Submit Manuscript  

Article Details


Protein Secondary Structure Determination (PSSD): A New and Simple Approach

[ Vol. 16 , Issue. 3 ]

Author(s):

Anindya Sundar Panja, Bidyut Bandopadhyay, Akash Nag and Smarajit Maiti*   Pages 246 - 253 ( 8 )

Abstract:


Background: Our present investigation was conducted to explore the computational algorithm for the protein secondary structure prediction as per the property of evolutionary transient and large number (each 50) of homologous mesophilic-thermophilic proteins.

Objectives: These mesophilic-thermophilic proteins were used for numerical measurement of helix-sheetcoil and turn tendency for which each amino-acid residue is screened to build up the propensity-table.

Methods: In the current study, two different propensity windows have been introduced that allowed predicting the secondary structure of protein more than 80% accuracy.

Results: Using this propensity matrix and dynamic algorithm-based programme, a significant and decisive outcome in the determination of protein (both thermophilic and mesophilic) secondary structure was noticed over the previous algorithm based programme. It was demonstrated after comparison with other standard methods including DSSP adopted by PDB with the help of multiple comparisons ANOVA and Dunnett’s t-test.

Conclusion: The PSSD is of great importance in the prediction of structural features of any unknown, unresolved proteins. It is also useful in the studies of proteins structure-function relationship.

Keywords:

PSSD and DSSP, GOR and Chou Fasman algorithm, thermophilic and mesophilic proteins, propensity matrix, helix sheet and turn, statistics.

Affiliation:

Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore-721102, West Bengal, Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore-721102, West Bengal, Post Graduate Department of Computer Science, The University of Burdwan, Burdwan, 713104, Westbengal, Post Graduate Department of Biochemistry and Biotechnology, Cell and Molecular Therapeutics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore- 721102, West Bengal



Read Full-Text article