Parametric sensitivity analysis of avian pancreatic polypeptide (APP)

Proteins
H ZhangH Rabitz

Abstract

Computer simulations utilizing a classical force field have been widely used to study biomolecular properties. It is important to identify the key force field parameters or structural groups controlling the molecular properties. In the present paper the sensitivity analysis method is applied to study how various partial charges and solvation parameters affect the equilibrium structure and free energy of avian pancreatic polypeptide (APP). The general shape of APP is characterized by its three principal moments of inertia. A molecular dynamics simulation of APP was carried out with the OPLS/Amber force field and a continuum model of solvation energy. The analysis pinpoints the parameters which have the largest (or smallest) impact on the protein equilibrium structure (i.e., the moments of inertia) or free energy. A display of the protein with its atoms colored according to their sensitivities illustrates the patterns of the interactions responsible for the protein stability. The results suggest that the electrostatic interactions play a more dominant role in protein stability than the part of the solvation effect modeled by the atomic solvation parameters.

References

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Citations

Apr 13, 2011·The Journal of Physical Chemistry. B·Marcus P D HatfieldSándor Lovas
Jul 27, 2002·Annual Review of Pharmacology and Toxicology·Chung F Wong, J Andrew McCammon
Apr 23, 2004·Proteins·Alex KentsisRoman Osman
Nov 6, 2008·International Journal of Quantum Chemistry·Nicholas Y PalermoSándor Lovas
Nov 6, 2008·International Journal of Quantum Chemistry·Marcus P D HatfieldSándor Lovas
Oct 26, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Olivier Collet
Mar 1, 2006·Journal of Chemical Theory and Computation·Michael K Gilson
Apr 6, 2006·Journal of the American Chemical Society·Wei ChenMichael K Gilson

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