OHSU

Michael Chapman, Professor

chapman

Structural Biology of Viral-Host Interactions and Enzyme Mechanism

 

Michael Chapman, Professor

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

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

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 atomic structure of the whole virus allowed predictions of the binding site of the primary receptor and have guided the work of many others in retargeting gene therapy vectors. We are now elucidating the details of cellular interactions by visualizing virus complexed with antibodies and receptor molecules using x-ray crystallography, electron microscopy and mass spectrometry.

In methodological research, we develop computer algorithms for building the most accurate models of molecular structure by refinement and validation against x-ray crystallographic data and 3D images from electron microscopy. The most interesting biomolecular complexes are often those difficult to visualize at high resolution. Thus, a special interest is methods for supplementing the experimental data with restraints that impose our understanding of the fundamental physical chemistry of atomic interactions. Our favorite test case is the ribosome. High resolution crystal structures are now available. Electron microscopy of complexes at the different steps of protein synthesis, combined with our refinement methods, is providing a detailed picture of the motions of the constituent structures in this exquisite cellular machine.

The impression gleaned from Biochemistry text books is that many enzyme mechanisms are known. However, relatively few have withstood rigorous experimental testing. Many are plausible suggestions based largely on a static structure obtained by x-ray crystallography. Using a model enzyme, arginine kinase, we are elucidating the dynamic protein motions that are just as critical to function. This is through very high resolution crystallographic structures of the enzyme trapped at different steps in the catalytic cycle, combined with nuclear magnetic resonance (NMR) experiments that reveal the local rates of motion and allow us to associate motions with either substrate binding or chemical steps. Finally, we seek a more quantitative understanding of enzyme mechanism by building a computational model of the reaction that is based on quantum mechanics that, when complete, we hope can be validated by predicting the kinetic effects of active site mutations that we measure experimentally.


Link to PubMed Listing

Chapman Lab

Dr. Chapman's NIH Biosketch