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Nitric oxide dynamics in truncated hemoglobin : docking sites, migration pathways, and vibrational spectroscopy from molecular dynamics simulations
JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift)
 
ID 84347
Author(s) Mishra, Sabyashachi; Meuwly, Markus
Author(s) at UniBasel Meuwly, Markus
Year 2009
Title Nitric oxide dynamics in truncated hemoglobin : docking sites, migration pathways, and vibrational spectroscopy from molecular dynamics simulations
Journal Biophysical Journal
Volume 96
Number 6
Pages / Article-Number 2105-18
Abstract Atomistic simulations of nitric oxide (NO) dynamics and migration in the trHbN of Mycobacterium tuberculosis are reported. From extensive molecular dynamics simulations (48 ns in total), the structural and energetic properties of the ligand docking sites in the protein have been characterized and a connectivity network between the ligand docking sites has been built. Several novel migration and exit pathways are found and are analyzed in detail. The interplay between a hydrogen-bonding network involving residues Tyr(33) and Gln(58) and the bound O(2) ligand is discussed and the role of Phe(62) residue in ligand migration is examined. It is found that Phe(62) is directly involved in controlling ligand migration. This is reminiscent of His(64) in myoglobin, which also plays a central role in CO migration pathways. Finally, infrared spectra of the NO molecule in different ligand docking sites of the protein are calculated. The pocket-specific spectra are typically blue-shifted by 5-10 cm(-1), which should be detectable in future spectroscopic experiments.
Publisher Biophysical Society
ISSN/ISBN 0006-3495
edoc-URL http://edoc.unibas.ch/dok/A5250885
Full Text on edoc No
Digital Object Identifier DOI 10.1016/j.bpj.2008.11.066
PubMed ID http://www.ncbi.nlm.nih.gov/pubmed/19289037
ISI-Number WOS:000266376700007
Document type (ISI) Journal Article
 
   

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