메뉴 건너뛰기




Volumn 223, Issue 1, 2007, Pages 416-435

A boundary element formulation of protein electrostatics with explicit ions

Author keywords

Boundary element method; Coarse grained model; Computer simulation; Electrostatics; Explicit ions; Ionic strength; Potential of mean force; Protein

Indexed keywords

BIOINFORMATICS; BIOMOLECULES; BOLTZMANN EQUATION; BOUNDARY ELEMENT METHOD; COARSE-GRAINED MODELING; DISSOCIATION; ELECTROLYTES; INTELLIGENT SYSTEMS; IONIC STRENGTH; MOLECULES; MONTE CARLO METHODS; POISSON EQUATION; PROTEINS; SODIUM CHLORIDE;

EID: 33947198768     PISSN: 00219991     EISSN: 10902716     Source Type: Journal    
DOI: 10.1016/j.jcp.2006.09.011     Document Type: Article
Times cited : (11)

References (57)
  • 1
    • 0037529067 scopus 로고    scopus 로고
    • Electrostatics and dynamics of proteins
    • Simonson T. Electrostatics and dynamics of proteins. Rep. Prog. Phys. 66 (2003) 737-787
    • (2003) Rep. Prog. Phys. , vol.66 , pp. 737-787
    • Simonson, T.1
  • 2
    • 0029016182 scopus 로고
    • A classical electrostatics in biology and chemistry
    • Honig B., and Nicholls A. A classical electrostatics in biology and chemistry. Science 268 (1995) 1144-1149
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 3
    • 0036873086 scopus 로고    scopus 로고
    • The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology
    • Fogolari F., Brigo A., and Molinari H. The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J. Mol. Recognit. 15 (2002) 377-392
    • (2002) J. Mol. Recognit. , vol.15 , pp. 377-392
    • Fogolari, F.1    Brigo, A.2    Molinari, H.3
  • 4
    • 0035281357 scopus 로고    scopus 로고
    • Computer simulation of protein-protein interactions
    • Elcock A.H., and McCammon D.Sept.J.A. Computer simulation of protein-protein interactions. J. Phys. Chem. B 105 (2001) 1504-1518
    • (2001) J. Phys. Chem. B , vol.105 , pp. 1504-1518
    • Elcock, A.H.1    McCammon, D.2    Sept, J.A.3
  • 5
    • 0942266531 scopus 로고    scopus 로고
    • Calculation of affinities of peptides for proteins
    • Donnini S., and Juffer A.H. Calculation of affinities of peptides for proteins. J. Comput. Chem. 25 (2004) 393-411
    • (2004) J. Comput. Chem. , vol.25 , pp. 393-411
    • Donnini, S.1    Juffer, A.H.2
  • 6
    • 0025197061 scopus 로고
    • a's of ionizable groups in proteins: atomic detail from a continuum electrostatic model
    • a's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 29 (1990) 10219-10225
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 7
    • 0031237025 scopus 로고    scopus 로고
    • Calculating acid dissociation constants using the boundary element method
    • Juffer A.H., Argos P., and Vogel H.J. Calculating acid dissociation constants using the boundary element method. J. Phys. Chem. B 101 (1997) 7664-7673
    • (1997) J. Phys. Chem. B , vol.101 , pp. 7664-7673
    • Juffer, A.H.1    Argos, P.2    Vogel, H.J.3
  • 8
    • 0032189032 scopus 로고    scopus 로고
    • Calculation of HyHel10-lysozyme binding free energy changes: Effect of 10 point mutations
    • Sharp K.A. Calculation of HyHel10-lysozyme binding free energy changes: Effect of 10 point mutations. Proteins 33 (1998) 39-48
    • (1998) Proteins , vol.33 , pp. 39-48
    • Sharp, K.A.1
  • 10
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
    • Vorobjev Y.N., Almagro J.C., and Hermans J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins 32 (1998) 399-413
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 12
    • 84961981995 scopus 로고    scopus 로고
    • Comparison of solvent reaction field representations
    • Chipman D.M. Comparison of solvent reaction field representations. Theor. Chem. Acc. 107 (2002) 80-89
    • (2002) Theor. Chem. Acc. , vol.107 , pp. 80-89
    • Chipman, D.M.1
  • 14
    • 0020475509 scopus 로고
    • Calculation of the electric potential in the active site cleft due to α-helix dipoles
    • Warwicker J., and Watson H.C.J. Calculation of the electric potential in the active site cleft due to α-helix dipoles. J. Mol. Biol. 157 (1982) 671-679
    • (1982) J. Mol. Biol. , vol.157 , pp. 671-679
    • Warwicker, J.1    Watson, H.C.J.2
  • 15
    • 0022964504 scopus 로고
    • Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification
    • Klapper I., Hagstrom R., Fine R., Sharp K., and Honig B. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins 1 (1986) 47-59
    • (1986) Proteins , vol.1 , pp. 47-59
    • Klapper, I.1    Hagstrom, R.2    Fine, R.3    Sharp, K.4    Honig, B.5
  • 16
    • 0022429751 scopus 로고
    • A new method for computing the macromolecular electric potential
    • Zauhar R.J., and Morgan R.S.J. A new method for computing the macromolecular electric potential. J. Mol. Biol. 186 (1985) 815-820
    • (1985) J. Mol. Biol. , vol.186 , pp. 815-820
    • Zauhar, R.J.1    Morgan, R.S.J.2
  • 18
    • 84962478456 scopus 로고
    • A boundary element method for molecular electrostatics with electrolyte effects
    • Yoon B.J., and Lenhoff A.M.J. A boundary element method for molecular electrostatics with electrolyte effects. J. Comput. Chem. 11 (1990) 1080-1086
    • (1990) J. Comput. Chem. , vol.11 , pp. 1080-1086
    • Yoon, B.J.1    Lenhoff, A.M.J.2
  • 19
    • 0037328258 scopus 로고    scopus 로고
    • Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
    • Bordner A.J., and Huber G.A. Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution. J. Comput. Chem. 24 (2003) 353-367
    • (2003) J. Comput. Chem. , vol.24 , pp. 353-367
    • Bordner, A.J.1    Huber, G.A.2
  • 20
    • 85033849708 scopus 로고    scopus 로고
    • Finite-difference solution of the Poisson-Boltzmann equation: complete elimination of self-energy
    • Zhou Z., Payne P., Vasquez M., Kuhn N., and Levitt M. Finite-difference solution of the Poisson-Boltzmann equation: complete elimination of self-energy. J. Comput. Chem. 17 (1996) 1344-1351
    • (1996) J. Comput. Chem. , vol.17 , pp. 1344-1351
    • Zhou, Z.1    Payne, P.2    Vasquez, M.3    Kuhn, N.4    Levitt, M.5
  • 21
    • 0000486194 scopus 로고    scopus 로고
    • Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems
    • Baker N., Holst M., and Wang F. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems. J. Comput. Chem. 21 (2000) 1343-1352
    • (2000) J. Comput. Chem. , vol.21 , pp. 1343-1352
    • Baker, N.1    Holst, M.2    Wang, F.3
  • 22
    • 0035327566 scopus 로고    scopus 로고
    • The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers
    • Baker N.A., Sept D., Holst M.J., and McCammon J.A. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM J. Res. Devel. 45 (2001) 427-438
    • (2001) IBM J. Res. Devel. , vol.45 , pp. 427-438
    • Baker, N.A.1    Sept, D.2    Holst, M.J.3    McCammon, J.A.4
  • 23
    • 0001620743 scopus 로고    scopus 로고
    • An automatic three-dimensional finite element mesh generation system for the Poisson-Boltzmann equation
    • Cortis C.M., and Friesner R.A. An automatic three-dimensional finite element mesh generation system for the Poisson-Boltzmann equation. J. Comput. Chem. 18 (1997) 1570-1590
    • (1997) J. Comput. Chem. , vol.18 , pp. 1570-1590
    • Cortis, C.M.1    Friesner, R.A.2
  • 24
    • 0023280069 scopus 로고
    • Calculation of electrostatic potentials in an enzyme active site
    • Gilson M.K., and Honig B.H.J. Calculation of electrostatic potentials in an enzyme active site. Nature 330 (1987) 84-86
    • (1987) Nature , vol.330 , pp. 84-86
    • Gilson, M.K.1    Honig, B.H.J.2
  • 25
    • 0034863617 scopus 로고    scopus 로고
    • Rapid boundary element solvation electrostatics calculations in folding simulations: Successful folding of a 23-residue peptide
    • Totrov M., and Abagyan R. Rapid boundary element solvation electrostatics calculations in folding simulations: Successful folding of a 23-residue peptide. Biopolymers 60 (2001) 124-133
    • (2001) Biopolymers , vol.60 , pp. 124-133
    • Totrov, M.1    Abagyan, R.2
  • 26
    • 33751392187 scopus 로고
    • Computation of the electrostatic interaction energy between a protein and charged surface
    • Yoon B.J., and Lenhoff A.M. Computation of the electrostatic interaction energy between a protein and charged surface. J. Phys. Chem. 96 (1992) 3130-3134
    • (1992) J. Phys. Chem. , vol.96 , pp. 3130-3134
    • Yoon, B.J.1    Lenhoff, A.M.2
  • 27
    • 0027254625 scopus 로고
    • Boundary element solution of macromolecular electrostatic. Interaction energy between two proteins
