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Volumn 16, Issue 1, 2015, Pages

On the packing density of the unbound protein-protein interaction interface and its implications in dynamics

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICS;

EID: 84923902310     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-16-S1-S7     Document Type: Article
Times cited : (3)

References (40)
  • 1
    • 0037093645 scopus 로고    scopus 로고
    • Dissecting protein-protein recognition sites
    • Chakrabarti P, Janin J: Dissecting protein-protein recognition sites. Proteins 2002,47(3):334-343. 10.1002/prot.10085.
    • (2002) Proteins , vol.47 , Issue.3 , pp. 334-343
    • Chakrabarti, P.1    Janin, J.2
  • 2
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones S, Thornton JM: Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996,93(1):13-20. 10.1073/pnas.93.1.13.
    • (1996) Proc Natl Acad Sci USA , vol.93 , Issue.1 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 3
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L, Chothia C, Janin J: The atomic structure of protein-protein recognition sites. J Mol Biol 1999,285(5):2177-2198. 10.1006/jmbi.1998.2439.
    • (1999) J Mol Biol , vol.285 , Issue.5 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 4
    • 42449161827 scopus 로고    scopus 로고
    • The interface of protein-protein complexes: analysis of contacts and prediction of interactions
    • Bahadur RP, Zacharias M: The interface of protein-protein complexes: analysis of contacts and prediction of interactions. Cell Mol Life Sci 2008,65(7-8):1059-1072. 10.1007/s00018-007-7451-x.
    • (2008) Cell Mol Life Sci , vol.65 , Issue.7-8 , pp. 1059-1072
    • Bahadur, R.P.1    Zacharias, M.2
  • 5
    • 43149092276 scopus 로고    scopus 로고
    • Principles of protein-protein interactions: What are the preferred ways for proteins to interact?
    • Keskin O, Gursoy A, Ma B, Nussinov R: Principles of protein-protein interactions: What are the preferred ways for proteins to interact? Chem Rev 2008,108(4):1225-1244. 10.1021/cr040409x.
    • (2008) Chem Rev , vol.108 , Issue.4 , pp. 1225-1244
    • Keskin, O.1    Gursoy, A.2    Ma, B.3    Nussinov, R.4
  • 6
    • 77957771797 scopus 로고    scopus 로고
    • Transient protein-protein interactions: structural, functional, and network properties
    • Perkins JR, Diboun I, Dessailly BH, Lees JG, Orengo C: Transient protein-protein interactions: structural, functional, and network properties. Structure 2010,18(10):1233-1243. 10.1016/j.str.2010.08.007.
    • (2010) Structure , vol.18 , Issue.10 , pp. 1233-1243
    • Perkins, J.R.1    Diboun, I.2    Dessailly, B.H.3    Lees, J.G.4    Orengo, C.5
  • 7
    • 0242299201 scopus 로고    scopus 로고
    • Dissecting subunit interfaces in homodimeric proteins
    • Bahadur RP, Chakrabarti P, Rodier F, Janin J: Dissecting subunit interfaces in homodimeric proteins. Proteins 2003,53(3):708-719. 10.1002/prot.10461.
    • (2003) Proteins , vol.53 , Issue.3 , pp. 708-719
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 8
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: a structure based prediction program to identify the location of protein-protein binding sites
    • Neuvirth H, Raz R, Schreiber G: ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004,338(1):181-199. 10.1016/j.jmb.2004.02.040.
    • (2004) J Mol Biol , vol.338 , Issue.1 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 9
    • 0034769223 scopus 로고    scopus 로고
    • Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis
    • Norel R, Sheinerman F, Petrey D, Honig BH: Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis. Protein Sci 2001,10(11):2147.
    • (2001) Protein Sci , vol.10 , Issue.11 , pp. 2147
    • Norel, R.1    Sheinerman, F.2    Petrey, D.3    Honig, B.H.4
  • 10
    • 1842405464 scopus 로고    scopus 로고
    • Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect
    • Tsai CJ, Lin SL, Wolfson HJ, Nussinov R: Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci 1997,6(1):53-64.
    • (1997) Protein Sci , vol.6 , Issue.1 , pp. 53-64
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 11
    • 26444568633 scopus 로고    scopus 로고
    • Statistical analysis of predominantly transient protein-protein interfaces
    • Ansari S, Helms V: Statistical analysis of predominantly transient protein-protein interfaces. Proteins 2005,61(2):344-355. 10.1002/prot.20593.
