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Charge environments around phosphorylation sites in proteins
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Kitchen, James, Saunders, Rebecca E. and Warwicker, Jim (2008) Charge environments around phosphorylation sites in proteins. BMC Structural Biology, Vol.8 (No.1). p. 19. doi:10.1186/1472-6807-8-19 ISSN 1472-6807.
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Official URL: http://dx.doi.org/10.1186/1472-6807-8-19
Abstract
Background: Phosphorylation is a central feature in many biological processes. Structural analyses
have identified the importance of charge-charge interactions, for example mediating
phosphorylation-driven allosteric change and protein binding to phosphopeptides. Here, we
examine computationally the prevalence of charge stabilisation around phosphorylated sites in the
structural database, through comparison with locations that are not phosphorylated in the same
structures.
Results: A significant fraction of phosphorylated sites appear to be electrostatically stabilised,
largely through interaction with sidechains. Some examples of stabilisation across a subunit
interface are evident from calculations with biological units. When considering the immediately
surrounding environment, in many cases favourable interactions are only apparent after
conformational change that accompanies phosphorylation. A simple calculation of potential
interactions at longer-range, applied to non-phosphorylated structures, recovers the separation
exhibited by phosphorylated structures. In a study of sites in the Phospho.ELM dataset, for which
structural annotation is provided by non-phosphorylated proteins, there is little separation of the
known phospho-acceptor sites relative to background, even using the wider interaction radius.
However, there are differences in the distributions of patch polarity for acceptor and background
sites in the Phospho.ELM dataset.
Conclusion: In this study, an easy to implement procedure is developed that could contribute to
the identification of phospho-acceptor sites associated with charge-charge interactions and
conformational change. Since the method gives information about potential anchoring interactions
subsequent to phosphorylation, it could be combined with simulations that probe conformational
change. Our analysis of the Phospho.ELM dataset also shows evidence for mediation of
phosphorylation effects through (i) conformational change associated with making a solvent
inaccessible phospho-acceptor site accessible, and (ii) modulation of protein-protein interactions.
Item Type: | Journal Article | ||||
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Subjects: | Q Science > QP Physiology | ||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||
Library of Congress Subject Headings (LCSH): | Phosphorylation, Electrostatics | ||||
Journal or Publication Title: | BMC Structural Biology | ||||
Publisher: | BioMed Central Ltd. | ||||
ISSN: | 1472-6807 | ||||
Official Date: | 2008 | ||||
Dates: |
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Volume: | Vol.8 | ||||
Number: | No.1 | ||||
Page Range: | p. 19 | ||||
DOI: | 10.1186/1472-6807-8-19 | ||||
Status: | Peer Reviewed | ||||
Access rights to Published version: | Open Access (Creative Commons) | ||||
Date of first compliant deposit: | 17 December 2015 | ||||
Date of first compliant Open Access: | 17 December 2015 | ||||
Funder: | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC) |
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