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Volumn 72, Issue 1, 2008, Pages 44-49

Differentiation between two-state and multi-state folding proteins based on sequence

Author keywords

Amino acid composition; Amino acid volume; Chain length; Differentiation of folding kinetic pathway; Logistic regression; Two state and multi state folding proteins

Indexed keywords

AMINO ACID;

EID: 44949250893     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21893     Document Type: Article
Times cited : (16)

References (32)
  • 1
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • Baker D. A surprising simplicity to protein folding. Nature 2000;405:39-42.
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 2
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;277:985-994.
    • (1998) J Mol Biol , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 3
    • 0032506017 scopus 로고    scopus 로고
    • Limited internal fraction in the rate-limiting step of a two-state protein folding reaction
    • Plaxco KW, Baker D. Limited internal fraction in the rate-limiting step of a two-state protein folding reaction. Proc Natl Acad Sci USA 1998;95:13591-13596.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 13591-13596
    • Plaxco, K.W.1    Baker, D.2
  • 4
    • 0034687123 scopus 로고    scopus 로고
    • Topology, stability, sequence, and length: Defining the determinants of two-state folding protein folding kinetics
    • Plaxco KW, Simons KT, Ruczinski I, Baker D. Topology, stability, sequence, and length: defining the determinants of two-state folding protein folding kinetics. Biochemistry 2000;39:11177-11183.
    • (2000) Biochemistry , vol.39 , pp. 11177-11183
    • Plaxco, K.W.1    Simons, K.T.2    Ruczinski, I.3    Baker, D.4
  • 5
    • 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
    • Gromiha MM, Selvaraj S. 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 2001;310:27-32.
    • (2001) J Mol Biol , vol.310 , pp. 27-32
    • Gromiha, M.M.1    Selvaraj, S.2
  • 6
    • 0034984144 scopus 로고    scopus 로고
    • Protein folding theory: From lattice to all-atom models
    • Mimy L, Shalhnovich E. Protein folding theory: from lattice to all-atom models. Annu Rev Biophys Biomol Strnct 2001;30:361-396.
    • (2001) Annu Rev Biophys Biomol Strnct , vol.30 , pp. 361-396
    • Mimy, L.1    Shalhnovich, E.2
  • 7
    • 0037133574 scopus 로고    scopus 로고
    • How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
    • Makarov DE, Keller CA, Plaxco KW, Metiu H. How the folding rate constant of simple, single-domain proteins depends on the number of native contacts. Proc Natl Acad Sci USA 2002;99:3535-3539.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 3535-3539
    • Makarov, D.E.1    Keller, C.A.2    Plaxco, K.W.3    Metiu, H.4
  • 8
    • 0037432567 scopus 로고    scopus 로고
    • Local secondary structure content predicts folding rates for simple, two-state folding proteins
    • Gong H, Isom DG, Srinivasan R, Rose GD. Local secondary structure content predicts folding rates for simple, two-state folding proteins. J Mol Biol 2003;327:1149-1154.
    • (2003) J Mol Biol , vol.327 , pp. 1149-1154
    • Gong, H.1    Isom, D.G.2    Srinivasan, R.3    Rose, G.D.4
  • 9
    • 18344371857 scopus 로고    scopus 로고
    • A statistical model for predicting protein folding rates from amino acid sequence with structural class information
    • Gromiha MM. A statistical model for predicting protein folding rates from amino acid sequence with structural class information. J Chem Inf Model 2005;45:494-501.
    • (2005) J Chem Inf Model , vol.45 , pp. 494-501
    • Gromiha, M.M.1
  • 10
    • 33646028225 scopus 로고    scopus 로고
    • Amino acid sequence predicts folding rate of middle-size two-state proteins
    • Huang JT, Tian J. Amino acid sequence predicts folding rate of middle-size two-state proteins. Proteins 2006;63:551-554.
    • (2006) Proteins , vol.63 , pp. 551-554
    • Huang, J.T.1    Tian, J.2
  • 11
    • 33749035288 scopus 로고    scopus 로고
    • Direct correlation between proteins' folding rates and their amino acid compositions: An ab initio folding rate prediction
    • Ma BG, Guo JX, Zhang HY. Direct correlation between proteins' folding rates and their amino acid compositions: An ab initio folding rate prediction. Proteins 2006;65:362-372.
    • (2006) Proteins , vol.65 , pp. 362-372
