Molecular dynamics simulation shows large volume fluctuations of proteins

European Biophysics Journal

Volumn 29, Issue 7, 2000, Pages 472-480

  Tama, F ^a   Miyashita, O ^a   Kitao, A ^a   Go, N ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Compressibility; Human lysozyme; Principal component analysis

Indexed keywords

LYSOZYME; PROTEIN;

ARTICLE; CALCULATION; COMPRESSION; CONFORMATIONAL TRANSITION; HUMAN; HYDRATION; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN STRUCTURE; SIMULATION;

COMPUTER SIMULATION; HUMANS; MODELS, MOLECULAR; MODELS, THEORETICAL; MURAMIDASE; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOFTWARE; WATER;

EID: 0033636872     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002490000103     Document Type: Article

References (28)

1. Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
2. Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions
3. The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and dot surface contouring of molecular assemblies
4. Adiabatic compressibility of globular proteins
5. Compressibility-structure relationship of globular proteins
6. Compressibility of globular protein in water at 25 °C
7. Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion
8. Collective variable description of native proteins dynamics
9. Harmonic and anharmonic aspects in the dynamics of bpti: A normal mode analysis and principal component analysis
10. Canonical dynamics: Equilibrium phase-space distribution
11. Comparison of simple potential functions for simulating liquid water
12. Hydrational and intrinsic compressibilities of globular proteins
13. Normal mode refinement: Crystallographic refinement of protein dynamic structure. II. Application to human lysozyme
14. The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulation of melittin in water and in vacuum
15. Energy landscape of a native protein: Jumping-among-minima model
16. Mechanical property of a TIM-barrel protein
17. Crystal structure of hen eggwhite lysozyme at a hydrostatic pressure of 1000 atmospheres
18. Effect of pressure on individual hydrogen bonds in proteins. Basic pancreatic trypsin inhibitor
19. Heme protein fluorescence versus pressure
20. Pressure dependence of protein electron transfer reactions: Theory and simulation
21. PRESTO (protein engineering simulator): A vectorized molecular mechanics program for biopolymers
22. A molecular dynamics method for simulations in the canonical ensemble
23. Intrinsic compressibility and volume compression in solvated proteins by molecular dynamics simulation at high pressure
24. On the volume of macromolecules
25. Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, v57a
26. An all atom force field for simulations of proteins and nucleics acids
27. Conformational deformation in deoxymyoglobin by hydrostatic pressure
28. Photochemical holes under pressure: Compressibility and volume fluctuations of a protein