메뉴 건너뛰기




Volumn 18, Issue 5, 2012, Pages 2153-2161

Structure-based characterization of the binding of peptide to the human endophilin-1 Src homology 3 domain using position-dependent noncovalent potential analysis

Author keywords

Noncovalent interaction; Peptide2; Src homology 3 domain; Statistical modeling

Indexed keywords

ENDOPHILIN; PROTEIN SH3;

EID: 84861232310     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1197-y     Document Type: Article
Times cited : (7)

References (43)
  • 2
    • 49549083915 scopus 로고    scopus 로고
    • Peptide mediated interactions in biological systems: New discoveries and applications
    • Petsalaki E, Russell RB (2008) Peptide mediated interactions in biological systems: new discoveries and applications. Curr Opin Biotechnol 19:344-350
    • (2008) Curr Opin Biotechnol , vol.19 , pp. 344-350
    • Petsalaki, E.1    Russell, R.B.2
  • 4
    • 33645776269 scopus 로고    scopus 로고
    • Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain
    • Hou T, Chen K, McLaughlin WA, Lu B, Wang W (2006) Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput Biol 2:e1
    • (2006) PLoS Comput Biol , vol.2
    • Hou, T.1    Chen, K.2    McLaughlin, W.A.3    Lu, B.4    Wang, W.5
  • 6
    • 0028148629 scopus 로고    scopus 로고
    • Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains
    • Lim WA, Richards FM, Fox RO (1997) Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature 372:375-379
    • (1997) Nature , vol.372 , pp. 375-379
    • Lim, W.A.1    Richards, F.M.2    Fox, R.O.3
  • 9
    • 0026656122 scopus 로고
    • Spot-synthesis: An easy technique for the positionally addressable, parallel chemical synthesis on a membrane support
    • Frank R (1992) Spot-synthesis: an easy technique for the positionally addressable, parallel chemical synthesis on a membrane support. Tetrahedron 48:9217-9232
    • (1992) Tetrahedron , vol.48 , pp. 9217-9232
    • Frank, R.1
  • 11
    • 12144276041 scopus 로고    scopus 로고
    • Predicting protein-peptide interactions via a network-based motif sampler
    • DOI 10.1093/bioinformatics/bth922
    • Reiss DJ, Schwikowski B (2004) Predicting protein-peptide interactions via a network-based motif sampler. Bioinformatics 20(suppl 1):i274-i282 (Pubitemid 41296699)
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Reiss, D.J.1    Schwikowski, B.2
  • 13
    • 33947315301 scopus 로고    scopus 로고
    • A neural strategy for the inference of SH3 domain-peptide interaction specificity
    • Ferraro E, Via A, Ausiello G, Helmer-Citterich M (2005) A neural strategy for the inference of SH3 domain-peptide interaction specificity. BMC Bioinformatics 6(Suppl 4):S13
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 4
    • Ferraro, E.1    Via, A.2    Ausiello, G.3    Helmer-Citterich, M.4
  • 14
    • 39049111013 scopus 로고    scopus 로고
    • Characterization of domain-peptide interaction interface: A case study on the amphiphysin-1 SH3 domain
    • Hou T, Zhang W, Case DA, Wang W (2008) Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain. J Mol Biol 376:1201-1214
    • (2008) J Mol Biol , vol.376 , pp. 1201-1214
    • Hou, T.1    Zhang, W.2    Case, D.A.3    Wang, W.4
  • 15
    • 72449181810 scopus 로고    scopus 로고
    • Machine learning quantitative structure- activity relationships (QSAR) for peptides binding to the human amphiphysin-1 SH3 domain
    • Ivanciuc O (2009) Machine learning quantitative structure- activity relationships (QSAR) for peptides binding to the human amphiphysin-1 SH3 domain. Curr Proteomics 6:289-302
