ArticleScientific reports2019
A comprehensive computational study of amino acid interactions in membrane proteins.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 63 citations in OpenAlex.
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- Prediction of pathogenic mutations in human transmembrane proteins and their associated diseases via utilizing pre-trained Bio-LLMs.Communications biology · 2025Article
- Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces.Journal of chemical information and modeling · 2025Article
- A quantitative analysis of ligand binding at the protein-lipid bilayer interface.Communications chemistry · 2025Article
- Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3.Communications chemistry · 2025Article
- A roadmap to cysteine specific labeling of membrane proteins for single-molecule photobleaching studies.Methods (San Diego, Calif.) · 2025Article
- Illustrative Features and Utilities of MPAD: Thermodynamic Database for Membrane Protein-Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Identification of Kunitz-Type Inhibitor Gene Family ofInternational journal of molecular sciences · 2024Article
- KAT6A Condensates Impair PARP1 Trapping of PARP Inhibitors in Ovarian Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Regulation of the Function and Expression of EpCAM.Biomedicines · 2024Review
- Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques.bioRxiv : the preprint server for biology · 2024Article
- Metabolic profiling of bacteria with the application of polypyrrole-MOF SPME fibers and plasmonic nanostructured LDI-MS substrates.Scientific reports · 2024Article
- Missense3D-TM: Predicting the Effect of Missense Variants in Helical Transmembrane Protein Regions Using 3D Protein Structures.Journal of molecular biology · 2024Article
- Functional Role of an Unusual Transmembrane Acidic Residue in the Calcium Pump Regulator Myoregulin.Biochemistry · 2023Article
- Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications.Computational and structural biotechnology journal · 2023Review
- Cardiolipin occupancy profiles of YidC paralogs reveal the significance of respective TM2 helix residues in determining paralog-specific phenotypes.Frontiers in molecular biosciences · 2023Article
- Thermostability engineering of industrial enzymes through structure modification.Applied microbiology and biotechnology · 2022Review
- A Census of Human Methionine-Rich Prion-like Domain-Containing Proteins.Antioxidants (Basel, Switzerland) · 2022Article
- Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines.Entropy (Basel, Switzerland) · 2022Article
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Authors and funding
6 authors at 1 institution in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transmembrane proteins play a fundamental role in a wide series of biological processes but, despite their importance, they are less studied than globular proteins, essentially because their embedding in lipid membranes hampers their experimental characterization. In this paper, we improved our understanding of their structural stability through the development of new knowledge-based energy functions describing amino acid pair interactions that prevail in the transmembrane and extramembrane regions of membrane proteins. The comparison of these potentials and those derived from globular proteins yields an objective view of the relative strength of amino acid interactions in the different protein environments, and their role in protein stabilization. Separate potentials were also derived from α-helical and β-barrel transmembrane regions to investigate possible dissimilarities. We found that, in extramembrane regions, hydrophobic residues are less frequent but interactions between aromatic and aliphatic amino acids as well as aromatic-sulfur interactions contribute more to stability. In transmembrane regions, polar residues are less abundant but interactions between residues of equal or opposite charges or non-charged polar residues as well as anion-π interactions appear stronger. This shows indirectly the preference of the water and lipid molecules to interact with polar and hydrophobic residues, respectively. We applied these new energy functions to predict whether a residue is located in the trans- or extramembrane region, and obtained an AUC score of 83% in cross validation, which demonstrates their accuracy. As their application is, moreover, extremely fast, they are optimal instruments for membrane protein design and large-scale investigations of membrane protein stability.
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