메뉴 건너뛰기




Volumn 231, Issue 1, 2004, Pages 85-95

Cooperativity of the oxidization of cysteines in globular proteins

Author keywords

Amino acid composition; Bonding state of cysteines; Protein folding; Support vector machine; Two stage classifier

Indexed keywords

CYSTEINE; DISULFIDE; GLOBULAR PROTEIN; PROTEIN DERIVATIVE;

EID: 4444249440     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jtbi.2004.06.002     Document Type: Article
Times cited : (5)

References (57)
  • 1
    • 0034697986 scopus 로고    scopus 로고
    • What can disulfide bonds tell us about protein energetics, function and folding: Simulations and bioinformatics analysis
    • V.I. Abkevich, and E.I. Shakhnovich What can disulfide bonds tell us about protein energetics, function and folding simulations and bioinformatics analysis J. Mol. Biol. 300 2000 975 985
    • (2000) J. Mol. Biol. , vol.300 , pp. 975-985
    • Abkevich, V.I.1    Shakhnovich, E.I.2
  • 2
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • C.B. Anfinsen Principles that govern the folding of protein chains Science 181 1973 223 230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 4
    • 0027362677 scopus 로고
    • Disulfide bonds and the stability of globular proteins
    • S.F. Betz Disulfide bonds and the stability of globular proteins Protein Sci 2 1993 1551 1558
    • (1993) Protein Sci , vol.2 , pp. 1551-1558
    • Betz, S.F.1
  • 7
    • 0034436969 scopus 로고    scopus 로고
    • Support vector machines for prediction of protein subcellular location
    • Y.D. Cai, X.J. Liu, X.B. Xu, and K.C. Chou Support vector machines for prediction of protein subcellular location Mol. Cell Biol. Res. Commun. 4 2000 230 233
    • (2000) Mol. Cell Biol. Res. Commun. , vol.4 , pp. 230-233
    • Cai, Y.D.1    Liu, X.J.2    Xu, X.B.3    Chou, K.C.4
  • 8
    • 0036007085 scopus 로고    scopus 로고
    • Prediction of protein structural classes by support vector machines
    • Y.D. Cai, X.J. Liu, X.B. Xu, and K.C. Chou Prediction of protein structural classes by support vector machines Comput. Chem. 26 2002 293 296
    • (2002) Comput. Chem. , vol.26 , pp. 293-296
    • Cai, Y.D.1    Liu, X.J.2    Xu, X.B.3    Chou, K.C.4
  • 9
    • 0037423777 scopus 로고    scopus 로고
    • Support vector machines for prediction of protein subcellular location
    • Y.D. Cai, X.J. Liu, X.B. Xu, and K.C. Chou Support vector machines for prediction of protein subcellular location J. Theor. Biol. 221 2003 115 120
    • (2003) J. Theor. Biol. , vol.221 , pp. 115-120
    • Cai, Y.D.1    Liu, X.J.2    Xu, X.B.3    Chou, K.C.4
  • 10
    • 0842326624 scopus 로고    scopus 로고
    • Application of SVM to predict membrane protein types
    • Y.D. Cai, P.W. Ricardo, C.H. Jen, and K.C. Chou Application of SVM to predict membrane protein types J. Theor. Biol. 226 2004 373 376
    • (2004) J. Theor. Biol. , vol.226 , pp. 373-376
    • Cai, Y.D.1    Ricardo, P.W.2    Jen, C.H.3    Chou, K.C.4
  • 11
    • 0141990705 scopus 로고    scopus 로고
    • Predicting the disulfide bonding state of cysteines with combinations of kernel machines
    • A. Ceroni, P. Frasconi, A. Passerini, and A. Vullo Predicting the disulfide bonding state of cysteines with combinations of kernel machines J. VLSI Signal Process. 35 2003 287 295
    • (2003) J. VLSI Signal Process. , vol.35 , pp. 287-295
    • Ceroni, A.1    Frasconi, P.2    Passerini, A.3    Vullo, A.4
  • 12
    • 0037195776 scopus 로고    scopus 로고
    • Using functional domain composition and support vector machines for prediction of protein subcellular location
    • K.C. Chou, and Y.D. Cai Using functional domain composition and support vector machines for prediction of protein subcellular location J. Biol. Chem. 277 2002 45765 45769
    • (2002) J. Biol. Chem. , vol.277 , pp. 45765-45769
    • Chou, K.C.1    Cai, Y.D.2
  • 13
    • 0041819762 scopus 로고    scopus 로고
    • Relationship between protein structures and disulfide-bonding patterns
