Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 116, Issue 14, Pages 6329-6338Publisher
AMER INST PHYSICS
DOI: 10.1063/1.1457445
Keywords
-
Ask authors/readers for more resources
A good example of macromolecular recognition is found in the interaction of the two monomers of the dimeric superoxide dismutase protein found in Photobacterium leiognathi. We have produced, by molecular dynamics simulation techniques, a specific path for the rupture of the dimer and calculated the effective force involved in the process by extending a well established free energy calculation scheme, the molecular dynamics blue moon approach to rare events. Within this picture we have generalized the approach to a vectorial reaction coordinate and performed a number of different simulations in function of the monomer-momomer separation, at fixed relative orientation. We find a deep minimum and we compute the height of the free energy barrier to break the dimer. As for the system characterization we have found that, when the separation distance increases, the protein structure is stable and the monomer-monomer interface is uniformly hydrated. Moreover, identifying the crucial contacts for the stabilization of the dimer, we have found the sequence of the different microscopic events in the monomer-monomer recognition and we have developed a view of the process which requires a merging of standard explanations, in agreement with the recent picture of recognition as a dynamical process mixing the various mechanisms previously considered [Kimura , Biophys. J. 80 635 (2001)]. (C) 2002 American Institute of Physics.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available