Center for Bioinformatics at KU

As part of our public Seminar Series
http://bioinformatics.ku.edu/seminars

Apr 28, Fri, 2006
3:00pm - 4:30pm, 1005 Haworth

Alex MacKerell

Structure-function relationships of nucleic acids and protein-nucleic acid complexes studied via MD simulations

Nucleic acids alone and in complexes with proteins perform a wide variety of biological functions, including replication and gene regulation, among others. To perform these functions, nucleic acids and/or their protein partners must undergo conformational changes. For example, the genetic information in DNA is "hidden" in the Watson-Crick base pair interactions requiring that duplex DNA unwind and open in order for that information to be accessed. Results from MD simulation studies on the conformational changes associated with base flipping in DNA alone and in the presence of the methyltransferase from HhaI (M.HhaI) will be presented. The role of results from computation in interpreting experimental NMR imino proton exchange data as well as elucidating the flipping mechanism and specificity of M.HhaI will be discussed.