Coarse-grained representation of beta-helical protein building blocks.
A general strategy to develop coarse-grained models of beta-helical protein fragments is presented. The procedure has been applied to a building block formed by a two-turn repeat motif from E. coli galactoside acetyltransferase, which is able to provide a very stable self-assembled tubular nanoconstruct upon stacking of its replicas. For this purpose, first, we have developed a computational scheme to sample very efficiently the configurational space of the building block. This method, which is inspired by a strategy recently designed to study amorphous polymers and by an advanced Monte Carlo algorithm, provides a large ensemble of uncorrelated configurations at a very reasonable computational cost. The atomistic configurations provided by this method have been used to obtain a coarse-grained model that describes the amino acids with fewer particles than those required for full atomistic detail, i.e., two, three, or four depending on the chemical nature of the amino acid. Coarse-grained potentials have been developed considering the following types of interactions: (i) electrostatic and van der Waals interactions between residues i and i + n with n >/= 2; (ii) interactions between residues i and i + 1; and (c) intra-residue interactions. The reliability of the proposed model has been tested by comparing the atomistic and coarse-grained energies calculated for a large number of independent configurations of the beta-helical building block.
Curcó
David
D
Departament d'Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquees 1, Barcelona E-08028, Spain. curco@angel.qui.ub.es
Nussinov
Ruth
R
Aleman
Carlos
C
D000123:Acetyltransferases / Q000737:chemistry*; D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D004926:Escherichia coli / Q000201:enzymology; D008958:Models, Molecular; D009010:Monte Carlo Method; D043942:Nanotubes / Q000737:chemistry*; D017433:Protein Structure, Secondary; D055672:Static Electricity; D013816:Thermodynamics
D000596:Amino Acids; D000123:Acetyltransferases; C022770:galactoside acetyltransferase