Research Abstracts Online
January 2010 - March 2011
St. Olaf College
PI: Jeff Schwinefus
Correlating Glycine Betaine Interactions With Nucleic Acids by Molecular Dynamics Simulations
The long-term objective of this project is to elucidate the mechanism of cosolute-modulated folded nucleic acid stability, so as to better understand cosolute interactions with biopolymers and how these interactions influence biopolymer structural change and biochemical reactions. This research uses molecular dynamics (MD) simulations using AMBER 10 to quantify accumulation or exclusion of glycine betaine at 5'-nucleotide monophosphates (5'-NMPs). Insights from analysis of the accumulation of glycine betaine around specific chemical functional groups on the nucleobases during molecular dynamics simulations allow the researchers to correlate favorable glycine betaine interactions (measured in thermal unfolding and vapor pressure osmometry studies at St. Olaf College) with chemical functional groups that would be exposed during the unfolding of nucleic acids.
The group is also continuing their analysis of 5'-NMP and nucleoside torsion angles in the absence of glycine betaine. The 60 ns MD simulations of all 8 NMPs and nucleosides have been completed at MSI. The researchers found that all NMPs and nucleosides spend the majority of simulation time with the nucleobase in the syn position. While anticipated for adenine and guanine based on empirical data, pyrimidines are not expected to spend such a large fraction of time in the syn position. The researchers seek to identify correlations between nucleobase torsion angle and sugar pseudorotation angle using ptraj to explain this unexpected trend.
James W. Checco, Undergraduate Student
James M. Kohler, Undergraduate Student
Stuart T. Nelson, Undergraduate Student
Collin J. Pitts, Undergraduate Student
Elliot C. Schmidt, Undergraduate Student
Alexandra L. Thomas, Undergraduate Student
Lauren E. Vandeventer, Undergraduate Student