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Volumn 39, Issue 7, 2010, Pages 1051-1056

Temperature dependence of fluctuations in HIV1-protease

Author keywords

Elastic network models; HIV1 protease; Molecular dynamics; Self consistent pair contact probability method; Statistical mechanics

Indexed keywords

P16 PROTEASE, HUMAN IMMUNODEFICIENCY VIRUS 1; PROTEINASE;

EID: 77955271658     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-009-0443-z     Document Type: Conference Paper
Times cited : (5)

References (46)
  • 1
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • Atilgan A, Durrell S, Jernigan R, Demirel M, Keskin O, Bahar I (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.1    Durrell, S.2    Jernigan, R.3    Demirel, M.4    Keskin, O.5    Bahar, I.6
  • 2
    • 0032483483 scopus 로고    scopus 로고
    • Vibrational dynamics of transfer RNAs. Comparison of the free and enzyme-bound forms
    • Bahar I, Jernigan RL (1998) Vibrational dynamics of transfer RNAs. Comparison of the free and enzyme-bound forms. J Mol Biol 281:871-884
    • (1998) J Mol Biol , vol.281 , pp. 871-884
    • Bahar, I.1    Jernigan, R.L.2
  • 3
    • 0033596908 scopus 로고    scopus 로고
    • Cooperative fluctuations and subunit communication in tryptophan synthase
    • Bahar I, Jernigan R (1999) Cooperative fluctuations and subunit communication in tryptophan synthase. Biochemistry 38:3478-3490
    • (1999) Biochemistry , vol.38 , pp. 3478-3490
    • Bahar, I.1    Jernigan, R.2
  • 4
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in protein using a single parameter harmonic potential
    • Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in protein 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
  • 5
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
    • Brooks B, Karplus M (1983) Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Nat Acad Sci 80:6571-6575
    • (1983) Proc Nat Acad Sci , vol.80 , pp. 6571-6575
    • Brooks, B.1    Karplus, M.2
  • 6
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. methodology
    • Brooks B, Janezic D, Karplus M (1995) Harmonic analysis of large systems. I. methodology. J Comp Chem 16(12):1522-1542
    • (1995) J Comp Chem , vol.16 , Issue.12 , pp. 1522-1542
    • Brooks, B.1    Janezic, D.2    Karplus, M.3
  • 7
    • 0036904038 scopus 로고    scopus 로고
    • Changes in flexbility upon binding: Application of the self-consistent pair contact probability method to protein-protein-interaction
    • Canino L, Shen T, McCammon JA (2002) Changes in flexbility upon binding: application of the self-consistent pair contact probability method to protein-protein-interaction. J Chem Phys 117(21):9927-9933
    • (2002) J Chem Phys , vol.117 , Issue.21 , pp. 9927-9933
    • Canino, L.1    Shen, T.2    McCammon, J.A.3
  • 8
    • 12144268244 scopus 로고    scopus 로고
    • Protein interactions and fluctuations in a proteomic network using an elastic network model
    • Demirel MC, Keskin O (2005) Protein interactions and fluctuations in a proteomic network using an elastic network model. J Biomol Struct Dyn 22(4):381-386
    • (2005) J Biomol Struct Dyn , vol.22 , Issue.4 , pp. 381-386
    • Demirel, M.C.1    Keskin, O.2
  • 9
    • 48749126860 scopus 로고    scopus 로고
    • Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking
    • Dobbins SE, Lesk VI, Sternberg MJE (2008) Insights into protein flexibility: the relationship between normal modes and conformational change upon protein-protein docking. Proc Natl Acad Sci 105(30):10,390-10,395
    • (2008) Proc Natl Acad Sci , vol.105 , Issue.30 , pp. 10390-10395
    • Dobbins, S.E.1    Lesk, V.I.2    Sternberg, M.J.E.3
  • 10
    • 38949151546 scopus 로고    scopus 로고
    • Molecular simulations of protein dynamics: New windows on mechanisms in biology
    • Dodson GG, Lane DP, Verma CS (2008) Molecular simulations of protein dynamics: new windows on mechanisms in biology. EMBO Rep 9(2):144-150
    • (2008) EMBO Rep , vol.9 , Issue.2 , pp. 144-150
