A Monte Carlo simulation of a protein (CoVE) in a matrix of random barriers

R.B. Pandey

Physica A: Statistical Mechanics and its Applications, 2021, vol. 572, issue C

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.

Keywords: Monte Carlo simulation; Coarse-grained model; Protein; Corona virus envelope protein; Random media; Globular; Random coil (search for similar items in EconPapers)
Date: 2021
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/S0378437121001680
Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:572:y:2021:i:c:s0378437121001680

DOI: 10.1016/j.physa.2021.125896

Access Statistics for this article

Physica A: Statistical Mechanics and its Applications is currently edited by K. A. Dawson, J. O. Indekeu, H.E. Stanley and C. Tsallis

More articles in Physica A: Statistical Mechanics and its Applications from Elsevier
Bibliographic data for series maintained by Catherine Liu ().