메뉴 건너뛰기




Volumn 8, Issue 6, 2011, Pages

Local and non-local native topologies reveal the underlying folding landscape of proteins

Author keywords

[No Author keywords available]

Indexed keywords


EID: 82955201864     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/8/6/066011     Document Type: Article
Times cited : (19)

References (51)
  • 1
    • 34547909602 scopus 로고    scopus 로고
    • Assortative mixing in protein contact networks and protein folding kinetics
    • DOI 10.1093/bioinformatics/btm257
    • Bagler G and Sinha S 2007 Assortative mixing in protein contact networks and protein folding kinetics Bioinformatics 23 1760-7 (Pubitemid 47250308)
    • (2007) Bioinformatics , vol.23 , Issue.14 , pp. 1760-1767
    • Bagler, G.1    Sinha, S.2
  • 2
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • DOI 10.1038/35011000
    • Baker D 2000 A surprising simplicity to protein folding Nature 405 39-42 (Pubitemid 30321807)
    • (2000) Nature , vol.405 , Issue.6782 , pp. 39-42
    • Baker, D.1
  • 3
    • 0033080081 scopus 로고    scopus 로고
    • Is protein folding hierarchic? II. Folding intermediates and transition states
    • DOI 10.1016/S0968-0004(98)01345-0, PII S0968000498013450
    • Baldwin R L and Rose G D 1999 Is protein folding hierarchic? II. Folding intermediates and transition states Trends Biochem. Sci. 24 77-83 (Pubitemid 29346578)
    • (1999) Trends in Biochemical Sciences , vol.24 , Issue.2 , pp. 77-83
    • Baldwin, R.L.1    Rose, G.D.2
  • 5
    • 33846498387 scopus 로고    scopus 로고
    • Thermodynamics of protein denatured states
    • DOI 10.1039/b611895j
    • Bowler B E 2007 Thermodynamics of protein denatured states Mol. Biosystems 3 88-99 (Pubitemid 46155471)
    • (2007) Molecular BioSystems , vol.3 , Issue.2 , pp. 88-99
    • Bowler, B.E.1
  • 7
    • 1942521649 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of non-native interactions in protein folding: A single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state
    • DOI 10.1016/j.jmb.2004.02.073, PII S0022283604002918
    • Cho J H, Sato S and Raleigh D P 2004 Thermodynamics and kinetics of non-native interactions in protein folding: a single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state J. Mol. Biol. 338 827-37 (Pubitemid 38507425)
    • (2004) Journal of Molecular Biology , vol.338 , Issue.4 , pp. 827-837
    • Cho, J.-H.1    Sato, S.2    Raleigh, D.P.3
  • 8
    • 0035906650 scopus 로고    scopus 로고
    • Calculation of ensembles of structures representing the unfolded state of an SH3 domain
    • DOI 10.1006/jmbi.2001.4750
    • Choy W Y and Forman-Kay J D 2001 Calculation of ensembles of structures representing the unfolded state of an SH3 domain J. Mol. Biol. 308 1011-32 (Pubitemid 32577079)
    • (2001) Journal of Molecular Biology , vol.308 , Issue.5 , pp. 1011-1032
    • Choy, W.-Y.1    Forman-Kay, J.D.2
  • 9
    • 67849124732 scopus 로고    scopus 로고
    • Protein folding rates and stability: How much is there beyond size?
    • De Sancho D, Doshi U and Munoz V 2009 Protein folding rates and stability: how much is there beyond size? J. Am. Chem. Soc. 131 2074-5
    • (2009) J. Am. Chem. Soc. , vol.131 , Issue.6 , pp. 2074-2075
    • De Sancho, D.1    Doshi, U.2    Munoz, V.3
  • 11
    • 0025856806 scopus 로고
    • Denatured states of proteins
    • Dill K A and Shortle D 1991 Denatured states of proteins Annu. Rev. Biochem. 60 795-825
    • (1991) Annu. Rev. Biochem. , vol.60 , Issue.1 , pp. 795-825
    • Dill, K.A.1    Shortle, D.2
  • 14
    • 0034652206 scopus 로고    scopus 로고
    • Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
    • DOI 10.1073/pnas.97.4.1525
    • Fersht A R 2000 Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability and the extended nucleus mechanism Proc. Natl Acad. Sci. USA 97 1525-9 (Pubitemid 30118475)
    • (2000) Proceedings of the National Academy of Sciences of the United States of America , vol.97 , Issue.4 , pp. 1525-1529