    • Dodson, G.G.1    Lane, D.P.2    Verma, C.S.3
  • 11
    • 0034663710 scopus 로고    scopus 로고
    • Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to a-amylase inhibitor
    • Doruker P, Atilgan AR, Bahar I (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to a-amylase inhibitor. Proteins Struct Func Genet 40:512-524
    • (2000) Proteins Struct Func Genet , vol.40 , pp. 512-524
    • Doruker, P.1    Atilgan, A.R.2    Bahar, I.3
  • 12
    • 0037108176 scopus 로고    scopus 로고
    • Important fluctuation dynamics of large protein structures are preserved upon coarse-grained renormalization
    • Doruker P et al (2002) Important fluctuation dynamics of large protein structures are preserved upon coarse-grained renormalization. Int J Quantum Chem 90(2):822-837
    • (2002) Int J Quantum Chem , vol.90 , Issue.2 , pp. 822-837
    • Doruker, P.1
  • 13
    • 33751225684 scopus 로고    scopus 로고
    • The gaussian network model: Precise prediction of residue fluctuations and application to binding problems
    • Erman B (2006) The gaussian network model: precise prediction of residue fluctuations and application to binding problems. Biophys J 91(10):3589-3599
    • (2006) Biophys J , vol.91 , Issue.10 , pp. 3589-3599
    • Erman, B.1
  • 14
    • 43649085777 scopus 로고    scopus 로고
    • Toward a molecular understanding of the anisotropic response of proteins to external forces: Insights from elastic network models
    • Eyal E, Bahar I (2008) Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models. Biophys J 94:3424-3435
    • (2008) Biophys J , vol.94 , pp. 3424-3435
    • Eyal, E.1    Bahar, I.2
  • 15
    • 0004236492 scopus 로고    scopus 로고
    • 3rd edn. The Johns Hopkins University Press, Baltimore
    • Golub GH, Loan CFV (1996) Matrix Computations, 3rd edn. The Johns Hopkins University Press, Baltimore
    • (1996) Matrix Computations
    • Golub, G.H.1    Loan, C.F.V.2
  • 16
    • 44949215646 scopus 로고    scopus 로고
    • Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model
    • Haliloglu T, Seyrek E, Erman B (2008) Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model. Phys Rev Lett 100:228102
    • (2008) Phys Rev Lett , vol.100 , pp. 228102
    • Haliloglu, T.1    Seyrek, E.2    Erman, B.3
  • 17
    • 19944381505 scopus 로고    scopus 로고
    • On stochastic global optimization of onedimensional functions
    • Hamacher K (2005) On stochastic global optimization of onedimensional functions. Physica A 354:547-557
    • (2005) Physica A , vol.354 , pp. 547-557
    • Hamacher, K.1
  • 18
    • 33745667530 scopus 로고    scopus 로고
    • Adaptation in stochastic tunneling global optimization of complex potential energy landscapes
    • Hamacher K (2006) Adaptation in stochastic tunneling global optimization of complex potential energy landscapes. Europhys Lett 74(6):944-950
    • (2006) Europhys Lett , vol.74 , Issue.6 , pp. 944-950
    • Hamacher, K.1
  • 19
    • 35948976625 scopus 로고    scopus 로고
    • Information theoretical measures to analyze trajectories in rational molecular design
    • Hamacher K (2007) Information theoretical measures to analyze trajectories in rational molecular design. J Comp Chem 28(16):2576-2580
    • (2007) J Comp Chem , vol.28 , Issue.16 , pp. 2576-2580
    • Hamacher, K.1
  • 20
    • 49049087284 scopus 로고    scopus 로고
    • Relating sequence evolution of HIV1-protease to its underlying molecular mechanics
    • Hamacher K (2008) Relating sequence evolution of HIV1-protease to its underlying molecular mechanics. Gene 422:30-36
    • (2008) Gene , vol.422 , pp. 30-36
    • Hamacher, K.1
  • 21
    • 33846247964 scopus 로고    scopus 로고
    • Computing the amino acid specificity of fluctuations in biomolecular systems
    • Hamacher K, McCammon JA (2006) Computing the amino acid specificity of fluctuations in biomolecular systems. J Chem Theory Comput 2(3):873-878
    • (2006) J Chem Theory Comput , vol.2 , Issue.3 , pp. 873-878
    • Hamacher, K.1    McCammon, J.A.2
  • 22
    • 4244100012 scopus 로고    scopus 로고
