Computational validation of protein nanotubes

Idit Buch, Bernard R. Brooks, Haim J. Wolfson, Ruth Nussinov

Research output: Contribution to journalArticlepeer-review

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 hellcity, 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.

Original languageEnglish
Pages (from-to)1096-1102
Number of pages7
JournalNano Letters
Volume9
Issue number3
DOIs
StatePublished - 11 Mar 2009

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