Thermodynamics-Based Molecular Modeling of α-Helices in Membranes and Micelles
| Autor: | Kevin A. Schnitzer, Irina D. Pogozheva, Spencer C Todd, Andrei L. Lomize |
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| Rok vydání: | 2021 |
| Předmět: |
Protein Conformation
alpha-Helical 010304 chemical physics Molecular model Chemistry General Chemical Engineering Lipid Bilayers General Chemistry Crystal structure Library and Information Sciences 01 natural sciences Micelle Protein Structure Secondary 0104 chemical sciences Computer Science Applications Folding (chemistry) 010404 medicinal & biomolecular chemistry Crystallography Membrane 0103 physical sciences Helix Thermodynamics Lipid bilayer Peptide sequence Micelles |
| Zdroj: | Journal of chemical information and modeling. 61(6) |
| ISSN: | 1549-960X |
| Popis: | The Folding of Membrane-Associated Peptides (FMAP) method was developed for modeling α-helix formation by linear peptides in micelles and lipid bilayers. FMAP 2.0 identifies locations of α-helices in the amino acid sequence, generates their three-dimensional models in planar bilayers or spherical micelles, and estimates their thermodynamic stabilities and tilt angles, depending on temperature and pH. The method was tested for 723 peptides (926 data points) experimentally studied in different environments and for 170 single-pass transmembrane (TM) proteins with available crystal structures. FMAP 2.0 detected more than 95% of experimentally observed α-helices with an average error in helix end determination of around 2, 3, 4, and 5 residues per helix for peptides in water, micelles, bilayers, and TM proteins, respectively. Helical and nonhelical residue states were predicted with an accuracy from 0.86 to 0.96, and the Matthews correlation coefficient was from 0.64 to 0.88 depending on the environment. Experimental micelle- and membrane-binding energies and tilt angles of peptides were reproduced with a root-mean-square deviation of around 2 kcal/mol and 7°, respectively. The TM and non-TM states of hydrophobic and pH-triggered α-helical peptides in various lipid bilayers were reproduced in more than 95% of cases. The FMAP 2.0 web server (https://membranome.org/fmap) is publicly available to explore the structural polymorphism of antimicrobial, cell-penetrating, fusion, and other membrane-binding peptides, which is important for understanding the mechanisms of their biological activities. |
| Databáze: | OpenAIRE |
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