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Volumn 99, Issue 11, 2010, Pages 3704-3715

Interaction energy based protein structure networks

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EID: 78649883885     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.08.079     Document Type: Article
Times cited : (181)

References (51)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen, C. B. 1973. Principles that govern the folding of protein chains. Science (NY). 181:223-230.
    • (1973) Science (NY). , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 2
    • 9944223645 scopus 로고    scopus 로고
    • Network properties of protein structures
    • Bagler, G., and S. Sinha. 2004. Network properties of protein structures. Physica A. 346:27-33.
    • (2004) Physica A. , vol.346 , pp. 27-33
    • Bagler, G.1    Sinha, S.2
  • 3
    • 0033578690 scopus 로고    scopus 로고
    • Identification of side-chain clusters in protein structures by a graph spectral method
    • Kannan, N., and S. Vishveshwara. 1999. Identification of side-chain clusters in protein structures by a graph spectral method. J. Mol. Biol. 292:441-464.
    • (1999) J. Mol. Biol. , vol.292 , pp. 441-464
    • Kannan, N.1    Vishveshwara, S.2
  • 4
    • 28444453011 scopus 로고    scopus 로고
    • A network representation of protein structures: Implications for protein stability
    • Brinda, K. V., and S. Vishveshwara. 2005. A network representation of protein structures: implications for protein stability. Biophys. J. 89:4159-4170.
    • (2005) Biophys. J. , vol.89 , pp. 4159-4170
    • Brinda, K.V.1    Vishveshwara, S.2
  • 5
    • 33748207211 scopus 로고    scopus 로고
    • Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non-enzyme families
    • del Sol, A., H. Fujihashi, R. Nussinov. 2006. Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci. 15:2120-2128.
    • (2006) Protein Sci. , vol.15 , pp. 2120-2128
    • Del Sol, A.1    Fujihashi, H.2    Nussinov, R.3
  • 6
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • Greene, L. H., and V. A. Higman. 2003. Uncovering network systems within protein structures. J. Mol. Biol. 334:781-791.
    • (2003) J. Mol. Biol. , vol.334 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 8
    • 70350031205 scopus 로고    scopus 로고
    • Understanding protein structure from a percolation perspective
    • Deb, D., S. Vishveshwara, and S. Vishveshwara. 2009. Understanding protein structure from a percolation perspective. Biophys. J. 97:1787-1794.
    • (2009) Biophys. J. , vol.97 , pp. 1787-1794
    • Deb, D.1    Vishveshwara, S.2    Vishveshwara, S.3
  • 9
    • 55249123363 scopus 로고    scopus 로고
    • Variations in clique and community patterns in protein structures during allosteric communication: Investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes
    • Ghosh, A., and S. Vishveshwara. 2008. Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes. Biochemistry. 47:11398-11407.
    • (2008) Biochemistry. , vol.47 , pp. 11398-11407
    • Ghosh, A.1    Vishveshwara, S.2
  • 10
    • 35648944297 scopus 로고    scopus 로고
    • A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis
    • Ghosh, A., and S. Vishveshwara. 2007. A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis. Proc. Natl. Acad. Sci. USA. 104:15711-15716.
    • (2007) Proc. Natl. Acad. Sci. USA. , vol.104 , pp. 15711-15716
    • Ghosh, A.1    Vishveshwara, S.2
  • 11
    • 77952938726 scopus 로고    scopus 로고
    • Global dynamics of proteins: Bridging between structure and function
    • Bahar, I., T. R. Lezon, E. Eyal. 2010. Global dynamics of proteins: bridging between structure and function. Annu. Rev. Biophys. 39:23-42.
    • (2010) Annu. Rev. Biophys. , vol.39 , pp. 23-42
    • Bahar, I.1    Lezon, T.R.2    Eyal, E.3
  • 12
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • Atilgan, A. R., S. R. Durell, I. Bahar. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-515.
    • (2001) Biophys. J. , vol.80 , pp. 505-515
    • Atilgan, A.R.1    Durell, S.R.2    Bahar, I.3
  • 13
    • 0000496772 scopus 로고    scopus 로고
    • Vibrational dynamics of proteins: Signiicance of slow and fast modes in relation to function and stability
    • Bahar, I., A. R. Atilgan, . , B. Erman. 1998. Vibrational dynamics of proteins: signiicance of slow and fast modes in relation to function and stability. Phys. Rev. Lett. 80:2733-2736.
    • (1998) Phys. Rev. Lett. , vol.80 , pp. 2733-2736
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 14
    • 68149141470 scopus 로고    scopus 로고
    • Protein elastic network models and the ranges of cooperativity
    • Yang, L., G. Song, and R. L. Jernigan. 2009. Protein elastic network models and the ranges of cooperativity. Proc. Natl. Acad. Sci. USA. 106:12347-12352.
