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Volumn 86, Issue 1 I, 2004, Pages 85-91

Small-World Communication of Residues and Significance for Protein Dynamics

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; MOLECULAR DYNAMICS; MOLECULAR SIZE; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN STABILITY;

EID: 0346057951     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74086-2     Document Type: Article
Times cited : (286)

References (44)
  • 4
    • 0012015514 scopus 로고    scopus 로고
    • How much sequence variation can the functions of biological molecules tolerate?
    • H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors. Dahlem University Press, Berlin, Germany
    • Baase, W. A., N. C. Gassner, X.-J. Zhang, R. Kuroki, L. H. Weaver, D. E. Tronrud, and B. W. Matthews. 1999. How much sequence variation can the functions of biological molecules tolerate? In Simplicity and Complexity in Proteins and Nucleic Acid. H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors. Dahlem University Press, Berlin, Germany.
    • (1999) Simplicity and Complexity in Proteins and Nucleic Acid
    • Baase, W.A.1    Gassner, N.C.2    Zhang, X.-J.3    Kuroki, R.4    Weaver, L.H.5    Tronrud, D.E.6    Matthews, B.W.7
  • 5
    • 0036470527 scopus 로고    scopus 로고
    • Residue packing in proteins: Uniform distribution on a coarse-grained scale
    • Bagci, Z., R. L. Jernigan, and I. Bahar. 2002. Residue packing in proteins: uniform distribution on a coarse-grained scale. J. Chem. Phys. 116:2269-2276.
    • (2002) J. Chem. Phys. , vol.116 , pp. 2269-2276
    • Bagci, Z.1    Jernigan, R.L.2    Bahar, I.3
  • 6
    • 0000496772 scopus 로고    scopus 로고
    • Vibrational dynamics of folded proteins: Significance of slow and fast modes in relation to function and stability
    • Bahar, I., A. R. Atilgan, M. C. Demirel, and B. Erman. 1998a. Vibrational dynamics of folded proteins: significance 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    Demirel, M.C.3    Erman, B.4
  • 7
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential
    • Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential. Fold. Des. 2:173-181.
    • (1997) Fold. Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 8
    • 3342877839 scopus 로고    scopus 로고
    • Collective dynamics of Hiv-1 reverse transcriptase: Examination of flexibility and enzyme function
    • Bahar, I., B. Erman, R. L. Jernigan, A. R. Atilgan, and D. G. Covell. 1999. Collective dynamics of Hiv-1 reverse transcriptase: examination of flexibility and enzyme function. J. Mol. Biol. 285:1023-1037.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1023-1037
    • Bahar, I.1    Erman, B.2    Jernigan, R.L.3    Atilgan, A.R.4    Covell, D.G.5
  • 9
    • 0032570266 scopus 로고    scopus 로고
    • Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model
    • Bahar, I., A. Wallqvist, D. G. Covell, and R. L. Jernigan. 1998b. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry. 37:1067-1075.
    • (1998) Biochemistry , vol.37 , pp. 1067-1075
    • Bahar, I.1    Wallqvist, A.2    Covell, D.G.3    Jernigan, R.L.4
  • 10
    • 0035479570 scopus 로고    scopus 로고
    • Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2
    • Baysal, C., and A. R. Atilgan. 2001a. Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2. Proteins. 45:62-70.
    • (2001) Proteins , vol.45 , pp. 62-70
    • Baysal, C.1    Atilgan, A.R.2
  • 11
    • 0035342460 scopus 로고    scopus 로고
    • Elucidating the structural mechanisms for biological activity of the chemokine family
    • Baysal, C., and A. R. Atilgan. 2001b. Elucidating the structural mechanisms for biological activity of the chemokine family. Proteins. 43:150-160.
    • (2001) Proteins , vol.43 , pp. 150-160
    • Baysal, C.1    Atilgan, A.R.2
  • 12
    • 0035996982 scopus 로고    scopus 로고
    • Relaxation kinetics and the glassiness of proteins: The case of bovine pancreatic trypsin inhibitor
    • Baysal, C., and A. R, Atilgan. 2002. Relaxation kinetics and the glassiness of proteins: the case of bovine pancreatic trypsin inhibitor. Biophys. J. 83:699-705.
