Knowledge-Based Potential for Positioning Membrane-Associated Structures and Assessing Residue-Specific Energetic Contributions

Loading...
Thumbnail Image
Penn collection
Departmental Papers (Chemistry)
Degree type
Discipline
Subject
Biochemistry
Organic Chemistry
Funder
Grant number
License
Copyright date
Distributor
Related resources
Author
Schramm, Chaim A
Donald, Jason E
Keasar, Chen
Samish, Ilan
Contributor
Abstract

The complex hydrophobic and hydrophilic milieus of membrane-associated proteins pose experimental and theoretical challenges to their understanding. Here we produce a non-redundant database to compute knowledge-based asymmetric cross-membrane potentials from the per-residue distributions of Cβ, Cγ 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.

Advisor
Date Range for Data Collection (Start Date)
Date Range for Data Collection (End Date)
Digital Object Identifier
Series name and number
Publication date
2012-05-09
Journal title
Structure
Volume number
Issue number
Publisher
Publisher DOI
Journal Issue
Comments
Recommended citation
Collection