126
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.