    • C.C. Chuang, C.Y. Chen, J.M. Yang, P.C. Lyu, and J.K. Hwang Relationship between protein structures and disulfide-bonding patterns Proteins 53 2004 1 5
    • (2004) Proteins , vol.53 , pp. 1-5
    • Chuang, C.C.1    Chen, C.Y.2    Yang, J.M.3    Lyu, P.C.4    Hwang, J.K.5
  • 16
    • 0029653850 scopus 로고
    • Disulfide-coupled protein folding pathways
    • T. Creighton Disulfide-coupled protein folding pathways Philos. Trans. R. Soc. London B 348 1995 5 10
    • (1995) Philos. Trans. R. Soc. London B , vol.348 , pp. 5-10
    • Creighton, T.1
  • 17
    • 0026692715 scopus 로고
    • Protein engineering of a disulfide bond in a beta/alpha-barrel protein
    • J. Eder, and M. Wilmanns Protein engineering of a disulfide bond in a beta/alpha-barrel protein Biochemistry 31 1992 4437 4444
    • (1992) Biochemistry , vol.31 , pp. 4437-4444
    • Eder, J.1    Wilmanns, M.2
  • 18
    • 0034781580 scopus 로고    scopus 로고
    • Prediction of disulfide connectivity in proteins
    • P. Fariselli, and R. Casadio Prediction of disulfide connectivity in proteins Bioinformatics 17 2001 957 964
    • (2001) Bioinformatics , vol.17 , pp. 957-964
    • Fariselli, P.1    Casadio, R.2
  • 19
    • 0033566578 scopus 로고    scopus 로고
    • Role of evolutionary information in predicting the disulfide bonding state of cysteine in proteins
    • P. Fariselli, P. Riccobelli, and R. Casadio Role of evolutionary information in predicting the disulfide bonding state of cysteine in proteins Proteins 36 1999 340 346
    • (1999) Proteins , vol.36 , pp. 340-346
    • Fariselli, P.1    Riccobelli, P.2    Casadio, R.3
  • 21
    • 0034039497 scopus 로고    scopus 로고
    • Predicting the oxidation state of cysteines by multiple sequence alignment
    • A. Fiser, and I. Simon Predicting the oxidation state of cysteines by multiple sequence alignment Bioinformatics 16 2000 251 256
    • (2000) Bioinformatics , vol.16 , pp. 251-256
    • Fiser, A.1    Simon, I.2
  • 22
    • 0026579140 scopus 로고
    • Different sequence environment of cysteines and half cystines in proteins: Application to predict disulfide forming residues
    • A. Fiser, M. Cserzo, E. Tudos, and I. Simon Different sequence environment of cysteines and half cystines in proteins application to predict disulfide forming residues FEBS Lett. 302 1992 117 120
    • (1992) FEBS Lett. , vol.302 , pp. 117-120
    • Fiser, A.1    Cserzo, M.2    Tudos, E.3    Simon, I.4
  • 24
    • 0028063090 scopus 로고
    • Analysis and classification of disulphide connectivity in proteins: The entropic effect of cross-linkage
    • P.M. Harrison, and M.J.E. Sternberg Analysis and classification of disulphide connectivity in proteins the entropic effect of cross-linkage J. Mol. Biol. 244 1994 448 463
    • (1994) J. Mol. Biol. , vol.244 , pp. 448-463
    • Harrison, P.M.1    Sternberg, M.J.E.2
  • 25
    • 0035957531 scopus 로고    scopus 로고
    • A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach
    • S.J. Hua, and Z.R. Sun A novel method of protein secondary structure prediction with high segment overlap measure support vector machine approach J. Mol. Biol. 308 2001 397 407
    • (2001) J. Mol. Biol. , vol.308 , pp. 397-407
    • Hua, S.J.1    Sun, Z.R.2
  • 26
    • 0034843744 scopus 로고    scopus 로고
    • Support vector machine approach for protein subcellular localization prediction
    • S.J. Hua, and Z.R. Sun Support vector machine approach for protein subcellular localization prediction Bioinformatics 17 2001 721 728
    • (2001) Bioinformatics , vol.17 , pp. 721-728
    • Hua, S.J.1    Sun, Z.R.2
  • 27
    • 0033516514 scopus 로고    scopus 로고
    • Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions
    • E.S. Huang, R. Samudrala, and J.W. Ponder Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions J. Mol. Biol. 290 1999 267 281
    • (1999) J. Mol. Biol. , vol.290 , pp. 267-281
    • Huang, E.S.1    Samudrala, R.2    Ponder, J.W.3
  • 28
    • 0347093598 scopus 로고    scopus 로고
