메뉴 건너뛰기




Volumn 10, Issue , 2010, Pages

Comparing interfacial dynamics in protein-protein complexes: An elastic network approach

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DIMER; PROTEIN;

EID: 77955214740     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-10-26     Document Type: Article
Times cited : (32)

References (72)
  • 1
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • 10.1073/pnas.93.1.13.8552589
    • Principles of protein-protein interactions. S Jones JM Thornton, Proc Natl Acad Sci USA 1996 93 13 20 10.1073/pnas.93.1.13 8552589
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 2
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • 10.1006/jmbi.1998.2439. 9925793
    • The atomic structure of protein-protein recognition sites. LL Conte C Chothia J Janin, J Mol Biol 1999 285 2177 98 10.1006/jmbi.1998.2439 9925793
    • (1999) J Mol Biol , vol.285 , pp. 2177-98
    • Conte, L.L.1    Chothia, C.2    Janin, J.3
  • 3
    • 0037093645 scopus 로고    scopus 로고
    • Dissecting protein-protein recognition sites
    • 10.1002/prot.10085. 11948787
    • Dissecting protein-protein recognition sites. P Chakrabarti J Janin, Proteins 2002 47 334 343 10.1002/prot.10085 11948787
    • (2002) Proteins , vol.47 , pp. 334-343
    • Chakrabarti, P.1    Janin, J.2
  • 4
    • 0035178383 scopus 로고    scopus 로고
    • Protein-protein interfaces: Analysis of amino acid conservation in homodimers
    • 10.1002/1097-0134(20010101)42:1<108::AID-PROT110>3.0.CO;2-O. 11093265
    • Protein-protein interfaces: Analysis of amino acid conservation in homodimers. W Valdar J Thornton, Proteins 2001 42 108 124 10.1002/1097- 0134(20010101)42:1<108::AID-PROT110>3.0.CO;2-O 11093265
    • (2001) Proteins , vol.42 , pp. 108-124
    • Valdar, W.1    Thornton, J.2
  • 5
    • 0035366379 scopus 로고    scopus 로고
    • Protein functional epitopes: Hot spots, dynamics and combinatorial libraries
    • 10.1016/S0959-440X(00)00216-5. 11406388
    • Protein functional epitopes: hot spots, dynamics and combinatorial libraries. B Ma H Wolfson R Nussinov, Curr Opin Struct Biol 2001 11 364 369 10.1016/S0959-440X(00)00216-5 11406388
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 364-369
    • Ma, B.1    Wolfson, H.2    Nussinov, R.3
  • 6
    • 0031868211 scopus 로고    scopus 로고
    • Protein folding via binding and vice versa
    • 10.1016/S1359-0278(98)00032-7. 9710571
    • Protein folding via binding and vice versa. CJ Tsai D Xu R Nussinov, Fold Des 1998 3 71 80 10.1016/S1359-0278(98)00032-7 9710571
    • (1998) Fold des , vol.3 , pp. 1871-80
    • Tsai, C.J.1    Xu, D.2    Nussinov, R.3
  • 7
    • 0031678069 scopus 로고    scopus 로고
    • Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions
    • 10.1002/pro.5560071211. 9865952
    • Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. O Keskin I Bahar A Badretdinov O Ptitsyn R Jernigan, Protein Sci 1998 7 2578 2586 10.1002/pro.5560071211 9865952
    • (1998) Protein Sci , vol.7 , pp. 2578-2586
    • Keskin, O.1    Bahar, I.2    Badretdinov, A.3    Ptitsyn, O.4    Jernigan, R.5
  • 8
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • 10.1006/jmbi.1998.1843. 9653027
    • Anatomy of hot spots in protein interfaces. A Bogan K Thorn, J Mol Biol 1998 280 1 9 10.1006/jmbi.1998.1843 9653027
    • (1998) J Mol Biol , vol.280 , pp. 1-9
    • Bogan, A.1    Thorn, K.2
  • 9
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction. Y Zhang A Kolinski J Skolnick, Biophys J 2003 85 1145 1164 10.1016/S0006- 3495(03)74551-2 12885659 (Pubitemid 36909676)
    • (2003) Biophysical Journal , vol.85 , Issue.2 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 10
    • 23144459432 scopus 로고    scopus 로고
    • POPSCOMP: An automated interaction analysis of biomolecular complexes
    • 10.1093/nar/gki369. 15980485
    • POPSCOMP: an automated interaction analysis of biomolecular complexes. J Kleinjung F Fraternali, Nucleic Acids Res 2005 33 342 6 10.1093/nar/gki369 15980485
    • (2005) Nucleic Acids Res , vol.33 , pp. 23342-6
    • Kleinjung, J.1    Fraternali, F.2
  • 11
    • 0026572775 scopus 로고
    • Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
    • 10.1073/pnas.89.6.2195. 1549581
    • Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. E Katchalskikatzir I Shariv M Eisenstein A Friesem C Aalo I Vakser, Proc Natl Acad Sci USA 1992 89 2195 2199 10.1073/pnas.89.6.2195 1549581
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2195-2199
    • Katchalskikatzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.4    Aalo, C.5    Vakser, I.6
  • 12
    • 0032512424 scopus 로고    scopus 로고
    • Specificity in protein-protein recognition: Conserved Im9 residues are the major determinants of stability in the colicin E9 DNase-Tm9 complex
    • 10.1021/bi971884a. 9425068
    • Specificity in protein-protein recognition: Conserved Im9 residues are the major determinants of stability in the colicin E9 DNase-Tm9 complex. R Wallis K Leung M Osborne R James G Moore C Kleanthous, Biochemistry 1998 37 476 485 10.1021/bi971884a 9425068
    • (1998) Biochemistry , vol.37 , pp. 476-485
    • Wallis, R.1    Leung, K.2    Osborne, M.3    James, R.4    Moore, G.5    Kleanthous, C.6
  • 13
    • 0036776124 scopus 로고    scopus 로고
    • Sequence and structural differences between enzyme and nonenzyme homologs
    • 10.1016/S0969-2126(02)00861-4. 12377129
    • Sequence and structural differences between enzyme and nonenzyme homologs. A Todd C Orengo J Thornton, Structure 2002 10 1435 1451 10.1016/S0969-2126(02)00861-4 12377129
    • (2002) Structure , vol.10 , pp. 1435-1451
    • Todd, A.1    Orengo, C.2    Thornton, J.3
  • 15
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterisation and functional significance of transient protein-protein interactions
    • 10.1016/S0022-2836(02)01281-0. 12527304
    • Structural characterisation and functional significance of transient protein-protein interactions. IMA Nooren JM Thornton, J Mol Biol 2003 325 991 1018 10.1016/S0022-2836(02)01281-0 12527304
    • (2003) J Mol Biol , vol.325 , pp. 991-1018
    • Nooren, I.M.A.1    Thornton, J.M.2
  • 16
    • 3843091516 scopus 로고    scopus 로고
    • Anchor residues in protein-protein interactions
    • 10.1073/pnas.0401942101. 15269345
    • Anchor residues in protein-protein interactions. D Rajamani S Thiel S Vajda CJ Camacho, Proc Natl Acad Sci USA 2004 101 11287 92 10.1073/pnas. 0401942101 15269345
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 11287-92
    • Rajamani, D.1    Thiel, S.2    Vajda, S.3    Camacho, C.J.4
  • 17
    • 15244355250 scopus 로고    scopus 로고
    • The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
    • 10.1016/j.jmb.2005.01.058. 15784265
    • The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. GR Smith MJE Sternberg PA Bates, J Mol Biol 2005 347 1077 101 10.1016/j.jmb.2005.01.058 15784265
    • (2005) J Mol Biol , vol.347 , pp. 1077-101
    • Smith, G.R.1    Sternberg, M.J.E.2    Bates, P.A.3
  • 18
    • 7944225979 scopus 로고    scopus 로고
    • Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: Implications for docking
    • 10.1016/j.jmb.2004.09.051. 15533445
    • Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. X Li O Keskin B Ma R Nussinov J Liang, J Mol Biol 2004 344 781 95 10.1016/j.jmb.2004.09.051 15533445
    • (2004) J Mol Biol , vol.344 , pp. 781-95
    • Li, X.1    Keskin, O.2    Ma, B.3    Nussinov, R.4    Liang, J.5
  • 19
    • 43649093747 scopus 로고    scopus 로고
    • Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations
    • 10.1529/biophysj.107.114835. 18227135
    • Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations. ON Yogurtcu SB Erdemli R Nussinov M Turkay O Keskin, Biophys J 2008 94 3475 85 10.1529/biophysj.107.114835 18227135
    • (2008) Biophys J , vol.94 , pp. 3475-85
    • Yogurtcu, O.N.1    Erdemli, S.B.2    Nussinov, R.3    Turkay, M.4    Keskin, O.5
  • 20
    • 36148979311 scopus 로고    scopus 로고
    • NMR identification of transient complexes critical to adenylate kinase catalysis
    • 10.1021/ja075055g. 17935333
    • NMR identification of transient complexes critical to adenylate kinase catalysis. J Adén M Wolf-Watz, J Am Chem Soc 2007 129 14003 12 10.1021/ja075055g 17935333
    • (2007) J Am Chem Soc , vol.129 , pp. 14003-12
    • Adén, J.1    Wolf-Watz, M.2
  • 21
    • 0034696766 scopus 로고    scopus 로고
    • Transition-state ensemble in enzyme catalysis: Possibility, reality, or necessity?