    • (2002) Biophys. J. , vol.83 , pp. 699-705
    • Baysal, C.1    Atilgan, A.R.2
  • 14
    • 0000188718 scopus 로고    scopus 로고
    • Highly optimized tolerance: Robustness and design in complex systems
    • Carlson, J. M., and J. Doyle. 2000. Highly optimized tolerance: robustness and design in complex systems. Phys. Rev. Lett. 84:2529-2532.
    • (2000) Phys. Rev. Lett. , vol.84 , pp. 2529-2532
    • Carlson, J.M.1    Doyle, J.2
  • 15
    • 0033565815 scopus 로고    scopus 로고
    • Residue depth: A novel parameter for the analysis of protein structure and stability
    • Chakravarty, S., and R. Varadarajan. 1999. Residue depth: a novel parameter for the analysis of protein structure and stability. Structure. 7:723-732.
    • (1999) Structure , vol.7 , pp. 723-732
    • Chakravarty, S.1    Varadarajan, R.2
  • 16
    • 4243206713 scopus 로고    scopus 로고
    • Emergence of a small world from local interactions: Modeling acquaintance networks
    • Davidsen, J., H. Ebel, and S. Bornholdt. 2002. Emergence of a small world from local interactions: modeling acquaintance networks. Phys. Rev. Lett. 88:128701.
    • (2002) Phys. Rev. Lett. , vol.88 , pp. 128701
    • Davidsen, J.1    Ebel, H.2    Bornholdt, S.3
  • 17
    • 0029558960 scopus 로고
    • Conformational pathway of the polypeptide chain of chymotrypsin inhibitor-2 growing from its n terminus in vitro. Parallels with the protein folding pathway
    • de Prat Gay, G., J. Ruiz-Sanz, J. L. Neira, F. J. Corrales, D. E. Otzen, A. G. Ladurner, and A. R. Fersht. 1995. Conformational pathway of the polypeptide chain of chymotrypsin inhibitor-2 growing from its n terminus in vitro. Parallels with the protein folding pathway. J. Mol. Biol. 254:968-979.
    • (1995) J. Mol. Biol. , vol.254 , pp. 968-979
    • De Prat Gay, G.1    Ruiz-Sanz, J.2    Neira, J.L.3    Corrales, F.J.4    Otzen, D.E.5    Ladurner, A.G.6    Fersht, A.R.7
  • 19
    • 0033047710 scopus 로고    scopus 로고
    • A neural network based predictor of residue contacts in proteins
    • Fariselli, P., and R. Casadio. 1999. A neural network based predictor of residue contacts in proteins. Protein Eng, 12:15-21.
    • (1999) Protein Eng. , vol.12 , pp. 15-21
    • Fariselli, P.1    Casadio, R.2
  • 20
    • 0034652206 scopus 로고    scopus 로고
    • Transition-state structure as a unifying basis in protein folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
    • Fersht, A. R. 2000. Transition-state structure as a unifying basis in protein folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. Proc. Natl. Acad. Sci. USA. 97:1525-1529.
    • (2000) Proc. Natl. Acad. Sci. USA. , vol.97 , pp. 1525-1529
    • Fersht, A.R.1
  • 21
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong, H., S. P. Mason, A.-L. Barabasi, and Z. N. Oltvai. 2001. Lethality and centrality in protein networks. Nature. 411:41-42.
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.-L.3    Oltvai, Z.N.4
  • 22
    • 0035996975 scopus 로고    scopus 로고
    • Relating molecular flexibility to function: A case study of tubulin
    • Keskin, O., S. R. Durell, I. Bahar, R. L. Jernigan, and D. G. Covell. 2002. Relating molecular flexibility to function: a case study of tubulin. Biophys. J. 83:663-680.
    • (2002) Biophys. J. , vol.83 , pp. 663-680
    • Keskin, O.1    Durell, S.R.2    Bahar, I.3    Jernigan, R.L.4    Covell, D.G.5
  • 24
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar, S., B. Ma, C.-J. Tsai, N. Sinha, and R. Nussinov. 2000. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9:10-19.