    • (2009) Proc. Natl. Acad. Sci. USA. , vol.106 , pp. 12347-12352
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 15
    • 36549005182 scopus 로고    scopus 로고
    • Coarse-grained biomolecular simulation with REACH: Realistic extension algorithm via covariance Hessian
    • Moritsugu, K., and J. C. Smith. 2007. Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. Biophys. J. 93:3460-3469.
    • (2007) Biophys. J. , vol.93 , pp. 3460-3469
    • Moritsugu, K.1    Smith, J.C.2
  • 16
    • 34848882812 scopus 로고    scopus 로고
    • Signal propagation in proteins and relation to equilibrium fluctuations
    • Chennubhotla, C., and I. Bahar. 2007. Signal propagation in proteins and relation to equilibrium fluctuations. PLOS Comput. Biol. 3:1716-1726.
    • (2007) PLOS Comput. Biol. , vol.3 , pp. 1716-1726
    • Chennubhotla, C.1    Bahar, I.2
  • 17
    • 33750795402 scopus 로고    scopus 로고
    • Evaluation of energetic and dynamic coupling networks in a PDZ domain protein
    • Fuentes, E. J., S. A. Gilmore, . , A. L. Lee. 2006. Evaluation of energetic and dynamic coupling networks in a PDZ domain protein. J. Mol. Biol. 364:337-351.
    • (2006) J. Mol. Biol. , vol.364 , pp. 337-351
    • Fuentes, E.J.1    Gilmor, S.A.2    Lee, A.L.3
  • 18
    • 43949129091 scopus 로고    scopus 로고
    • Energy flow in proteins
    • Leitner, D. M. 2008. Energy flow in proteins. Annu. Rev. Phys. Chem. 59:233-259.
    • (2008) Annu. Rev. Phys. Chem. , vol.59 , pp. 233-259
    • Leitner, D.M.1
  • 21
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
    • (1983) Biopolymers. , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 22
    • 65649089458 scopus 로고    scopus 로고
    • Intra and intermolecular communications through protein structure network
    • Vishveshwara, S., A. Ghosh, and P. Hansia. 2009. Intra and intermolecular communications through protein structure network. Curr. Protein Pept. Sci. 10:146-160.
    • (2009) Curr. Protein Pept. Sci. , vol.10 , pp. 146-160
    • Vishveshwara, S.1    Ghosh, A.2    Hansia, P.3
  • 23
    • 34247639886 scopus 로고    scopus 로고
    • Exploring subdomain cooperativity in T4 lysozyme II: Uncovering the C-terminal subdomain as a hidden intermediate in the kinetic folding pathway
    • Cellitti, J., R. Bernstein, and S. Marqusee. 2007. Exploring subdomain cooperativity in T4 lysozyme II: uncovering the C-terminal subdomain as a hidden intermediate in the kinetic folding pathway. Protein Sci. 16:852-862.
    • (2007) Protein Sci. , vol.16 , pp. 852-862
    • Cellitti, J.1    Bernstein, R.2    Marqusee, S.3
  • 24
    • 0031891493 scopus 로고    scopus 로고
    • Subdomain interactions as a determinant in the folding and stability of T4 lysozyme
    • Llinás, M., and S. Marqusee. 1998. Subdomain interactions as a determinant in the folding and stability of T4 lysozyme. Protein Sci. 7: 96-104.
    • (1998) Protein Sci. , vol.7 , pp. 96-104
    • Llinás, M.1    Marqusee, S.2
  • 25
    • 0033517740 scopus 로고    scopus 로고
    • Methionine and alanine substitutions show that the formation of wild-type-like structure in the carboxy-terminal domain of T4 lysozyme is a ratelimiting step in folding
    • Gassner, N. C., W. A. Baase, B. W. Matthews. 1999. Methionine and alanine substitutions show that the formation of wild-type-like structure in the carboxy-terminal domain of T4 lysozyme is a ratelimiting step in folding. Biochemistry. 38:14451-14460.
    • (1999) Biochemistry. , vol.38 , pp. 14451-14460
    • Gassner, N.C.1    Baase, W.A.2    Matthews, B.W.3
  • 26
    • 0037438594 scopus 로고    scopus 로고
    • Multiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability
    • Gassner, N. C., W. A. Baase, . , B. W. Matthews. 2003. Multiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability. Biophys. Chem. 100:325-340.
    • (2003) Biophys. Chem. , vol.100 , pp. 325-340
    • Gassner, N.C.1    Baase., W.A.2    Matthews, B.W.3
  • 27
    • 65649094471 scopus 로고    scopus 로고
    • Evaluation at atomic resolution of the role of strain in destabilizing the temperaturesensitive T4 lysozyme mutant Arg 96 → His
    • Mooers, B. H., D. E. Tronrud, and B. W. Matthews. 2009. Evaluation at atomic resolution of the role of strain in destabilizing the temperaturesensitive T4 lysozyme mutant Arg 96 → His. Protein Sci. 18:863-870.
