University of Minnesota
University Relations

Minnesota Supercomputing Institute

Log out of MyMSI

Research Abstracts Online
January - December 2011

Main TOC

St. Olaf College
Department of Chemistry

PI: Jeff Schwinefus

Blycosyl Torsion Angles in 5'-NMP Molecular Dynamics Simulations

The long-term objective of this project is to illuminate the reason for the preferential syn position of the nucleobase in 5'-nucleotide monophosphates (5'-NMPs) and nucleosides during molecular dynamics (MD) simulations. NMR has been used to demonstrate that purine 5'-monophosphates such as guanosine monophosphate do have a sizeable fraction of time spent in the syn position. However, previous MD simulations have shown all 5'-NMPs and nucleosides studied to date have a greater fraction of syn versus anti occupancy. The researchers have obtained 60 ns simulation time for all 8 NMPs and nucleosides at MSI using AMBER 10. They are extending these simulations to 120 ns. These investigations will use MD simulations using AMBER 10, available at MSI, to quantify the fraction of time 5'-nucleotide monophosphates (5'-NMPs) and corresponding nucleosides spend in the syn and anti positions and correlate these times with nucleobase and sugar pseudorotation torsion angles, atomic distances, hydrogen bonding, and ionic interactions.

Group Members

Samuel Engelsgjerd, Undergraduate Student
Elliot C. Schmidt, Undergraduate Student
Andrew Menssen, Undergraduate Student