    • The scaling behaviour of stochastic minimization algorithms in a perfect funnel landscape
    • Hamacher K, Wenzel W (1999) The scaling behaviour of stochastic minimization algorithms in a perfect funnel landscape. Phys Rev E 59(1):938-941
    • (1999) Phys Rev E , vol.59 , Issue.1 , pp. 938-941
    • Hamacher, K.1    Wenzel, W.2
  • 23
    • 33749047118 scopus 로고    scopus 로고
    • A minimal model for stabilization of biomolecules by hydrocarbon cross-linking
    • Hamacher K, Hübsch A, McCammon JA (2006a) A minimal model for stabilization of biomolecules by hydrocarbon cross-linking. J Chem Phys 124(16):164907
    • (2006) J Chem Phys , vol.124 , Issue.16 , pp. 164907
    • Hamacher, K.1    Hübsch, A.2    McCammon, J.A.3
  • 24
  • 25
    • 50149091918 scopus 로고    scopus 로고
    • Analysis of ligand binding to proteins using molecular dynamics simulations
    • Housaindokht M, Bozorgmehr M, Bahrololoom M (2008) Analysis of ligand binding to proteins using molecular dynamics simulations. J Theo Biol 254(2):294-300
    • (2008) J Theo Biol , vol.254 , Issue.2 , pp. 294-300
    • Housaindokht, M.1    Bozorgmehr, M.2    Bahrololoom, M.3
  • 27
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M, McCammon J (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9(9):646-52
    • (2002) Nat Struct Biol , vol.9 , Issue.9 , pp. 646-52
    • Karplus, M.1    McCammon, J.2
  • 28
    • 0034029144 scopus 로고    scopus 로고
    • Proteins with similar architecture exhibit similar large-scale dynamic behavior
    • http://www.biophysj.org/cgi/reprint/78/4/2093.pdf
    • Keskin O, Jernigan RL, Bahar I (2000) Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic Behavior. Biophys J 78(4):2093-2106, URL http://www.biophysj.org/ cgi/content/abstract/78/4/2093, http://www.biophysj. org/cgi/ reprint/78/4/2093.pdf
    • (2000) Biophys J , vol.78 , Issue.4 , pp. 2093-2106
    • Keskin, O.1    Jernigan, R.L.2    Bahar, I.3
  • 29
    • 0035996975 scopus 로고    scopus 로고
    • Relating molecular flexibility to function: A case study of tubulin
    • Keskin O, Durell S, Bahar I, Jernigan R, Covell D (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.2    Bahar, I.3    Jernigan, R.4    Covell, D.5
  • 30
    • 0033117937 scopus 로고    scopus 로고
    • Investigating protein dynamics in collective coordinate space
    • Kitao A, Go N (1999) Investigating protein dynamics in collective coordinate space. Curr Op Struct Biol 9:164-169
    • (1999) Curr Op Struct Biol , vol.9 , pp. 164-169
    • Kitao, A.1    Go, N.2
  • 31
    • 0037963159 scopus 로고    scopus 로고
    • Cooperative fluctuations of unliganded and substrate-bound HIV-1-protease: A structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations
    • Kurt N, Scott W, Schiffer C, Haliloglu T (2003) Cooperative fluctuations of unliganded and substrate-bound HIV-1-protease: A structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations. Proteins Struct Func Genet 51:409-422
    • (2003) Proteins Struct Func Genet , vol.51 , pp. 409-422
    • Kurt, N.1    Scott, W.2    Schiffer, C.3    Haliloglu, T.4
  • 32
    • 0036890285 scopus 로고    scopus 로고
    • Binding affinity and specifity from computational studies
    • Lazaridis T (2002) Binding affinity and specifity from computational studies. Curr Org Chem 6:1319-1332
    • (2002) Curr Org Chem , vol.6 , pp. 1319-1332
    • Lazaridis, T.1
  • 34
    • 55749115445 scopus 로고    scopus 로고
    • A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography
    • Lu M, Ma J (2008) A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography. Proc Natl Acad Sci 105(40):15358-15363
    • (2008) Proc Natl Acad Sci , vol.105 , Issue.40 , pp. 15358-15363
    • Lu, M.1    Ma, J.2
  • 35
    • 0035920986 scopus 로고    scopus 로고
    • Conformations of proteins in equilibrium
    • Micheletti C, Banavar JR, Maritan A (2001) Conformations of proteins in equilibrium. Phys Rev Lett 87(8):088102-1
    • (2001) Phys Rev Lett , vol.87 , Issue.8 , pp. 088102-1
