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1. Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C Virus IRES pseudoknot domain

Author

Lavender, Christopher A., Feng Ding, Dokholyan, Nikolay V., and Weeks, Kevin M.

Subjects
Computational biology -- Analysis, Hepatitis C virus -- Genetic aspects, Hepatitis C virus -- Physiological aspects, Molecular dynamics -- Usage, Ribosomes -- Research, Biological sciences, Chemistry
Abstract

A generic discrete molecular dynamics-based modeling system that uses long-range constraints inferred from diverse biochemical or bioinformatic analyses is developed to generate statistically significant nativelike folds for RNAs of known structure ranging from 45 to 158 nucleotides. The unknown structure of the hepatitis C virus internal ribosome entry site (IRES) pseudoknot domain predicted by the model which showed that the pseudoknot domain positions the AUG start codon near the mRNA channel and is tRNA-like, revealed that IRES employs molecular mimicry as a functional strategy.

Published
2010

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