PDB Community Focus: Angela Gronenborn, University of Pittsburgh

ANGELA GRONENBORN, PH. D. is one of the country's leading structural biologists and an internationally renowned specialist in the application of nuclear magnetic resonance (NMR) spectroscopy for investigating structure, dynamics and folding of biological macromolecules. She joined the faculty of the University of Pittsburgh as a Professor in the School of Medicine in 2004. In 2005, the Department of Structural Biology was established with Prof. Gronenborn holding the Rosalind Franklin Professorship and Chair. The department is located in the new Biomedical Science Tower, housing state of the art equipment devoted to NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy. Prior to her move to Pittsburgh, Prof. Gronenborn was a member of the Senior Biomedical Research Service and Chief of the Structural Biology in the National Institute of Diabetes and Digestive and Kidney Diseases at the National Institutes of Health (NIH). She received both her undergraduate and Ph.D. degrees from the University of Cologne, Germany. After postdoctoral training she joined the Scientific Staff in the Divisions of Molecular Pharmacology and Physical Biochemistry at the National Institute for Medical Research, Mill Hill, London. In 1984, she moved to the Max-Planck Institute in Munich as head of the Biological NMR Group, and in 1988 to the NIH.

Prof. Gronenborn's research harnesses the power of NMR in two major areas: understanding biochemical mechanisms and the structural basis of cellular regulation as well as HIV pathogenesis. She has authored more than 350 publications, including structural studies on interleukins, chemokines, the tumor suppressor protein p53, various transcription factors and enzymes, and a number of HIV-encoded proteins including integrase and protease. She also is noted for her contributions to advancing technology on how best to apply NMR to elucidate important problems in the biosciences.

How would you compare X-ray and NMR methods for determining structure?

I truly believe both methods are complementary. Each provides a model for the 3D structure of a molecule and as such, each presents a picture of the spatial architecture, one in the solid state and the other in solution. Naturally, the environment and conditions in which the structural studies are conducted will influence the outcome to a certain degree. pH, temperature, and ionic strength are rarely identical if both methods have yielded structures, and details may vary accordingly. For example, sidechain orientations may differ depending on the protonation state, and loop regions may get 'locked in' in the crystalline state. In addition, since a much larger degree of order is required for crystals to form, the oligomerization state may be different in solution and the crystal. Indeed, there are numerous examples of proteins for which dimers and higher oligomers are observed by X-ray crystallography, but the solution NMR structures are monomeric.

In terms of methodological maturity, it is evident that X-ray crystallography is 25 years ahead of NMR as a structural method, thus it is a robust method. This is reflected in the significantly larger numbers of X-ray structures in the PDB compared to NMR structures. If one looks at the growth rate, however, I believe NMR follows exactly the trend that was seen 25 years ago in the crystallographic field. Structural NMR is still evolving, with novel and advanced approaches being introduced all the time. A case in point was the introduction of R(esidual) D(ipolar) C(coupling)-based methodologies that led to better defined structures and allows for unambiguous positioning of relative structural elements.

What aspects of structural biology are more accessible by NMR than X-ray methods?

As we all know, the rate-limiting step in X-ray crystallography frequently is the time it takes to obtain well-diffracting single crystals - NMR solution structural work is not hampered by this requirement.Crystallization may be prevented if, for instance, a protein is very flexible or contains mobile regions, but NMR can investigate such 'floppy' proteins. Examples of this type are folding intermediates or partially folded proteins, for which NMR is probably the only method that allows one to carry out structural characterizations (see for example ref.¹).

In addition, structures of weakly interacting systems are another area where NMR excels. Tight binding is often required for complexes to be amenable to crystallization, and exchanging systems present major challenges (sometimes overcome by cross-linking the components). NMR can deal with exchanging systems and structures of "weak" complexes can be determined (see for example ref.²). This property of NMR was exploited early on in studies of protein-ligand complexes and the transferred NOE methodology has been widely used in pharmaceutical applications.

What were the most exciting projects in which you have been involved?

There have been numerous exciting projects all along the way - and I still can get thrilled about seeing a new structure for the first time or coming up with some crazy idea.

One exhilarating period that comes to mind was the late eighties/early nineties when we were all in the bowels of Building 2 at the NIH. Marius Clore and myself had just moved from the Max-Planck. Together with Ad Bax, who already was working there, and a combined group of congenial post-docs, we developed and implemented 3- and 4D NMR and its application for protein structure determination.

Also, my work on cyanovirin (CVN) - starting with the initial structure of a protein whose sequence had no relatives in any database via dissecting its folding and domain-swapping, to carbohydrate binding and the structural basis of its anti-HIV activity has kept me captivated for years. Indeed, it inspired me to embark on a fishing expedition - for its gene - which in turn has now led to the discovery of CVN homologs in truffles and plants, whose structures we are currently working on.