    • Micheletti, C.1    Banavar, J.R.2    Maritan, A.3
  • 36
    • 0036073320 scopus 로고    scopus 로고
    • Crucial stages of protein folding through a solvable model: Prediciting target sites for enzyme-inhibiting drugs
    • Micheletti C, Cecconi F, Flammini A, Maritan A (2002) Crucial stages of protein folding through a solvable model: prediciting target sites for enzyme-inhibiting drugs. Prot Sci 11:1878-1887
    • (2002) Prot Sci , vol.11 , pp. 1878-1887
    • Micheletti, C.1    Cecconi, F.2    Flammini, A.3    Maritan, A.4
  • 37
    • 2442543557 scopus 로고    scopus 로고
    • Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and gaussian models
    • Micheletti C, Carloni P, Maritan A (2004) Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and gaussian models. Proteins 55:635
    • (2004) Proteins , vol.55 , pp. 635
    • Micheletti, C.1    Carloni, P.2    Maritan, A.3
  • 38
    • 1842454635 scopus 로고    scopus 로고
    • HIV-1-protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs
    • Perryman A, Lin JH, McCammon J (2004) HIV-1-protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Prot Sci 13:1108-1123
    • (2004) Prot Sci , vol.13 , pp. 1108-1123
    • Perryman, A.1    Lin, J.H.2    McCammon, J.3
  • 39
    • 77955661514 scopus 로고
    • Numerical recipes in C. Cambridge University Press, Cambridge
    • Press WH et al (1995) Numerical recipes in C. Cambridge University Press, Cambridge
    • (1995)
    • Press, W.H.1
  • 40
    • 0037046143 scopus 로고    scopus 로고
    • Anisotropic dynamics of the je-2147-HIV protease complex: Drug resistance and thermodynamic binding mode examined in a 1.09 a structure
    • Reiling K, Endres N, Dauber D, Craik C, Stroud R (2002) Anisotropic dynamics of the je-2147-HIV protease complex: drug resistance and thermodynamic binding mode examined in a 1.09 a structure. Biochemistry 41:4582
    • (2002) Biochemistry , vol.41 , pp. 4582
    • Reiling, K.1    Endres, N.2    Dauber, D.3    Craik, C.4    Stroud, R.5
  • 41
    • 0023863112 scopus 로고
    • The normal modes of the gramicidin-A dimer channel
    • Roux B, Karplus M (1988) The normal modes of the gramicidin-A dimer channel. Biophys J 53(3):297-309
    • (1988) Biophys J , vol.53 , Issue.3 , pp. 297-309
    • Roux, B.1    Karplus, M.2
  • 42
    • 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
    • Sen TZ, Fend Y, Garcia JV, Kolczkowski A, Jernigan RL (2006) The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. J Chem Theo Comp 2(3):696-704
    • (2006) J Chem Theo Comp , vol.2 , Issue.3 , pp. 696-704
    • Sen, T.Z.1    Fend, Y.2    Garcia, J.V.3    Kolczkowski, A.4    Jernigan, R.L.5
  • 43
    • 48949119100 scopus 로고    scopus 로고
    • Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic b-factors
    • 026,008
    • Soheilifard R, Makarov DE, Rodin GJ (2008) Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic b-factors. Phys Biol 5:026,008
    • (2008) Phys Biol , vol.5
    • Soheilifard, R.1    Makarov, D.E.2    Rodin, G.J.3
  • 44
    • 0036307741 scopus 로고    scopus 로고
    • The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus
    • Tama F, Brooks I CL (2002) The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J Mol Biol 318(3):733-747
    • (2002) J Mol Biol , vol.318 , Issue.3 , pp. 733-747
    • Tama, F.1    Brooks I, C.L.2
  • 45
    • 0034308140 scopus 로고    scopus 로고
    • A building block approach for determining low-frequency normal modes of macromolecules
    • Tama F, Gadea F, Marques O (2000) A building block approach for determining low-frequency normal modes of macromolecules. Proteins Struct Func Genet 41:1-7
    • (2000) Proteins Struct Func Genet , vol.41 , pp. 1-7
    • Tama, F.1    Gadea, F.2    Marques, O.3
  • 46
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion M (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77(9):1905-1908
    • (1996) Phys Rev Lett , vol.77 , Issue.9 , pp. 1905-1908
    • Tirion, M.1


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