Wang, Lu and Duan, Yong and Shortle, Rebecca and Imperiali, Barbara and Kollman, Peter A. (1999) Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures. Protein Science, 8 (6). pp. 1292-1304. ISSN 0961-8368 http://resolver.caltech.edu/CaltechAUTHORS:20120112-142040537
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BBA1 is a designed protein that has only 23 residues. It is the smallest protein without disulfide bridges that has a well‐defined tertiary structure in solution. We have performed unfolding molecular dynamics simulations on BBA1 and some of its mutants at 300, 330, 360, and 400 K to study their kinetic stability as well as the unfolding mechanism of BBA1. It was shown that the unfolding simulations can provide insights into the forces that stabilize the protein. Packing, hydrophobic interactions, and a salt bridge between Asp12 and Lys16 were found to be important to the protein' stability. The unfolding of BBA1 goes through two major steps: (1) disruption of the hydrophobic core and (2) unfolding of the helix. The β‐hairpin remains stable in the unfolding because of the high stability of the type II' turn connecting the two β‐strands.
|Additional Information:||© 1999 The Protein Society. Received November 2, 1998; Accepted March 4, 1999 This work has been supported by NIH (Grant GM-29072) and a University of California Biotechnology Star grant from AMGEN (to P.A.K.). Supercomputing time was provided by Pittsburgh Supercomputer Center (PSC). The facilities of the UCSF computer graphics laboratory, supported by NIH P41-RR01081, T. Ferrin, principal investigator, are gratefully acknowledged. R. S. acknowledges the support of a Department of Defense ONR predoctoral fellowship.|
|Subject Keywords:||BBA1; energetics; molecular dynamics simulation; protein stability; unfolding mechanism|
|Official Citation:||Wang, L., Duan, Y., Shortle, R., Imperiali, B. and Kollman, P. A. (1999), Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures. Protein Science, 8: 1292–1304. doi: 10.1110/ps.8.6.1292|
|Usage Policy:||No commercial reproduction, distribution, display or performance rights in this work are provided.|
|Deposited By:||Jason Perez|
|Deposited On:||13 Jan 2012 00:01|
|Last Modified:||13 Jan 2012 00:01|
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