A molecular dynamics study of solvent behavior around a protein

Proteins: Structure, Function, and Bioinformatics

Volumn 16, Issue 3, 1993, Pages 268-277

  Komeiji, Yuto ^a,d   Uebayasi, Masami ^b   Someya, Jun‐ichiro ^b   Yamato, Ichiro ^c  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c TOKYO UNIVERSITY OF SCIENCE   (Japan)

^d ELECTROTECHNICAL LABORATORY   (Japan)

Author keywords

AMBER; diffusion coefficient; hydrogen bond; hydrophobic shell; radial distribution; TIP3P water; trp repressor

Indexed keywords

PROTEIN; SOLVENT; WATER;

ARTICLE; CHEMICAL STRUCTURE; DIFFUSION COEFFICIENT; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; REPRESSOR GENE;

AMINO ACIDS; COMPUTER SIMULATION; COMPUTERS; DIFFUSION; HYDROGEN BONDING; REPRESSOR PROTEINS; SOFTWARE; SOLUBILITY; SOLUTIONS; SOLVENTS; WATER;

EID: 0027211701     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.340160305     Document Type: Article

References (24)

1. The water structure surrounding proteins
2. Protein hydration from water oxygen‐17 magnetic relaxation
3. 1H multiple quantum coherence NMR spectroscopy
4. Determination of the positions of bound water molecules in the solution structure of reduced human thioredoxin by heteronuclear three‐dimensional nuclear magnetic resonance spectroscopy
5. Water‐protein interactions: Theory and experiment
6. Computer simulation and the design of new biological molecules
7. Accurate simulation of protein dynamics in solution
8. Solvent effects on protein motion and protein effects on solvent motion‐dynamics of the active site region of lysozyme
9. Molecular dynamics simulation of trp‐aporepressor in a solvent
10. Flexibility of the DNA‐ binding domains of trp represser
11. Environment and exposure of solvent of protein atoms. Lysozyme and insulin
12. A new force field for molecular mechanical simulation oi nucleic acids and proteins
13. Molecular dynamics with coupling to an external bath
14. Comparison of simple potential functions for simulating liquid water
15. An NMR‐based molecular dynamics simulation of the interaction of the lac represser headpiece and its operator in aqueous solution
16. Solvent influence on protein dynamics
17. Self‐diffusion in normal and heavy water in the range 1–45°
18. Experimentally verifying molecular dynamics simulations through fluorescence anisotropy measurements
19. Computer experiments on aqueous solutions. III. Monte Carlo calculation on the hydration of tertiary butyl alcohol in an infinitely dilute aqueous solution with a new water‐butanol pair potential
20. Hydration structure around a non‐electrolyte molecule as revealed by Monte Carlo calculation: Have you seen the ‘iceberg’
21. Computer experiments on aqueous solution. I. Monte Carlo calculation on the hydration of methanol in an infinitely dilute aqueous solution with a new water‐methanoi pair potential
22. A Monte Carlo study on the size dependence in hydrophobic hydration