Document Type
Article
Publication Date
5-17-2011
Description
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. Conclusion: 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.
Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.
Citation Information
Firoz, Ahmad; Malik, Adeel; Joplin, Karl H.; Ahmad, Zulfiqar; Jha, Vivekanand; and Ahmad, Shandar. 2011. Residue Propensities, Discrimination and Binding Site Prediction of Adenine and Guanine Phosphates. BMC Biochemistry. Vol.12(1). https://doi.org/10.1186/1471-2091-12-20 PMID: 21569447
Copyright Statement
© 2011 Firoz et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.