Membrane protein structure quality in molecular dynamics simulation Richard J. Law a, * , Charlotte Capener a , Marc Baaden b , Peter J. Bond a , Jeff Campbell a , George Patargias a , Yalini Arinaminpathy a , Mark S.P. Sansom a a Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK b Institut de Biologie Physico-Chimique, CNRS-UPR9080, 13 rue Pierre et Marie Curie, F-75005 Paris, France Accepted 4 May 2005 Available online 15 August 2005 Abstract Our goal was to assess the relationship between membrane protein quality, output from protein quality checkers and output from molecular dynamics (MD) simulations. Membrane transport proteins are essential for a wide range of cellular processes. Structural features of integral membrane proteins are still under-explored due to experimental limitations in structure determination. Computational techniques can be used to exploit biochemical and medium resolution structural data, as well as sequence homology to known structures, and enable us to explore the structure–function relationships in several transmembrane proteins. The quality of the models produced is vitally important to obtain reliable predictions. An examination of the relationship between model stability in molecular dynamics (MD) simulations derived from RMSD (root mean squared deviation) and structure quality assessment from various protein quality checkers was undertaken. The results were compared to membrane protein structures, solved at various resolution, by either X-ray or electron diffraction techniques. The checking programs could predict the potential success of MD in making functional conclusions. MD stability was shown to be a good indicator for the quality of structures. The quality was also shown to be dependent on the resolution at which the structures were determined. # 2005 Elsevier Inc. All rights reserved. Keywords: Protein structure; Homology modeling; Simulation; Protein quality checking; X-ray crystallography; Electron microscopy 1. Introduction It is theoretically possible for every protein structure solved to be at atomic resolution, without the need for model refinement, in this case the quality would not need to be checked [1]. But this is not the case. For membrane proteins, in particular, the situation is worse due to the added difficulties with solving their structures [2]. This explains why only structures for 82 different membrane proteins (including homologous proteins from different organisms) (http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html) have been solved so far (<1% of the estimated total number of membrane proteins) even though they represent about 30% of most genomes. However, this number is rapidly increasing with the release of several recent membrane protein structures with diverse biological function [3–11]. Homology modeling is a process that attempts to redress the balance somewhat. One caveat is that significant uncertainty remains concerning the atomic coordinates of both homology models and medium resolution structures and therefore it is important that we have methods to check their validity. The accuracy of a structure has direct implications on the elucidation of structure–function relationships and protein quality check- ers can avoid drawing invalid mechanistic conclusions from bad starting structures. There is a need to assess the quality of a homology model, as well as asking how well it compares to experimentally determined structures of various resolutions. The large number of models for aquaporins and potassium channels is one area where model and experi- mental structure can readily be compared, and will be www.elsevier.com/locate/JMGM Journal of Molecular Graphics and Modelling 24 (2005) 157–165 * Corresponding author at: Chemistry and Biochemistry Department, 9500 Gilman Drive, University of California, San Diego, La Jolla, CA 92093-0365, USA. Tel.: +1 858 349 6369; fax: +1 858 349 6369. E-mail address: rlaw@mccammon.ucsd.edu (R.J. Law). 1093-3263/$ – see front matter # 2005 Elsevier Inc. All rights reserved. doi:10.1016/j.jmgm.2005.05.006