title: Structural interrogation of phosphoproteome identified by mass spectrometry reveals allowed and disallowed regions of phosphoconformation.
abstract: BACKGROUND
  High-throughput mass spectrometric (HT-MS) study is the method of choice for monitoring global changes in proteome. Data derived from these studies are meant for further validation and experimentation to discover novel biological insights. Here we evaluate use of relative solvent accessible surface area (rSASA) and DEPTH as indices to assess experimentally determined phosphorylation events deposited in PhosphoSitePlus.
  
  
  RESULTS
  Based on accessibility, we map these identifications on allowed (accessible) or disallowed (inaccessible) regions of phosphoconformation. Surprisingly a striking number of HT-MS/MS derived events (1461/5947 sites or 24.6%) are present in the disallowed region of conformation. By considering protein dynamics, autophosphorylation events and/or the sequence specificity of kinases, 13.8% of these phosphosites can be moved to the allowed region of conformation. We also demonstrate that rSASA values can be used to increase the confidence of identification of phosphorylation sites within an ambiguous MS dataset.
  
  
  CONCLUSIONS
  While MS is a stand-alone technique for the identification of vast majority of phosphorylation events, identifications within disallowed region of conformation will benefit from techniques that independently probe for phosphorylation and protein dynamics. Our studies also imply that trapping alternate protein conformations may be a viable alternative to the design of inhibitors against mutation prone drug resistance kinases.
authors.forename: Arun Kumar
authors.initials: AK
authors.lastname: Somavarapu
authors.forename: Satish
authors.initials: S
authors.lastname: Balakrishnan
authors.forename: Amit Kumar Singh
authors.initials: AK
authors.lastname: Gautam
authors.forename: David S
authors.initials: DS
authors.lastname: Palmer
authors.affiliation: Protein Interactome Lab for Structural and Functional Biology, Advanced Center for Treatment Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India. vprasanna@actrec.gov.in.
authors.forename: Prasanna
authors.initials: P
authors.lastname: Venkatraman
mesh_terms: D000818:Animals; D019295:Computational Biology; D030541:Databases, Genetic; D006801:Humans; D013058:Mass Spectrometry; D008958:Models, Molecular; D010750:Phosphoproteins / Q000737:chemistry*; D010766:Phosphorylation; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D020543:Proteome / Q000737:chemistry*
chemical_list: D010750:Phosphoproteins; D020543:Proteome