    • (2005) Proteins , vol.61 , Issue.2 , pp. 344-355
    • Ansari, S.1    Helms, V.2
  • 12
    • 0029109468 scopus 로고
    • Protein-protein interactions: a review of protein dimer structures
    • Jones S, Thornton JM: Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol 1995,63(1):31-65. 10.1016/0079-6107(94)00008-W.
    • (1995) Prog Biophys Mol Biol , vol.63 , Issue.1 , pp. 31-65
    • Jones, S.1    Thornton, J.M.2
  • 13
    • 0016610491 scopus 로고
    • Computer simulation of protein folding
    • Levitt M, Warshel A: Computer simulation of protein folding. Nature 1975,253(5494):694-698. 10.1038/253694a0.
    • (1975) Nature , vol.253 , Issue.5494 , pp. 694-698
    • Levitt, M.1    Warshel, A.2
  • 14
    • 0017776823 scopus 로고
    • Dynamics of folded proteins
    • McCammon JA, Gelin BR, Karplus M: Dynamics of folded proteins. Nature 1977,267(5612):585-590. 10.1038/267585a0.
    • (1977) Nature , vol.267 , Issue.5612 , pp. 585-590
    • McCammon, J.A.1    Gelin, B.R.2    Karplus, M.3
  • 15
    • 0017251977 scopus 로고
    • Bicycle-pedal model for the first step in the vision process
    • Warshel A: Bicycle-pedal model for the first step in the vision process. Nature 1976,260(5553):679-683. 10.1038/260679a0.
    • (1976) Nature , vol.260 , Issue.5553 , pp. 679-683
    • Warshel, A.1
  • 16
    • 0036285978 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biological reactions
    • Warshel A: Molecular dynamics simulations of biological reactions. Accounts Chem Res 2002,35(6):385-395. 10.1021/ar010033z.
    • (2002) Accounts Chem Res , vol.35 , Issue.6 , pp. 385-395
    • Warshel, A.1
  • 17
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor
    • Brooks B, Karplus M: Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 1983,80(21):6571. 10.1073/pnas.80.21.6571.
    • (1983) Proc Natl Acad Sci USA , vol.80 , Issue.21 , pp. 6571
    • Brooks, B.1    Karplus, M.2
  • 18
    • 0026663419 scopus 로고
    • Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data
    • Kidera A, Go N: Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data. J Mol Biol 1992,225(2):457-475. 10.1016/0022-2836(92)90932-A.
    • (1992) J Mol Biol , vol.225 , Issue.2 , pp. 457-475
    • Kidera, A.1    Go, N.2
  • 19
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt M, Sander C, Stern PS: Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 1985,181(3):423-447. 10.1016/0022-2836(85)90230-X.
    • (1985) J Mol Biol , vol.181 , Issue.3 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stern, P.S.3
  • 21
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I, Atilgan A, Erman B: Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding & Design 1997,2(3):173-181. 10.1016/S1359-0278(97)00024-2.
    • (1997) Folding & Design , vol.2 , Issue.3 , pp. 173-181
    • Bahar, I.1    Atilgan, A.2    Erman, B.3
  • 22
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino acid sequence and atomic coordinates
    • Ming D, Kong Y, Lambert M, Huang Z, Ma J: How to describe protein motion without amino acid sequence and atomic coordinates. Proc Natl Acad Sci USA 2002,99(13):8620-8625. 10.1073/pnas.082148899.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.13 , pp. 8620-8625
    • Ming, D.1    Kong, Y.2    Lambert, M.3    Huang, Z.4    Ma, J.5
  • 23
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion M: Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996,77(9):1905-1908. 10.1103/PhysRevLett.77.1905.
    • (1996) Phys Rev Lett , vol.77 , Issue.9 , pp. 1905-1908
    • Tirion, M.1
  • 24
    • 84871612755 scopus 로고    scopus 로고
    • On the structural characteristics of the protein active sites and their relation to thermal fluctuations
    • Edited by: Yang N-S. InTech
    • Huang S-W, Hwang J-K: On the structural characteristics of the protein active sites and their relation to thermal fluctuations. In Systems and Computational Biology - Molecular and Cellular Experimental Systems. Edited by: Yang N-S. InTech; 2011:53-68.
    • (2011) Systems and Computational Biology - Molecular and Cellular Experimental Systems , pp. 53-68
    • Huang, S.-W.1    Hwang, J.-K.2
  • 25
    • 0037022347 scopus 로고    scopus 로고
    • Flexibility and packing in proteins
    • Halle B: Flexibility and packing in proteins. Proc Natl Acad Sci USA 2002,99(3):1274-1279. 10.1073/pnas.032522499.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.3 , pp. 1274-1279
