Structural Chemistry

, Volume 28, Issue 3, pp 625–633 | Cite as

Structure and dynamics of a free aquaporin (AQP1) by a coarse-grained Monte Carlo simulation

Original Research
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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.

Keywords

Protein folding Aquaporin Coarse-grained model Monte Carlo simulation 

Notes

Acknowledgments

We thank Minttu Virkki for suggesting us to look at AQP1.

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of Physics and AstronomyUniversity of Southern MississippiHattiesburgUSA
  2. 2.Materials and Manufacturing Directorate, Air Force Research LaboratoryWright Patterson Air Force BaseDaytonUSA

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