Structure and Dynamics of a Free Aquaporin (AQP1) by a Coarse-Grained Monte Carlo Simulation

Authors

R.B. Pandey, University of Southern MississippiFollow
B.L. Farmer, Air Force Research LaboratoryFollow

Document Type

Article

Publication Date

6-2017

Department

Physics and Astronomy

Abstract

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.

Publication Title

Structural Chemistry

Volume

28

Issue

3

First Page

625

Last Page

633

Recommended Citation

Pandey, R., Farmer, B. (2017). Structure and Dynamics of a Free Aquaporin (AQP1) by a Coarse-Grained Monte Carlo Simulation. Structural Chemistry, 28(3), 625-633.
Available at: https://aquila.usm.edu/fac_pubs/17678