    • 10.1006/jtbi.2000.1097. 10736215
    • Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity? B Ma S Kumar CJ Tsai Z Hu R Nussinov, J Theor Biol 2000 203 383 97 10.1006/jtbi.2000.1097 10736215
    • (2000) J Theor Biol , vol.203 , pp. 383-97
    • Ma, B.1    Kumar, S.2    Tsai, C.J.3    Hu, Z.4    Nussinov, R.5
  • 22
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • 10.1038/nature06407. 18026087
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. KA Henzler-Wildman M Lei V Thai SJ Kerns M Karplus D Kern, Nature 2007 450 913 6 10.1038/nature06407 18026087
    • (2007) Nature , vol.450 , pp. 913-6
    • Henzler-Wildman, K.A.1    Lei, M.2    Thai, V.3    Kerns, S.J.4    Karplus, M.5    Kern, D.6
  • 24
    • 21244440196 scopus 로고    scopus 로고
    • Conservation of s-ms enzyme motions in the apo- and substrate-mimicked state
    • 10.1021/ja0514949. 15969595
    • Conservation of s-ms enzyme motions in the apo- and substrate-mimicked state. H Beach R Cole ML Gill JP Loria, J Am Chem Soc 2005 127 9167 76 10.1021/ja0514949 15969595
    • (2005) J Am Chem Soc , vol.127 , pp. 9167-76
    • Beach, H.1    Cole, R.2    Gill, M.L.3    Loria, J.P.4
  • 26
    • 58749094825 scopus 로고    scopus 로고
    • Small- and large-scale conformational changes of adenylate kinase: A molecular dynamics study of the subdomain motion and mechanics
    • 10.1529/biophysj.108.135467. 18931260
    • Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics. F Pontiggia A Zen C Micheletti, Biophys J 2008 95 5901 12 10.1529/biophysj.108.135467 18931260
    • (2008) Biophys J , vol.95 , pp. 5901-12
    • Pontiggia, F.1    Zen, A.2    Micheletti, C.3
  • 28
    • 30044434744 scopus 로고    scopus 로고
    • Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
    • 10.1073/pnas.0507603102. 16354836
    • Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. D Tobi I Bahar, Proc Natl Acad Sci USA 2005 102 18908 13 10.1073/pnas.0507603102 16354836
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 18908-13
    • Tobi, D.1    Bahar, I.2
  • 29
    • 34250001164 scopus 로고    scopus 로고
    • Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: A case study of antibodies
    • 10.1186/1472-6807-7-31. 17509130
    • Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies. O Keskin, BMC Struct Biol 2007 7 31 10.1186/1472-6807-7-31 17509130
    • (2007) BMC Struct Biol , vol.7 , pp. 31
    • Keskin, O.1
  • 30
    • 48749126860 scopus 로고    scopus 로고
    • Insights into protein exibility: The relationship between normal modes and conformational change upon protein-protein docking
    • 10.1073/pnas.0802496105. 18641126
    • Insights into protein exibility: The relationship between normal modes and conformational change upon protein-protein docking. SE Dobbins VI Lesk MJE Sternberg, Proc Natl Acad Sci USA 2008 105 10390 5 10.1073/pnas.0802496105 18641126
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 10390-5
    • Dobbins, S.E.1    Lesk, V.I.2    Sternberg, M.J.E.3
  • 31
    • 33746651090 scopus 로고    scopus 로고
    • Convergent dynamics in the protease enzymatic superfamily
    • 10.1021/ja060896t. 16866533
    • Convergent dynamics in the protease enzymatic superfamily. V Carnevale S Raugei C Micheletti P Carloni, J Am Chem Soc 2006 128 9766 72 10.1021/ja060896t 16866533
    • (2006) J Am Chem Soc , vol.128 , pp. 9766-72
    • Carnevale, V.1    Raugei, S.2    Micheletti, C.3    Carloni, P.4
  • 32
    • 36348968387 scopus 로고    scopus 로고
    • Essential dynamics of helices provide a functional classification of EF-hand proteins
    • 10.1021/pr070314m. 17935310
