메뉴 건너뛰기




Volumn 55, Issue 2, 2004, Pages 383-394

Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model

Author keywords

Generalized Born approximation; Macromolecules; Molecular dynamics

Indexed keywords

BARNASE; BARSTAR; PROTEIN; PROTEIN A; THIOREDOXIN; UBIQUITIN;

EID: 1842479952     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20033     Document Type: Article
Times cited : (2145)

References (38)
  • 1
    • 84961981091 scopus 로고    scopus 로고
    • Implicit solvation models: Equilibria, structure, spectra, and dynamics
    • Cramer CJ, Truhlar DG. Implicit solvation models: equilibria, structure, spectra, and dynamics. Chem Rev 1999;9:2161-2200.
    • (1999) Chem Rev , vol.9 , pp. 2161-2200
    • Cramer, C.J.1    Truhlar, D.G.2
  • 2
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science 1995;268:1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 3
    • 0032319206 scopus 로고    scopus 로고
    • Calculation of proton binding thermodynamics in proteins
    • Beroza P, Case DA. Calculation of proton binding thermodynamics in proteins. Methods Enzymol 1998;295:170-189.
    • (1998) Methods Enzymol , vol.295 , pp. 170-189
    • Beroza, P.1    Case, D.A.2
  • 5
    • 0029066848 scopus 로고
    • Theory of electrostatic interactions in macromolecules
    • Gilson MK. Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol 1995;5:216-223.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 216-223
    • Gilson, M.K.1
  • 6
    • 0031248940 scopus 로고    scopus 로고
    • Continuum electrostatic energies of macromolecules in aqueous solutions
    • Scarsi M, Apostolakis J, Caflisch A. Continuum electrostatic energies of macromolecules in aqueous solutions. J Phys Chem A 1997;101:8098-8106.
    • (1997) J Phys Chem A , vol.101 , pp. 8098-8106
    • Scarsi, M.1    Apostolakis, J.2    Caflisch, A.3
  • 7
    • 0036771626 scopus 로고    scopus 로고
    • Accelerated Poisson-Boltzmann calculations for static and dynamic systems
    • Luo R, David L, Gilson MK. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comp Chem 2002;23:1244-1253.
    • (2002) J Comp Chem , vol.23 , pp. 1244-1253
    • Luo, R.1    David, L.2    Gilson, M.K.3
  • 8
    • 0012818236 scopus 로고
    • Testing and comparison of empirical force fields: Techniques and problems
    • van Gunsteren WF, Weiner PK, Wilkinson AJ, editors. Leiden: ESCOM
    • Gelin BR. Testing and comparison of empirical force fields: techniques and problems. In: van Gunsteren WF, Weiner PK, Wilkinson AJ, editors. Computer simulation of biomolecular sytems. Vol. 2. Leiden: ESCOM; 1993. p 127-146.
    • (1993) Computer Simulation of Biomolecular Sytems , vol.2 , pp. 127-146
    • Gelin, B.R.1
  • 10
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechnics and dynamics
    • Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechnics and dynamics. J Am Chem Soc 1990;112:6127-6129.
    • (1990) J Am Chem Soc , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 11
    • 0012227656 scopus 로고    scopus 로고
    • A comprehensive analytical treatment of continuum electrostatics
    • Schaefer M, Karplus M. A comprehensive analytical treatment of continuum electrostatics. J Phys Chem 1996;100:1578-1599.
    • (1996) J Phys Chem , vol.100 , pp. 1578-1599
    • Schaefer, M.1    Karplus, M.2
  • 12
    • 0031075977 scopus 로고    scopus 로고
    • Solvation free energies of peptides: Comparison of approximate continuum solvation models with accurate solution of Poisson-Boltzman equation
    • Edinger S, Cortis C, Shenkin P, Friesner R. Solvation free energies of peptides: comparison of approximate continuum solvation models with accurate solution of Poisson-Boltzman equation. J Phys Chem B 1997;101:1190-1197.
    • (1997) J Phys Chem B , vol.101 , pp. 1190-1197
    • Edinger, S.1    Cortis, C.2    Shenkin, P.3    Friesner, R.4
  • 13
    • 0000741414 scopus 로고    scopus 로고
    • A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts
    • Jayaram B, Liu Y, Beveridge DJ. A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts. J Chem Phys 1998;109:1465-1470.
    • (1998) J Chem Phys , vol.109 , pp. 1465-1470
    • Jayaram, B.1    Liu, Y.2    Beveridge, D.J.3
  • 14
    • 0001246294 scopus 로고    scopus 로고
    • A generalized Born model based on a surface integral formulation