    • (2009) Protein Sci. , vol.18 , pp. 863-870
    • Mooers, B.H.1    Tronrud, D.E.2    Matthews, B.W.3
  • 28
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: A plausible model
    • Monod, J., J. Wyman, and J. P. Changeux. 1965. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12:88-118.
    • (1965) J. Mol. Biol. , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 29
    • 0013863816 scopus 로고
    • Comparison of experimental binding data and theoretical models in proteins containing subunits
    • Koshland, Jr., D. E., G. Némethy, and D. Filmer. 1966. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry. 5:365-385.
    • (1966) Biochemistry. , vol.5 , pp. 365-385
    • Koshland Jr., D.E.1    Némethy, G.2    Filmer, D.3
  • 30
    • 0015528157 scopus 로고
    • Ligand binding and internal equilibria in proteins
    • Weber, G. 1972. Ligand binding and internal equilibria in proteins. Biochemistry. 11:864-878.
    • (1972) Biochemistry. , vol.11 , pp. 864-878
    • Weber, G.1
  • 31
    • 33745461893 scopus 로고    scopus 로고
    • Residues crucial for maintaining short paths in network communication mediate signaling in proteins
    • del Sol, A., H. Fujihashi, . , R. Nussinov. 2006. Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol. Sys. Biol. 2:0019.
    • (2006) Mol. Sys. Biol. , vol.2 , pp. 0019
    • Del Sol, A.1    Fujihashi ., H.2    Nussinov, R.3
  • 32
    • 58949102247 scopus 로고    scopus 로고
    • Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis
    • Kong, Y., and M. Karplus. 2009. Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Proteins. 74:145-154.
    • (2009) Proteins. , vol.74 , pp. 145-154
    • Kong, Y.1    Karplus, M.2
  • 33
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless, S. W., and R. Ranganathan. 1999. Evolutionarily conserved pathways of energetic connectivity in protein families. Science (NY). 286:295-299.
    • (1999) Science (NY). , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 34
    • 33749029273 scopus 로고    scopus 로고
    • Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
    • Sharp, K., and J. J. Skinner. 2006. Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Proteins. 65:347-361.
    • (2006) Proteins. , vol.65 , pp. 347-361
    • Sharp, K.1    Skinner, J.J.2
  • 35
    • 41149104308 scopus 로고    scopus 로고
    • Allostery: Absence of a change in shape does not imply that allostery is not at play
    • Tsai, C. J., A. del Sol, and R. Nussinov. 2008. Allostery: absence of a change in shape does not imply that allostery is not at play. J. Mol. Biol. 378:1-11.
    • (2008) J. Mol. Biol. , vol.378 , pp. 1-11
    • Tsai, C.J.1    Del Sol, A.2    Nussinov, R.3
  • 36
    • 48249141040 scopus 로고    scopus 로고
    • Allostery and cooperativity revisited
    • Cui, Q., and M. Karplus. 2008. Allostery and cooperativity revisited. Protein Sci. 17:1295-1307.
    • (2008) Protein Sci. , vol.17 , pp. 1295-1307
    • Cui, Q.1    Karplus, M.2
  • 37
    • 70450228871 scopus 로고    scopus 로고
    • Long-range energy transfer in proteins
    • Piazza, F., and Y. H. Sanejouand. 2009. Long-range energy transfer in proteins. Phys. Biol. 6:046014.
    • (2009) Phys. Biol. , vol.6 , pp. 046014
    • Piazza, F.1    Sanejouand, Y.H.2
  • 38
    • 27744493897 scopus 로고    scopus 로고
    • Structural observation of the primary isomerization in vision with femtosecondstimulated Raman
    • Kukura, P., D. W. McCamant, . , R. A. Mathies. 2005. Structural observation of the primary isomerization in vision with femtosecondstimulated Raman. Science (NY). 310:1006-1009.
    • (2005) Science (NY). , vol.310 , pp. 1006-1009
    • Kukura, P.1    McCamant ., D.W.2    Mathies, R.A.3
  • 39
    • 68049093193 scopus 로고    scopus 로고
    • Direct observation of the dynamic process underlying allosteric signal transmission
    • Brüschweiler, S., P. Schanda, M. Tollinger. 2009. Direct observation of the dynamic process underlying allosteric signal transmission. J. Am. Chem. Soc. 131:3063-3068.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 3063-3068
    • Brüschweiler, S.1    Schanda, P.2    Tollinger, M.3
  • 40
    • 23244447873 scopus 로고    scopus 로고
    • Functional dynamics of PDZ binding domains: A normal-mode analysis
    • De Los Rios, P., F. Cecconi, . , B. Juanico. 2005. Functional dynamics of PDZ binding domains: a normal-mode analysis. Biophys. J. 89: 14-21.
