Structure and dynamics of a free aquaporin (AQP1) by a coarse-grained Monte Carlo simulation
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Structure and dynamics of a free aquaporin (AQP1) are studied by a coarse-grained Monte Carlo simulation as a function of temperature using a phenomenological potential with the input of a knowledge-based residue–residue interaction. Response of the radius of gyration (R g) of the protein to the temperature (T) is found to be nonlinear: Decay of R g at T ≤ T c is followed by a continuous increase at T ≥ T c before reaching its saturation. In thermo-responsive regime, the protein exhibits segmental globularization with the persistence of three regions along its sequence involving residues 1M–25V and 250V–269K toward the beginning and end segments with a narrow intermediate region around 155A–163D. A detail analysis of the structure factor S(q) shows a global random coil conformation at high temperatures with an effective dimension D e ~ 1.74 and a globular structure (D e ~ 3) at low temperatures. In thermo-responsive regime, the variation of S(q) with the wave vector q reveals a systematic redistribution of self-organizing residues (in globular and fibrous sections) that depends on the length scale and the temperature.
KeywordsProtein folding Aquaporin Coarse-grained model Monte Carlo simulation
We thank Minttu Virkki for suggesting us to look at AQP1.
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