    • Ma, B.G.1    Guo, J.X.2    Zhang, H.Y.3
  • 12
    • 0037402639 scopus 로고    scopus 로고
    • Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics
    • Galzitskaya OV, Garbuzynskiy SO, Ivanlov DN, Finkelstein AV. Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics. Proteins 2003;51:162-166.
    • (2003) Proteins , vol.51 , pp. 162-166
    • Galzitskaya, O.V.1    Garbuzynskiy, S.O.2    Ivanlov, D.N.3    Finkelstein, A.V.4
  • 13
    • 2942689229 scopus 로고    scopus 로고
    • Prediction of protein folding rates from the amino acid sequence-predicted secondary structure
    • Ivankov DN, Finkelstein AV. Prediction of protein folding rates from the amino acid sequence-predicted secondary structure. Proc Natl Acad Sci USA 2004;101:8942-8944.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 8942-8944
    • Ivankov, D.N.1    Finkelstein, A.V.2
  • 14
    • 33847367710 scopus 로고    scopus 로고
    • Secondary structure length as a determinant of folding rate of proteins with twoand three-state kinetics
    • Huang JT, Cheng JP, Chen H. Secondary structure length as a determinant of folding rate of proteins with twoand three-state kinetics. Proteins 2007;67:12-17.
    • (2007) Proteins , vol.67 , pp. 12-17
    • Huang, J.T.1    Cheng, J.P.2    Chen, H.3
  • 16
    • 0031815749 scopus 로고    scopus 로고
    • How do small single-domain proteins folds?
    • Jackson SE. How do small single-domain proteins folds? Fold Design 1998;3:R81-R91.
    • (1998) Fold Design , vol.3
    • Jackson, S.E.1
  • 17
    • 0021118508 scopus 로고
    • Principles that determine the structure of proteins
    • Chothia C. Principles that determine the structure of proteins. Annu Rev Biochem 1984;53:537-572.
    • (1984) Annu Rev Biochem , vol.53 , pp. 537-572
    • Chothia, C.1
  • 18
    • 0031897962 scopus 로고    scopus 로고
    • Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete
    • Berger B, Leighton T. Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete. J Comput Biol 1998;5:27-40.
    • (1998) J Comput Biol , vol.5 , pp. 27-40
    • Berger, B.1    Leighton, T.2
  • 19
    • 0029002720 scopus 로고
    • The hydrophobic effect in protein folding
    • Lins L, Brasseur R. The hydrophobic effect in protein folding. FASEB J 1995;9:535-540.
    • (1995) FASEB J , vol.9 , pp. 535-540
    • Lins, L.1    Brasseur, R.2
  • 24
    • 33847255036 scopus 로고    scopus 로고
    • K-Fold: A tool for the prediction of the protein folding kinetic order and rate
    • Capriotti E, Casadio R. K-Fold: a tool for the prediction of the protein folding kinetic order and rate. Bioinformatics 2007;23:385-386.
    • (2007) Bioinformatics , vol.23 , pp. 385-386
    • Capriotti, E.1    Casadio, R.2
  • 25
    • 34250194031 scopus 로고    scopus 로고
    • What determines protein folding type? An investigation of intrinsic structural properties and its implications for understanding folding mechanisms
    • Ma BG, Chen LL, Zhang HY. What determines protein folding type? An investigation of intrinsic structural properties and its implications for understanding folding mechanisms. J Mo Biol 2007;370:439-448.
    • (2007) J Mo Biol , vol.370 , pp. 439-448
    • Ma, B.G.1    Chen, L.L.2    Zhang, H.Y.3
  • 26
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 27
    • 33747822326 scopus 로고    scopus 로고
    • FOLD-RATE: Prediction of protein folding rates from amino acid sequence
    • Gromiha MM, Thangakani AM, Selvara S. FOLD-RATE: prediction of protein folding rates from amino acid sequence. Nucl Acid Res 2006;34:W70-W74.
    • (2006) Nucl Acid Res , vol.34
    • Gromiha, M.M.1    Thangakani, A.M.2    Selvara, S.3
  • 28
    • 33846041078 scopus 로고    scopus 로고
    • The universal protein resource (UniProt)
    • UniProt Consortium
    • UniProt Consortium. The universal protein resource (UniProt). Nucl Acid Res 2007;35:D193-D197.
    • (2007) Nucl Acid Res , vol.35
  • 29
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucl Acid Res 2007;35:D301-D303.
    • (2007) Nucl Acid Res , vol.35
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 31
    • 0030305457 scopus 로고    scopus 로고
    • R: A language for data analysis and graphics
    • Ihaka R, Gentleman R. R: a language for data analysis and graphics. J Comput Graphical Stat 1996;5:299-314.
    • (1996) J Comput Graphical Stat , vol.5 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.