Predoctoral Trainee

Ryan M. Bannen Biochemistry Doctoral Training Program Dept. of Biochemistry Faculty Supervisor: George N. Phillips, Jr. Email: rbannen@biochem.wisc.edu 263-5923

The Gaussian Network Model (GNM) is a simplified protein dynamics model that uses the alpha-carbon atomic coordinates from x-ray crystallography and nuclear magnetic resonance (NMR) to predict how the protein will move in solution. The alpha carbons are connected by a system of 'springs' between each atom. This allows each atom to have a certain amplitude based on how many springs are connected to it. If there are many springs attached to one atom, the carbon alpha will have a lower amplitude of movement compared to an atom with only a few springs. Previous research used a fixed spring length for the entire protein data set. It has been suggested however that by choosing a different spring length for each individual protein, the GNM will report more accurate temperature factors when compared to the factors reported in the published x-ray crystallography and NMR protein files. My work tests this idea on a data set of 113 proteins and finds that with using this variable spring length approach, the correlation coefficient is statistically improved. Future work will look at using the anisotropic network model (ANM) which gives vector movements of all the carbon alphas in addition to the amplitudes which the GNM produces.

Resume

Resume 2002 (.doc format)

Publications

Phillips GN, Jr, McCoy J, Bannen R, and Kundu S. Models of Dynamic Disorder in Protein Crystals: Theory and New Analysis. Abstract, American Crystallographic Association Meeting, 2003.

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File last modified: August 14, 2003
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