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The effects of the L29F mutation on the ligand migration kinetics in crystallized myoglobin as revealed by molecular dynamics simulations
Proteins, structure, function, and bioinformatics, 2011-03, Vol.79 (3), p.867-879
Anselmi, Massimiliano
Di Nola, Alfredo
Amadei, Andrea
2011
Volltextzugriff (PDF)
Details
Autor(en) / Beteiligte
Anselmi, Massimiliano
Di Nola, Alfredo
Amadei, Andrea
Titel
The effects of the L29F mutation on the ligand migration kinetics in crystallized myoglobin as revealed by molecular dynamics simulations
Ist Teil von
Proteins, structure, function, and bioinformatics, 2011-03, Vol.79 (3), p.867-879
Ort / Verlag
Hoboken: Wiley Subscription Services, Inc., A Wiley Company
Erscheinungsjahr
2011
Quelle
Wiley-Blackwell Journals
Beschreibungen/Notizen
By using multiple molecular dynamics (MD) trajectories, a quantitative description of carbon monoxide (CO) migration within crystal of L29F myoglobin mutant (L29F‐Mb) was obtained. The aim was to provide a detailed model for ligand diffusion in the protein to be compared to the available L29F‐Mb experimental‐computational data and to the corresponding model kinetics we previously obtained for photolyzed CO within crystallized wild‐type myoglobin (wt‐Mb). Results suggest a clear migration pathway from distal pocket to the proximal site, similar to the one observed in wt‐Mb, with a relaxation kinetics differing from the wt‐Mb one essentially for the escape rate which is much higher in the mutant. Moreover MD data indicated a clear correlation between CO location within the protein and the conformation adopted by Phe29, well matching the available experimental data as obtained by time‐resolved X‐ray density maps. Such data, further validating the model used in the simulations, point out the subtle mutual effect between ligand diffusion and protein functional motions possibly explaining the observed dramatic variation of CO exit rate in L29F‐Mb. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Sprache
Englisch
Identifikatoren
ISSN: 0887-3585
eISSN: 1097-0134
DOI: 10.1002/prot.22924
Titel-ID: cdi_proquest_miscellaneous_849012157
Format
–
Schlagworte
binding sites
,
cavities
,
Crystallization
,
Crystallography, X-Ray
,
Kinetics
,
ligand diffusion
,
Ligands
,
MD simulations
,
Models, Molecular
,
Molecular Dynamics Simulation
,
Mutation
,
myoglobin
,
Myoglobin - chemistry
,
Myoglobin - genetics
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