Paper Citing NAMD - Abstract
Salimi, Neema L.; Ho, Bosco; Agard, David A.
Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable alpha-Lytic Protease
PLOS COMPUTATIONAL BIOLOGY, 6 Art. No. e1000689, FEB 2010
Kinetically stable proteins, those whose stability is derived from their slow unfolding kinetics and not thermodynamics, are examples of evolution's best attempts at suppressing unfolding. Especially in highly proteolytic environments, both partially and fully unfolded proteins face potential inactivation through degradation and/or aggregation, hence, slowing unfolding can greatly extend a protein's functional lifetime. The prokaryotic serine protease alpha-lytic protease (alpha LP) has done just that, as its unfolding is both very slow (t(1/2) similar to 1 year) and so cooperative that partial unfolding is negligible, providing a functional advantage over its thermodynamically stable homologs, such as trypsin. Previous studies have identified regions of the domain interface as critical to alpha LP unfolding, though a complete description of the unfolding pathway is missing. In order to identify the alpha LP unfolding pathway and the mechanism for its extreme cooperativity, we performed high temperature molecular dynamics unfolding simulations of both alpha LP and trypsin. The simulated alpha LP unfolding pathway produces a robust transition state ensemble consistent with prior biochemical experiments and clearly shows that unfolding proceeds through a preferential disruption of the domain interface. Through a novel method of calculating unfolding cooperativity, we show that alpha LP unfolds extremely cooperatively while trypsin unfolds gradually. Finally, by examining the behavior of both domain interfaces, we propose a model for the differential unfolding cooperativity of alpha LP and trypsin involving three key regions that differ between the kinetically stable and thermodynamically stable classes of serine proteases.
