ArticleBiophysical journal2010
Quantitative analysis of ligand migration from transition networks.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 16 citations in OpenAlex.
- Implications of short time scale dynamics on long time processes.Structural dynamics (Melville, N.Y.) · 2017Review
- Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N.PLoS computational biology · 2017Article
- Markov state models of protein misfolding.The Journal of chemical physics · 2016Article
- Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin.Journal of chemical theory and computation · 2015Article
- Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations.Journal of the American Chemical Society · 2015Article
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this work we use transition network analysis for the first time to investigate ligand migration in truncated hemoglobin (trHbN) and obtain kinetic information about the docking-site dynamics in the protein. A comparison with explicit water molecular dynamics simulations (100 ns in total) shows that the rate constants derived from the network analysis are realistic. The transition network analysis provides 1) The time-resolved connectivity network in the protein; 2) The half-lives of the docking sites; 3) The transition timescales between two given docking sites; and 4) The extent of population transfer among different docking sites of the protein as a function of lag time. We investigate the role of the Tyr33 and Gln58 residues in ligand migration by studying ligand migration in four mutants of trHbN. The mutation study suggests that residues Tyr33 and Gln58 stabilize the NO ligand in the Xe2 docking site of trHbN, thus facilitating the efficiency of the NO detoxification reaction.
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