    • Essential dynamics of helices provide a functional classification of EF-hand proteins. F Capozzi C Luchinat C Micheletti F Pontiggia, J Proteome Res 2007 6 4245 55 10.1021/pr070314m 17935310
    • (2007) J Proteome Res , vol.6 , pp. 4245-55
    • Capozzi, F.1    Luchinat, C.2    Micheletti, C.3    Pontiggia, F.4
  • 33
    • 43049104657 scopus 로고    scopus 로고
    • Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families
    • 10.1110/ps.073390208. 18369194
    • Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families. A Zen V Carnevale AM Lesk C Micheletti, Protein Sci 2008 17 918 29 10.1110/ps.073390208 18369194
    • (2008) Protein Sci , vol.17 , pp. 918-29
    • Zen, A.1    Carnevale, V.2    Lesk, A.M.3    Micheletti, C.4
  • 34
    • 67650745346 scopus 로고    scopus 로고
    • Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: An application to OB-fold domains
    • 10.1093/bioinformatics/btp339. 19487258
    • Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains. A Zen C de Chiara A Pastore C Micheletti, Bioinformatics 2009 25 1876 83 10.1093/bioinformatics/btp339 19487258
    • (2009) Bioinformatics , vol.25 , pp. 1876-83
    • Zen, A.1    De Chiara, C.2    Pastore, A.3    Micheletti, C.4
  • 35
    • 1842507022 scopus 로고    scopus 로고
    • A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
    • 10.1110/ps.03484604. 15044734
    • A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. O Keskin C Tsai H Wolfson R Nussinov, Protein Sci 2004 13 1043 1055 10.1110/ps.03484604 15044734
    • (2004) Protein Sci , vol.13 , pp. 1043-1055
    • Keskin, O.1    Tsai, C.2    Wolfson, H.3    Nussinov, R.4
  • 36
    • 47849091218 scopus 로고    scopus 로고
    • Architectures and functional coverage of protein-protein interfaces
    • 10.1016/j.jmb.2008.04.071. 18620705
    • Architectures and functional coverage of protein-protein interfaces. N Tuncbag A Gursoy E Guney R Nussinov O Keskin, J Mol Biol 2008 381 785 802 10.1016/j.jmb.2008.04.071 18620705
    • (2008) J Mol Biol , vol.381 , pp. 785-802
    • Tuncbag, N.1    Gursoy, A.2    Guney, E.3    Nussinov, R.4    Keskin, O.5
  • 37
    • 17144366191 scopus 로고    scopus 로고
    • Favorable scaffolds: Proteins with different sequence, structure and function may associate in similar ways
    • 10.1093/protein/gzh095. 15790576
    • Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. O Keskin R Nussinov, Protein Eng Des Sel 2005 18 11 24 10.1093/protein/gzh095 15790576
    • (2005) Protein Eng des Sel , vol.18 , pp. 11-24
    • Keskin, O.1    Nussinov, R.2
  • 38
    • 33847768378 scopus 로고    scopus 로고
    • Similar binding sites and different partners: Implications to shared proteins in cellular pathways
    • 10.1016/j.str.2007.01.007. 17355869
    • Similar binding sites and different partners: implications to shared proteins in cellular pathways. O Keskin R Nussinov, Structure 2007 15 341 54 10.1016/j.str.2007.01.007 17355869
    • (2007) Structure , vol.15 , pp. 341-54
    • Keskin, O.1    Nussinov, R.2
  • 39
    • 0000197372 scopus 로고    scopus 로고
    • Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis
    • 10.1103/PhysRevLett.77.1905. 10063201
    • Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. M Tirion, Phys Rev Lett 1996 77 1905 1908 10.1103/PhysRevLett. 77.1905 10063201
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.1
  • 40
    • 0345973041 scopus 로고    scopus 로고
    • Gaussian dynamics of folded proteins
    • 10.1103/PhysRevLett.79.3090
    • Gaussian dynamics of folded proteins. T Haliloglu I Bahar B Erman, Phys Rev Lett 2000 79 3090 3093 10.1103/PhysRevLett.79.3090
    • (2000) Phys Rev Lett , vol.79 , pp. 3090-3093