    • Halle, B.1
  • 28
    • 23344451687 scopus 로고    scopus 로고
    • Structure, function, and evolution of transient and obligate protein-protein interactions
    • Mintseris J, Weng Z: Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 2005,102(31):10930-10935. 10.1073/pnas.0502667102.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.31 , pp. 10930-10935
    • Mintseris, J.1    Weng, Z.2
  • 29
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983,22(12):2577-2637. 10.1002/bip.360221211.
    • (1983) Biopolymers , vol.22 , Issue.12 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 31
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: CAPRI 3rd Edition
    • Lensink MF, Méndez R, Wodak SJ: Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 2007,69(4):704-718. 10.1002/prot.21804.
    • (2007) Proteins , vol.69 , Issue.4 , pp. 704-718
    • Lensink, M.F.1    Méndez, R.2    Wodak, S.J.3
  • 32
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Mendez R, Leplae R, Lensink M, Wodak S: Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005,60(2):150-169. 10.1002/prot.20551.
    • (2005) Proteins , vol.60 , Issue.2 , pp. 150-169
    • Mendez, R.1    Leplae, R.2    Lensink, M.3    Wodak, S.4
  • 33
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • Rost B, Sander C: Conservation and prediction of solvent accessibility in protein families. Proteins 1994,20(3):216-226. 10.1002/prot.340200303.
    • (1994) Proteins , vol.20 , Issue.3 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 34
    • 22444434743 scopus 로고    scopus 로고
    • Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces
    • Ben-Shimon A, Eisenstein M: Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces. J Mol Biol 2005,351(2):309-326. 10.1016/j.jmb.2005.06.047.
    • (2005) J Mol Biol , vol.351 , Issue.2 , pp. 309-326
    • Ben-Shimon, A.1    Eisenstein, M.2
  • 35
    • 80052257762 scopus 로고    scopus 로고
    • On the relationship between catalytic residues and their protein contact number
    • Huang SW, Yu SH, Shih CH, Guan HW, Huang TT, Hwang JK: On the relationship between catalytic residues and their protein contact number. Curr Protein Pept Sc 2011,12(6):574-579. 10.2174/138920311796957676.
    • (2011) Curr Protein Pept Sc , vol.12 , Issue.6 , pp. 574-579
    • Huang, S.W.1    Yu, S.H.2    Shih, C.H.3    Guan, H.W.4    Huang, T.T.5    Hwang, J.K.6
  • 36
    • 27344440132 scopus 로고    scopus 로고
    • Conservation and relative importance of residues across protein-protein interfaces
    • Guharoy M, Chakrabarti P: Conservation and relative importance of residues across protein-protein interfaces. Proc Natl Acad Sci USA 2005,102(43):15447-15452. 10.1073/pnas.0505425102.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.43 , pp. 15447-15452
    • Guharoy, M.1    Chakrabarti, P.2
  • 37
    • 79959593991 scopus 로고    scopus 로고
    • Characterization of protein-protein interaction interfaces from a single species
    • Talavera D, Robertson DL, Lovell SC: Characterization of protein-protein interaction interfaces from a single species. PLoS ONE 2011,6(6):e21053. 10.1371/journal.pone.0021053.
    • (2011) PLoS ONE , vol.6 , Issue.6 , pp. e21053
    • Talavera, D.1    Robertson, D.L.2    Lovell, S.C.3
  • 38
    • 33751076785 scopus 로고    scopus 로고
    • Cell biology: brief encounters bolster contacts
    • Blundell TL, Fernandez-Recio J: Cell biology: brief encounters bolster contacts. Nature 2006,444(7117):279-280. 10.1038/nature05306.
    • (2006) Nature , vol.444 , Issue.7117 , pp. 279-280
    • Blundell, T.L.1    Fernandez-Recio, J.2
  • 39
    • 33751086423 scopus 로고    scopus 로고
    • Visualization of transient encounter complexes in protein-protein association
    • Tang C, Iwahara J, Clore GM: Visualization of transient encounter complexes in protein-protein association. Nature 2006,444(7117):383-386. 10.1038/nature05201.
    • (2006) Nature , vol.444 , Issue.7117 , pp. 383-386
    • Tang, C.1    Iwahara, J.2    Clore, G.M.3
  • 40
    • 0016708122 scopus 로고
    • Principles of protein-protein recognition
    • Chothia C, Janin J: Principles of protein-protein recognition. Nature 1975,256(5520):705-708. 10.1038/256705a0.
    • (1975) Nature , vol.256 , Issue.5520 , pp. 705-708
    • Chothia, C.1    Janin, J.2


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