We are analyzing https://link.springer.com/article/10.1186/1472-6807-8-19.

Title:
Charge environments around phosphorylation sites in proteins | BMC Structural Biology
Description:
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.
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Keywords {🔍}

sites, phosphorylation, phosphorylated, article, google, scholar, cas, interactions, protein, figure, charge, phosphoelm, nonphosphorylated, proteins, set, structural, structures, sequence, site, change, pdb, interaction, conformational, solvent, tyr, database, ser, thr, calculations, dataset, radius, prediction, authors, phosphoacceptor, surface, accessibility, file, original, analysis, data, stabilisation, sidechains, favourable, model, structurally, sets, burial, full, separation, distributions,

Topics {✒️}

protein post-translational modification open access article post-translational modifications serotonin n-acetyltransferase complex finite difference poisson-boltzmann β-catenin/e-cadherin complex phosphorylation/charge-driven conformational change phosphoserine-lysine salt bridge phosphorylated serotonin n-acetyltransferase adipocyte lipid-binding protein site-specific phosphorylation dynamics high-throughput proteomics data related subjects article download pdf arginine-phosphate electrostatic interaction pk-specific phosphorylation sites protein-protein interaction databases β-catenin repeat interactions polar area/total area charge/electrostatic potential neighbourhood model-building torsional angles surrounding residues colour-coded structural systems biology post-translational phosphorylation full size image favourable charge-charge interactions water-dominated interaction scheme p-loop mainchain interaction group-based phosphorylation predicting privacy choices/manage cookies related pdb entries cancer research uk authors’ original file amino acid sequence phosphorylation-induced conformational change α-helix terminus larger burial depth α-helix stability article kitchen low solvent accessibility specific phosphorylation pathways phospho-acceptor sites relative protein-protein interactions full access support vector machines cyclin-dependent kinase bioinformatics resource dedicated charge interaction energies acceptor site geometry ptr representing phosphoserine

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         description: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. 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. 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.
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            Cystic Fibrosis Transmembrane Conductance Regulator
            Burial Depth
            Solvent Accessibility
            Charge Interaction
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            general
            Protein Science
            Crystallography and Scattering Methods
            Mass Spectrometry
            Spectroscopy/Spectrometry
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      headline:Charge environments around phosphorylation sites in proteins
      description: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. 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. 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.
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         Phosphorylation Site
         Cystic Fibrosis Transmembrane Conductance Regulator
         Burial Depth
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         general
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         Crystallography and Scattering Methods
         Mass Spectrometry
         Spectroscopy/Spectrometry
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