Designing a nanotube using naturally occurring protein building blocks

Chung Jung Tsai, Jie Zheng, Ruth Nussinov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

39 Scopus citations

Abstract

Here our goal is to carry out nanotube design using naturally occurring protein building blocks. Inspection of the protein structural database reveals the richness of the conformations of proteins, their parts, and their chemistry. Given target functional protein nanotube geometry, our strategy involves scanning a library of candidate building blocks, combinatorially assembling them into the shape and testing its stability. Since self-assembly takes place on time scales not affordable for computations, here we propose a strategy for the very first step in protein nanotube design: we map the candidate building blocks onto a planar sheet and wrap the sheet around a cylinder with the target dimensions. We provide examples of three nanotubes, two peptide and one protein, in atomistic model detail for which there are experimental data. The nanotube models can be used to verify a nanostructure observed by low-resolution experiments, and to study the mechanism of tube formation.

Original languageEnglish
Pages (from-to)311-319
Number of pages9
JournalPLoS Computational Biology
Volume2
Issue number4
DOIs
StatePublished - Apr 2006

Funding

FundersFunder number
National Cancer InstituteZ01BC010441

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