    • (2009) Curr Proteomics , vol.6 , pp. 289-302
    • Ivanciuc, O.1
  • 16
    • 30744471940 scopus 로고    scopus 로고
    • Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis
    • DOI 10.1021/pr0502267
    • Hou T, McLaughlin W, Lu B, Chen K, Wang W (2006) Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. J Proteome Res 5:32-43 (Pubitemid 43100795)
    • (2006) Journal of Proteome Research , vol.5 , Issue.1 , pp. 32-43
    • Hou, T.1    McLaughlin, W.2    Lu, B.3    Chen, K.4    Wang, W.5
  • 18
    • 60849108682 scopus 로고    scopus 로고
    • Modeling and prediction of binding affinities between the human amphiphysin SH3 domain and its peptide ligands using genetic algorithm-Gaussian processes
    • Zhou P, Tian F, Chen X, Shang Z (2008) Modeling and prediction of binding affinities between the human amphiphysin SH3 domain and its peptide ligands using genetic algorithm-Gaussian processes. Biopolymers (Pept Sci) 90:792-802
    • (2008) Biopolymers (Pept Sci) , vol.90 , pp. 792-802
    • Zhou, P.1    Tian, F.2    Chen, X.3    Shang, Z.4
  • 19
    • 80052891491 scopus 로고    scopus 로고
    • Exploring the activity space of peptides binding to diverse SH3 domains using principal property descriptors derived from amino acid rotamers
    • He P, Wu W, Yang K, Jing T, Liao K, Zhang W, Wang H, Hua X (2011) Exploring the activity space of peptides binding to diverse SH3 domains using principal property descriptors derived from amino acid rotamers. Biopolymers (Pept Sci) 96:288-301
    • (2011) Biopolymers (Pept Sci) , vol.96 , pp. 288-301
    • He, P.1    Wu, W.2    Yang, K.3    Jing, T.4    Liao, K.5    Zhang, W.6    Wang, H.7    Hua, X.8
  • 21
    • 59749084158 scopus 로고    scopus 로고
    • Quantitative sequence-activity model (QSAM): Applying QSAR strategy to model and predict bioactivity and function of peptides, proteins and nucleic acids
    • Zhou P, Tian F, Wu Y, Li Z, Shang Z (2008) Quantitative sequence-activity model (QSAM): applying QSAR strategy to model and predict bioactivity and function of peptides, proteins and nucleic acids. Curr Comput Aided Drug Des 4:311-321
    • (2008) Curr Comput Aided Drug des , vol.4 , pp. 311-321
    • Zhou, P.1    Tian, F.2    Wu, Y.3    Li, Z.4    Shang, Z.5
  • 23
    • 0033527653 scopus 로고    scopus 로고
    • The SH3 domains of endophilin and amphiphysin bind to the proline-rich region of synaptojanin 1 at distinct sites that display an unconventional binding specificity
    • Cestra G, Castagnoli L, Dente L, Minenkova O, Petrelli A (1999) The SH3 domains of endophilin and amphiphysin bind to the proline-rich region of synaptojanin 1 at distinct sites that display an unconventional binding specificity. J Biol Chem 274:32001-32007
    • (1999) J Biol Chem , vol.274 , pp. 32001-32007
    • Cestra, G.1    Castagnoli, L.2    Dente, L.3    Minenkova, O.4    Petrelli, A.5
  • 24
    • 0028148629 scopus 로고    scopus 로고
    • Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains
    • DOI 10.1038/372375a0
    • Lim WA, Richards FM, Fox RO (1994) Structural determinants of peptidebinding orientation and of sequence specificity in SH3 domains. Nature 372:375-379 (Pubitemid 24363441)
    • (1994) Nature , vol.372 , Issue.6504 , pp. 375-379
    • Lim, W.A.1    Richards, F.M.2    Fox, R.O.3
  • 25
    • 33646940952 scopus 로고
    • Numerical integration of Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert J, Ciccotti G, Berendsen HJC (1977) Numerical integration of Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327-341
