Globular Structure of a Human Immunodeficiency Virus-1 Protease (1DIFA dimer) in an Effective Solvent Medium by a Monte Carlo Simulation
Abstract
A coarse-grained model is used to study the structure and dynamics of a human immunodeficiency virus-1 protease 1DIFA dimer consisting of 198 residues in an effective solvent medium on a cubic lattice by Monte Carlo simulations for a range of interaction strengths. Energy and mobility profiles of residues are found to depend on the interaction strength and exhibit remarkable segmental symmetries in two monomers. Lowest energy residues such as Arg41 and Arg140 most electrostatic and polar are not the least mobile; despite the higher energy, the hydrophobic residues Ile, Leu, and Val are least mobile and form the core by pinning down the local segments for the globular structure. Variations in the gyration radius Rg and energy Ec of the protein show nonmonotonic dependence on the interaction strength with the smallest Rg around the largest value of Ec. Pinning of the conformations by the hydrophobic residues at high interaction strength seems to provide seed for the protein chain to collapse.
Document Details
- Document Type
- Technical Report
- Publication Date
- Mar 22, 2010
- Accession Number
- ADA517038
Entities
People
- B. L. Farmer
- R. B. Pandey
Organizations
- University of Southern Mississippi