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Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling.

Title: Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling.
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Name(s): Lv, Chao, author
Aitchison, Erick W, author
Wu, Dongsheng, author
Zheng, Lianqing, author
Cheng, Xiaolin, author
Yang, Wei, author
Type of Resource: text
Genre: Journal Article
Text
Date Issued: 2016-03-05
Physical Form: computer
online resource
Extent: 1 online resource
Language(s): English
Abstract/Description: Hydrogen sulfide (H2 S), a commonly known toxic gas compound, possesses unique chemical features that allow this small solute molecule to quickly diffuse through cell membranes. Taking advantage of the recent orthogonal space tempering (OST) method, we comparatively mapped the transmembrane free energy landscapes of H2 S and its structural analogue, water (H2 O), seeking to decipher the molecular determinants that govern their drastically different permeabilities. As revealed by our OST sampling results, in contrast to the highly polar water solute, hydrogen sulfide is evidently amphipathic, and thus inside membrane is favorably localized at the interfacial region, that is, the interface between the polar head-group and nonpolar acyl chain regions. Because the membrane binding affinity of H2 S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the transmembrane free energy barriers to encounter by this toxic molecule are very small. Moreover when H2 S diffuses from the bulk solution to the membrane center, the above two effects nearly cancel each other, so as to lead to a negligible free energy difference. This study not only explains why H2 S can quickly pass through cell membranes but also provides a practical illustration on how to use the OST free energy sampling method to conveniently analyze complex molecular processes. © 2015 Wiley Periodicals, Inc.
Identifier: FSU_pmch_26119423 (IID), 10.1002/jcc.23982 (DOI), PMC4959446 (PMCID), 26119423 (RID), 26119423 (EID)
Keywords: Enhanced sampling, Free energy calculation, Membrane permeation
Grant Number: R01 GM111886
Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959446.
Subject(s): Cell Membrane/chemistry
Cell Membrane/metabolism
Cell Membrane Permeability
Computer Simulation
Diffusion
Humans
Hydrogen Sulfide/chemistry
Hydrogen Sulfide/metabolism
Hydrophobic and Hydrophilic Interactions
Models, Biological
Thermodynamics
Water/chemistry
Water/metabolism
Persistent Link to This Record: http://purl.flvc.org/fsu/fd/FSU_pmch_26119423
Owner Institution: FSU
Is Part Of: Journal of computational chemistry.
1096-987X
Issue: iss. 6, vol. 37

Choose the citation style.
Lv, C., Aitchison, E. W., Wu, D., Zheng, L., Cheng, X., & Yang, W. (2016). Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling. Journal Of Computational Chemistry. Retrieved from http://purl.flvc.org/fsu/fd/FSU_pmch_26119423