  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.

Biological Physics;Biomolecules