Ab-initio protein structure prediction of Leucosporidium antarcticum antifreeze proteins using I-TASSER simulations

Abdul Rahman, Mohd Basyaruddin and Zulkifli, Mohamad Fairuz and Basri, Mahiran and Raja Abdul Rahman, Raja Noor Zaliha and Salleh, Abu Bakar (2008) Ab-initio protein structure prediction of Leucosporidium antarcticum antifreeze proteins using I-TASSER simulations. In: 9th WSEAS International Conference on Mathematics & Computers in Biology & Chemistry (MCBC '08), June 24-26, 2008, Bucharest, Romania.

Full text not available from this repository.

Official URL: http://www.wseas.us/e-library/conferences/2008/rho...

Abstract

Organisms living in cold environment produce some Antifreeze Protein (AFP) which exhibit special functions as a result of cold adaption. AFP is currently being identified in many organisms such as bacteria, plants, fish, and fungi that exposed to freezing stress. Due to the limited structural information from fold library, it gave a big challenge in its structure prediction. Therefore, this study seeks to predict the three-dimensional (3D) model of the Leucosporidium antarcticum antifreeze protein by using homology modeling, threading and ab-initio methods. As low of percentage of sequence identity, not more than 25% (‘twilight zone’) and poor results in threading methods, the search proceeded with ab-initio method by using I-TASSER simulations, where 5 predicted models were obtained. All the models were then evaluated with PROCHECK and Verify3D servers. Ramachandran Plot showed that the residues in most favored regions were 75.2% with only 4 residues in disallowed regions (Ser21, Phe29, Ala100 and Ala114). For the Verify3D, the structurally and functionally important residues in AFP have scored from 0.30-0.60. These results suggest that ab-initio methods as I-TASSER may soon become useful for low-resolution structure prediction for proteins that lack of close homologue of known structure.

Item Type:Conference or Workshop Item (Paper)
Keyword:antifreeze proteins (AFP), Leucosporidium, homology modeling, fold recognition/threading, ab-initio, I-TASSER
Subject:Antifreeze proteins
Faculty or Institute:Faculty of Science
ID Code:8872
Deposited By: Samsida Samsudin
Deposited On:23 Dec 2010 07:33
Last Modified:23 Dec 2010 07:34

Repository Staff Only: item control page


Universiti Putra Malaysia Institutional Repository

Universiti Putra Malaysia Institutional Repository is an on-line digital archive that serves as a central collection and storage of scientific information and research at the Universiti Putra Malaysia.

Currently, the collections deposited in the IR consists of Master and PhD theses, Master and PhD Project Report, Journal Articles, Journal Bulletins, Conference Papers, UPM News, Newspaper Cuttings, Patents and Inaugural Lectures.

As the policy of the university does not permit users to view thesis in full text, access is only given to the first 24 pages only.