Computer simulations of the folding process of apomyoglobin

PHYS 429

Mariangela Dametto, mdametto@mail.usf.edu and Alfredo E Cardenas, cardenas@cas.usf.edu. Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, CHE 205, Tampa, FL 33620
We study the folding mechanism of the protein apomyoglobin by performing computer simulations with atomic detail. The mechanisms of folding of this protein have been extensively studied by experiment, providing a large amount of data that allows comparison with simulations. Apomyoglobin is a protein composed of seven alpha helices arranged in a globular shape. In the present study, we compute several folding trajectories of apomyoglobin starting from coiled structures. Conformations for the initial unfolded state were obtained by collecting structures obtained by high temperature molecular dynamics simulations. The room-temperature folding trajectories are obtained using the Stochastic Difference Equation in Length algorithm of Elber. Our folding results (that show a late collapse of the structure of the protein) are compared with recent experimental results (Uzawa et al, PNAS 2004) and a previous MD simulation (Onufriev et al., J. Mol. Biol. 2003).
 

Poster Session
7:30 PM-10:00 PM, Wednesday, 13 September 2006 Moscone Center -- Hall D, Poster

Division of Physical Chemistry

The 232nd ACS National Meeting, San Francisco, CA, September 10-14, 2006