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 27
    • 70450106216 scopus 로고    scopus 로고
    • Improved prediction of protein side-chain conformations with SCWRL4
    • Krivov GG, Shapovalov MV, Dunbrack RL Jr (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins 77:778-795
    • (2009) Proteins , vol.77 , pp. 778-795
    • Krivov, G.G.1    Shapovalov, M.V.2    Dunbrack Jr., R.L.3
  • 28
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word JM, Lovell SC, Richardson JS, Richardson D.C.
    • Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285:1735-1747
    • (1999) J Mol Biol , vol.285 , pp. 1735-1747
  • 29
    • 44349194048 scopus 로고    scopus 로고
    • Side chain substitution benchmark for peptide/MHC interaction
    • DOI 10.1110/ps.073402508
    • Knapp B, Omasits U, Schreiner W (2008) Side chain substitution benchmark for peptide/MHC interaction. Protein Sci 17:977-982 (Pubitemid 351749203)
    • (2008) Protein Science , vol.17 , Issue.6 , pp. 977-982
    • Knapp, B.1    Omasits, U.2    Schreiner, W.3
  • 30
    • 66249145702 scopus 로고    scopus 로고
    • Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins
    • Zhou P, Tian F, Lv F, Shang Z (2009) Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins. Proteins 76:151-163
    • (2009) Proteins , vol.76 , pp. 151-163
    • Zhou, P.1    Tian, F.2    Lv, F.3    Shang, Z.4
  • 31
    • 77951943794 scopus 로고    scopus 로고
    • Predicting the binding affinity of epitope peptides with HLA-A*0201 by encoding atom-pair non-covalent interaction information between receptor and ligands
    • Hu L, Ai Z, Liu P, Xiong Q, Min M, Lan C, Wang J, Fan L, Chen D (2010) Predicting the binding affinity of epitope peptides with HLA-A*0201 by encoding atom-pair non-covalent interaction information between receptor and ligands. Chem Biol Drug Des 75:597-606
    • (2010) Chem Biol Drug des , vol.75 , pp. 597-606
    • Hu, L.1    Ai, Z.2    Liu, P.3    Xiong, Q.4    Min, M.5    Lan, C.6    Wang, J.7    Fan, L.8    Chen, D.9
  • 32
    • 77951666362 scopus 로고    scopus 로고
    • Toward quantitative characterization of the binding profile between the human amphiphysin-1 SH3 domain and its peptide ligands
    • He P, Wu W, Wang H, Yang K, Liao K, Zhang W (2010) Toward quantitative characterization of the binding profile between the human amphiphysin-1 SH3 domain and its peptide ligands. Amino Acids 38:1209-1218
    • (2010) Amino Acids , vol.38 , pp. 1209-1218
    • He, P.1    Wu, W.2    Wang, H.3    Yang, K.4    Liao, K.5    Zhang, W.6
  • 33
    • 33847105892 scopus 로고    scopus 로고
    • A structure-based, quantitative structure-activity relationship approach for predicting HLA-A*0201-restricted cytotoxic T lymphocyte epitopes
    • DOI 10.1111/j.1747-0285.2007.00472.x
    • Zhou P, Tian F, Li Z (2007) A structure-based, quantitative structureactivity relationship approach for predicting H.L.A.A. 0201-restricted cytotoxic T lymphocyte epitopes. Chem Biol Drug Des 69:56-67 (Pubitemid 46277786)
    • (2007) Chemical Biology and Drug Design , vol.69 , Issue.1 , pp. 56-67
    • Zhou, P.1    Tian, F.2    Li, Z.3
  • 34
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg D, McLachlan AD (1986) Solvation energy in protein folding and binding. Nature 319:199-203 (Pubitemid 16128783)
    • (1986) Nature , vol.319 , Issue.6050 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 35
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Sanner MF, Olson AJ, Spehner JC (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38:305-320
