NDLI: Evaluating Tilt Angles of Membrane-Associated Helices: Comparison of Computational and NMR Techniques

Content Provider	PubMed Central
Author	Ulmschneider, Martin B. Sansom, Mark S. P. Nola, Alfredo Di
Copyright Year	2006
Abstract	A computational method to calculate the orientation of membrane-associated α-helices with respect to a lipid bilayer has been developed. It is based on a previously derived implicit membrane representation, which was parameterized using the structures of 46 α-helical membrane proteins. The method is validated by comparison with an independent data set of six transmembrane and nine antimicrobial peptides of known structure and orientation. The minimum energy orientations of the transmembrane helices were found to be in good agreement with tilt and rotation angles known from solid-state NMR experiments. Analysis of the free-energy landscape found two types of minima for transmembrane peptides: i), Surface-bound configurations with the helix long axis parallel to the membrane, and ii), inserted configurations with the helix spanning the membrane in a perpendicular orientation. In all cases the inserted configuration also contained the global energy minimum. Repeating the calculations with a set of solution NMR structures showed that the membrane model correctly distinguishes native transmembrane from nonnative conformers. All antimicrobial peptides investigated were found to orient parallel and bind to the membrane surface, in agreement with experimental data. In all cases insertion into the membrane entailed a significant free-energy penalty. An analysis of the contributions of the individual residue types confirmed that hydrophobic residues are the main driving force behind membrane protein insertion, whereas polar, charged, and aromatic residues were found to be important for the correct orientation of the helix inside the membrane.
Related Links	http://dx.doi.org/10.1529/biophysj.105.065367
Starting Page	1650
File Format	PDF
ISSN	15420086
e-ISSN	15420086
Journal	Biophysical Journal
Issue Number	5
Volume Number	90
Language	English
Publisher	Biophysical Society
Publisher Date	2006-03-01
Access Restriction	Open
Rights Holder	Biophysical Society
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Biophysics

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