    • Fersht, A.R.1
  • 15
    • 0000381972 scopus 로고
    • Protein core assembly processes
    • Fiebig K M and Dill K A 1993 Protein core assembly processes J. Chem. Phys. 98 3475-87
    • (1993) J. Chem. Phys. , vol.98 , Issue.4 , pp. 3475-3487
    • Fiebig, K.M.1    Dill, K.A.2
  • 17
    • 34948869804 scopus 로고    scopus 로고
    • The ultimate speed limit to protein folding is conformational searching
    • DOI 10.1021/ja066785b
    • Ghosh K, Ozkan S B and Dill K A 2007 The ultimate speed limit to protein folding is conformational searching J. Am. Chem. Soc. 129 11920-7 (Pubitemid 47515346)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.39 , pp. 11920-11927
    • Ghosh, K.1    Ozkan, S.B.2    Dill, K.A.3
  • 18
    • 77949598393 scopus 로고    scopus 로고
    • Union of geometric constraint-based simulations with molecular dynamics for protein structure prediction
    • Glembo T J and Ozkan S B 2010 Union of geometric constraint-based simulations with molecular dynamics for protein structure prediction Biophys. J. 98 1046-54
    • (2010) Biophys. J. , vol.98 , Issue.6 , pp. 1046-1054
    • Glembo, T.J.1    Ozkan, S.B.2
  • 19
    • 66149112049 scopus 로고    scopus 로고
    • Multiple contact network is a key determinant to protein folding rates
    • Gromiha M M 2009 Multiple contact network is a key determinant to protein folding rates J. Chem. Inf. Model. 49 1130-5
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.4 , pp. 1130-1135
    • Gromiha, M.M.1
  • 20
    • 0035967862 scopus 로고    scopus 로고
    • Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Application of long-range order to folding rate prediction
    • DOI 10.1006/jmbi.2001.4775
    • Gromiha M M and Selvaraj S 2001 Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction J. Mol. Biol. 310 27-32 (Pubitemid 32619950)
    • (2001) Journal of Molecular Biology , vol.310 , Issue.1 , pp. 27-32
    • Gromiha, M.M.1    Selvaraj, S.2
  • 21
    • 33747822326 scopus 로고    scopus 로고
    • FOLD-RATE: Prediction of protein folding rates from amino acid sequence
    • Gromiha M M, Thangakani A M and Selvaraj S 2006 FOLD-RATE: prediction of protein folding rates from amino acid sequence Nucleic Acids Res. 34 W70-4
    • (2006) Nucleic Acids Res. , vol.34 , Issue.WEB SERVER
    • Gromiha, M.M.1    Thangakani, A.M.2    Selvaraj, S.3
  • 23
    • 70350168415 scopus 로고    scopus 로고
    • Refinement of the long-range order parameter in predicting folding rates of two-state proteins
    • Harihar B and Selvaraj S 2009 Refinement of the long-range order parameter in predicting folding rates of two-state proteins Biopolymers 91 928-35
    • (2009) Biopolymers , vol.91 , Issue.11 , pp. 928-935
    • Harihar, B.1    Selvaraj, S.2
  • 24
    • 63449129633 scopus 로고    scopus 로고
    • Insights from coarse-grained go models for protein folding and dynamics
    • Hills R D and Brooks C L 2009 Insights from coarse-grained go models for protein folding and dynamics Int. J. Mol. Sci. 10 889-905
    • (2009) Int. J. Mol. Sci. , vol.10 , Issue.3 , pp. 889-905
    • Hills, R.D.1    Brooks, C.L.2
  • 25
    • 33847367710 scopus 로고    scopus 로고
    • Secondary structure length as a determinant of folding rate of proteins with two- and three-state kinetics
    • DOI 10.1002/prot.21282
    • Huang J T, Cheng J P and Chen H 2007 Secondary structure length as a determinant of folding rate of proteins with two- and three-state kinetics Proteins: Struct. Funct. Bioinformatics 67 12-7 (Pubitemid 46340122)
    • (2007) Proteins: Structure, Function and Genetics , vol.67 , Issue.1 , pp. 12-17
    • Huang, J.-T.1    Cheng, J.-P.2    Chen, H.3
  • 26
    • 0028868995 scopus 로고
    • The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
    • Itzhaki L S, Otzen D E and Fersht A R 1995 The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding J. Mol. Biol. 254 260-88
    • (1995) J. Mol. Biol. , vol.254 , Issue.2 , pp. 260-288
    • Itzhaki, L.S.1    Otzen, D.E.2    Fersht, A.R.3
