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• W2335699326 abstract "Conceptually, the simplistic lock and key model has been superseded by more realistic views of molecular recognition that take into account the intrinsic dynamics of biological macromolecules. However, it is still common for structure-based drug discovery methods to represent the receptor as static structures. The practical advantages of this approximation, the notable success attained over the past few decades with such simple models and the absence of clear guidelines for weighing the pros and cons of accounting for flexibility may prompt some investigators to stretch the rigid model beyond its scope. Here, we investigate the relationship between protein flexibility and binding free energy and present some useful hints for understanding when, and to what extent, flexibility should be considered. Using molecular dynamics simulations of hen egg-white lysozyme (HEWL) with explicit aqueous/organic solvent mixtures and a range of restraint conditions, we find out how artificially restricted mobility affects binding hot spots. Barring sampling errors or an inappropriate choice of reference structure, we find that decreased mobility (measured as B-factors) leads to artifactually more negative binding free energies, but a logarithmic relationship between both terms attenuates the errors. Consequently, ignoring flexibility may be an acceptable approximation for intrinsically rigid regions (such as the active site of enzymes) but may lead to larger errors elsewhere. For the same reason, local conformational sampling yields very accurate predictions and, owing to its practical advantages, may be preferable to full conformational sampling for many applications." @default.
• W2335699326 created "2016-06-24" @default.
• W2335699326 creator A5004496357 @default.
• W2335699326 creator A5037789245 @default.
• W2335699326 date "2014-05-30" @default.
• W2335699326 modified "2023-10-17" @default.
• W2335699326 title "Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design" @default.
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• W2335699326 doi "https://doi.org/10.1021/ct500182z" @default.
• W2335699326 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/26580781" @default.
• W2335699326 hasPublicationYear "2014" @default.
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