MOLECULAR DYNAMICS &FREE ENERGY CALCULATIONS OF RNA PROTEIN INTERACTIONS

$2,181P41FY2000RRNIH

University Of California San Francisco, San Francisco CA

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Abstract

The spliceosomal protein, U1A, binds to a hairpin RNA and to an internal loop RNA with sub-nanomolar affinities. To understand the driving forces of RNA protein recognition, we performed molecular dynamics simulations and Poisson-Boltzmann solvation free energy calculations. Our goals for this project are to 1) estimate the absolute binding free energy of the U1A-RNA complex; 2) calculate the binding free energy of different U1A-hairpin mutations and compare with experimental values; and, 3) predict deleterious mutations for the U1A-internal loop complex. We are using the Computer Graphics Laboratory facilities to view the structures over the course of our simulations using MidasPlus.

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