Computational Validation of Protein Nanotubes
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- 作者：Idit Buch† ; ; Bernard R. Brooks‡ ; ; Haim J. Wolfson§ ; ; Ruth Nussinov*† ;
- 刊名：Nano Letters
- 出版年：2009
- 出版时间：March 11, 2009
- 年：2009
- 卷：9
- 期：3
- 页码：1096-1102
- 全文大小：362K
- 年卷期：v.9,no.3(March 11, 2009)
- ISSN：1530-6992
文摘
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.