Document Type

Article

Publication Date

6-15-2021

Department

Physics and Astronomy

School

Mathematics and Natural Sciences

Abstract

Monte Carlo simulations are performed to study structure and dynamics of a protein CoVE in random media generated by a random distribution of barriers at concentration c with a coarse-grained model in its native (low temperature) and denatured (high temperature) phase. The stochastic dynamics of the protein is diffusive in denature phase at low c, it slows down on increasing c and stops moving beyond a threshold (cth ≈ 0.10). In native phase, the protein moves extremely slow at low c but speeds up on further increasing c in a characteristic range (c =0.10–0.20) before getting trapped at high c (cth ≈ 0.30). The radius of gyration (Rg) of CoVE shows different non-monotonic dependence on c (increase followed by decay) in native and denature phase with a higher and sharper rate of change in former. Effective dimension (D) of CoVE is estimated from the scaling of structure factor: in denatured phase, D ≈ 2 (a random coil conformation) at low c (= 0.01–0.10) with appearance of some globularization i.e. D ≈ 2.3, 2.5 at higher c (= 0.2, 0.3). Increasing c seems to reduce the globularity (D ≈ 3) of CoVE in native phase.

Comments

Published version found at 10.1016/j.physa.2021.125896.

Publication Title

Physica A: Statistical Mechanics and its Applications

Volume

572

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