Computational analysis of the folding pathway of a mutant cold shock protein

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Sergio Urahata, surahata@dasher.wustl.edu1, Adam Clarke, clarkea@mail.usf.edu2, and Alfredo E Cardenas, cardenas@cas.usf.edu2. (1) Department of Biochemistry and Molecular Biophysics, Washington University, 660 S. Euclid Ave., Box 8231, Saint Louis, MO 63110, (2) Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE 205, Tampa, FL 33620
In this work, we use the Stochastic Difference Equation in length algorithm to compute folding trajectories for the Cold Shock protein Bc-CspR3E (Protein Data Bank 1I5F) which is a mutant species of Bc-CspB from Bacillus subtilis (Protein Data Bank 1C90). These proteins have the same sequence with the only difference being the presence of a glutamic acid in position 3 in Bc-CspR3E instead of arginine. In total, 25 complete trajectories were obtained at room temperature and each of them has 400 intermediate slices. We present detailed results of the folding process for this protein that indicates an early collapse event without formation of the beta turns. This hydrophobic collapse occurs by collaborative interactions between different parts of the protein. Finally, the role of the glutamic acid in position 3 is also analyzed.