Virtual Quantification of Protein Stability using Applied Kinetic and Thermodynamic Parameters

S. Prasanth Kumar¹ and M. Meenachi

¹Bioinformatics Laboratory, Department of Botany, University School of Sciences, Gujarat University, Ahmedabad - 380 009, Gujarat, India.

2.Department of Bioinformatics, Achariya Arts and Science College, Villianur, Pondicherry - 605 110, India.

Abstract

Protein stability, the most important aspect of molecular dynamics and simulations, requires sophisticated instrumentations of molecular biology to analyze its kinetic and thermodynamic background. Sequence- and structure-based programs on protein stability exist which relies only on single point mutations and sequence optimality. The energy distribution conferred by each amino acid essentially paves way for understanding protein stability. To the best of our knowledge, Protein Stability is a first program of its kind, developed to explore the energy requirement of each amino acid in the protein sequence derived from various applied kinetic and thermodynamic quantities. The algorithm is strongly dependent both on kinetic quantities such as atomic solvation energies and solvent accessible surface area and thermodynamic quantities viz. enthalpy, entropy, heat capacity, etc. The hydrophobicity pattern of protein was considered as the important component of protein stabilization. A program was developed to provide the energy distribution and its overall stability.

Keywords: Molecular modeling, kinetics, thermodynamics, protein stability.

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