozyme
    • Alber T, Matthews BW (1987) Structure and thermal stability of phage T4 lysozyme. Methods Enzymol 154:511-533.
    • (1987) Methods Enzymol , vol.154 , pp. 511-533
    • Alber, T.1    Matthews, B.W.2
  • 34
    • 24344479918 scopus 로고    scopus 로고
    • An improved experimental system for determining small folding entropy changes resulting from proline to alanine substitutions
    • Street TO, Bradley CM, Barrick D (2005) An improved experimental system for determining small folding entropy changes resulting from proline to alanine substitutions. Protein Sci 14:2429-2435.
    • (2005) Protein Sci , vol.14 , pp. 2429-2435
    • Street, T.O.1    Bradley, C.M.2    Barrick, D.3
  • 35
    • 33845797576 scopus 로고    scopus 로고
    • Enhancing the stability and folding rate of a repeat protein through the addition of consensus repeats
    • Tripp KW, Barrick D (2007) Enhancing the stability and folding rate of a repeat protein through the addition of consensus repeats. J Mol Biol 365:1187-1200.
    • (2007) J Mol Biol , vol.365 , pp. 1187-1200
    • Tripp, K.W.1    Barrick, D.2
  • 36
    • 42649092133 scopus 로고    scopus 로고
    • Rerouting the folding pathway of the notch ankyrin domain by reshaping the energy landscape
    • Tripp KW, Barrick D (2008) Rerouting the folding pathway of the notch ankyrin domain by reshaping the energy landscape. J Am Chem Soc 130:5681-5688.
    • (2008) J Am Chem Soc , vol.130 , pp. 5681-5688
    • Tripp, K.W.1    Barrick, D.2
  • 37
    • 0028327236 scopus 로고
    • Protein folding dynamics: The diffusion-collision model and experimental data
    • Karplus M, Weaver DL (1994) Protein folding dynamics: the diffusion-collision model and experimental data. Prot Sci 3:650-668.
    • (1994) Prot Sci , vol.3 , pp. 650-668
    • Karplus, M.1    Weaver, D.L.2
  • 38
    • 0032554626 scopus 로고    scopus 로고
    • Protein folding dynamics: Quantitative comparison between theory and experiment
    • Burton RE, Myers JK, Oas TG (1998) Protein folding dynamics: quantitative comparison between theory and experiment. Biochemistry 37:5337-5343.
    • (1998) Biochemistry , vol.37 , pp. 5337-5343
    • Burton, R.E.1    Myers, J.K.2    Oas, T.G.3
  • 39
    • 0033523097 scopus 로고    scopus 로고
    • Reinterpretation of GCN4-p1 folding kinetics: Partial helix formation precedes dimerization in coiled coil folding
    • Myers JK, Oas TG (1999) Reinterpretation of GCN4-p1 folding kinetics: partial helix formation precedes dimerization in coiled coil folding. J Mol Biol 289:205-209.
    • (1999) J Mol Biol , vol.289 , pp. 205-209
    • Myers, J.K.1    Oas, T.G.2
  • 40
    • 0035005366 scopus 로고    scopus 로고
    • Preorganized secondary structure as an important determinant of fast protein folding
    • Myers JK, Oas TG (2001) Preorganized secondary structure as an important determinant of fast protein folding. Nat Struct Biol 8:552-558.
    • (2001) Nat Struct Biol , vol.8 , pp. 552-558
    • Myers, J.K.1    Oas, T.G.2
  • 41
    • 0036307683 scopus 로고    scopus 로고
    • Application of the diffusion-collision model to the folding of three-helix bundle proteins
    • Islam SA, Karplus M, Weaver DL (2002) Application of the diffusion-collision model to the folding of three-helix bundle proteins. J Mol Biol 318:199-215.
    • (2002) J Mol Biol , vol.318 , pp. 199-215
    • Islam, S.A.1    Karplus, M.2    Weaver, D.L.3
  • 42
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco KW, Simons KT, Baker D (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277:985-994.
    • (1998) J Mol Biol , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 43
    • 27744531924 scopus 로고    scopus 로고
    • The energy landscape of modular repeat proteins: Topology determines folding mechanism in the ankyrin family
    • Ferreiro DU, Cho SS, Komives EA, Wolynes PG (2005) The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family. J Mol Biol 354:679-692.
    • (2005) J Mol Biol , vol.354 , pp. 679-692
    • Ferreiro, D.U.1    Cho, S.S.2    Komives, E.A.3    Wolynes, P.G.4
  • 44
    • 18744380008 scopus 로고    scopus 로고
    • Consensus-derived structural determinants of the ankyrin repeat motif
    • Mosavi LK, Minor DL, Jr, Peng ZY (2002) Consensus-derived structural determinants of the ankyrin repeat motif. Proc Natl Acad Sci USA 99:16029-16034.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 16029-16034
    • Mosavi, L.K.1    Minor Jr, D.L.2    Peng, Z.Y.3
  • 45
    • 0035807867 scopus 로고    scopus 로고
    • Studies of the ankyrin repeats of the Drosophila melanogaster notch receptor, Part 1: Solution conformational and hydrodynamic properties
    • Zweifel ME, Barrick D (2001) Studies of the ankyrin repeats of the Drosophila melanogaster notch receptor, Part 1: Solution conformational and hydrodynamic properties. Biochemistry 40:14344-14356.
    • (2001) Biochemistry , vol.40 , pp. 14344-14356
    • Zweifel, M.E.1    Barrick, D.2
  • 46
    • 34247579591 scopus 로고    scopus 로고
    • Predicting coupling limits from an experimentally determined energy landscape
    • Street TO, Bradley CM, Barrick D (2007) Predicting coupling limits from an experimentally determined energy landscape. Proc Natl Acad Sci USA 104:4907-4912.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 4907-4912
    • Street, T.O.1    Bradley, C.M.2    Barrick, D.3
  • 47
    • 34848916114 scopus 로고    scopus 로고
    • Anatomy of energetic changes accompanying urea-induced protein denaturation
    • Auton M, Holthauzen LM, Bolen DW (2007) Anatomy of energetic changes accompanying urea-induced protein denaturation. Proc Natl Acad Sci USA 104:15317-15322.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 15317-15322
    • Auton, M.1    Holthauzen, L.M.2    Bolen, D.W.3
  • 48
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • Gillespie DT (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput Phys 22:403-434.
    • (1976) J Comput Phys , vol.22 , pp. 403-434
    • Gillespie, D.T.1
  • 49
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340-2361.
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1


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