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Miloshevsky GV, Hassanein A, Jordan PC. Shape-Dependent Global Deformation Modes of Large Protein Structures. J Mol Struct. 2010;972(1):41-50doi: 10.1016/j.molstruc.2010.01.009.
Miloshevsky, G. V., Hassanein, A., & Jordan, P. C. (2010). Shape-Dependent Global Deformation Modes of Large Protein Structures. Journal of molecular structure, 972(1), 41-50. https://doi.org/10.1016/j.molstruc.2010.01.009
Miloshevsky, Gennady V, et al. "Shape-Dependent Global Deformation Modes of Large Protein Structures." Journal of molecular structure vol. 972,1 (2010): 41-50. doi: https://doi.org/10.1016/j.molstruc.2010.01.009
Miloshevsky GV, Hassanein A, Jordan PC. Shape-Dependent Global Deformation Modes of Large Protein Structures. J Mol Struct. 2010 May 19;972(1):41-50. doi: 10.1016/j.molstruc.2010.01.009. PMID: 20526444; PMCID: PMC2878971.
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J Mol Struct. 2010 May 19;972(1):41-50. doi: 10.1016/j.molstruc.2010.01.009.

Shape-Dependent Global Deformation Modes of Large Protein Structures.

Journal of molecular structure

Gennady V Miloshevsky, Ahmed Hassanein, Peter C Jordan

Affiliations

  1. School of Nuclear Engineering, Purdue University, West Lafayette, IN 47907, USA.

PMID: 20526444 PMCID: PMC2878971 DOI: 10.1016/j.molstruc.2010.01.009

Abstract

Conformational changes are central to the functioning of pore-forming proteins that open and close their molecular gates in response to external stimuli such as pH, ionic strength, membrane voltage or ligand binding. Normal mode analysis (NMA) is used to identify and characterize the slowest motions in the gA, KcsA, ClC-ec1, LacY and LeuT(Aa) proteins at the onset of gating. Global deformation modes of the essentially cylindrical gA, KcsA, LacY and LeuT(Aa) biomolecules are reminiscent of global twisting, transverse and longitudinal motions in a homogeneous elastic rod. The ClC-ec1 protein executes a splaying motion in the plane perpendicular to the lipid bilayer. These global collective deformations are determined by protein shape. New methods, all-atom Monte Carlo Normal Mode Following and its simplification using a rotation-translation of protein blocks (RTB), are described and applied to gain insight into the nature of gating transitions in gA and KcsA. These studies demonstrate the severe limitations of standard NMA in characterizing the structural rearrangements associated with gating transitions. Comparison of all-atom and RTB transition pathways in gA clearly illustrates the impact of the rigid protein block approximation and the need to include all degrees of freedom and their relaxation in computational studies of protein gating. The effects of atomic level structure, pH, hydrogen bonding and charged residues on the large scale conformational changes associated with gating transitions are discussed.

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