ArticleProteins2016
Refining the treatment of membrane proteins by coarse-grained models.
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- Understanding hypertrophic cardiomyopathy and its regulation by myosin drugs.Protein science : a publication of the Protein Society · 2025Article
- Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators.Journal of chemical information and modeling · 2025Article
- Computational and Experimental Study of the Conformational Variation of the Catalytic Residue His41 of the SARS-CoV-2 Main Protease.The journal of physical chemistry. B · 2025Article
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- Exploring the Activation Process of the Glycine Receptor.Journal of the American Chemical Society · 2024Article
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- Exploring the activation mechanism of metabotropic glutamate receptor 2.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Energetic and structural insights behind calcium induced conformational transition in calmodulin.Proteins · 2024Article
- Predicting Mutational Effects on CaJournal of the American Chemical Society · 2024Article
- Exploring the Phospholipid Transport Mechanism of ATP8A1-CDC50.Biomedicines · 2023Article
- The Nature of Functional Features of Different Classes of G-Protein-Coupled Receptors.Biology · 2022Article
- Application of Computational Biology and Artificial Intelligence in Drug Design.International journal of molecular sciences · 2022Review
- Mechanism Study of Proteins under Membrane Environment.Membranes · 2022Article
- Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange process.Journal of computational chemistry · 2022Article
- Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines.Entropy (Basel, Switzerland) · 2022Article
- Electrostatic influence on IL-1 transport through the GSDMD pore.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Obtaining a quantitative description of the membrane proteins stability is crucial for understanding many biological processes. However the advance in this direction has remained a major challenge for both experimental studies and molecular modeling. One of the possible directions is the use of coarse-grained models but such models must be carefully calibrated and validated. Here we use a recent progress in benchmark studies on the energetics of amino acid residue and peptide membrane insertion and membrane protein stability in refining our previously developed coarse-grained model (Vicatos et al., Proteins 2014;82:1168). Our refined model parameters were fitted and/or tested to reproduce water/membrane partitioning energetics of amino acid side chains and a couple of model peptides. This new model provides a reasonable agreement with experiment for absolute folding free energies of several β-barrel membrane proteins as well as effects of point mutations on a relative stability for one of those proteins, OmpLA. The consideration and ranking of different rotameric states for a mutated residue was found to be essential to achieve satisfactory agreement with the reference data.
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