    • Zhou H.-X. Boundary element solution of macromolecular electrostatic. Interaction energy between two proteins. Biophys. J. 65 (1993) 955-963
    • (1993) Biophys. J. , vol.65 , pp. 955-963
    • Zhou, H.-X.1
  • 28
    • 1242328838 scopus 로고    scopus 로고
    • The extent of anisotropic interactions between protein molecules in electrolyte solutions
    • Song X. The extent of anisotropic interactions between protein molecules in electrolyte solutions. Mol. Simult. 29 (2003) 643-647
    • (2003) Mol. Simult. , vol.29 , pp. 643-647
    • Song, X.1
  • 29
    • 21244431972 scopus 로고    scopus 로고
    • Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method
    • Lu B., Zhang D., and McCammon J.A. Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J. Chem. Phys. 122 (2005) 214102-214108
    • (2005) J. Chem. Phys. , vol.122 , pp. 214102-214108
    • Lu, B.1    Zhang, D.2    McCammon, J.A.3
  • 30
    • 33845910351 scopus 로고    scopus 로고
    • Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals
    • Lu B., Cheng X., Hou T., and McCammon J.A. Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals. J. Chem. Phys. 123 (2005) 84904-84911
    • (2005) J. Chem. Phys. , vol.123 , pp. 84904-84911
    • Lu, B.1    Cheng, X.2    Hou, T.3    McCammon, J.A.4
  • 32
    • 0034477212 scopus 로고    scopus 로고
    • A simulation method of combining boundary element method with generalized Langevin dynamics
    • Chen W., Lu B.Z., and Wang C. A simulation method of combining boundary element method with generalized Langevin dynamics. Chi. Sci. Bull. 45 (2000) 2227-2231
    • (2000) Chi. Sci. Bull. , vol.45 , pp. 2227-2231
    • Chen, W.1    Lu, B.Z.2    Wang, C.3
  • 33
    • 0034230032 scopus 로고    scopus 로고
    • A stochastic dynamics simulation study associated with hydration force and friction memory effect
    • Lu B.Z., Wang C.X., Chen W.Z., Wan S.Z., and Shi Y.Y. A stochastic dynamics simulation study associated with hydration force and friction memory effect. J. Phys. Chem. B 104 (2000) 6877-6883
    • (2000) J. Phys. Chem. B , vol.104 , pp. 6877-6883
    • Lu, B.Z.1    Wang, C.X.2    Chen, W.Z.3    Wan, S.Z.4    Shi, Y.Y.5
  • 34
    • 0035101696 scopus 로고    scopus 로고
    • Protein-membrane electrostatic interactions: application of the Lekner summation technique
    • Juffer A.H., Shepherd C.M., and Vogel H.J. Protein-membrane electrostatic interactions: application of the Lekner summation technique. J. Chem. Phys. 114 (2001) 1892-1905
    • (2001) J. Chem. Phys. , vol.114 , pp. 1892-1905
    • Juffer, A.H.1    Shepherd, C.M.2    Vogel, H.J.3
  • 35
    • 0028222670 scopus 로고
    • Treatment of electrostatic effects in proteins: multigrid-based Newton iterative method for solution of the full non-linear Poisson-Boltzmann equation
    • Holst M., Kozack R.E., Saied F., and Subramaniam S. Treatment of electrostatic effects in proteins: multigrid-based Newton iterative method for solution of the full non-linear Poisson-Boltzmann equation. Proteins 18 (1994) 231-245
    • (1994) Proteins , vol.18 , pp. 231-245
    • Holst, M.1    Kozack, R.E.2    Saied, F.3    Subramaniam, S.4
  • 36
    • 0001547345 scopus 로고
    • A combined iterative and boundary element approach for the solution of the non-linear Poisson-Boltzmann equation
    • Vorobjev Y.N., Grant J.A., and Scheraga H.A. A combined iterative and boundary element approach for the solution of the non-linear Poisson-Boltzmann equation. J. Am. Chem. Soc. 114 (1992) 3189-3196
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 3189-3196
    • Vorobjev, Y.N.1    Grant, J.A.2    Scheraga, H.A.3
  • 37
    • 2342454337 scopus 로고    scopus 로고
    • Hybrid boundary element and finite difference method for solving the non-linear Poisson-Boltzmann equation
    • Boschitsch A.H., and Fenley M.O. Hybrid boundary element and finite difference method for solving the non-linear Poisson-Boltzmann equation. J. Comput. Chem. 25 (2004) 935-955
    • (2004) J. Comput. Chem. , vol.25 , pp. 935-955
    • Boschitsch, A.H.1    Fenley, M.O.2
  • 40
    • 0032615301 scopus 로고    scopus 로고
    • Transport coefficients of electrolyte solutions from smart Brownian dynamics simulations
