Ligand diffusion in the catalase from Proteus mirabilis: A molecular dynamics study

Protein Science

Volumn 10, Issue 10, 2001, Pages 1927-1935

  Amara, Patricia ^a   Andreoletti, Pierre ^a   Jouve, Hélène Marie ^a   Field, Martin J ^a  

^a INSTITUT DE BIOLOGIE STRUCTURALE   (France)

Author keywords

Catalase; Cavities; Channels; Free energy; Ligand diffusion; Molecular dynamics

Indexed keywords

CATALASE; HEME; LIGAND; OXYGEN; SERINE; WATER;

ARTICLE; CATALYSIS; CONTROLLED STUDY; DIFFUSION; ENZYME ACTIVE SITE; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEUS MIRABILIS; REACTION ANALYSIS; SIMULATION; STRUCTURE ANALYSIS; X RAY ANALYSIS;

BINDING SITES; CATALASE; COMPUTER SIMULATION; DIFFUSION; ENERGY METABOLISM; HYDROGEN PEROXIDE; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; OXYGEN; PROTEIN CONFORMATION; PROTEUS MIRABILIS; REPRODUCIBILITY OF RESULTS; WATER;

EID: 0034813458     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.14201     Document Type: Article

References (33)

1. Prediction of pH-dependent properties of proteins
2. Structure of catalases
3. Structure of catalase HPII from Escherichia coli at 1.9 Å resolution
4. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
5. Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
6. Structural dynamics of myoglobin
7. Structural dynamics of ligand diffusion in the protein matrix: A study of a new myoglobin mutant Y(B10) Q(E7) R(E10)
8. Accessibility to internal cavities and ligand binding sites monitored by crystallographic thermal factors
9. Dynamics of ligand binding to heme proteins
10. Molecular dynamics simulations of P450 BM3 - Examination of a substrate-induced conformational change
11. Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian dynamics program
12. Enhanced sampling in molecular dynamics: Use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
13. Alternate pathways for acetic acid and acetate ion release from acetylcholinesterase: A molecular dynamics study
14. The active center of catalase
15. Crystal structure of Proteus mirabilis PR catalase with and without bound NADPH
16. Intramolecular cavities in globular proteins
17. Purification and properties of the Proteus mirabilis catalase
18. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
19. How do substrates enter and products exit the buried active site of cytochrome P450cam? I. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms
20. How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways
21. All-atom empirical potential for molecular modeling and dynamics studies of proteins
22. Structure of catalase-A form Saccharomyces cerevisiae
23. Gas access to the active site of Ni-Fe hydrogenases probed by X-ray crystallography and molecular dynamics
24. Enzymology and structure of catalases
25. NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules
26. Role of the lateral channel in catalase HPII of Escherichia coli
27. Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A
28. Computational studies of the interaction of myoglobin and xenon
29. Protein-ligand dynamics: A 96 picosecond simulation of a myoglobin-xenon complex
30. Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones lluid
31. Spéléologie des hydrogénases à nickel et à fer
32. Site-directed mutagenesis of the lower parts of the major substrate channel of yeast cattalos A leads to highly increased peroxidatic activity