Paper Citing NAMD - Abstract
Hamacher, K.; Hubsch, A.; McCammon, J.A.
A minimal model for stabilization of biomolecules by hydrocarbon cross-linking
JOURNAL OF CHEMICAL PHYSICS, 124 Art. No. 164907, APR 28 2006
Programmed cell death regulating protein motifs play an essential role in the development of an organism, its immune response, and disease-related cellular mechanisms. Among those motifs the BH3 domain of the BCL-2 family is found to be of crucial importance. Recent experiments showed how the isolated, otherwise unstructured BH3 peptide can be modified by a hydrocarbon linkage to regain function. We parametrized a reduced, dynamic model for the stability effects of such covalent cross-linking and confirmed that the model reproduces the reinforcement of the structural stability of the BH3 motif by cross-linking. We show that an analytically solvable model for thermostability around the native state is not capable of reproducing the stabilization effect. This points to the crucial importance of the peptide dynamics and the fluctuations neglected in the analytic model for the cross-linking system to function properly. This conclusion is supported by a thorough analysis of a simulated G (o) over bar model. The resulting model is suitable for rational design of generic cross-linking systems in silicio. (c) 2006 American Institute of Physics.
