PDB Community Focus: Dr. Wah Chiu
Dr. Wah Chiu is the Alvin Romansky Professor of Biochemistry at
Baylor College of Medicine. He is a leading investigator in the
structural determination of biological nanomachines using
cryo-electron microscopy (cryoEM) towards atomic resolution.
His laboratory has pioneered various experimental and
computational methods in biological cryoEM. He has determined
cryoEM structures of filament bundles, ion channels, viruses
and chaperonins at subnanometer resolutions. He is the founding
director of two NIH-supported research centers: the National
Center for Macromolecular Imaging (ncmi.bcm.edu)
and the Center for Protein Folding Machinery (proteinfoldingcenter.org).
Both involve investigators from diverse disciplines in biology,
medicine, physics, chemistry, engineering and computing from
different institutions and industries across the U.S. He is the
founding director of the Graduate Program in Structural and
Computational Biology and Molecular Biophysics at Baylor
College of Medicine (scbmb.bcm.tmc.edu)
with 68 faculty members from multiple academic institutions in
the greater Houston area to train future scientists at the
interface between biomedicine and physical, chemical,
mathematical, computational and engineering sciences. He is
also the co-founder of the Gulf Coast Consortia for
Collaborative Research and Training in the Houston-Galveston
Area with faculty and trainees from Baylor College of Medicine,
Rice University, University of Houston, MD Anderson Cancer
Center, University of Texas Houston Medical School and
University of Texas Galveston Medical Branch. Dr. Chiu has been
a leading investigator in the development of cryoEM to solve
structures of macromolecular assemblies at increasingly higher
resolutions. Experimentally, he was the first to show the
benefits of a liquid helium cryo-specimen stage and a medium
voltage microscope for high resolution data collection from
frozen, hydrated biological assemblies. Computationally, his
group has developed single particle reconstruction software,
which has been widely adopted by other investigators. His group
has consistently set high resolution standards in
macromolecular electron cryomicroscopy.
Among the many cryoEM structures determined by his group, Chiu is noted for his two seminal studies on the acrosomal bundle
(1000 Å wide and 50 µm long) and herpesvirus capsid (1250 Å in diameter). While both assemblies are similar in
terms of complexity and large size, different computational methods for are required retrieving their structures.
The two structures represent types of assemblies that are not readily solved by crystallography. Chiu's decade-long effort
on the cryo-EM study of these specimens gradually progressed from 40 to 9 Å, at which long alpha helices and large beta
sheets of protein components could begin to be seen. The bundle structure reveals how actin-scruin packing varies along the
filament to allow the bundle switching from coiled to straight conformation under different physiological conditions. The
herpesvirus study uncovered new folds for the four major capsid proteins and led to a novel approach for deriving a pseudo
atomic model of a large assembly by
combining sub-nanometer resolution cryo-EM and computational methods.
Q: What was your path into the field of cryo-electron microscopy (cryoEM)?
A: I entered the field of electron microscopy while I was a graduate student. The field of cryoEM was started in the lab at Berkeley where I did my PhD thesis.
Q: What is cryoEM? Why do you think the number of cryoEM structures is increasing?
A: CryoEM is the use of transmission electron microscope with frozen, hydrated specimens kept at low temperature (below liquid nitrogen temperature). The number of cryoEM structures is increasing partly because the technology has become simpler for biologists to use and partly because the biologists are interested in studying large complexes that are too difficult for conventional crystallography or that are complementary to the crystal structures of the molecular components or the entire complex in one crystalline state.
Q: How far can single particle cryoEM technology be pushed - will it eventually be possible to attain truly atomic resolution
A: The best single particle cryoEM study is now capable of producing a density map of large macromolecular assembly at ~4 Å. I expect that combining the bioinformatics and available PDB structures of component homologs, the cryoEM map will be interpretable in terms of a polypeptide backbone trace and bulky side chains in the near future. To determine single particle structure at truly atomic resolution (i.e. 2 Å or better), numerous technical hurdles have to be overcome.
Q: What is the next frontier in terms of structures that will be observable by cryoEM?
A: CryoEM is currently focused on the study of biological assemblies which are composed of multiple molecular components and have multiple conformations at different functional states. There is also tremendous enthusiasm to pursue cryo-electron tomography of cells and organelles.
Q: Currently, cryoEM maps can be deposited at the EBI, and then coordinates fitted into the maps are deposited into the PDB. How can the processes of depositing and archiving cryoEM data be improved?
A: We would like to deposit both the cryoEM density map and the associated models to one site. Currently, we lack both uniform standards for data representation and tools for visualizing low resolution cryoEM maps. In addition, validation of the observed map and model requires more technical development. To make a successful repository site, we need collaborations among the cryoEM specialists, biology end-users, computational and mathematical specialists and the experienced staff at the RCSB PDB and EBI-MSD. Equally important, steady federal support to initiate and maintain such an infrastructure is necessary.
Q: What is the work of the National Center for Macromolecular Imaging (NCMI)?
A: NCMI (http://ncmi.bcm.edu) is a national facility for macromolecular cryoEM supported by National Center of Research Resource of the NIH. We have the missions of core technology research and development, collaboration, service, training and dissemination. Our Center serves the biological community in a manner similar to synchrotron beam lines in that users can apply to use our facility. The approved projects will be carried out by the users or in collaboration with our experienced staff. We also engage in development of data processing and structure interpretation software, all of which are freely available through our web site. NCMI also sponsors annual workshops to train users to use the newest cryoEM technologies.