Document Detail


Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions.
MedLine Citation:
PMID:  22579257     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The complex hydrophobic and hydrophilic milieus of membrane-associated proteins pose experimental and theoretical challenges to their understanding. Here, we produce a nonredundant database to compute knowledge-based asymmetric cross-membrane potentials from the per-residue distributions of C(β), C(γ) and functional group atoms. We predict transmembrane and peripherally associated regions from genomic sequence and position peptides and protein structures relative to the bilayer (available at http://www.degradolab.org/ez). The pseudo-energy topological landscapes underscore positional stability and functional mechanisms demonstrated here for antimicrobial peptides, transmembrane proteins, and viral fusion proteins. Moreover, experimental effects of point mutations on the relative ratio changes of dual-topology proteins are quantitatively reproduced. The functional group potential and the membrane-exposed residues display the largest energetic changes enabling to detect native-like structures from decoys. Hence, focusing on the uniqueness of membrane-associated proteins and peptides, we quantitatively parameterize their cross-membrane propensity, thus facilitating structural refinement, characterization, prediction, and design.
Authors:
Chaim A Schramm; Brett T Hannigan; Jason E Donald; Chen Keasar; Jeffrey G Saven; William F Degrado; Ilan Samish
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  Structure (London, England : 1993)     Volume:  20     ISSN:  1878-4186     ISO Abbreviation:  Structure     Publication Date:  2012 May 
Date Detail:
Created Date:  2012-05-14     Completed Date:  2012-09-10     Revised Date:  2014-09-11    
Medline Journal Info:
Nlm Unique ID:  101087697     Medline TA:  Structure     Country:  United States    
Other Details:
Languages:  eng     Pagination:  924-35     Citation Subset:  IM    
Copyright Information:
Copyright © 2012 Elsevier Ltd. All rights reserved.
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Databases, Factual
Hydrophobic and Hydrophilic Interactions
Knowledge Bases
Membrane Proteins / chemistry*
Models, Molecular
Proteins / chemistry*
Thermodynamics
Grant Support
ID/Acronym/Agency:
GM54616/GM/NIGMS NIH HHS; HL085303/HL/NHLBI NIH HHS; R01 GM054616/GM/NIGMS NIH HHS; R01 GM054616-08/GM/NIGMS NIH HHS; R01 HL085303/HL/NHLBI NIH HHS; R37 GM054616/GM/NIGMS NIH HHS; R37 GM054616-18/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Membrane Proteins; 0/Proteins
Comments/Corrections

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