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Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures

Published online by Cambridge University Press:  01 June 1999

LU WANG ,
YONG DUAN ,
REBECCA SHORTLE ,
BARBARA IMPERIALI  and
PETER A. KOLLMAN
LU WANG
Affiliation:
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
YONG DUAN
Affiliation:
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
REBECCA SHORTLE
Affiliation:
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143
BARBARA IMPERIALI
Affiliation:
Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
PETER A. KOLLMAN
Affiliation:
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
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Abstract

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's 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.

Keywords

BBA1energeticsmolecular dynamics simulationprotein stabilityunfolding mechanism
Type
Research Article
Information
Protein Science , Volume 8 , Issue 6 , June 1999 , pp. 1292 - 1304
Copyright
© 1999 The Protein Society

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