Computational Biochemistry

My research focuses on development and application of computational chemistry tools for solving biochemical problems. I believe that some of the fundamental questions in biochemistry, such as

can be answered with the help of computational methods.

Research Strategies

"Computers can answer questions but only an educated person can question the answers"
A powerful strategy of computational analysis of biomacromolecules involves the combination of reductionism and systems approach. In the first, reductionist stage, a necessary description of components of a biological macromolecule is obtained using quantum mechanics. Then, during the systems approach stage, molecular simulation techniques based on a simplified hamiltonian are used to describe the structure, dynamics, and energetics of the whole system. More ...

Molecular Recognition

The essential elements of life--self-replication, information processing, and metabolism--occur largely by specific interaction between biological molecules. Understanding how two molecules recognize each other is thus one of the fundamental issues in biochemistry. Molecular recognition is also a central topic in applied biochemistry because it determines whether a compound posesses useful clinical properties. More ...

Enzyme Catalysis

Most enzymes accelerate specific biochemical reactions enormously. For example, the enzyme rate constant kcat for decarboxylation of the amino acid arginine is 7*1019 times larger than the rate constant for spontaneous decarboxylation of amino acids (Snider & Wolfenden, J. Am. Chem. Soc. 2000, 122,11507). Our group is interested in understanding how enzymes bring about such enormous rate accelerations. More ...

Urate Oxidase

My graduate research focused on experimental studies of the kinetics and mechanism of urate oxidase. Urate oxidase is an unusual enzyme because it does not contain transition metals or redox cofactors, yet it catalyzes the oxidation of singlet organic molecule using molecular oxygen. We determined the kinetic mechanism of this reaction, identified the true enzymatic product, and elucidated the decomposition pathway of this unstable product to the final stable metabolite. More ...

Scientific Publications

"Scientific endeavor is not complete until it has been written up".
These words by Peter Feibelman remind me constantly about few of my unfinished endeavors. The ones that are complete can be found in my Publications List

This document was last updated on Sept 13, 2004. Visits are counted by Nedstad