Document Detail


Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations.
MedLine Citation:
PMID:  17012325     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Understanding the solvation of amino acids in biomembranes is an important step to better explain membrane protein folding. Several experimental studies have shown that polar residues are both common and important in transmembrane segments, which means they have to be solvated in the hydrophobic membrane, at least until helices have aggregated to form integral proteins. In this work, we have used computer simulations to unravel these interactions on the atomic level, and classify intramembrane solvation properties of amino acids. Simulations have been performed for systematic mutations in poly-Leu helices, including not only each amino acid type, but also every z-position in a model helix. Interestingly, many polar or charged residues do not desolvate completely, but rather retain hydration by snorkeling or pulling in water/headgroups--even to the extent where many of them exist in a microscopic polar environment, with hydration levels corresponding well to experimental hydrophobicity scales. This suggests that even for polar/charged residues a large part of solvation cost is due to entropy, not enthalpy loss. Both hydration level and hydrogen bonding exhibit clear position-dependence. Basic side chains cause much less membrane distortion than acidic, since they are able to form hydrogen bonds with carbonyl groups instead of water or headgroups. This preference is supported by sequence statistics, where basic residues have increased relative occurrence at carbonyl z-coordinates. Snorkeling effects and N-/C-terminal orientation bias are directly observed, which significantly reduces the effective thickness of the hydrophobic core. Aromatic side chains intercalate efficiently with lipid chains (improving Trp/Tyr anchoring to the interface) and Ser/Thr residues are stabilized by hydroxyl groups sharing hydrogen bonds to backbone oxygens.
Authors:
Anna C V Johansson; Erik Lindahl
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2006-09-29
Journal Detail:
Title:  Biophysical journal     Volume:  91     ISSN:  0006-3495     ISO Abbreviation:  Biophys. J.     Publication Date:  2006 Dec 
Date Detail:
Created Date:  2006-11-28     Completed Date:  2007-02-08     Revised Date:  2013-06-07    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  United States    
Other Details:
Languages:  eng     Pagination:  4450-63     Citation Subset:  IM    
Affiliation:
Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden.
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MeSH Terms
Descriptor/Qualifier:
Amino Acids / chemistry*
Cell Membrane*
Computer Simulation*
Hydrogen Bonding
Membrane Proteins / chemistry*
Models, Molecular*
Protein Folding*
Protein Structure, Secondary
Water / chemistry
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Membrane Proteins; 7732-18-5/Water
Comments/Corrections

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