    • Haliloglu, T.1    Bahar, I.2    Erman, B.3
  • 41
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • 10.1016/S1359-0278(97)00024-2. 9218955
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. I Bahar AR Atilgan B Erman, Fold Des 1997 2 173 81 10.1016/S1359-0278(97)00024-2 9218955
    • (1997) Fold des , vol.2 , pp. 173-81
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 42
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8. 9829700
    • Analysis of domain motions by approximate normal mode calculations. K Hinsen, Proteins 1998 33 417 29 10.1002/(SICI)1097-0134(19981115)33:3<417:: AID-PROT10>3.0.CO;2-8 9829700
    • (1998) Proteins , vol.33 , pp. 417-29
    • Hinsen, K.1
  • 43
    • 0034029144 scopus 로고    scopus 로고
    • Proteins with similar architecture exhibit similar large-scale dynamic behavior
    • 10.1016/S0006-3495(00)76756-7. 10733987
    • Proteins with similar architecture exhibit similar large-scale dynamic behavior. O Keskin RL Jernigan I Bahar, Biophys J 2000 78 2093 2106 10.1016/S0006-3495(00)76756-7 10733987
    • (2000) Biophys J , vol.78 , pp. 2093-2106
    • Keskin, O.1    Jernigan, R.L.2    Bahar, I.3
  • 44
    • 0035920986 scopus 로고    scopus 로고
    • Conformations of Proteins in Equilibrium
    • 10.1103/PhysRevLett.87.088102. 11497984
    • Conformations of Proteins in Equilibrium. C Micheletti JR Banavar A Maritan, Phys Rev Lett 2001 87 088102 10.1103/PhysRevLett.87.088102 11497984
    • (2001) Phys Rev Lett , vol.87 , pp. 088102
    • Micheletti, C.1    Banavar, J.R.2    Maritan, A.3
  • 45
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • 10.1016/S0006-3495(01)76033-X. 11159421
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model. AR Atilgan SR Durell RL Jernigan MC Demirel O Keskin I Bahar, Biophys J 2001 80 505 15 10.1016/S0006-3495(01)76033-X 11159421
    • (2001) Biophys J , vol.80 , pp. 505-15
    • Atilgan, A.R.1    Durell, S.R.2    Jernigan, R.L.3    Demirel, M.C.4    Keskin, O.5    Bahar, I.6
  • 46
    • 0036077875 scopus 로고    scopus 로고
    • Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model
    • 10.1016/S0022-2836(02)00562-4. 12126621
    • Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. M Delarue YH Sanejouand, J Mol Biol 2002 320 1011 24 10.1016/S0022-2836(02)00562-4 12126621
    • (2002) J Mol Biol , vol.320 , pp. 1011-24
    • Delarue, M.1    Sanejouand, Y.H.2
  • 47
    • 2442543557 scopus 로고    scopus 로고
    • Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models
    • 10.1002/prot.20049. 15103627
    • Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models. C Micheletti P Carloni A Maritan, Proteins 2004 55 635 45 10.1002/prot.20049 15103627
    • (2004) Proteins , vol.55 , pp. 635-45
    • Micheletti, C.1    Carloni, P.2    Maritan, A.3
  • 48
    • 33748189629 scopus 로고    scopus 로고
    • The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models
    • 10.1021/ct600060d. 17710199
    • The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models. TZ Sen Y Feng JV Garcia A Kloczkowski RL Jernigan, J Chem Theory Comput 2006 2 696 704 10.1021/ct600060d 17710199
    • (2006) J Chem Theory Comput , vol.2 , pp. 696-704
    • Sen, T.Z.1    Feng, Y.2    Garcia, J.V.3    Kloczkowski, A.4    Jernigan, R.L.5
  • 49
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • 10.1093/protein/14.1.1. 11287673
    • Conformational change of proteins arising from normal mode calculations. F Tama YH Sanejouand, Protein Eng 2001 14 1 6 10.1093/protein/14.1.1 11287673
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 50
    • 24144441220 scopus 로고    scopus 로고
