title: Computational validation of protein nanotubes.
abstract: We present a novel generic computational method to assess protein nanotubes with variable diameter sizes at the atomic level given their low resolution protomeric structures. The method is based on the symmetrical assembly of a repeating protein subunit into a nanotube. Given the protein unit-cell, and the tube diameter and helicity, we carry out all-atom molecular dynamics simulations, combined with a unique mathematical transformation. This allows us to mimic nanotubes of even huge sizes without end or edge effects. All our simulation setups attempt to explicitly adhere to the conditions under which the experiments were conducted. Thus, we are able to obtain high resolution atomic-scale structures at reasonable computational costs. We expect that our approach would prove useful in assessing protein nanotubes, as well as in silico constructions of novel nanobiomaterials.
authors.affiliation: Department of Human Molecular Genetics and Biochemistry, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
authors.forename: Idit
authors.initials: I
authors.lastname: Buch
authors.forename: Bernard R
authors.initials: BR
authors.lastname: Brooks
authors.forename: Haim J
authors.initials: HJ
authors.lastname: Wolfson
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D000465:Algorithms; D001672:Biocompatible Materials / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D015497:HIV-1 / Q000378:metabolism; D015233:Models, Statistical; D008968:Molecular Conformation; D053761:Nanocomposites / Q000737:chemistry*; D036103:Nanotechnology / Q000379:methods*; D043942:Nanotubes / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D012984:Software; D014764:Viral Proteins / Q000737:chemistry
chemical_list: D001672:Biocompatible Materials; D010455:Peptides; D011506:Proteins; D014764:Viral Proteins