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

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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.

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Acknowledgments

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

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Authors and Affiliations

  1. Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, MS, 39406, USA

    R. B. Pandey

  2. Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Dayton, OH, 45433, USA

    B. L. Farmer

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  1. R. B. Pandey
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  2. B. L. Farmer
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Correspondence to R. B. Pandey.

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Pandey, R.B., Farmer, B.L. Structure and dynamics of a free aquaporin (AQP1) by a coarse-grained Monte Carlo simulation. Struct Chem 28, 625–633 (2017). https://doi.org/10.1007/s11224-016-0836-4

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  • DOI: https://doi.org/10.1007/s11224-016-0836-4

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