ArticleBMC bioinformatics2016
A hydrophobic spine stabilizes a surface-exposed α-helix according to analysis of the solvent-accessible surface area.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Heparan sulfate as an attachment factor for ASFV is restricted by host HB-EGF.Cellular and molecular life sciences : CMLS · 2026Article
- Thermal denaturation of porcine myofibrillar proteins at different heating temperatures: A focus on the surface hydrophobicity.Food chemistry: X · 2025Article
- Cationic Surface Charge Engineering of Recombinant Transthyretin Remarkably Increases the Inhibitory Potency Against Amyloid β-Protein Fibrillogenesis.Molecules (Basel, Switzerland) · 2024Article
- Random Coils of Proteins Situated Between a Beta Strand and an Alpha Helix Demonstrate Decreased Solvent Accessibility.The protein journal · 2020Article
- Physicochemical Position-Dependent Properties in the Protein Secondary StructuresIranian biomedical journal · 2019Article
- Bioinformatics and systems biology research update from the 15BMC bioinformatics · 2016Article
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3 authors.
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Abstract
backgroundMost of hydrophilic and hydrophobic residues are thought to be exposed and buried in proteins, respectively. In contrast to the majority of the existing studies on protein folding characteristics using protein structures, in this study, our aim was to design predictors for estimating relative solvent accessibility (RSA) of amino acid residues to discover protein folding characteristics from sequences.
methodsThe proposed 20 real-value RSA predictors were designed on the basis of the support vector regression method with a set of informative physicochemical properties (PCPs) obtained by means of an optimal feature selection algorithm. Then, molecular dynamics simulations were performed for validating the knowledge discovered by analysis of the selected PCPs.
resultsThe RSA predictors had the mean absolute error of 14.11% and a correlation coefficient of 0.69, better than the existing predictors. The hydrophilic-residue predictors preferred PCPs of buried amino acid residues to PCPs of exposed ones as prediction features. A hydrophobic spine composed of exposed hydrophobic residues of an α-helix was discovered by analyzing the PCPs of RSA predictors corresponding to hydrophobic residues. For example, the results of a molecular dynamics simulation of wild-type sequences and their mutants showed that proteins 1MOF and 2WRP_H16I (Protein Data Bank IDs), which have a perfectly hydrophobic spine, have more stable structures than 1MOF_I54D and 2WRP do (which do not have a perfectly hydrophobic spine).
conclusionsWe identified informative PCPs to design high-performance RSA predictors and to analyze these PCPs for identification of novel protein folding characteristics. A hydrophobic spine in a protein can help to stabilize exposed α-helices.
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