Structure and dynamics of aquaporin-1

Structural response of a AQP1 is examined by a coarse-grained model with a phenomenological interaction potential with a knowledge-based residue-residue interaction (derived from an ensemble of protein structures in PDB). The thermal response of the protein chain exhibits an unexpected characteristics in its native phase where the radius of gyration of the protein decreases on raising the temperature. The radius of gyration of AQP1 increases on increasing the temperature before saturating to a random-coil morphology in denatured phase at high temperatures. Three regions of persistent globularization are identified, toward the end segments 1M-25V and 250V-269K and a narrow region in the middle 155A-163D along the backbone. Varying the temperature leads to a systematic redistribution of self-organizing residues with globular and fibrous morphologies with an effective dimension D~2 (random coil) at high temperature and D~3 (globular conformation) in native phase. A preliminary analysis is also presented on the effect of a crowded membrane environment on the protein structure by incorporating effective solute constituents. Conformation of the protein is found to be pinned by selective binding of solute to specific targets; the matrix directed structure differs considerably from that of a protein in a generic solvent. The structure of AQP1 can be controlled by temperature and constitutive elements of the underlying matrix.