A tool for the qualitative comparison of membrane-embedded and detergent-solubilized membrane protein structures in projection

Jeckelmann, Jean-Marc; Palacin, Manuel; Fotiadis, Dimitrios (2011). A tool for the qualitative comparison of membrane-embedded and detergent-solubilized membrane protein structures in projection. Journal of structural biology, 173(2), pp. 375-81. San Diego, Calif.: Elsevier 10.1016/j.jsb.2010.09.005

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The calculation of projection structures (PSs) from Protein Data Bank (PDB)-coordinate files of membrane proteins is not well-established. Reports on such attempts exist but are rare. In addition, the different procedures are barely described and thus difficult if not impossible to reproduce. Here we present a simple, fast and well-documented method for the calculation and visualization of PSs from PDB-coordinate files of membrane proteins: the projection structure visualization (PSV)-method. The PSV-method was successfully validated using the PS of aquaporin-1 (AQP1) from 2D crystals and cryo-transmission electron microscopy, and the PDB-coordinate file of AQP1 determined from 3D crystals and X-ray crystallography. Besides AQP1, which is a relatively rigid protein, we also studied a flexible membrane transport protein, i.e. the L-arginine/agmatine antiporter AdiC. Comparison of PSs calculated from the existing PDB-coordinate files of substrate-free and L-arginine-bound AdiC indicated that conformational changes are detected in projection. Importantly, structural differences were found between the PSV-method calculated PSs of the detergent-solubilized AdiC proteins and the PS from cryo-TEM of membrane-embedded AdiC. These differences are particularly exciting since they may reflect a different conformation of AdiC induced by the lateral pressure in the lipid bilayer.

Item Type:	Journal Article (Original Article)
Division/Institute:	04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Biochemistry and Molecular Medicine
UniBE Contributor:	Jeckelmann, Jean-Marc, Fotiadis, Dimitrios José
ISSN:	1047-8477
Publisher:	Elsevier
Language:	English
Submitter:	Factscience Import
Date Deposited:	04 Oct 2013 14:23
Last Modified:	05 Dec 2022 14:06
Publisher DOI:	10.1016/j.jsb.2010.09.005
PubMed ID:	20837147
Web of Science ID:	000286846700020
URI:	https://boris.unibe.ch/id/eprint/8147 (FactScience: 213634)