Biophysical chemistry: structure of proteins; protein crystallographyand Cryo EM
Office: Mayer Hall 4513
University of California, Berkeley
Universite de Paris, Sorbonne, France
Ecole Superieure d'Electricite, Paris, France
Ecole Superieure d'Electricite, Paris, France
Awards and Academic Honors
UCSD Chancellor Associate Award
Union of Pacific Asian Award
NIH Fogerty Fellowship (unable to accept)
NATO Senior Fellowship
Physicist, Lawrence Radiation Laboratory
Assistant Research Physicist, University of California, San Diego
Our laboratory pursues two directions of research on determination of protein structures. The first is to improve the methodology, including making new instruments for Protein Crystallography and Cyro Electron Microscopy. For Protein Crystallography we are designing and building a direct detection, photon counting, x-ray pixel array detector that could collect data at least an order of magnitude faster than the standard detector. For Cyro-EM, we are designing and building a large Mosaic CCD camera with very high resolution (8K x 8K pixels) and sensitivity. We are also exploring different solid state electron counting detectors.
The second direction is to use existing protein crystallography methods to solve 3D structures of new and interesting proteins, incuding the following:
Structure of the cAMP-dependent Protein Kinase
Our long term goals are to understand the structure and function of the catalytic (C) and regulatory subunits of cAMP-dependent protein kinase (cAPK). By probing this simple protein kinase, we hope to elucidate the general rules for this large family of enzymes that play critical roles in signal transduction. A major goal for many years was to solve the crystal structure of the C-subunit. We published the first protein kinase structure in 1991. We subsequently solved a variety of structures of the catalytic subunit, complexed with different cofactors and substrate analogs. These structures represented both closed and open conformations of the enzyme and allowed us to begin to evaluate the conformational flexibility of the enzyme. We are now solving the structure of the apoenzyme as well as a complex that contains bound balinol, a high affinity natural product inhibitor of PKA and PKC.
We have also succeeded in solving the structure of the regulatory subunit of cAPK. This is also the first structure of a regulatory subunit and allows us to see the molecular features of the cAMP binding sites. Furthermore, one can begin to understand how the cooperative binding of cAMP might lead to kinase activation. A major future goal will be to solve the structure of a holoenzyme complex. This investigation is being carried out in collaboration with Professor Susan Taylor.
Structure of anthranilate synthase
The crystal structure of anthranilate synthase (AS) from Serratia marcescens, a mesophilic bacterium, has been solved in the presence of its substrates, chorismate and glutamine, and one product, glutamate, at 1.95 Å, and with its bound feedback inhibitor, trytophan, at 2.4 Å. In comparison with the AS structure from the hyperthermophile Sulfolobus solfactaricus, the S. marcescens structure shows similar subunit structures but a markedly different oligomeric organization. One crystal form of the S. marcescens enzyme displays a bound pyruvate as well as a putative anthranilate (the nitrogen group is ambiguous) in the TrpE subunit. It also confirms the presence of a covalently bound glutamyl thioester intermediate in the TrpG subunit. The tryptophan-bound form reveals that the inhibitor binds at a site distinct from that of the substrate, chorismate. Bound tryptophan appears to prevent chorismate binding by a demonstrable conformational effect, and the structure reveals how occupancy of only one of the two feedback inhibition sites can immobilize the catalytic activity of both TrpE subunits. The presence of effectors in the structure provides a view of the locations of some of the amino acid residues in the active sites. Our findings are discussed in terms of the previously described AS Structure of S. solfactaricus, mutational data obtained from enteric bacteria, and the enzyme's mechanism of action. This investigation is being carried out in collaboration with Professor Stanley Mills of the UCSD Biology Division.
Structure of anthranilate phosphoribosyltransferase
Phosphoribosyltransferases catalyze the Mg2+ -dependent group transfer of 5'-phosphoribose from ±-D-5-phosphoribosyl-1-pyrophosphate (PRPP) to the nitrogen atom of NH3 as well as various aromatic hetrerocyclic and benzene-derived nucleophiles. The nitrogen acceptor for anthranilate phosphoribosyltransferase (APRT) reported here is anthranilate. These enzymes are essential components of nucleotide salvage as well as biosynthetic pathways for purines, pyrimidines, niacin, and the amino acids histidine and tryptophan.
The structure of APRT from the enterobacterium Pectobacterium carotovorum has been solved at 2.4 Å in the complex with Mn2+ -pyrophosphate (PPi), and 1.86 Å without ligands. The enzyme structure has a novel PRT fold, and displays close homology to the structure of pyrimidine nucleoside phosphorylase. The nature of the active site is inferred from the trapped MnPPi complex and detailed knowledge of the active sites of other phosphoribosyltransferases. This investigation is being carried out in collaboration with Professor Stanley Mills of the UCSD Biology Division.
Primary Research Area
- Crystal Structure of a Transition State Mimic of the Catalytic Subunit of cAMP-dependent Protein Kinase. With Madhusudan, P. Akamine, and S. S. Taylor. Nature Struc. Biol. 9, 273 (2002).
- The Structures of Anthranilate Synthase of Serratia Marcescens Crystallized in the Presence of (i) its substrates, Chorismate and Glutamine, and a Product, Glutamate, and (ii) its End-product Inhibitor, L-tryptophan. With G. Spraggon, C. Kim, M. C. Yee, C. Yanofsky, and S. E. Mills. PNAS 98, 6021 (2001).
- Status of the Digital Pixel Array Detector for Protein Crystallography. With P. Datte, A. Birkbeck, E. Beuville, N. Enres, F. Druillole, L. Luo, and J. Millaud. Nuclear Instru. & Methods Phys. Res. A-421, 576 (1999).
- ASIC-Based Event-Driven 2D Digital Electron Counter for TEM Imaging. With G.Y. Fan, P. Datte, E. Beuville, J.-F. Beche, J. Millaud, K.H. Downing, F.T. Burkard, and M.H. Ellisman. Ultramicroscopy 70, 107 (1998).