Globular structure of a human immunodeficiency virus-1 protease (1DIFA dimer) in an effective solvent medium by a Monte Carlo simulation

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 Arg(41) and Arg(140) (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 (R-g) and energy (E-c) of the protein show nonmonotonic dependence on the interaction strength with the smallest R-g around the largest value of E-c. Pinning of the conformations by the hydrophobic residues at high interaction strength seems to provide seed for the protein chain to collapse.