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 36
    • 78650218200 scopus 로고    scopus 로고
    • Predicting the flexibility profile of ribosomal RNAs
    • Tian F, Zhang C, Fan X, Yang X, Wang X, Liang H (2010) Predicting the flexibility profile of ribosomal RNAs. Mol Inf 29:707-715
    • (2010) Mol Inf , vol.29 , pp. 707-715
    • Tian, F.1    Zhang, C.2    Fan, X.3    Yang, X.4    Wang, X.5    Liang, H.6
  • 38
    • 34249753618 scopus 로고
    • Support vector networks
    • Cortes C, Vapnik V (1995) Support vector networks. Mach Learn 20:273-293
    • (1995) Mach Learn , vol.20 , pp. 273-293
    • Cortes, C.1    Vapnik, V.2
  • 39
    • 62249165045 scopus 로고    scopus 로고
    • Comprehensive comparison of eight statistical modelling methods used in quantitative structure-retention relationship studies for liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome
    • Zhou P, Tian F, Lv F, Shang Z (2009) Comprehensive comparison of eight statistical modelling methods used in quantitative structure-retention relationship studies for liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome. J Chromatogr A 1216:3107-3116
    • (2009) J Chromatogr A , vol.1216 , pp. 3107-3116
    • Zhou, P.1    Tian, F.2    Lv, F.3    Shang, Z.4
  • 40
    • 0023192524 scopus 로고
    • Peptide quantitative structure-activity relationships, a multivariate approach
    • Hellberg S, Sjostrom M, Skagerberg B, Wold S (1987) Peptide quantitative structure-activity relationships, a multivariate approach. J Med Chem 30:1126-1135 (Pubitemid 17117970)
    • (1987) Journal of Medicinal Chemistry , vol.30 , Issue.7 , pp. 1126-1135
    • Hellberg, S.1    Sjostrom, M.2    Skagerberg, B.3    Wold, S.4
  • 41
    • 67349182211 scopus 로고    scopus 로고
    • Silico quantitative prediction of peptides binding affinity to human MHC molecule: An intuitive quantitative structure-activity relationship approach
    • Tian F, Yang L, Lv F, Yang Q, Zhou P (2009) In silico quantitative prediction of peptides binding affinity to human MHC molecule: an intuitive quantitative structure-activity relationship approach. Amino Acids 36:535-554
    • (2009) Amino Acids , vol.36 , pp. 535-554
    • Tian, F.1    Yang, L.2    Lv, F.3    Yang, Q.4    Zhou, P.5
  • 42
    • 54249165105 scopus 로고    scopus 로고
    • Toward prediction of binding affinities between the MHC protein and its peptide ligands using quantitative structure-affinity relationship approach
    • Tian F, Lv F, Zhou P, Yang Q, Jalbout AF (2008) Toward prediction of binding affinities between the MHC protein and its peptide ligands using quantitative structure-affinity relationship approach. Protein Pept Lett 15:1033-1043
    • (2008) Protein Pept Lett , vol.15 , pp. 1033-1043
    • Tian, F.1    Lv, F.2    Zhou, P.3    Yang, Q.4    Jalbout, A.F.5
  • 43
    • 40449106762 scopus 로고    scopus 로고
    • Factor analysis scales of generalized amino acid information as applied in predicting interactions between the human amphiphysin-1 SH3 domains and their peptide ligands
    • DOI 10.1111/j.1747-0285.2008.00641.x
    • Liang G, Chen G, Niu W, Li Z (2008) Factor analysis scales of generalized amino acid information as applied in predicting interactions between the human amphiphysin-1 SH3 domains and their peptide ligands. Chem Biol Drug Des 71:345-351 (Pubitemid 351347792)
    • (2008) Chemical Biology and Drug Design , vol.71 , Issue.4 , pp. 345-351
    • Liang, G.1    Chen, G.2    Niu, W.3    Li, Z.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.