Asymmetry in structural response of inner and outer transmembrane segments of CorA protein by a coarse-grain model

Abstract

Structure of CorA protein and its inner (i.corA) and outer (o.corA) transmembrane (TM) components are investigated as a function of temperature by a coarse-grained Monte Carlo simulation. Thermal response of i.corA is found to differ considerably from that of the outer component, o.corA. Analysis of the radius of gyration reveals that the inner TM component undergoes a continuous transition from a globular conformation to a random coil structure on raising the temperature. In contrast, the outer transmembrane component exhibits an abrupt (nearly discontinuous) thermal response in a narrow range of temperature. Scaling of the structure factor shows a globular structure of i.corA at a low temperature with an effective dimension D ∼ 3 and a random coil at a high temperature with D ∼ 2. The residue distribution in o.corA is slightly sparser than that of i.corA in a narrow thermos-responsive regime. The difference in thermos-response characteristics of these components (i.corA and o.corA) may reflect their unique transmembrane functions.

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

“…It is worth pointing out that we have already examined the structure and dynamics of CorA in absence of environmental complexity and found interesting thermal response of inner and outer segments of the protein [10,11]. For example, the thermal response of the inner segment shows a continuous transition from globular to random-coil structure on raising the temperature while the outer segment exhibits an abrupt (nearly discontinuous) thermal response in a narrow range of temperature.…”

“…A bond-fluctuation mechanism [13] is used to model the protein [10][11][12], a chain of 351 nodes, each representing unique specificity of corresponding residue. The simulation is performed on a cubic lattice with ample degrees of freedom for each residue to perform its stochastic moves and corresponding peptide bonds to fluctuate.…”

“…The transmembrane protein CorA consists of 351 residues with a well-defined inner (iCorA) and outer (oCorA) segments in cells [4][5][6][7][8][9][10]. Numerous elements in a cell such as lipid molecules, ions, osmolytes, different types of proteins, etc.…”

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

“…We consider a coarse-grained model of protein on a cubic lattice where a residue is represented by a cubic node of size (2a) 3 where a is the lattice constant [33][34][35][36][37][38]. CoVE protein consists of 76 residues in a specific sequence [10] and is represented by 76 nodes tethered together by flexible covalent bonds; the bond length between consecutive nodes varies between 2 and (10) in unit of the lattice constant [39].…”

“…There are numerous coarse-grained methods [20][21][22][23][24][25][26][27][28][29][30][31][32] used in such studies. We have been using a coarse-grain approach to examine structure and dynamics of a number of proteins over the years [33][34][35][36][37][38]. It involves (i) a bond-fluctuation mechanism used extensively in modeling polymer on a cubic lattice with ample degrees of freedom [39], a lesson learnt from computational polymer and (ii) knowledge-based residue-residue interactions used extensively in protein folding to capture specificity [40][41][42][43][44][45].…”