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• W2002302312 startingPage "e32" @default.
• W2002302312 abstract "Post-translational phosphorylation is a ubiquitous mechanism for modulating protein activity and protein-protein interactions. In this work, we examine how phosphorylation can modulate the conformation of a protein by changing the energy landscape. We present a molecular mechanics method in which we phosphorylate proteins in silico and then predict how the conformation of the protein will change in response to phosphorylation. We apply this method to a test set comprised of proteins with both phosphorylated and non-phosphorylated crystal structures, and demonstrate that it is possible to predict localized phosphorylation-induced conformational changes, or the absence of conformational changes, with near-atomic accuracy in most cases. Examples of proteins used for testing our methods include kinases and prokaryotic response regulators. Through a detailed case study of cyclin-dependent kinase 2, we also illustrate how the computational methods can be used to provide new understanding of how phosphorylation drives conformational change, why substituting Glu or Asp for a phosphorylated amino acid does not always mimic the effects of phosphorylation, and how a phosphatase can “capture” a phosphorylated amino acid. This work illustrates how computational methods can be used to elucidate principles and mechanisms of post-translational phosphorylation, which can ultimately help to bridge the gap between the number of known sites of phosphorylation and the number of structures of phosphorylated proteins." @default.
• W2002302312 created "2016-06-24" @default.
• W2002302312 creator A5001224002 @default.
• W2002302312 creator A5039078525 @default.
• W2002302312 creator A5086944007 @default.
• W2002302312 date "2006-04-21" @default.
• W2002302312 modified "2023-09-27" @default.
• W2002302312 title "Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation" @default.
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• W2002302312 doi "https://doi.org/10.1371/journal.pcbi.0020032" @default.
• W2002302312 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/1440919" @default.
• W2002302312 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/16628247" @default.
• W2002302312 hasPublicationYear "2006" @default.
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