    • (2000) Protein Sci. , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.-J.3    Sinha, N.4    Nussinov, R.5
  • 25
    • 0034901412 scopus 로고    scopus 로고
    • Are proteins well packed?
    • Liang, J., and K. A. Dill. 2001. Are proteins well packed? Biophys. J. 81:751-766.
    • (2001) Biophys. J. , vol.81 , pp. 751-766
    • Liang, J.1    Dill, K.A.2
  • 26
    • 0000818624 scopus 로고
    • Crystal and molecular structure of chymotrypsin inhibitor 2 from barley seeds in complex with subtilisin novo
    • McPhalen, C. A., I. Svendsen, I. Jonassen, and M. N. G. James. 1985. Crystal and molecular structure of chymotrypsin inhibitor 2 from barley seeds in complex with subtilisin novo. Proc. Natl. Acad. Sci. USA. 82:7242-7246.
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 7242-7246
    • McPhalen, C.A.1    Svendsen, I.2    Jonassen, I.3    James, M.N.G.4
  • 27
    • 0037422581 scopus 로고    scopus 로고
    • Substructure synthesis method for simulation large molecular complexes
    • Ming, D., Y. Kong, Y. Wu, and J. Ma. 2003. Substructure synthesis method for simulation large molecular complexes. Proc. Natl. Acad. Sci. USA. 100:104-109.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 104-109
    • Ming, D.1    Kong, Y.2    Wu, Y.3    Ma, J.4
  • 28
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa, S., and R. L. Jernigan. 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256:623-644.
    • (1996) J. Mol. Biol. , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 29
    • 0034310033 scopus 로고    scopus 로고
    • Models of the small world
    • Newman, M. E. J. 2000. Models of the small world. J. Stat. Phys. 101:819-841.
    • (2000) J. Stat. Phys. , vol.101 , pp. 819-841
    • Newman, M.E.J.1
  • 30
    • 0037043004 scopus 로고    scopus 로고
    • Optimal design, robustness, and risk aversion
    • Newman, M. E. J., M. Girvan, and J. D. Farmer. 2002. Optimal design, robustness, and risk aversion. Phys. Rev. Lett. 89:028301.
    • (2002) Phys. Rev. Lett. , vol.89 , pp. 028301
    • Newman, M.E.J.1    Girvan, M.2    Farmer, J.D.3
  • 31
    • 0035420732 scopus 로고    scopus 로고
    • Random graphs with arbitrary degree distributions and their applications
    • Newman, M. E. J., S. H. Strogatz, and D. J. Watts. 2001. Random graphs with arbitrary degree distributions and their applications. Phys. Rev. E 64:026118.
    • (2001) Phys. Rev. E , vol.64 , pp. 026118
    • Newman, M.E.J.1    Strogatz, S.H.2    Watts, D.J.3
  • 32
    • 0037133342 scopus 로고    scopus 로고
    • Biological water at the protein surface: Dynamical solvation probed directly with femtosecond resolution
    • Pal, S. K., J. Peon, and A. H. Zewail. 2002. Biological water at the protein surface: dynamical solvation probed directly with femtosecond resolution. Proc. Natl. Acad. Sci. USA. 99:1763-1768.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1763-1768
    • Pal, S.K.1    Peon, J.2    Zewail, A.H.3
  • 33
    • 0030850226 scopus 로고    scopus 로고
    • Ideal architecture of residue packing and its observation in protein structures
    • Raghunathan, G., and R. Jernigan. 1997. Ideal architecture of residue packing and its observation in protein structures. Protein Sci. 6:2072-2083.
    • (1997) Protein Sci. , vol.6 , pp. 2072-2083
    • Raghunathan, G.1    Jernigan, R.2
  • 34
    • 0034287449 scopus 로고    scopus 로고
    • Voronoi tessellation reveals the condensed matter character of folded proteins
    • Soyer, A., J. Chomilier, J.-P. Mornon, R. Jullien, and J.-F. Sadoc. 2000. Voronoi tessellation reveals the condensed matter character of folded proteins. Phys. Rev. Lett. 85:3532-3535.
