Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session II

73-POS Board 26 Bond Orientation Order Parameters Explain the Influence of Contact Density and Protein Geometry on Fluctuations Osman B. Okan 1 , Deniz Turgut 1 , Aravind Rammohan 2 , Angel E. Garcia 3 , Rahmi Ozisik 1 . 1 Rensselaer Polytechnic Institute, Troy, NY, USA, 2 Corning Inc., Painted Post, NY, USA, 3 Rensselaer Polytechnic Institute, Troy, NY, USA. The Anisotropic Network Model (ANM) was used to investigate the fluctuations of 210 globular proteins. The results of ANM were compared with molecular dynamics (MD) simulations and experimental findings. The ANM results were analyzed using Bond Orientation Order (BOO) parameters, which were reformulated as a sum of contact density and geometrical distribution of contacts in space. This reformulation of BOO expression makes it possible to investigate the role of each individual component and identify cut–off ranges where each component dominates protein fluctuations. The results indicate that the two components of the BOO dominate protein fluctuations at different length scales: contact density at small length scales and geometric distribution of residues at length scales comparable to the protein size. In addition, their probability distributions change with respect to cut–off distance. The combination of these two effects (length scale and cut–off dependence) leads to a unique outcome such that at small length scales, where most simulations or analysis is performed, only the contact density’s effect is seen even though the geometric component is most important for the overall stability of proteins.

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