Michael Chapman, Professor


Structural Biology: Viral-Host Interactions and Enzyme Dynamics


Michael Chapman, PhD, Professor, Interim Chair

Phone: 503-494-1025 Fax: 503-494-8393
Location:  MRB 534A

Atomic structure, interactions and dynamics are core to understanding bio-molecular mechanism. Structural biology underpins the basic science of how things work in the cell, and is often a foundation for design of therapeutic interventions. The Chapman group develops biophysical methods for visualizing molecular interactions and applies them in the distinct areas of viral-host interactions and enzyme mechanism/dynamics.

Adeno-associated virus (AAV) is a human virus that does not cause disease and is being developed as a vector for delivering gene therapies in patients with genetic diseases. Delivery requires circumvention of the host immune response to viruses, and an understanding of the interactions of the virus with cellular receptors so that the therapy can be more specifically directed towards targeted tissues. Our X-ray atomic structures of the whole virus provide a key foundation for a molecular understanding its host interactions and have guided the work of many others in retargeting gene therapy vectors. We have used electron microscopy (EM) to visualize the interactions with neutralizing antibodies and combined it with surface plasmon resonance to characterize the specificity with which AAV attaches to cell surface glycans. Having identified (with Jan Carette, PhD) the protein receptor through a genomic screen, we are now characterizing the interactions of endosomal cell entry.

In methodological research, we develop computer algorithms for building the most accurate models of molecular structure by refinement against data from x-ray crystallography, EM and NMR. The most interesting biomolecular complexes are often difficult to visualize at high resolution, so we are developing innovative approaches for the combination of individually sparse datasets, for eliminating unnecessary degrees of freedom in the model and for adding additional information through restraints to general stereochemical and biophysical principles.

From Biochemistry text books, the impression might be that proteins have fixed structure. Although they have been much more challenging to characterize, we realize increasingly that a protein's motions are critical to function. Using arginine kinase as a paradigm, we are elucidating the dynamic motions of a "typical" enzyme during its reaction cycle. This involves combining crystal structures in various intermediate states, together with nuclear magnetic resonance (NMR) experiments that reveal the local rates of motion in the functionally critical (but experimentally challenging) milli- and micro-second regimes. We have demonstrated that the loop and domain motions have the same activation barrier as turnover, implying that protein motions, and not substrate chemistry, is rate-limiting, and are now dissecting where, in the reaction cycle, each of these motions is critical.

Link to PubMed Listing

Chapman Lab

Dr. Chapman's NIH Biosketch