ArticleBioinformatics (Oxford, England)2017
Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed, 3 citations in OpenAlex.
- GeTFEP: A general transfer free energy profile of transmembrane proteins.Protein science : a publication of the Protein Society · 2020Article
- High-resolution structure prediction ofProceedings of the National Academy of Sciences of the United States of America · 2018Article
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4 authors at 2 institutions in 1 country.
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Abstract
motivationTransmembrane beta-barrel proteins (TMBs) serve a multitude of essential cellular functions in Gram-negative bacteria, mitochondria and chloroplasts. Transfer free energies (TFEs) of residues in the transmembrane (TM) region provides fundamental quantifications of thermodynamic stabilities of TMBs, which are important for the folding and the membrane insertion processes, and may help in understanding the structure-function relationship. However, experimental measurement of TFEs of TMBs is challenging. Although a recent computational method can be used to calculate TFEs, the results of which are in excellent agreement with experimentally measured values, this method does not scale up, and is limited to small TMBs.
resultsWe have developed an approximation method that calculates TFEs of TM residues in TMBs accurately, with which depth-dependent transfer free energy profiles can be derived. Our results are in excellent agreement with experimental measurements. This method is efficient and applicable to all bacterial TMBs regardless of the size of the protein. AVAILABILITY AND IMPLEMENTATION: An online webserver is available at http://tanto.bioe.uic.edu/tmb-tfe . CONTACT: : jliang@uic.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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