Interview with Dr. Willa Appel, Executive Director of the New York Structural Biology Center
by Howard B. Johnson
I met with Willa Appel recently at the Upper Manhattan offices of the New York Structural Biology Center. The NYSBC is one of the most advanced sites in the world for instrumentation for structural biology – one of the most important scientific frontiers in biomedical research and drug development. It provides the detailed structure of molecules that are essential for life and the targets of drug therapies. NYSBC represents a breakthrough model for shared resources in the United States. Founded in 2002 by nine eminent New York academic research institutions to provide cutting-edge instrumentation to their faculties, the NYSBC has a professional staff of 30 serving more than 100 Principal Investigators. NYSBC also offers its services to outside academics and for-profit research companies.
In addition to providing resources and services, NYSBC is an intellectual center for structural biology known throughout the world. It conducts in-house research and sponsors multi-institutional research collaborations, symposia and conferences. It alsooffers accredited graduate-level courses and training workshops available to students from all 9 member institutions such as: Cryoelectron Microscopy of Macromolecular Assemblies, Biomolecular NMR Spectroscopy, and NMR Spectroscopy of Macromolecules.
Willa Appel was one of the founders and chief organizers of the NYSBC. She has been with the NYSBC since its inception and serves as its Executive Director.
I recently asked Willa a few questions of potential importance to New York City bioscience entrepreneurs.
1. Tell us about what NYSBC has brought to New York’s scientific community.
Having advanced resources available to visualize proteins in three dimensions has enabled NY researchers to pursue projects that otherwise would not have been possible.
One example is the study of the nuclear pore complex via Cryoelectron Microscopy that provides insights into this important transport activity in and out of the nucleus that is implicated in certain types of cancer and developmental defects. Another is research to understand why Parkinsons and Alzheimer’s diseases develop; this work uses advanced atomic resolution spectroscopic methods to visualize the proteins that are associated with the development of those diseases. These are two among hundreds of research projects that have been made possible by our advanced instrumentation.
Each of the different technologies of structural biology provides detailed images of proteins which provide insight into how these critical molecules function. At NYSBC, we are fortunate to have the three major technologies of structural biology under one roof. These technologies are complementary and having all three allows us to determine protein structures at the atomic level of resolution – via x-ray crystallography and Nuclear Magnetic Resonance Spectroscopy – as well as the macro level through Cryoelectron Microscopy which entails visualizing molecular molecular machines or assemblies.
2. Tell us about the leading-edge instrumentation at the NYSBC.
Nuclear Magnetic Resonance Spectroscopy (NMR) uses extremely powerful magnets to analyze the arrangements and movements of atoms within a protein. It’s a technology similar to MRIs in hospitals but in NMR, the magnets are far more powerful and the focus is far smaller – individual proteins as opposed to organs. The data generated are then modeled into three-dimensional images of a biomolecule at the atomic level. The value of this information is that it provides exquisite detail of protein interactions, the behavior of molecules as they move, and drug interactions with molecules. All this makes it possible to understand molecular behavior in normal and pathological states. NYSBC’s NMR facility is the most advanced in the world.
NYSBC’s expert staff operates nine NMRs including: two at 900 megahertz (MHz); three at 800 MHz; one at 750 MHz and one at 700 MHz – all equipped with cryoprobes to increase sensitivity. We have recently installed a high-field Dynamic Nuclear Polarization spectrometer, the first commercially available in the U.S., whose technology may revolutionize the field by increasing sensitivity by several orders of magnitude. NYSBC’s NMR facility is the most advanced in the world.
X-ray Crystallography uses light a billion times more powerful than that of the sun, generated by a synchrotron, to reveal the architecture of molecules in crystal form at atomic scale. NYSBC operates two synchrotron beamlines at the Brookhaven National Laboratory (BNL) on Long Island. We are building a new, next-generation next-generation beamline, “NYX”, that will exploit the increase energy of the new $1 billion synchrotron being completed at BNL. We expect that NYX will be the most advanced beamline for x-ray crystallography in the world. Of course, we also have ‘home source’ generators at our main facility in Manhattan that are suitable for crystal screening and some structure determination.
Cryolectron Microscopy (CEM) uses electrons to reveal images of individual molecules and molecular assemblies. In CEM, the samples are frozen to preserve them in their native states — unlike conventional electron microscopes that require samples to be fixed and stained. The electrons illuminate the sample much as light does in an ordinary microscope, but the electromagnetic lenses magnify the image up to one million fold. CEM is highly complementary to NMR and X-ray Crystallography as it can create images of transient, large, multi-molecular complexes. NYSBC operates one of the most advanced CEM facilities in the U.S.