  • 30
    • 0037215268 scopus 로고    scopus 로고
    • The topomer search model: A simple, quantitative theory of two-state protein folding kinetics
    • DOI 10.1110/ps.0220003
    • Makarov D E and Plaxco K W 2003 The topomer search model: a simple, quantitative theory of two-state protein folding kinetics Protein Sci. 12 17-26 (Pubitemid 36020130)
    • (2003) Protein Science , vol.12 , Issue.1 , pp. 17-26
    • Makarov, D.E.1    Plaxco, K.W.2
  • 32
    • 0037375366 scopus 로고    scopus 로고
    • Prediction of folding rates and transition-state placement from native-state geometry
    • DOI 10.1002/prot.10342
    • Micheletti C 2003 Prediction of folding rates and transition-state placement from native-state geometry Proteins: Struct. Funct. Bioinformatics 51 74-84 (Pubitemid 36293034)
    • (2003) Proteins: Structure, Function and Genetics , vol.51 , Issue.1 , pp. 74-84
    • Micheletti, C.1
  • 33
    • 0028075953 scopus 로고
    • Protein stability for single substitution mutants and the extent of local compactness in the denatured state
    • Miyazawa S and Jernigan R L 1994 Protein stability for single substitution mutants and the extent of local compactness in the denatured state Protein Eng. 7 1209-20 (Pubitemid 24319399)
    • (1994) Protein Engineering , vol.7 , Issue.10 , pp. 1209-1220
    • Miyazawa, S.1    Jernigan, R.L.2
  • 35
    • 0034872511 scopus 로고    scopus 로고
    • Transition states and the meaning of Φ-values in protein folding kinetics
    • DOI 10.1038/nsb0901-765
    • Ozkan S B, Bahar I and Dill K A 2001 Transition states and the meaning of Phi-values in protein folding kinetics Nature Struct. Biol. 8 765-9 (Pubitemid 32803593)
    • (2001) Nature Structural Biology , vol.8 , Issue.9 , pp. 765-769
    • Ozkan, S.B.1    Bahar, I.2    Dill, K.A.3
  • 37
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • DOI 10.1006/jmbi.1998.1645
    • Plaxco K W, Simons K T and David B 1998 Contact order, transition state placement and the refolding rates of single domain proteins J. Mol. Biol. 277 985-94 (Pubitemid 28195995)
    • (1998) Journal of Molecular Biology , vol.277 , Issue.4 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 38
    • 0034687123 scopus 로고    scopus 로고
    • Topology, stability, sequence and length: Defining the determinants of two-state protein folding kinetics
    • Plaxco K W, Simons K T, Ruczinski I and David B 2000 Topology, stability, sequence and length: defining the determinants of two-state protein folding kinetics Biochemistry 39 11177-83
    • (2000) Biochemistry , vol.39 , Issue.37 , pp. 11177-11183
    • Plaxco, K.W.1    Simons, K.T.2    Ruczinski, I.3    David, B.4
  • 39
    • 67649607259 scopus 로고    scopus 로고
    • Structure, stability, and folding of ribonuclease H1 from the moderately thermophilic chlorobium tepidum: Comparison with thermophilic and mesophilic homologues
    • Ratcliff K, Corn J and Marqusee S 2009 Structure, stability, and folding of ribonuclease H1 from the moderately thermophilic chlorobium tepidum: comparison with thermophilic and mesophilic homologues Biochemistry 48 5890-8
    • (2009) Biochemistry , vol.48 , Issue.25 , pp. 5890-5898
    • Ratcliff, K.1    Corn, J.2    Marqusee, S.3
  • 40
    • 77953905699 scopus 로고    scopus 로고
    • Identification of residual structure in the unfolded state of ribonuclease H1 from the moderately thermophilic chlorobium tepidum: Comparison with thermophilic and mesophilic homologues
    • Ratcliff K and Marqusee S 2010 Identification of residual structure in the unfolded state of ribonuclease H1 from the moderately thermophilic chlorobium tepidum: comparison with thermophilic and mesophilic homologues Biochemistry 49 5167-75
    • (2010) Biochemistry , vol.49 , Issue.25 , pp. 5167-5175
    • Ratcliff, K.1    Marqusee, S.2
  • 42
    • 61549140397 scopus 로고    scopus 로고
    • Blind test of physics-based prediction of protein structures