    • The influence of conformational fluctuations on enzymatic activity: Modelling the functional motion of β-secretase
    • DOI 10.1088/0953-8984/17/18/014
    • The influence of conformational fluctuations on enzymatic activity: modelling the functional motion of beta secretase. Neri MM Cascella C Micheletti, J Phys Condens Matter 2005 17 1581 S1593 10.1088/0953-8984/17/18/014 (Pubitemid 41237357)
    • (2005) Journal of Physics Condensed Matter , vol.17 , Issue.18
    • Neri, M.1    Cascella, M.2    Micheletti, C.3
  • 51
    • 33745024278 scopus 로고    scopus 로고
    • Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
    • 10.1146/annurev.biophys.35.040405.102010. 16689630
    • Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. F Tama CL Brooks, Annu Rev Biophys Biomol Struct 2006 35 115 33 10.1146/annurev.biophys.35.040405.102010 16689630
    • (2006) Annu Rev Biophys Biomol Struct , vol.35 , pp. 115-33
    • Tama, F.1    Brooks, C.L.2
  • 52
    • 40549141130 scopus 로고    scopus 로고
    • Predicting the order in which contacts are broken during single molecule protein stretching experiments
    • 10.1002/prot.21652. 17932935
    • Predicting the order in which contacts are broken during single molecule protein stretching experiments. JI Sulkowska A Kloczkowski TZ Sen M Cieplak RL Jernigan, Proteins 2008 71 45 60 10.1002/prot.21652 17932935
    • (2008) Proteins , vol.71 , pp. 45-60
    • Sulkowska, J.I.1    Kloczkowski, A.2    Sen, T.Z.3    Cieplak, M.4    Jernigan, R.L.5
  • 55
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm
    • 10.1006/jmbi.1999.3110. 10550212
    • Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. PE Wright HJ Dyson, J Mol Biol 1999 293 321 31 10.1006/jmbi.1999.3110 10550212
    • (1999) J Mol Biol , vol.293 , pp. 321-31
    • Wright, P.E.1    Dyson, H.J.2
  • 56
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • 10.1002/jcc.540161209
    • Harmonic analysis of large systems. I. Methodology. B Brooks D Janezic M Karplus, J Comput Chem 1995 16 1522 1542 10.1002/jcc.540161209
    • (1995) J Comput Chem , vol.16 , pp. 1522-1542
    • Brooks, B.1    Janezic, D.2    Karplus, M.3
  • 57
    • 0032374086 scopus 로고    scopus 로고
    • Energy landscape of a native protein: Jumping-among-minima model
    • 10.1002/(SICI)1097-0134(19981201)33:4<496::AID-PROT4>3.0.CO;2-1. 9849935
    • Energy landscape of a native protein: jumping-among-minima model. A Kitao S Hayward N Go, Proteins 1998 33 496 517 10.1002/(SICI)1097-0134(19981201)33: 4<496::AID-PROT4>3.0.CO;2-1 9849935
    • (1998) Proteins , vol.33 , pp. 496-517
    • Kitao, A.1    Hayward, S.2    Go, N.3
  • 58
    • 15744387343 scopus 로고    scopus 로고
    • Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases
    • 10.1021/ja044608+. 15771507
    • Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases. M Cascella C Micheletti U Rothlisberger P Carloni, J Am Chem Soc 2005 127 3734 42 10.1021/ja044608+ 15771507
    • (2005) J Am Chem Soc , vol.127 , pp. 3734-42
    • Cascella, M.1    Micheletti, C.2    Rothlisberger, U.3    Carloni, P.4
  • 60
    • 38049141556 scopus 로고    scopus 로고
    • Large-scale motions and electrostatic properties of furin and HIV-1 protease
    • 10.1021/jp0751716. 18001009
    • Large-scale motions and electrostatic properties of furin and HIV-1 protease. V Carnevale S Raugei C Micheletti P Carloni, J Phys Chem A 2007 111 12327 32 10.1021/jp0751716 18001009
    • (2007) J Phys Chem A , vol.111 , pp. 12327-32
    • Carnevale, V.1    Raugei, S.2    Micheletti, C.3    Carloni, P.4
  • 61
    • 68949144755 scopus 로고    scopus 로고
