Analysis of Steered Molecular Dynamics Study of Sickle Hemoglobin Protein in Water*

Abstract

ANALYSIS OF STEERED MOLECULAR DYNAMICS

STUDY OF SICKLE HEMOGLOBIN PROTEIN IN

WATER

Jhulan Powrel ^1,2 and Narayan Prasad Adhikari <sup>2

1</sup>Department of Physics, Butwal Multiple Campus, Tribhuvan University, Nepal

² Central Department of Physics, Tribhuvan University, Nepal

E-mail: npadhikari@gmail.com

Abstract

Recent practice providing the important qualitative insight in to the bio-physical relevant problems. So this work is focusing for identifying binding components and their folding pathways to explore the elastic properties of sickled hemoglobin proteins(HbS) in SMD simulation. Time dependent external force is applied and the responses are analyzed. The study of sickled hemoglobin protein using nano scale molecular dynamics(NAMD) is performed for analyzing the binding mechanism and stability of protein. The first peak in the SMD graph shows the force required for breaking the H-bond in the secondary and tertiary structure of protein chains. In sickle hemoglobin protein the H-bond binding energy is ranging from 7073.74 pN to 12646.80 pN for pulling velocities of 0.0020 Å/ps to 0.0040 Å/ps for the spring constant of 8 kcal mol⁻¹ Å⁻². SASA of beta chain of HbS protein is increased for the spring constant of k=5 kcal mol⁻¹ Å⁻² to k=8 kcal mol^-1Å^-2 with increase in time which indicating the hydrophilic nature of beta chain. The hydrophobic, van der Waals(vdw) and electrostatics interactions are the stronger and seven salt bridges are also involved in binding mechanism of beta chain in sickle hemoglobin protein for their structural conformation.