Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation

Proteins: Structure, Function and Genetics

Volumn 48, Issue 3, 2002, Pages 497-504

  Lu, Ben Zhuo ^a,b   Chen, Wei Zu ^b   Wang, Cun Xin ^a,b   Xu, Xiao Jie ^c  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b BEIJING UNIVERSITY OF TECHNOLOGY   (China)

^c PEKING UNIVERSITY   (China)

Author keywords

Finite difference stochastic dynamics; Insulin dimer; Protein dielectric constant; Solvent effect

Indexed keywords

SOLVENT;

ARTICLE; CALCULATION; DIELECTRIC CONSTANT; ELECTRICITY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; POISSON DISTRIBUTION; PRIORITY JOURNAL; SIMULATION; SOLVATION; STOCHASTIC MODEL;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ELECTROSTATICS; HYDROGEN BONDING; INSULIN; KINETICS; MODELS, MOLECULAR; MODELS, THEORETICAL; POISSON DISTRIBUTION; PROTEINS; SOLVENTS; STOCHASTIC PROCESSES;

EID: 0037103014     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10172     Document Type: Article

References (31)

1. Proteins: A theoretical perspective of dynamics, structure and thermodynamics
2. Identification and characterization of the unfolding transition state of chymtrypsin inhibitor 2 by molecular dynamics simulations
3. β-hairpin stability and folding: Molecular dynamics studies of the first β-hairpin of tendamistat
4. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
5. Solvation energy in protein folding and binding
6. The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations
7. Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson-Boltzmann model
8. Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
9. Molecular dynamics simulation with a continuum electrostatic model of the solvent
10. Incorporating hydration force determined by boundary element method into stochastic dynamics
11. A stochastic dynamics simulation study associated with hydration force and friction memory effect
12. Comparison of continuum and explicit models of solvation: Potentials of mean force for alanine dipeptide
13. Classical electrostatics in biology and chemistry
14. Conformation and hydrogen ion titration of proteins: A continuum electrostatic model with conformational flexibility
15. pH-dependence of protein stability: Absolute electrostatic free energy differences between conformations
16. Prediction of pH-dependent properties of proteins
17. Comparison of generalized Born and Poison methods: Energetics and dynamics of HIV protease
18. Protein molecular dynamics with the generalized Born/ACE solvent model
19. The inclusion of electrostatic hydration energies in molecular mechanics calculations
20. The low dielectric interior of proteins is sufficient to cause major structural changes in DNA on association
21. Application of Poisson-Boltzmann solvation forces to macromolecular simulations
22. Investigating the dielectric effects of channel pore water on the electrostatic barriers of the permeation ion by the finite difference Poisson-Boltzmann method
23. What are the dielectric "constants" of proteins and how to validate electrostatic model?
24. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
25. A leap-frog algorithm for stochastic dynamics
26. Biological applications of electrostatic calculations and Brownian dynamics simulations
27. The structure of 2Zn pig insulin crystals at 1.5 angstroms resolution
28. Conformational sampling with Poisson-Boltzmann forces and a stochastic dynamics/Monte Carlo method: Application to alanine dipeptide
29. Numerical integration of the cartesian equations of motion for a system with constraints: Molecular dynamics of n-alkanes
30. MD of plastocyanin: Structure and dynamics