    • Prediction of protein subcellular locations using fuzzy k-NN method
    • Y. Huang, and Y.D. Li Prediction of protein subcellular locations using fuzzy k-NN method Bioinformatics 20 2004 21 28
    • (2004) Bioinformatics , vol.20 , pp. 21-28
    • Huang, Y.1    Li, Y.D.2
  • 31
    • 0141593924 scopus 로고    scopus 로고
    • Protein secondary prediction based on an improved support vector machines approach
    • H. Kim, and H. Park Protein secondary prediction based on an improved support vector machines approach Protein Eng. 16 2003 553 560
    • (2003) Protein Eng. , vol.16 , pp. 553-560
    • Kim, H.1    Park, H.2
  • 32
    • 0028138294 scopus 로고
    • The adsorption protein of filamentous phage fd: Assignment of its disulphide bridges and identification of the domain incorporated in the coat
    • A. Kremser, and I. Rasched The adsorption protein of filamentous phage fd assignment of its disulphide bridges and identification of the domain incorporated in the coat Biochemistry 33 1994 13954 13958
    • (1994) Biochemistry , vol.33 , pp. 13954-13958
    • Kremser, A.1    Rasched, I.2
  • 34
    • 0036937367 scopus 로고    scopus 로고
    • Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks
    • P.L. Martelli, P. Fariselli, L. Malaguti, and R. Casadio Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks Protein Eng. 15 2002 951 953
    • (2002) Protein Eng. , vol.15 , pp. 951-953
    • Martelli, P.L.1    Fariselli, P.2    Malaguti, L.3    Casadio, R.4
  • 35
    • 0036839271 scopus 로고    scopus 로고
    • Prediction of the disulfide bonding state of cysteines in proteins at 88% accuracy
    • P.L. Martelli, P. Fariselli, L. Malaguti, and R. Casadio Prediction of the disulfide bonding state of cysteines in proteins at 88% accuracy Protein Sci. 11 2002 2735 2739
    • (2002) Protein Sci. , vol.11 , pp. 2735-2739
    • Martelli, P.L.1    Fariselli, P.2    Malaguti, L.3    Casadio, R.4
  • 36
    • 0024564552 scopus 로고
    • Control of enzyme activity by an engineered disulfide bond
    • M. Matsumura, and B. Matthews Control of enzyme activity by an engineered disulfide bond Science 243 1989 792 794
    • (1989) Science , vol.243 , pp. 792-794
    • Matsumura, M.1    Matthews, B.2
  • 37
    • 0026319603 scopus 로고
    • Stabilization of functional proteins by introduction of multiple disulfide bonds
    • M. Matsumura, and B. Matthews Stabilization of functional proteins by introduction of multiple disulfide bonds Method Enzymot. 202 1991 336 355
    • (1991) Method Enzymot. , vol.202 , pp. 336-355
    • Matsumura, M.1    Matthews, B.2
  • 38
    • 0016772212 scopus 로고
    • Comparison of predicted and observed secondary structure of T4 phage lysozyme
    • B.W. Matthews Comparison of predicted and observed secondary structure of T4 phage lysozyme Biophys. Acta 405 1975 442 451
    • (1975) Biophys. Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 39
    • 0022425563 scopus 로고
    • A new method for rapid assignment of s-s bridges in proteins
    • H. Morris, and P. Pucci A new method for rapid assignment of s-s bridges in proteins Biochem. Biophys. Res. Commun. 126 1985 1122 1128
    • (1985) Biochem. Biophys. Res. Commun. , vol.126 , pp. 1122-1128
    • Morris, H.1    Pucci, P.2
  • 40
    • 0037083493 scopus 로고    scopus 로고
    • Predicting the disulfide bonding state of cysteines using protein descriptors
    • M.H. Mucchielli-Giorgi, S. Hazout, and P. Tuffery Predicting the disulfide bonding state of cysteines using protein descriptors Proteins 46 2002 243 249
    • (2002) Proteins , vol.46 , pp. 243-249
    • Mucchielli-Giorgi, M.H.1    Hazout, S.2    Tuffery, P.3
  • 41
    • 0025118064 scopus 로고
    • Prediction of the disulfide-bonding state of cysteine in proteins
    • S.M. Muskal, S.R. Holbrook, and S.H. Kim Prediction of the disulfide-bonding state of cysteine in proteins Protein Eng. 3 1990 667 672
    • (1990) Protein Eng. , vol.3 , pp. 667-672