    • Aghosh A, Rapp CS, Friesner RA. A generalized Born model based on a surface integral formulation. J Phys Chem 1998;102:10983-10990.
    • (1998) J Phys Chem , vol.102 , pp. 10983-10990
    • Aghosh, A.1    Rapp, C.S.2    Friesner, R.A.3
  • 15
    • 0033654297 scopus 로고    scopus 로고
    • Generalized Born models of macromolecular solvation effects
    • Bashford D, Case D. Generalized Born models of macromolecular solvation effects. Annu Rev Phys Chem 2000;51:129-152.
    • (2000) Annu Rev Phys Chem , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.2
  • 16
    • 20644449471 scopus 로고    scopus 로고
    • Modification of the Generalized Born model suitable for macromolecules
    • Onufriev A, Bashford D, Case D. Modification of the Generalized Born model suitable for macromolecules. J Phys Chem B 2000;104:3712-3720.
    • (2000) J Phys Chem B , vol.104 , pp. 3712-3720
    • Onufriev, A.1    Bashford, D.2    Case, D.3
  • 18
    • 84961985307 scopus 로고    scopus 로고
    • Development of a Generalized Born model parametrization for proteins and nucleic acids
    • Dominy BN, Brooks CL. Development of a Generalized Born model parametrization for proteins and nucleic acids. J Phys Chem B 1999;103:3765-3773.
    • (1999) J Phys Chem B , vol.103 , pp. 3765-3773
    • Dominy, B.N.1    Brooks, C.L.2
  • 19
    • 0042139644 scopus 로고    scopus 로고
    • Comparison of generalized Born and Poisson models: Energetics and dynamics of HIV protease
    • David L, Luo R, Gilson MK. Comparison of generalized Born and Poisson models: energetics and dynamics of HIV protease. J Comp Chem 2000;21:295-309.
    • (2000) J Comp Chem , vol.21 , pp. 295-309
    • David, L.1    Luo, R.2    Gilson, M.K.3
  • 20
    • 0037194983 scopus 로고    scopus 로고
    • Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models
    • Spassov VZ, Yan L, Szalma S. Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models. J Phys Chem B 2002;106:8726-8738.
    • (2002) J Phys Chem B , vol.106 , pp. 8726-8738
    • Spassov, V.Z.1    Yan, L.2    Szalma, S.3
  • 21
    • 0035501755 scopus 로고    scopus 로고
    • Protein molecular dynamics with the generalized Born/ACE solvent model
    • Calimet N, Schaefer M, Simonson T. Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins 2001;45:144-158.
    • (2001) Proteins , vol.45 , pp. 144-158
    • Calimet, N.1    Schaefer, M.2    Simonson, T.3
  • 22
    • 0034701222 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids using a generalized Born solvation model
    • Tsui V, Case D. Molecular dynamics simulations of nucleic acids using a generalized Born solvation model. J Am Chem Soc 2000;122:2489-2498.
    • (2000) J Am Chem Soc , vol.122 , pp. 2489-2498
    • Tsui, V.1    Case, D.2
  • 23
    • 0037230970 scopus 로고    scopus 로고
    • Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation
    • Wang T, Wade R. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins 2003;50:158-169.
    • (2003) Proteins , vol.50 , pp. 158-169
    • Wang, T.1    Wade, R.2
  • 24
    • 0033468737 scopus 로고    scopus 로고
    • Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects
    • Srinivasan J, Trevathan M, Beroza P, Case D. Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects. Theor Chem Accts 1999;101:426-434.
    • (1999) Theor Chem Accts , vol.101 , pp. 426-434
    • Srinivasan, J.1    Trevathan, M.2    Beroza, P.3    Case, D.4
  • 25
    • 0037110472 scopus 로고    scopus 로고
    • Effective Born radii in the Generalized Born approximation: The importance of being perfect
    • Onufriev A, Case D, Bashford D. Effective Born radii in the Generalized Born approximation: the importance of being perfect. J Comp Chem 2002;23:1297-1304.
    • (2002) J Comp Chem , vol.23 , pp. 1297-1304
    • Onufriev, A.1    Case, D.2    Bashford, D.3
  • 26
    • 4043171970 scopus 로고    scopus 로고
    • The GB/SA continuum model for solvation: A fast analytical method for the calculation of approximate Born radii
    • Qiu D, Shenkin P, Hollinger F, Still WC. The GB/SA continuum model for solvation: a fast analytical method for the calculation of approximate Born radii. J Phys Chem A 1997;101:3005-3014.
    • (1997) J Phys Chem A , vol.101 , pp. 3005-3014
    • Qiu, D.1    Shenkin, P.2    Hollinger, F.3    Still, W.C.4
  • 27
