ArticleBiophysical journal2009
Nitric oxide dynamics in truncated hemoglobin: docking sites, migration pathways, and vibrational spectroscopy from molecular dynamics simulations.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Membrane-Mediated Action of Phosphodiesterase 5 Inhibitors.Pharmaceutics · 2025Article
- Molecular Dynamics Simulations of Nitric Oxide Scattering Off Graphene.Chemphyschem : a European journal of chemical physics and physical chemistry · 2022Article
- Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.Journal of the Royal Society, Interface · 2019Article
- Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations.Journal of chemical theory and computation · 2019Article
- Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N.PLoS computational biology · 2017Article
- A quantitative model for oxygen uptake and release in a family of hemeproteins.Bioinformatics (Oxford, England) · 2016Article
- Bactericidal activity of PA-824 against Mycobacterium tuberculosis under anaerobic conditions and computational analysis of its novel analogues against mutant Ddn receptor.BMC microbiology · 2013Article
- Hemoglobin: a nitric-oxide dioxygenase.Scientifica · 2012Review
- Quantitative analysis of ligand migration from transition networks.Biophysical journal · 2010Article
- Theoretical investigations of nitric oxide channeling in Mycobacterium tuberculosis truncated hemoglobin N.Biophysical journal · 2009Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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