Combined Knowledge And Physics Based Approaches Towards Predicting Protein Structures
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Date
2009-12
Authors
Ahmad Khairudin, Nurul Bahiyah
Journal Title
Journal ISSN
Volume Title
Publisher
Universiti Sains Malaysia
Abstract
Proteins are the building blocks of life. Knowledge structure of proteins is of fundamental importance in understanding protein function. In this study, a new computational method was developed to predict these structures by combining the knowledge-based homology modelling and the physic based molecular dynamic simulation methods. The core region of the protein was initially constructed via homology modelling based on sequence similarity with other solved protein templates. Then, the remaining end-terminal region were allowed to fold towards the core region via MD simulation a few residue at a time. The method was categorized into three parts; the development of the core region of the protein, the development of the complete protein structure and the MD refinement simulation. This proposed technique was tested on three proteins with different size, cholesterol esterase (534 resedue), CC Chemokine Eotaxin-3 (71 residues) and chicken villin headpiece subdomain (36 resideues). The developed models were analysed and compared with their respective native structures, From the results, it was found that this method could successfully predict the structure of a small protein but showed a negative result for larger size proteins. Another important highlight of the current work is the identification of a ‘nucletaion center’ which facilitated the folding process of a small protein.
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Keywords
Combined Knowledge And Physics Based Approaches , Towards Predicting Protein Structures