Bioorganic Chemistry: nucleic acid-protein complexes.
Our group uses chemical approaches to address biological
problems. In particular, we seek to determine the identity and relative energetic
contributions of specific molecular interactions that control affinity and
specificity in the formation of RNA-protein complexes. RNA is important in
all steps of gene expression and usually acts in concert with proteins.
Thus, an understanding of RNA recognition by proteins is necessary for a
complete description of biological processes involving RNA and the development
of small molecules capable of modifying these processes. Ultimately, we will
use the information gained in these projects to design peptides and small
molecules that specifically bind RNA with high affinity. We are investigating the RNA recognition motif (RRM),
one of the most common RNA-binding domains. We have chosen to study RRMs
from two proteins, the U1A protein and Sex lethal protein. The U1A protein
is a component of U1 snRNP, a subunit of the spliceosome that splices most
eukaryotic pre-mRNA. The Sex lethal protein is important in alternative splice
site selection that ultimately influences sex determination in Drosophila.
The U1A-RNA and Sex lethal-RNA complexes are good models for RRM-RNA complexes
because both have been structurally characterized alone and bound to RNA,
allowing us to dissect the energetic contributions of interactions observed
structurally. Comparison of RNA recognition by the U1A and Sex lethal proteins
will begin to reveal the general features of the RRM that enable it to be
a ubiquitous RNA binding domain.
To identify the energetic components of binding affinity
and specificity in RRM-RNA complexes, we systematically modify protein side
chains and RNA nucleotides and measure the stability of the modified complexes.
We complement these experiments with structural and theoretical methods in
order to fully understand the effects of the modifications on both the free
and bound components of the complex. Currently, we are investigating the
energetic contribution of stacking interactions between highly conserved
aromatic amino acids and RNA bases to RRM-RNA stability and the role of RNA
and protein conformation in RRM-RNA complexes. We have compared the energetic
contribution of stacking interactions and networks of hydrogen bonds to complex
stability by mutating U1A and substituting modified bases into the RNA target
site that have a range of abilities to participate in stacking interactions
and hydrogen bonds.
We are developing small peptide models of RRMs in which
the interactions that have been observed to be most important for RNA recognition
are maintained. We are using both rational design and combinatorial selection
techniques to discover these peptides. In the process of design and
selection of RNA binding peptides, we are learning which general characteristics
of small peptides are most important for RNA recognition. In addition, small
peptides are easier to chemically manipulate and structurally characterize
than the full length RRMs from the U1A or Sex lethal proteins.
Selected Publications:
- "Accessory Factor-bZIP DNA Interactions" Baranger, A. M., Curr.
Opin. Chem. Biol., 2, 18 (1998).
- "Recognition of an Essential Adenine at a Protein-RNA Interface:
Comparison of the Contributions of Hydrogen Bonds and a Stacking Interaction"
Nolan, S.J.; Shiels, J.C.; Tuite, J.B.; Cecere, K.L.; Baranger, A.M.
J. Am. Chem. Soc. 121, 8951 (1999).
- "Contribution of RNA Conformation to the Stability of a High-Affinity
RNA-Protein Complex" Luchanscky, S.J.; Nolan, S.J.; Baranger, A.M. J.
Am. Chem. Soc. 122, 7130 (2000).
- "Molecular Dynamics and Thermodynamics of a Protein-RNA Complex:
Mutation of a Conserved Aromatic Residue Modifies Stacking Interactions
and Structural Adaptation in the U1A-stem loop 2 RNA Complex" Blakaj, D.M.;
McConnell, K.J.; Beveridge, D.L.; Baranger, A.M. J.Am. Chem. Soc.
123 , 2548 (2001).
- "RNA-DNA Hybrids Containing Damaged DNA are Substrates for RNase
H" Shiels, J.C.; Jerkovic, B.; Baranger, A.M.; Bolton, P.H. , Bioorg.
Med. Chem. Lett.,11, 2623 (2001).
- "Investigation of a Conserved Stacking Interaction in Target Site
Recognition by the U1A Protein" Shiels, J.C.; Tuite, J.B.; Nolan, S.J.; Baranger,
A.M., Nucleic Acids Res., 30, 550 (2002).
- "Molecular Dynamics Simulation Studies of Induced Fit and Conformational
Capture in U1A-RNA Binding: Do Molecular Substates Code for Specificity?"
Felicia P., .Beveridge, D.L., and Baranger, A.M., Biopolymers,
65, 424 (2002).
- “Inhibition of the U1A-RNA Complex by an Aminoacridine Derivative”
Gayle, A.Y.; Baranger, A.M. Bioorg. Med. Chem. Lett., 12
, 2839 (2002).
- “Substitution of an Essential Adenine in the U1A-RNA Complex with
a Non-polar Isostere” Tuite, J.B.; Shiels, J.C.; Baranger, A.M. , Nucleic
Acids Res., 30, 5269 (2002).
-
"Design of an Adenosine Analog that Selectively Improves the Affinity
of a Mutant U1A Protein for RNA" Zhao, Y.; Baranger, A.M. J. Am. Chem.
Soc., 125, 2480 (2003).
-
"Binding of an Aminoacridine Derivative to a Tetralopp RNA"
Yan, Z., Baranger, A.M. Bioorganic and medicinal Chemistry Letters, 14,
5889 (2004).
-
"Synthesis of Fluoro-substituted Phenyl Ribonucleosides"
Benitex, Y., Baranger, A.M. submitted for publication (2004).
Education
- B.S. 1988 Massachusetts Institute of Technology
- Ph.D.1993 University of California, Berkeley
[Chemistry]
[Wesleyan]
Last updated: August 15, 2008 (AMB/rncb)