    • 33748390341 scopus 로고    scopus 로고
    • Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
    • Hawkins GD, Cramer CJ, Truhlar DG. Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J Phys Chem 1996;100:19824-19836.
    • (1996) J Phys Chem , vol.100 , pp. 19824-19836
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 28
    • 0025661993 scopus 로고
    • A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution
    • Schaefer M, Froemmel C. A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution. J Mol Biol 1990;216:1045-1066.
    • (1990) J Mol Biol , vol.216 , pp. 1045-1066
    • Schaefer, M.1    Froemmel, C.2
  • 29
    • 0017429069 scopus 로고
    • Areas, volumes, packing and protein structure
    • Richards FM. Areas, volumes, packing and protein structure. Annu Rev Biochem Bioeng 1977;6:151-176.
    • (1977) Annu Rev Biochem Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 30
    • 0346971105 scopus 로고    scopus 로고
    • Performance comparison of Generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
    • Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL. Performance comparison of Generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comp Chem 2004;25:265-284.
    • (2004) J Comp Chem , vol.25 , pp. 265-284
    • Feig, M.1    Onufriev, A.2    Lee, M.S.3    Im, W.4    Case, D.A.5    Brooks, C.L.6
  • 31
    • 0037225277 scopus 로고    scopus 로고
    • Structural details, pathways, and energetics of unfolding apomyoglobin
    • Onufriev A, Case DA, Bashford D. Structural details, pathways, and energetics of unfolding apomyoglobin. J Mol Biol 2003;325:555-567.
    • (2003) J Mol Biol , vol.325 , pp. 555-567
    • Onufriev, A.1    Case, D.A.2    Bashford, D.3
  • 32
    • 0031932824 scopus 로고    scopus 로고
    • Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding
    • Eliezer D, Yao J, Dyson HJ, Wright PE. Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding. Nat Struct Biol 1998;5:148-155.
    • (1998) Nat Struct Biol , vol.5 , pp. 148-155
    • Eliezer, D.1    Yao, J.2    Dyson, H.J.3    Wright, P.E.4
  • 33
    • 0347602124 scopus 로고    scopus 로고
    • Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
    • Gohlke H, Case DA. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J Comp Chem 2004;25:238-250.
    • (2004) J Comp Chem , vol.25 , pp. 238-250
    • Gohlke, H.1    Case, D.A.2
  • 34
    • 14244273182 scopus 로고    scopus 로고
    • Theory and applications of the Generalized Born solvation model in macromolecular simulations
    • Tsui V, Case D. Theory and applications of the Generalized Born solvation model in macromolecular simulations. Biopolymers 2001;56:275-291.
    • (2001) Biopolymers , vol.56 , pp. 275-291
    • Tsui, V.1    Case, D.2
  • 35
    • 0030745939 scopus 로고    scopus 로고
    • Accurate ab initio quantum chemical determinantion of the relative energies of peptide conformations and assessement of empirical force fields
    • Beachy MD, Chasman D, Murphy RB, Halgren TA, Friesner RA. Accurate ab initio quantum chemical determinantion of the relative energies of peptide conformations and assessement of empirical force fields. J Am Chem Soc 1997;119:5908-5920.
    • (1997) J Am Chem Soc , vol.119 , pp. 5908-5920
    • Beachy, M.D.1    Chasman, D.2    Murphy, R.B.3    Halgren, T.A.4    Friesner, R.A.5
  • 36
    • 0035865992 scopus 로고    scopus 로고
    • Exploring the energy landscape of a β-hairpin in explicit solvent
    • Garcia AE, Sanbonmatsu KY. Exploring the energy landscape of a β-hairpin in explicit solvent. Proteins 2001;42:345-354.
    • (2001) Proteins , vol.42 , pp. 345-354
    • Garcia, A.E.1    Sanbonmatsu, K.Y.2
  • 37
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling C, Strockbine B, Roitberg AE. All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 2002;124:11258-11259.
    • (2002) J Am Chem Soc , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 38
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm, utilizing successive over relaxation to solve the Poisson-Boltzmann equation
    • Nicholls A, Honig B. A rapid finite difference algorithm, utilizing successive over relaxation to solve the Poisson-Boltzmann equation. J Comp Chem 1991;12:435-445.
    • (1991) J Comp Chem , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.