You are the chair of the BMRB Advisory Committee. How do you see the interaction of the BMRB with the PDB?

The BMRB is the arm of the PDB that deals with NMR structure determinations. Its mission is to collect, archive, and disseminate data derived from NMR spectroscopic investigations of biological macromolecules. Initially structures, irrespective of their origin (i.e., the method with which they were determined) were all deposited in the PDB. Likewise, the constraints that were used for generating these structures were archived there, whereas other NMR parameters such as chemical shifts were deposited at BMRB. Now that BMRB is part of wwPDB, it is becoming more of an integral part of the overall depository and it is envisaged that no matter at which site a deposition is made, all data will be retrievable in identical format from any of the sites. I strongly believe that an open and collegial atmosphere is essential for science to thrive, unencumbered by national interests - to that end the PDB data is maintained as a single global archive whose contents is freely and publicly available. The NMR community and BMRB has a stake in contributing to the international and interdisciplinary nature of the PDB by providing and archiving high quality and consistent NMR data, thereby playing an active role in the continued success of this global resource.

How has NMR changed and/or advanced as a technique over the course of your career?

In one word - tremendously! Just considering instrumentation alone, we have seen unbelievable advances. During my thesis work I recorded spectra on 60MHz spectrometers, with the HA100 our most advanced instrument. When I started in "biological NMR" during my post-doctoral training, 2D NMR had not been invented and protein NMR was in its infancy. We were thrilled to see individual resonances for histidine residues in 1D proton spectra! High field magnets were 270 MHz; and we would read in pulse programs from paper tapes. These days we routinely record heteronuclear, multidimensional (2-, 3- and 4D) spectra on uniformly (¹³C/¹⁵N/²H) labeled biological macromolecules at 600MHz, with 700, 800 and 900 MHz magnets available in regional and national NMR facilities for the most demanding applications and samples. Whereas initially it was feared that NMR would be limited to studying proteins of less than ~100 amino acids - certainly true if one were restricted to proton 2D NMR only - we now can tackle much larger systems. Indeed, structure determinations of systems up to ~100kDa are possible and good quality spectra have been obtained for much bigger systems like the 800-kDa tetradecameric GroEL chaperone. Using selective or segmental labeling approaches in conjunction with clever spectroscopy no doubt will lead to further advances - we haven't reached our limits yet.

What do you see as the future of NMR?

I believe we will see continuous advances in the development of NMR methodology as well as its application to more and more challenging systems. As alluded to above, NMR is particularly powerful to look at dynamic systems, such as unfolded or partially folded proteins, exchanging systems or regions in multi-component systems that are flexible. I predict that we will see increasing activities in the NMR community directed at characterizing protein dynamics and relating motions to biological activities.

You recently moved to the University of Pittsburgh to chair the structural biology department there. What were the challenges involved in setting up that program?

As is often the case when one embarks on a new venture, one is excited about the opportunities. Challenges and opportunities usually go hand in hand, and setting up Structural Biology at the University of Pittsburgh Medical School presented a tremendous opportunity. I firmly believed that it was necessary to embrace the continuum of structural methodologies if one wanted to understand biological systems at the most fundamental level - cryo-electron microscopy, X-ray crystallography and NMR - and needed to assemble faculty and instrumentation of the highest caliber. Naturally, this comes at considerable cost. Fortunately for Pittsburgh and myself, the institution and the Senior Vice Chancellor for the Health Sciences, Art Levine, not only shared this view, but had already embraced structural biology as being crucial for medical research. As a result, he supported me all along the way. We have now completed the first round of hiring, and the new Structural Biology Department already has a number of faculty who moved to Pittsburgh from all over the US and Europe. We are housed in a state-of-the-art new research building, BST3, that was designed to optimally site all our instrumentation. Despite its location on one of the busiest streets in Pittsburgh, 5th Avenue, the NMR spectrometers and electron microscopes are shielded from vibrations and other environmental influences. Working with an extremely competent and responsible architectural firm made this possible - as well as getting natural light into the NMR facility, a pleasure for those of us who have worked underground for most of our careers. We are now looking forward to carrying out exciting new biomedical research and entering into adventurous collaborations with our clinical and biological colleagues.

1. Byeon, I. J., Louis, J. M. & Gronenborn, A. M. A captured folding intermediate involved in dimerization and domain-swapping of GB1. J Mol Biol 340, 615-25 (2004).
2. Garrett, D. S., Seok, Y. J., Peterkofsky, A., Gronenborn, A. M. & Clore, G. M. Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr. Nat Struct Biol 6, 166-73 (1999).