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Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Protein-RNA Recognition: Insight into U1A-RNA from Molecular Dynamics Simulations

A comprehensive description of protein-RNA recognition is necessary for a complete understanding of the posttranscriptional regulation of gene expression. Sequence, structure, energetics, dynamical motions and cooperativity are all factors that contribute to protein-RNA recognition. The individual contributions of these factors to binding affinity and specificity can be difficult to isolate and examine experimentally. With this in mind, molecular dynamics (MD) simulations are used to contribute to a better understanding of the protein-RNA recognition process. The focus of this study is the complex formed between the protein U1A and stem loop 2 of U1 snRNA. We are using MD methods to investigate the contributions of structure, dynamical motions and energetics to the U1A-RNA recognition process. A number of techniques have been employed to analyze MD simulations of U1A-RNA with the intent of contributing to an understanding of the issues that contribute both to affinity and specificity in the protein-RNA recognition process.

Bethany L. Kormos1
Anne M. Baranger2and
David L. Beveridge1*

Chemistry Dept1 & Molecular Biophysics,
Wesleyan University,
Middletown, CT 06459

Dept of Chemistry2
Univ. of Illinois at Urbana-Champaign,
Urbana, IL 61801

Phone: 860-685-4963
Fax: 860-685-2211
Eamil: bkormos@wesleyan.edu