Pinning the conformation of a protein (CorA) in a solute matrix with selective binding

• Published in: Physica A 2020-10, Vol.556, p.124823, Article 124823
• Main Authors: Rangubpit, Warin, Kitjaruwankul, Sunan, Sompornpisut, Pornthep, Pandey, R.B.
• Format: Article
• Language: English
• Subjects: Coarse-grained model; Interacting solute matrix; Monte Carlo simulation; Protein CorA; Protein folding
• ISSN: 0378-4371; 1873-2119
• DOI: 10.1016/j.physa.2020.124823

Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute–residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach their targeted residue due to their unique interactions with the residues. Degree of slowing down of the protein depends on the interaction strength f. Unlike a predictable dependence of the radius of gyration of the same protein on interaction in an effective medium, it does not show a systematic dependence on interaction due to pinning caused by the solute binding. Spread of the protein chain is quantified by estimating its effective dimension (D) from scaling of the structure factor. Even with a lower solute–residue interaction, the protein chain appears to conform to a random-coil conformation (D∼2) in its native phase where it is globular in absence of such solute environment. The structural spread at small length scale differs from that at large scale in presence of stronger interactions: D∼2.3 at smaller length scale and D∼1.4 on larger scale with f = 3.5 while D∼1.4 at smaller length scale and D∼2.5 at larger length scales with f = 4.0.