alexa Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding
ISSN: 0974-276X

Journal of Proteomics & Bioinformatics
Open Access

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Research Article

Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding

Yoojin Hong1,2#, Dimitra Chalkia3#, Kyung Dae Ko1,3, Gaurav Bhardwaj1,3, Gue Su Chang1,3, Damian B. van Rossum1,3*, Randen L. Patterson1,3*

1Center for Computational Proteomics

2Department of Computer Science

3Department of Biology, The Pennsylvania State University

#These authors contributed equally to this work

*Corresponding Author:
Dr. Randen L. Patterson
230 Life Science Bldg
University Park, PA 16802
Tel: 001-814-865-1668
Fax : 001-814-863-1357
E-mail: [email protected]

Dr. Damian B. van Rossum
518 Wartik Labs
University Park, PA 16802
Tel: 001-814-863-1007
Fax : 001-814-863-1357
E-mail: [email protected]

Received Date: February 12, 2009; Accepted Date: March 20, 2009; Published Date: March 21, 2009

Citation: Hong Y, Chalkia D, Ko KD, Bhardwaj G, Chang GS, et al. (2009) Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding. J Proteomics Bioinform 2: 139-149. doi: 10.4172/jpb.1000071

Copyright: © 2009 Hong Y, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.



One of the major challenges in the genomic era is a nnotating structure/function to the vast quantities of se- quence information now available. Indeed, most of t he protein sequence database lacks comprehensive an nota- tion, even when experimental evidence exists. Furth er, within structurally resolved and functionally a nnotated protein domains, additional functionalities contain ed in these domains are not apparent. To add furthe r complica- tion, small changes in the amino-acid sequence can lead to profound changes in both structure and func tion, underscoring the need for rapid and reliable method s to analyze these types of data. Phylogenetic prof iles pro- vide a quantitative method that can relate the stru ctural and functional properties of proteins, as we ll as their evolutionary relationships. Using all of the struct urally resolved Src-Homology-2 (SH2) domains, we de mon- strate that knowledge-bases can be used to create s ingle-amino acid phylogenetic profiles which reliab ly anno- tate lipid-binding. Indeed, these measures isolate the known phosphotyrosine and hydrophobic pockets a s inte- gral to lipid-binding function. In addition, we det ermined that the SH2 domain of Tec family kinases b ind to lipids with varying affinity and specificity. Simulating mutations in Bruton’s tyrosine kinase (BTK) that ca use X-Linked Agammaglobulinemia (XLA) predict that these mutatio ns alter lipid-binding, which we confirm experiment ally. In light of these results, we propose that XLA-caus ing mutations in the SH3-SH2 domain of BTK alter li pid- binding, which could play a causative role in the X LA-phenotype. Overall, our study suggests that the number of lipid-binding proteins is drastically underestimate d and, with further development, phylogenetic profi les can provide a method for rapidly increasing the functio nal annotation of protein sequences.

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