Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

U1A-RNA Complex Formation: Insights from Molecular Dynamics Simulations

Protein-RNA complexes are involved in most steps of gene expression, including the editing, modification, transportation, translation. and degradation of RNA. A thorough description of the protein-RNA recognition process is absolutely critical for a complete understanding of the posttranscriptional regulation of gene expression, but has thus far been elusive. Both sequence and structure play integral roles in the recognition process. However, the individual contributions of these issues to binding affinity and specificity involved in the protein-RNA recognition process can be difficult to isolate and examine experimentally. As such, molecular dynamics (MD) simulations are an ideal complement to experimental studies in this field, and can contribute to a better understanding of the protein-RNA recognition process.

The focus of this study is a particularly well-characterized system, the complex formed between the N-terminal domain of the protein U1A and stem loop 2 of U1 snRNA. Recognition of single-stranded RNA by U1A occurs through a structural motif called the RNA recognition motif (RRM), also known as the ribonucleoprotein (RNP) domain or the RNA binding domain (RBD). The RRM consists of a βαββαβ fold, which forms a four-stranded antiparallel β-sheet supported by two α-helices. The N-terminal RRM of U1A contains two out of three highly conserved aromatic amino acids that are found on the surface of the β-sheet and are known to stack with RNA bases upon binding. Baranger and co-workers have found that mutation of one of these highly conserved residues, Phe56, can lead to up to a 5.5 kcal mol-1 destabilization of the complex.

We are using MD methods to investigate the role of the conserved Phe56 residue in the U1A-RNA recognition process. Simulations of U1A and stem loop 2 RNA have been performed in both free and bound states for wild type and Phe56Ala, Phe56Leu and Phe56Trp mutants. A variety of techniques have been used to analyze these simulations with the intent of contributing to an understanding of the loss in binding energy seen experimentally, as well as to probe the greater issue of structural adaptation. Analyses of both the local and global structural changes in protein and RNA associated with the mutation of Phe56 and the energetics of complex formation will be presented.

Bethany L. Kormos
David L. Beveridge
Anne M. Baranger

Department of Chemistry
Wesleyan University
237 Church St.
Middletown, CT 06459-0180

Phone: 860.685.4963
Fax: 860.685.2211
Email: bkormos@wesleyan.edu