Coarse-graining the self-assembly of beta-helical protein building blocks.
Nanotubular structures constructed using self-assembled beta-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.
Curcó
David
D
Departament d'Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona E-08028, Spain. curco@angel.qui.ub.es
Nussinov
Ruth
R
Alemán
Carlos
C
D003198:Computer Simulation; D008958:Models, Molecular; D043942:Nanotubes / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
D011506:Proteins