Its instrumentation includes: one 300 kilovolt (kV) microscope, two 200 kV microscopes, and one 120 kV microscope all with field emission guns, and a Dual-Beam Scanning Electron and Focused Ion Beam microscope, that can produce 3D reconstructions of tissue from 1-10 microns. The latter is of especial interest to cell biologists, especially neuroscientists who want to quickly visualize the pathway through a cell.
The NYSBC also operates a high throughput protein production facility that uses robotic methods to produce hundreds of functional integral membrane and other proteins in bacterial, insect and mammalian expression systems. One great advantage we have is that we can make multiple proteins in parallel, simultaneously testing the benefits of different conditions and different vectors. This is a different scale of operations from most academic labs that are capable of making proteins do not use high throughput techniques. Many other labs can’t make proteins at all and simply buy them from commercial vendors and these are often low quality. Because NYSBC produces high quality proteins rapidly, our facility is increasingly asked to do work for outside research labs.
3. Who are your Member Institutions? How do they access the resources at the NYSBC?
Albert Einstein College of Medicine, City University of New York, Columbia University, New York University, Memorial Sloan-Kettering Cancer Center, Mount Sinai School of Medicine, State University of New York, The Rockefeller University, Wadsworth Center, New York Department of Health, Weill Medical College of Cornell University. Faculty from all of these institutions can access our instrumentation and our staff. Right now, we provide resources to more than 100 laboratories working on a range of problems. A few examples of these research efforts include: developing inhibitors to prevent HIV from entering the cell; working on receptors that are critical to the cardiovascular system and hypertension; and understanding why morphological defects in mitochondrial membranes explain the symptom of Barth Syndrome. All of this work relies on access to the New York Structural Biology Center and its scientific staff.
4. Do you conduct your own research? What does this research focus on? Do you patent your inventions?
Yes, we do. We have a great deal of expertise on membrane proteins that are critical for effective drug development thanks to large, multiyear grants to NYSBC for work on these challenging proteins. Our Scientific Director, Dr. Wayne Hendrickson, is the Principal Investigator of the New York Consortium on Membrane Protein Structure (NYCOMPS) and has 8 full time staff dedicated to it. Another multiyear NIH grant uses Cryoelectron Microscopy to determine the 2-D structures of membrane proteins, also with dedicated staff. A separate research group at NYSBC has made major advances in the understanding of acetylcholinesterase, an enzyme critical to human nervous system and a target of chemical weapons such as Sarin, and we have patented those results.
5. Do you work with the private sector as well? Tell us about how New York City bioscience entrepreneurs can take advantage of your instrumentation and expertise.
Yes, we opened our doors this past year to the private sector. We have structural biology equipment and expertise that rival or surpass what many large pharmaceutical companies; these resources are far more advanced than what bioscience entrepreneurs might have. We offer our services to these groups. While some may just need access to instrumentation, most have particular projects where they would like our expertise. Usually, a project relates to drug development where seeing exactly where and how a protein binds to a target is extremely useful for drug design and optimization. Our expertise in membrane proteins is also a big draw since so many drugs involve them. We encourage bioscience entrepreneurs to contact us if they’d like to hear about our services. I should add that when these projects create new intellectual property, the entrepreneur or company engaging us maintains ownership.
6. How have you raised your funding?
When they joined the consortium, each of our Member Institutions made a capital contribution that in the aggregate was about $10 million. Since then, we have raised another $65+ million for new instrumentation and housing the new equipment. Our facility now comprises 45,000 square feet. Most funding has come through grants, primarily peer reviewed grants and contracts.
7. Can you tell us about how your site was retrofitted to handle your instrumentation? It sounds like an architectural engineering feat.
The gut renovation of our first building was pretty special. It was a former gymnasium — basketball court and swimming pool — on the City College campus that had been vacant for years. The engineering challenge was placing four high field magnets (NMRs) in the old basketball court without the magnets interfering with each other while minimizing vibrationwhich these instruments can’t tolerate. We ended up placing each magnet on a solid concrete column that extended 30 feet from the floor of the former basketball court down through the swimming pool and then down to bedrock. Each column required 600 tons of concrete. The columns look like a cross between ‘Star Wars’ and James Bond.