ArticleEuropean biophysics journal : EBJ2008
Molecular dynamics simulations and membrane protein structure quality.
Article in European biophysics journal : EBJ, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Effect of THz Waves of Different Orientations on KInternational journal of molecular sciences · 2023Article
- Probing the Interactions Responsible for the Structural Stability of Trypanothione Reductase Through Computer Simulation and Biophysical Characterization.The protein journal · 2022Article
- Ins and outs of AlphaFold2 transmembrane protein structure predictions.Cellular and molecular life sciences : CMLS · 2022Article
- Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators.RSC medicinal chemistry · 2021Review
- The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment.PloS one · 2018Article
- Jump into a New Fold-A Homology Based Model for the ABCG2/BCRP Multidrug Transporter.PloS one · 2016Article
- On the origin of large flexibility of P-glycoprotein in the inward-facing state.The Journal of biological chemistry · 2013Article
- Characterization of adenosine receptor in its native environment: insights from molecular dynamics simulations of palmitoylated/glycosylated, membrane-integrated human A(2B) adenosine receptor.Journal of molecular modeling · 2012Article
- Structural insights into human GPCR protein OA1: a computational perspective.Journal of molecular modeling · 2012Article
- Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex.PLoS computational biology · 2011Article
- Computational study of the Na+/H + antiporter from Vibrio parahaemolyticus.Journal of molecular modeling · 2011Article
- Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes.Nature communications · 2011Article
- Article
- Molecular dynamics simulations of membrane channels and transporters.Current opinion in structural biology · 2009Review
- A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach.Computational biology and chemistry · 2009Article
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Authors and funding
2 authors.
Funding
Abstract
Despite a growing repertoire of membrane protein structures (currently approximately 120 unique structures), considerations of low resolution and crystallization in the absence of a lipid bilayer require the development of techniques to assess the global quality of membrane protein folds. This is also the case for assessment of, e.g. homology models of human membrane proteins based on structures of (distant) bacterial homologues. Molecular dynamics (MD) simulations may be used to help evaluate the quality of a membrane protein structure or model. We have used a structure of the bacterial ABC transporter MsbA which has the correct transmembrane helices but an incorrect handedness and topology of their packing to test simulation methods of quality assessment. An MD simulation of the MsbA model in a lipid bilayer is compared to a simulation of another bacterial ABC transporter, BtuCD. The latter structure has demonstrated good conformational stability in the same bilayer environment and over the same timescale (20 ns) as for the MsbA model simulation. A number of comparative analyses of the two simulations were performed to assess changes in the structural integrity of each protein. The results show a significant difference between the two simulations, chiefly due to the dramatic structural deformations of MsbA. We therefore propose that MD could become a useful quality control tool for membrane protein structural biology. In particular, it provides a way in which to explore the global conformational stability of a model membrane protein fold.
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