    • Muskal, S.M.1    Holbrook, S.R.2    Kim, S.H.3
  • 44
    • 0032788590 scopus 로고    scopus 로고
    • Amino acid neighbours and detailed conformational analysis of cysteines in proteins
    • M.T. Petersen, P.H. Jonson, and S.B. Petersen Amino acid neighbours and detailed conformational analysis of cysteines in proteins Protein Eng. 12 1999 535 548
    • (1999) Protein Eng. , vol.12 , pp. 535-548
    • Petersen, M.T.1    Jonson, P.H.2    Petersen, S.B.3
  • 45
    • 0031575423 scopus 로고    scopus 로고
    • MONSSTER: A method for folding globular proteins with a small number of distance restraints
    • J. Skolnick, A. Kolinski, and A.R. Ortiz MONSSTER a method for folding globular proteins with a small number of distance restraints J. Mol. Biol. 265 1997 217 241
    • (1997) J. Mol. Biol. , vol.265 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.R.3
  • 48
    • 0346493041 scopus 로고    scopus 로고
    • A novel database of disulfide patterns and its application to the discovery of distantly related homologs
    • H.W. Van Vlijmen, A. Gupta, L.S. Narasimhan, and J. Singh A novel database of disulfide patterns and its application to the discovery of distantly related homologs J. Mol. Biol. 335 2004 1083 1092
    • (2004) J. Mol. Biol. , vol.335 , pp. 1083-1092
    • Van Vlijmen, H.W.1    Gupta, A.2    Narasimhan, L.S.3    Singh, J.4
  • 49
    • 1842455284 scopus 로고    scopus 로고
    • Disulfide connectivity prediction using recursive neural networks and evolutionary information
    • A. Vullo, and P. Frasconi Disulfide connectivity prediction using recursive neural networks and evolutionary information Bioinformatics 20 2004 653 659
    • (2004) Bioinformatics , vol.20 , pp. 653-659
    • Vullo, A.1    Frasconi, P.2
  • 50
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • G. Wang, and R.L. Dunbrack Jr. PISCES a protein sequence culling server Bioinformatics 19 2003 1589 1591
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 51
    • 0842265197 scopus 로고    scopus 로고
    • Support vector machines for prediction of peptidyl prolyl cis/trans isomerization
    • M.L. Wang, W.J. Li, and W.B. Xu Support vector machines for prediction of peptidyl prolyl cis/trans isomerization J. Peptide Res. 63 2003 23 28
    • (2003) J. Peptide Res. , vol.63 , pp. 23-28
    • Wang, M.L.1    Li, W.J.2    Xu, W.B.3
  • 54
    • 0028943316 scopus 로고
    • Disulfide bond formation and eukaryotic secretory productivity
    • K.D. Wittrup Disulfide bond formation and eukaryotic secretory productivity Curr. Opin. in Biotechnol. 6 1995 203 208
    • (1995) Curr. Opin. in Biotechnol. , vol.6 , pp. 203-208
    • Wittrup, K.D.1
  • 55
    • 0027998241 scopus 로고
    • Determination of the disulfide bridges in factor va heavy rain
    • J. Xue, M. Kalafatis, J.R. Silveira, C. Kung, and K.G. Mann Determination of the disulfide bridges in factor va heavy rain Biochemistry 33 1994 13019 13116
    • (1994) Biochemistry , vol.33 , pp. 13019-13116
    • Xue, J.1    Kalafatis, M.2    Silveira, J.R.3    Kung, C.4    Mann, K.G.5
  • 56
    • 0035819416 scopus 로고    scopus 로고
    • A new approach to predict the helix/strand content of globular Proteins
    • Z. Zhang, Z.R. Sun, and C.T. Zhang A new approach to predict the helix/strand content of globular Proteins J. Theor. Biol. 208 2001 65 78
    • (2001) J. Theor. Biol. , vol.208 , pp. 65-78
    • Zhang, Z.1    Sun, Z.R.2    Zhang, C.T.3
  • 57
    • 0027480940 scopus 로고
    • Disulfide bond contribution to protein stability: Positional effects of substitution in the hydrophobic core of the two-stranded alpha-helical coiled-coil
    • N.E. Zhou, C.M. Kay, and R.S. Hodges Disulfide bond contribution to protein stability positional effects of substitution in the hydrophobic core of the two-stranded alpha-helical coiled-coil Biochemistry 32 1993 178 187
    • (1993) Biochemistry , vol.32 , pp. 178-187
    • Zhou, N.E.1    Kay, C.M.2    Hodges, R.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.