Paper Citing NAMD - Abstract
Curco, David; Nussinov, Ruth; Aleman, Carlos
Coarse-graining the self-assembly of beta-helical protein building blocks
JOURNAL OF PHYSICAL CHEMISTRY B, 111:14006-14011, DEC 20 2007
Nanotubular structures constructed using self-assembled P-helical protein building blocks one atop the other have been coarsened to develop a mesoscopic potential that reproduces the intermolecular interaction energies provided by atomistic force-fields. The resulting potential consists of an analytical expression that depends exclusively on the distance and the relative orientation between the two interacting entities. In spite of its complexity, this coarse-grained potential reproduces satisfactorily the energetic properties of two interacting building blocks. The coarse-grained potential has been used to predict that the interaction between building blocks formed by residues 131-165 of E. coli galactoside acteyltransferase becomes repulsive when the size of the nanotube is larger than a threshold, that is, about 45 self-assembled building blocks.