    • Jardat M., Bernard O., and Turq P. Transport coefficients of electrolyte solutions from smart Brownian dynamics simulations. J. Phys. Chem. 110 (1999) 7993-7999
    • (1999) J. Phys. Chem. , vol.110 , pp. 7993-7999
    • Jardat, M.1    Bernard, O.2    Turq, P.3
  • 44
    • 0000623669 scopus 로고
    • On the representation of orientation space
    • Evans D.J. On the representation of orientation space. Mol. Phys. 34 (1977) 317-325
    • (1977) Mol. Phys. , vol.34 , pp. 317-325
    • Evans, D.J.1
  • 46
    • 0035146576 scopus 로고    scopus 로고
    • A molecular dynamics study of peptide-bilayer adsorption
    • Shepherd C.M., Schaus K.A., Vogel H.J., and Juffer A.H. A molecular dynamics study of peptide-bilayer adsorption. Biophys. J. 80 (2001) 579-596
    • (2001) Biophys. J. , vol.80 , pp. 579-596
    • Shepherd, C.M.1    Schaus, K.A.2    Vogel, H.J.3    Juffer, A.H.4
  • 47
    • 0032059253 scopus 로고    scopus 로고
    • A flexible triangulation method to describe the solvent-accessible surface of biopolymers
    • Juffer A.H., and Vogel H.J. A flexible triangulation method to describe the solvent-accessible surface of biopolymers. J. Comput.-Aided Mol. Design. 12 (1998) 289-299
    • (1998) J. Comput.-Aided Mol. Design. , vol.12 , pp. 289-299
    • Juffer, A.H.1    Vogel, H.J.2
  • 49
    • 84977266737 scopus 로고
    • Die Berechnung optischer und elektrostatischer Gitterpotentiale
    • Ewald P. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phy. 64 (1921) 253-287
    • (1921) Ann. Phy. , vol.64 , pp. 253-287
    • Ewald, P.1
  • 50
    • 34547887373 scopus 로고
    • Summation of Coulomb fields in computer-simulated disordered systems
    • Lekner J. Summation of Coulomb fields in computer-simulated disordered systems. Phys. A 176 (1991) 485-498
    • (1991) Phys. A , vol.176 , pp. 485-498
    • Lekner, J.1
  • 51
    • 0035861430 scopus 로고    scopus 로고
    • Reality simulation - observe while it happens
    • Berendsen H.J.C. Reality simulation - observe while it happens. Science 294 (2001) 2304-2305
    • (2001) Science , vol.294 , pp. 2304-2305
    • Berendsen, H.J.C.1
  • 52
    • 0012227656 scopus 로고    scopus 로고
    • A comprehensive analytical treatment of continuum electrostatics
    • Schaefer M., and Karplus M.A. A comprehensive analytical treatment of continuum electrostatics. J. Phys. Chem. 100 (1996) 1578-1599
    • (1996) J. Phys. Chem. , vol.100 , pp. 1578-1599
    • Schaefer, M.1    Karplus, M.A.2
  • 53
    • 0034225199 scopus 로고    scopus 로고
    • Electrostatic free energy calculations for macromolecules: a hybrid molecular dynamics/continuum electrostatics approach
    • Simonson T. Electrostatic free energy calculations for macromolecules: a hybrid molecular dynamics/continuum electrostatics approach. J. Phys. Chem. B 104 (2000) 6509-6513
    • (2000) J. Phys. Chem. B , vol.104 , pp. 6509-6513
    • Simonson, T.1
  • 54
    • 0031028837 scopus 로고    scopus 로고
    • Multiconformational NMR analysis of sandostatin (octreotide): Equilibrium between β-sheet and partially helical structures
    • Melacini G., Zhu Q., and Goodman M. Multiconformational NMR analysis of sandostatin (octreotide): Equilibrium between β-sheet and partially helical structures. Biochemistry 36 (1997) 1233-1241
    • (1997) Biochemistry , vol.36 , pp. 1233-1241
    • Melacini, G.1    Zhu, Q.2    Goodman, M.3
  • 55
    • 0035789518 scopus 로고    scopus 로고
    • Gromacs 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E E., Hess B., and van der Spoel D. Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 7 (2001) 306-317
    • (2001) J. Mol. Mod. , vol.7 , pp. 306-317
    • Lindahl E, E.1    Hess, B.2    van der Spoel, D.3
  • 57
    • 0000804322 scopus 로고
    • Interaction energy between identical spherical colloidal particles: the linearized Poisson-Boltzmann theory
    • Carnie S.L., and Chan D.Y.C. Interaction energy between identical spherical colloidal particles: the linearized Poisson-Boltzmann theory. J. Colloid Interf. Sci. 155 (1993) 297-312
    • (1993) J. Colloid Interf. Sci. , vol.155 , pp. 297-312
    • Carnie, S.L.1    Chan, D.Y.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.