title: Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates.
abstract: BACKGROUND
  Adenine and guanine phosphates are involved in a number of biological processes such as cell signaling, metabolism and enzymatic cofactor functions. Binding sites in proteins for these ligands are often detected by looking for a previously known motif by alignment based search. This is likely to miss those where a similar binding site has not been previously characterized and when the binding sites do not follow the rule described by predefined motif. Also, it is intriguing how proteins select between adenine and guanine derivative with high specificity.
  
  
  RESULTS
  Residue preferences for AMP, GMP, ADP, GDP, ATP and GTP have been investigated in details with additional comparison with cyclic variants cAMP and cGMP. We also attempt to predict residues interacting with these nucleotides using information derived from local sequence and evolutionary profiles. Results indicate that subtle differences exist between single residue preferences for specific nucleotides and taking neighbor environment and evolutionary context into account, successful models of their binding site prediction can be developed.
  
  
  CONCLUSIONS
  In this work, we explore how single amino acid propensities for these nucleotides play a role in the affinity and specificity of this set of nucleotides. This is expected to be helpful in identifying novel binding sites for adenine and guanine phosphates, especially when a known binding motif is not detectable.
authors.affiliation: Biomedical Informatics Center, PGIMER, Chandigarh-160012, India. adeel@netasa.org
authors.forename: Ahmad
authors.initials: A
authors.lastname: Firoz
authors.forename: Adeel
authors.initials: A
authors.lastname: Malik
authors.forename: Karl H
authors.initials: KH
authors.lastname: Joplin
authors.forename: Zulfiqar
authors.initials: Z
authors.lastname: Ahmad
authors.forename: Vivekanand
authors.initials: V
authors.lastname: Jha
authors.forename: Shandar
authors.initials: S
authors.lastname: Ahmad
mesh_terms: D000227:Adenine Nucleotides / Q000378:metabolism*; D001185:Artificial Intelligence; D001665:Binding Sites; D019295:Computational Biology; D000242:Cyclic AMP / Q000378:metabolism; D006152:Cyclic GMP / Q000378:metabolism; D006150:Guanine Nucleotides / Q000378:metabolism*; D006801:Humans; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012044:Regression Analysis; D013379:Substrate Specificity
chemical_list: D000227:Adenine Nucleotides; D006150:Guanine Nucleotides; D011506:Proteins; D000242:Cyclic AMP; D006152:Cyclic GMP