1,804 research outputs found
Mechanisms underlying sequence-independent beta-sheet formation
We investigate the formation of beta-sheet structures in proteins without
taking into account specific sequence-dependent hydrophobic interactions. To
accomplish this, we introduce a model which explicitly incorporates both
solvation effects and the angular dependence (on the protein backbone) of
hydrogen bond formation. The thermodynamics of this model is studied by
comparing the restricted partition functions obtained by "unfreezing"
successively larger segments of the native beta-sheet structure. Our results
suggest that solvation dynamics together with the aforementioned angular
dependence gives rise to a generic cooperativity in this class of systems; this
result explains why pathological aggregates involving beta-sheet cores can form
from many different proteins. Our work provides the foundation for the
construction of phenomenological models to investigate the competition between
native folding and non-specific aggregation.Comment: 20 pages, 5 figures, Revtex4, simulation mpeg movie available at
http://www-physics.ucsd.edu/~guochin/Images/sheet1.mp
Simulation of Pressure-Induced and Temperature-Induced Denaturation of Phosphoglycerate Kinase
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