    • Coarse-grained description of protein internal dynamics: An optimal strategy for decomposing proteins in rigid subunits
    • 10.1016/j.bpj.2009.03.051. 19527659
    • Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits. R Potestio F Pontiggia C Micheletti, Biophys J 2009 96 4993 5002 10.1016/j.bpj.2009.03.051 19527659
    • (2009) Biophys J , vol.96 , pp. 4993-5002
    • Potestio, R.1    Pontiggia, F.2    Micheletti, C.3
  • 62
    • 70349978984 scopus 로고    scopus 로고
    • PiSQRD: A web server for decomposing proteins into quasi-rigid dynamical domains
    • 10.1093/bioinformatics/btp512. 19696046
    • PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains. T Aleksiev R Potestio F Pontiggia S Cozzini C Micheletti, Bioinformatics 2009 25 2743 4 10.1093/bioinformatics/btp512 19696046
    • (2009) Bioinformatics , vol.25 , pp. 2743-4
    • Aleksiev, T.1    Potestio, R.2    Pontiggia, F.3    Cozzini, S.4    Micheletti, C.5
  • 63
    • 0028360307 scopus 로고
    • The contribution of vibrational entropy to molecular association. The dimerization of insulin
    • 10.1006/jmbi.1994.1300. 8176732
    • The contribution of vibrational entropy to molecular association. The dimerization of insulin. B Tidor M Karplus, J Mol Biol 1994 238 405 14 10.1006/jmbi.1994.1300 8176732
    • (1994) J Mol Biol , vol.238 , pp. 405-14
    • Tidor, B.1    Karplus, M.2
  • 64
    • 0041852853 scopus 로고    scopus 로고
    • The role of dynamics in enzyme activity
    • 10.1146/annurev.biophys.32.110601.142445. 12471064
    • The role of dynamics in enzyme activity. RM Daniel RV Dunn JL Finney JC Smith, Annu Rev Biophys Biomol Struct 2003 32 69 92 10.1146/annurev.biophys.32. 110601.142445 12471064
    • (2003) Annu Rev Biophys Biomol Struct , vol.32 , pp. 69-92
    • Daniel, R.M.1    Dunn, R.V.2    Finney, J.L.3    Smith, J.C.4
  • 66
    • 75149177173 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt)
    • 10.1093/nar/gkn141. 18045787
    • The Universal Protein Resource (UniProt). UniProt Consortium, Nucleic Acids Res 2008 36 190 5 10.1093/nar/gkn141 18045787
    • (2008) Nucleic Acids Res , vol.36 , pp. 4190-5
    • Consortium, U.1
  • 67
    • 58149191270 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) 2009
    • 10.1093/nar/gkn664. 18836194
    • The Universal Protein Resource (UniProt) 2009. UniProt Consortium, Nucleic Acids Res 2009 37 169 74 10.1093/nar/gkn664 18836194
    • (2009) Nucleic Acids Res , vol.37 , pp. 4169-74
    • Consortium, U.1
  • 68
    • 33644639293 scopus 로고    scopus 로고
    • NOXclass: Prediction of protein protein interaction types
    • 10.1186/1471-2105-7-27. 16423290
    • NOXclass: prediction of protein protein interaction types. H Zhu FS Domingues I Sommer T Lengauer, BMC Bioinformatics 2006 7 27 10.1186/1471-2105-7- 27 16423290
    • (2006) BMC Bioinformatics , vol.7 , pp. 27
    • Zhu, H.1    Domingues, F.S.2    Sommer, I.3    Lengauer, T.4
  • 69
    • 0031565729 scopus 로고    scopus 로고
    • Analysis of protein-protein interaction sites using surface patches
    • 10.1006/jmbi.1997.1234. 9299342
    • Analysis of protein-protein interaction sites using surface patches. S Jones JM Thornton, J Mol Biol 1997 272 121 32 10.1006/jmbi.1997.1234 9299342
    • (1997) J Mol Biol , vol.272 , pp. 121-32
    • Jones, S.1    Thornton, J.M.2
  • 71
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • 10.1002/bip.360221211. 6667333
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. W Kabsch C Sander, Biopolymers 1983 22 2577 637 10.1002/bip.360221211 6667333
    • (1983) Biopolymers , vol.22 , pp. 2577-637
    • Kabsch, W.1    Sander, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.