Evelyn A. Mayaan, Ph.D.

Research Associate
York Group
Department of Chemistry
University of Minnesota

207 Pleasant St SE
Minneapolis, MN 55455-0431
evelyn@zymeworks.com
(604) 678-1388 x27

curriculum vitae (word doc format)

Phosphate Hydrolysis Reactions in RNA Catalysis

Since the discovery that RNA can have catalytic activity, ribozyme reaction mechanisms have become an increasingly interesting area of study. Ribozymes are capable of cleaving the phosphate backbone of RNA in a highly specific manner. This allows for many exciting bio-applications, such as gene expression inhibitors for the treatment of genetic diseases like cancer and AIDS. Furthermore, RNAs ability to function both as an enzyme and as a carrier of genetic information has important implications for the origins of life on earth.

We are studying the self-cleaving phosphate hydrolysis reaction of the hammerhead ribozyme (HR) as a prototype ribozyme system due to the wealth of experiment studies and x-ray crystallographic structure data available for reference. The HR system contains an active site undergoing phosphate hydrolysis in the presence of divalent metal ions. A fairly substantial conformational rearrangement of the active site appears necessary to bring the reacting phosphate into a "in-line" geometry consistent with an SN2 type reaction. The transition state is believed to be phosphorane-like although it exists on a time scale too small to be captured by experimental methods. It is also believed that divalent metal ions are necessary in vivo for catalytic reaction rates to be achieved, however, the exact role of these metal ions is yet to be fully understood. Our group is using computational methods to add insight to questions such as these on a molecular detail level.

Force Field Development for Molecular Mechanics of RNA Catalysis

To develop a more accurate molecular dynamics (MD) force field and quantum mechanics (QM) Hamiltonian for ribozyme studies, Density Functional Theory (DFT) calculations have been run to determine geometry and energy data for small, representative phosphate and phosphorane molecules and their binding interactions with divalent metal ion complexes. These calculations are useful for predicting trends in geometries, ligand binding and protonation energies with which to parameterize an accurate Hamiltonian for phosphate hydrolysis reactions. Additions and modifications to the CHARMM force field have also been made based on these calculations to allow for more accurate study of conformational rearrangements in the HR environment without more computationally expensive quantum mechanical methods.

Molecular Mechanical Simulation of the Hammerhead Ribozyme

MD is being used to study the large scale conformational changes of the HR active site which allow a catalytically active conformation to be achieved. Simulations of the available HR ground state, early-intermediate, late-intermediate and product x-ray crystal structure have been undertaken to observe the important interactions and occurrences that allow for this conformational rearrangement to occur.

Quantum Mechanical/Molecular Mechanical (QM/MM) simulations are also being explored to characterize reaction intermediates and transitions states of proposed mechanisms for the HR. These mechanisms involve a variety of possible protonation states and metal ion roles which have been discussed in recent literature. Data from these simulations will provide detailed energetic information for determining the catalytic pathway occurring in the HR.

Publications

"Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes", Evelyn Mayaan, Kevin Range and Darrin M. York, J. Biol. Inorg. Chem., 9, 2004, 807-817.

"The contribution of phosphate-phosphate repulsions to the free energy of DNA bending", Kevin Range, Evelyn Mayaan, L. James Maher, III, and Darrin M. York, Nucleic Acids Res., 33, 2005, 1257-1268.

"CHARMM force field development for MD simulation studies of RNA catalysis", Evelyn Mayaan, Adam Moser Alexander D. MacKerell and Darrin M. York, accepted J. Comput. Chem., Feb. 7, 2006.

"Application of a new CHARMM force field for MD simulations studies of RNA catalysis", Evelyn Mayaan and Darrin M. York, in progress.

"Artificial metalloenzymes based on protein cavities: Exploring the effect of altering the metal ligand attachment position by site directed mutagenesis", Ronald R. Davies, Hao Kuang, Dongfeng Qi, Aram Mazhary, Evelyn Mayaan and Mark Distefano, Bioorg. Med. Chem. Letts., 9, 1999, 79-84.

Links of Interest

What is RNA? Click here for a fun, interactive site to learn more about DNA, RNA and many other genetic topics.

Find out how hammerhead ribozyme is being used to help develop new drugs for genetic diseases.

cmm.info.nih.gov/intro_simulation/course_for_html.html A great site for learning the basics of molecular and quantum mechanics.

Introduction to hybrid quantum mechanical/molecular mechanical (QM/MM) simulations.

http://www.charmm.org Link to the official Chemistry at HARvard Molecular Mechanics (CHARMM) website.

Links to the RCSB Protein Data Bank and the Nucleic Acids Database where you can download pdb structures of published molecules.

Learn more about the implications ribozymes have for life on earth. The RNA World Hypothesis

Evelyn's LINUX Cheat Sheet If you are new to our group and feeling clueless about LINUX, visit my LINUX "Cheat Sheet" to learn some basic commands you'll need to become acquainted with. (Most of these commands work for UNIX too.)