Biochemistry and Biophysics Center

The Biochemistry and Biophysics Center carries out research that brings chemical and physical approaches to the study of biological problems. The principal investigators of the Center focus on topics that range from DNA transcription to cellular degeneration. To understand the mechanisms involved in these diverse processes, the investigators develop instruments and techniques to resolve, quantify, model, manipulate, and simulate biological mechanisms at molecular and cellular levels. The focus of Center research is to develop both experimental and theoretical models of biomolecular structure, and use these models to discover the link between the structure, function, and regulation of biologically active molecules and processes. This basic research helps fuel scientific discovery that may one day help advance research related to heart, lung, blood, and sleep conditions or other fields.

Our Labs

Advanced Microscopy and Biophotonics

Visualizing the workings of living cells has transformed biological understanding. Today, optical technologies allow us to detect the movements of macromolecules in cells embedded within living tissues, but there is still a need to improve resolution, speed, and minimize tissue damage. The Laboratory of Advanced Microscopy and Biophotonics, led by Dr. Jay R. Knutson, uses optical physics and fluorescence to create better instruments for examining the inner workings of cells and the macromolecular (proteins, lipids, and DNA) complexes within. 

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Biochemical Dynamics

The enzymatic activity of many proteins is regulated by certain chemical modifications. Research in the Laboratory of Biochemical Dynamics involves understanding biochemical mechanisms of enzyme action and cellular regulation with a focus on the regulatory roles of reversible protein modifications. Led by Dr. P. Boon Chock, the lab is also interested in free radicals and reactive oxygen species-mediated oxidative modification of proteins and RNA. Dr. Chock’s work revealed the advantages of reversible modification cascades in cell signaling in view of their enormous potential for signal and rate amplification and regulatory flexibility. Dr. Chock also showed the role of protein glutathionylation in regulating the activity of tyrosine phosphatase 1B and 2-Cys-peroxiredoxin, in growth factor-mediated actin polymerization, and in translocation.

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Biochemistry

Because eukaryotic cells depend on molecular oxygen for normal metabolism, they generate reactive oxygen species (ROS) that can cause multiple forms of cellular stress and damage. For several years, the Laboratory of Biochemistry, led by Dr. Rodney L. Levine, has focused its research on the identification of oxidative modifications of proteins. Dr. Levine is interested in the conditions that give rise to modifications in which amino acids are modified, and the impact those modifications have on enzymatic function or structural integrity. Dr. Levine is pursuing the hypothesis that oxidative modifications of proteins are not always a negative effect of stress, but also participate in normal cellular signaling.

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Bioseparation Technology

The Laboratory of Bioseparation Technology’s primary interest is in inventing methods of isolating, purifying, or analyzing materials of biomedical interest—including cells, macromolecules, and small molecular weight compounds—by means of counter-current chromatography and elutriation. This lab is led by Dr. Yoichiro Ito, who has helped develop innovative separation methods, including the coil planet centrifuge for blood cells, and a novel rotary seal-free centrifuge device for blood that limits the damage to platelets caused by the commonly used rotary seal.

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Computational Biophysics

The Computational Biophysics Section of the Laboratory of Computational Biology is a group of researchers, led by Dr. Bernard Brooks, who use high-performance computing and macromolecular simulation to investigate problems in biophysics and chemistry. Their research efforts involve the development of new methods to assist the interpretation of experiments for calculating binding free energies and partition coefficients, including those with pKa changes; for integrating multiple computational models into a multiscale computation; for new enhanced sampling methods and normal mode techniques; and for techniques for finding reaction pathways in complex systems. These developments are integrated into CHARMM and several other macromolecular simulation and quantum mechanical software packages, providing a complete set of tools for complementing and enhancing experimental research.

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