    • (2000) Phys. Rev. Lett. , vol.85 , pp. 3532-3535
    • Soyer, A.1    Chomilier, J.2    Mornon, J.-P.3    Jullien, R.4    Sadoc, J.-F.5
  • 35
    • 0035826155 scopus 로고    scopus 로고
    • Exploring complex networks
    • Strogatz, S. H. 2001. Exploring complex networks. Nature. 410:268-276.
    • (2001) Nature , vol.410 , pp. 268-276
    • Strogatz, S.H.1
  • 36
    • 0033747018 scopus 로고    scopus 로고
    • Molecular dynamics of solid-state lysozyme as affected by glycerol and water: A neutron scattering study
    • Tsai, A. M., D. A. Neumann, and L. N. Bell. 2000. Molecular dynamics of solid-state lysozyme as affected by glycerol and water: a neutron scattering study. Biophys. J. 79:2728-2732.
    • (2000) Biophys. J. , vol.79 , pp. 2728-2732
    • Tsai, A.M.1    Neumann, D.A.2    Bell, L.N.3
  • 37
    • 0036084260 scopus 로고    scopus 로고
    • Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins
    • Tsai, C.-J., P. P. de Laureto, A. Fontana, and R. Nussinov. 2002. Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins. Protein Sci. 11:1753-1770.
    • (2002) Protein Sci. , vol.11 , pp. 1753-1770
    • Tsai, C.-J.1    De Laureto, P.P.2    Fontana, A.3    Nussinov, R.4
  • 38
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: Shifts in energy landscapes
    • Tsai, C.-J., B. Ma, and R. Nussinov. 1999. Folding and binding cascades: shifts in energy landscapes. Proc. Natl. Acad. Sci. USA. 96:9970-9972.
    • (1999) Proc. Natl. Acad. Sci. USA. , vol.96 , pp. 9970-9972
    • Tsai, C.-J.1    Ma, B.2    Nussinov, R.3
  • 39
    • 41349118690 scopus 로고    scopus 로고
    • Small-world view of the amino acids that play a key role in protein folding
    • Vendruscolo, M., N. V. Dokholyan, E. Paci, and M. Karplus. 2002. Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E 65:061910.
    • (2002) Phys. Rev. E , vol.65 , pp. 061910
    • Vendruscolo, M.1    Dokholyan, N.V.2    Paci, E.3    Karplus, M.4
  • 40
    • 0004081447 scopus 로고    scopus 로고
    • Princeton University Press, Princeton, NJ
    • Watts, D. J. 1999. Small Worlds. Princeton University Press, Princeton, NJ.
    • (1999) Small Worlds
    • Watts, D.J.1
  • 41
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of "small-world" networks
    • Watts, D. J., and S. H. Strogatz. 1998. Collective dynamics of "small-world" networks. Nature. 393:440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 42
    • 0031021778 scopus 로고    scopus 로고
    • Entropy difference between the face-centered cubic and hexagonal close-packed structures
    • Woodcock, L. V. 1997. Entropy difference between the face-centered cubic and hexagonal close-packed structures. Nature. 385:141-143.
    • (1997) Nature , vol.385 , pp. 141-143
    • Woodcock, L.V.1
  • 43
    • 0034622725 scopus 로고    scopus 로고
    • Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts
    • Yilmaz, L. S., and A. R. Atilgan. 2000. Identifying the adaptive mechanism in globular proteins: fluctuations in densely packed regions manipulate flexible parts. J. Chem. Phys. 113:4454-4464.
    • (2000) J. Chem. Phys. , vol.113 , pp. 4454-4464
    • Yilmaz, L.S.1    Atilgan, A.R.2
  • 44
    • 0034595671 scopus 로고    scopus 로고
    • How soft is a protein? A protein dynamics force constant measured by neutron scattering
    • Zaccai, G. 2000. How soft is a protein? A protein dynamics force constant measured by neutron scattering. Science. 288:1604-1607.
    • (2000) Science , vol.288 , pp. 1604-1607
    • Zaccai, G.1


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