ArticleBMC structural biology2008
Charge environments around phosphorylation sites in proteins.
Article in BMC structural biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 33 citations in OpenAlex.
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- Features of reactive cysteines discovered through computation: from kinase inhibition to enrichment around protein degrons.Scientific reports · 2017Article
- Phosphorylation regulates the secondary structure and function of dentin phosphoprotein peptides.Bone · 2017Article
- Phosphorylation of Human Choline Kinase Beta by Protein Kinase A: Its Impact on Activity and Inhibition.PloS one · 2016Article
- Structural interrogation of phosphoproteome identified by mass spectrometry reveals allowed and disallowed regions of phosphoconformation.BMC structural biology · 2014Article
- Calcium/Calmodulin-dependent protein kinase is negatively and positively regulated by calcium, providing a mechanism for decoding calcium responses during symbiosis signaling.The Plant cell · 2013Article
- Phosphorylation variation during the cell cycle scales with structural propensities of proteins.PLoS computational biology · 2013Article
- Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.Nucleic acids research · 2011Article
- Calculating pKa values in the cAMP-dependent protein kinase: the effect of conformational change and ligand binding.Protein science : a publication of the Protein Society · 2010Article
- Local control of a disorder-order transition in 4E-BP1 underpins regulation of translation via eIF4E.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- The K-segment of maize DHN1 mediates binding to anionic phospholipid vesicles and concomitant structural changes.Plant physiology · 2009Article
- Sequence based residue depth prediction using evolutionary information and predicted secondary structure.BMC bioinformatics · 2008Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPhosphorylation 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.
resultsA 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.
conclusionIn 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.
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