    • (2005) Biophys. J. , vol.89 , pp. 14-21
    • De Los Rios, P.1    Cecconi ., F.2    Juanico, B.3
  • 41
    • 68149157248 scopus 로고    scopus 로고
    • The origin of allosteric functional modulation: Multiple pre-existing pathways
    • del Sol, A., C. J. Tsai, . , R. Nussinov. 2009. The origin of allosteric functional modulation: multiple pre-existing pathways. Structure. 17:1042-1050.
    • (2009) Structure. , vol.17 , pp. 1042-1050
    • Del Sol, A.1    Tsai, C.J.2    Nussinov, R.3
  • 42
    • 0347753736 scopus 로고    scopus 로고
    • Ligand-dependent dynamics and intramolecular signaling in a PDZ domain
    • Fuentes, E. J., C. J. Der, and A. L. Lee. 2004. Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. J. Mol. Biol. 335:1105-1115.
    • (2004) J. Mol. Biol. , vol.335 , pp. 1105-1115
    • Fuentes, E.J.1    Der, C.J.2    Lee, A.L.3
  • 43
    • 0028081650 scopus 로고
    • Genetic analysis of bacteriophage T4 lysozyme structure and function
    • Poteete, A. R., and L. W. Hardy. 1994. Genetic analysis of bacteriophage T4 lysozyme structure and function. J. Bacteriol. 176: 6783-6788.
    • (1994) J. Bacteriol. , vol.176 , pp. 6783-6788
    • Poteete, A.R.1    Hardy, L.W.2
  • 44
    • 0036708444 scopus 로고    scopus 로고
    • Electrostatic contributions to T4 lysozyme stability: Solvent-exposed charges versus semi-buried salt bridges
    • Dong, F., and H. X. Zhou. 2002. Electrostatic contributions to T4 lysozyme stability: solvent-exposed charges versus semi-buried salt bridges. Biophys. J. 83:1341-1347.
    • (2002) Biophys. J. , vol.83 , pp. 1341-1347
    • Dong, F.1    Zhou, H.X.2
  • 45
    • 0030671578 scopus 로고    scopus 로고
    • Alteration of T4 lysozyme structure by second-site reversion of deleterious mutations
    • Poteete, A. R., D. Rennell, L. W. Hardy. 1997. Alteration of T4 lysozyme structure by second-site reversion of deleterious mutations. Protein Sci. 6:2418-2425.
    • (1997) Protein Sci. , vol.6 , pp. 2418-2425
    • Poteete, A.R.1    Rennell, D.2    Hardy, L.W.3
  • 46
    • 0031893269 scopus 로고    scopus 로고
    • The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect
    • Xu, J., W. A. Baase, B. W. Matthews. 1998. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Protein Sci. 7:158-177.
    • (1998) Protein Sci. , vol.7 , pp. 158-177
    • Xu, J.1    Baase, W.A.2    Matthews, B.W.3
  • 47
    • 0037083363 scopus 로고    scopus 로고
    • Essential domain motions in barnase revealed by MD simulations
    • Nolde, S. B., A. S. Arseniev, M. Billeter. 2002. Essential domain motions in barnase revealed by MD simulations. Proteins. 46:250-258.
    • (2002) Proteins. , vol.46 , pp. 250-258
    • Nolde, S.B.1    Arseniev, A.S.2    Billeter, M.3
  • 49
    • 0033560065 scopus 로고    scopus 로고
    • PDZ domains: Fundamental building blocks in the organization of protein complexes at the plasma membrane
    • Fanning, A. S., and J. M. Anderson. 1999. PDZ domains: fundamental building blocks in the organization of protein complexes at the plasma membrane. J. Clin. Invest. 103:767-772.
    • (1999) J. Clin. Invest. , vol.103 , pp. 767-772
    • Fanning, A.S.1    Anderson, J.M.2
  • 50
    • 0036300569 scopus 로고    scopus 로고
    • Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL
    • Walma, T., C. A. Spronk, G. W. Vuister. 2002. Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL. J. Mol. Biol. 316:1101-1110.
    • (2002) J. Mol. Biol. , vol.316 , pp. 1101-1110
    • Walma, T.1    Spronk, C.A.2    Vuister, G.W.3
  • 51
    • 22444450449 scopus 로고    scopus 로고
    • Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
    • Ota, N., and D. A. Agard. 2005. Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J. Mol. Biol. 351:345-354.
    • (2005) J. Mol. Biol. , vol.351 , pp. 345-354
    • Ota, N.1    Agard, D.A.2


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