Hydrophobic-hydrophilic forces and their effects on protein structural similarity

Hydrophobic-hydrophilic interactions have a strong impact on the three-dimensional structure a protein will adopt. Because structure, not amino acid sequence order, carry out certain functions it is important to understand how these forces affect the protein folding process. In recent years, a lot of focus has been dedicated towards ab initio protein folding prediction, which tries to predict a proteins native conformation from its sequence alone. To aid this type of prediction sub-conformations from already known proteins are used to limit the free energy conformational search space. In this paper we looked into the sub-conformations’ hydrophobic-hydrophilic nature by incorporating a HP approach and proposed a way of evaluating how these type of forces affect the protein folding process. By doing this, we can gain insight into how hydrophobic-hydrophilic interactions affect protein structural similarity, and thus aid us in picking more suitable sub-conformations based off their HP shape for use in protein structure prediction. PRIB 2008 proceedings found at: http://dx.doi.org/10.1007/978-3-540-88436-1 Contributors: Monash University. Faculty of Information Technology. Gippsland School of Information Technology ; Chetty, Madhu ; Ahmad, Shandar ; Ngom, Alioune ; Teng, Shyh Wei ; Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB) (3rd : 2008 : Melbourne, Australia) ; Coverage: Rights: Copyright by Third IAPR International Conference on Pattern Recognition in Bioinformatics. All rights reserved.