    • Shell M S, Ozkan S B, Voelz V, Wu G H A and Dill K A 2009 Blind test of physics-based prediction of protein structures Biophys. J. 96 917-24
    • (2009) Biophys. J. , vol.96 , Issue.3 , pp. 917-924
    • Shell, M.S.1    Ozkan, S.B.2    Voelz, V.3    Wu, G.H.A.4    Dill, K.A.5
  • 43
    • 0030032461 scopus 로고    scopus 로고
    • The denatured state (the other half of the folding equation) and its role in protein stability
    • Shortle D 1996 The denatured state (the other half of the folding equation) and its role in protein stability FASEB J. 10 27-34 (Pubitemid 26035503)
    • (1996) FASEB Journal , vol.10 , Issue.1 , pp. 27-34
    • Shortle, D.1
  • 44
    • 0035919635 scopus 로고    scopus 로고
    • Persistence of native-like topology in a denatured protein in 8 M urea
    • DOI 10.1126/science.1060438
    • Shortle D and Ackerman M S 2001 Persistence of native-like topology in a denatured protein in 8 M urea Science 293 487-9 (Pubitemid 32679075)
    • (2001) Science , vol.293 , Issue.5529 , pp. 487-489
    • Shortle, D.1    Ackerman, M.S.2
  • 45
    • 0027050824 scopus 로고
    • Modeling the effects of mutations on the denatured states of proteins
    • Shortle D, Chan H S and Dill K A 1992 Modeling the effects of mutations on the denatured states of proteins Protein Sci. 1 201-5
    • (1992) Protein Sci. , vol.1 , Issue.2 , pp. 201-205
    • Shortle, D.1    Chan, H.S.2    Dill, K.A.3
  • 46
    • 0030789351 scopus 로고    scopus 로고
    • Laser temperature jump study of the helix⇆coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model
    • DOI 10.1021/bi9704764
    • Thompson P A, Eaton W A and Hofrichter J 1997 Laser temperature jump study of the helix reversible arrow coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model Biochemistry 36 9200-10 (Pubitemid 27329505)
    • (1997) Biochemistry , vol.36 , Issue.30 , pp. 9200-9210
    • Thompson, P.A.1    Eaton, W.A.2    Hofrichter, J.3
  • 47
    • 24644460584 scopus 로고    scopus 로고
    • Loop-closure events during protein folding: Rationalizing the shape of Φ-value distributions
    • DOI 10.1002/prot.20504
    • Weikl T R 2005 Loop-closure events during protein folding: Rationalizing the shape of Phi-value distributions Proteins: Struct. Funct. Bioinformatics 60 701-11 (Pubitemid 41266427)
    • (2005) Proteins: Structure, Function and Genetics , vol.60 , Issue.4 , pp. 701-711
    • Weikl, T.R.1
  • 48
    • 1342268048 scopus 로고    scopus 로고
    • Cooperativity in two-state protein folding kinetics
    • DOI 10.1110/ps.03403604
    • Weikl T R, Palassini M and Dill K A 2004 Cooperativity in two-state protein folding kinetics Protein Sci. 13 822-9 (Pubitemid 38252578)
    • (2004) Protein Science , vol.13 , Issue.3 , pp. 822-829
    • Weikl, T.R.1    Palassini, M.2    Dill, K.A.3
  • 49
    • 0034628913 scopus 로고    scopus 로고
    • Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding
    • Wong K B, Clarke J, Bond C J, Neira J L, Freund S M V, Fersht A R and Daggett V 2000 Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding J. Mol. Biol. 296 1257-82
    • (2000) J. Mol. Biol. , vol.296 , Issue.5 , pp. 1257-1282
    • Wong, K.B.1    Clarke, J.2    Bond, C.J.3    Neira, J.L.4    Freund, S.M.V.5    Fersht, A.R.6    Daggett, V.7
  • 50
    • 46449120907 scopus 로고    scopus 로고
    • Predicting protein folding rates from geometric contact and amino acid sequence
    • Zheng O Y and Jie L 2008 Predicting protein folding rates from geometric contact and amino acid sequence Protein Sci. 17 1256-63
    • (2008) Protein Sci. , vol.17 , Issue.7 , pp. 1256-1263
    • Zheng, O.Y.1    Jie, L.2
  • 51
    • 0036215854 scopus 로고    scopus 로고
    • Folding rate prediction using total contact distance
    • Zhou H Y and Zhou Y Q 2002 Folding rate prediction using total contact distance Biophys. J. 82 458-63
    • (2002) Biophys. J. , vol.82 , Issue.1 , pp. 458-463
    • Zhou, H.Y.1    Zhou, Y.Q.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.