Computational and Mathematical Methods in Medicine
Volume 2013 (2013), Article ID 470390, 11 pages
Uses of Phage Display in Agriculture: Sequence Analysis and Comparative Modeling of Late Embryogenesis Abundant Client Proteins Suggest Protein-Nucleic Acid Binding Functionality
1Agricultural Science Center, Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA
2Seed Biology Group, University of Kentucky, Lexington, KY 40546, USA
3Plant Science Building, Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA
4Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
5Center for Computational Sciences, University of Kentucky, Lexington, KY 40506, USA
Received 27 February 2013; Accepted 2 April 2013
Academic Editor: Jian Huang
Copyright © 2013 Rekha Kushwaha et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
A group of intrinsically disordered, hydrophilic proteins—Late Embryogenesis Abundant (LEA) proteins—has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules.