1. STRUCTURAL GENOMICS OF M. JANNASCHII
By Art Robinson
Contact: SHKim@lbl.gov

In structural genomics, researchers look for clues to the function of a protein in its three-dimensional structure. In the early stages of a pilot project to test the feasibility of structural genomics, UC Berkeley and Berkeley Lab researchers conducting protein crystallography experiments at the ALS have determined the structures of two proteins of previously unknown function. In one case, the structure suggested a small number of possible functions from which biochemical assays could then be used to pinpoint the actual function.

One of the important objectives of cataloging the DNA sequences of organisms (as in the Human Genome Project) is to understand the cellular and molecular (biochemical and biophysical) functions of all the gene products (mostly proteins) encoded in the genome. Unfortunately, the function of a protein cannot be readily inferred from the DNA sequence of a gene unless that sequence is significantly similar to that of a gene whose function is already known.

Assessing function by determining the structures of all the gene products of an organism would be an overwhelming task. Fortunately, the current database of protein structures strongly suggests that most proteins are classifiable in terms of a finite set of folds, the "folding basis set," and that each fold may be represented by a small number of biochemical or biophysical functions. Accordingly, large-scale projects to determine the structures of a few representatives from each fold family can provide a foundation for the functional genomics. This information can be combined with cellular functions derivable from mutational studies, transcription tracking, translation tracking, and interaction tracking.

To this end, the UC Berkeley and Berkeley Lab researchers are using the Macromolecular Crystallography Facility (MCF) in a pilot study of the fully sequenced model hyperthermophilic archaebacterium Methanococcus jannaschii. The group has chosen several gene products from this organism—some with known cellular functions but without known molecular functions and some without any known functions—and have begun to determine their structures. The long-term goal of this project is to determine the structures of representative gene products in order to establish a folding basis set for the approximately 1800 gene products expressed in the microbe. The principal focus on finding a large number of new folds makes determination of the phases of diffracted beams by multiple-wavelength anomalous diffraction (MAD) analysis a necessity.

Early results have already allowed the roles of two "hypothetical" proteins (proteins for which there is no other protein in the database with a gene having a similar sequence and a known function) to be tentatively identified from their structure alone. With data gathered at the MCF, for example, the group has determined the structure of hypothetical protein MJ0577 from M. jannaschii. (A highlight showing the solved structure is available on the Web at http://www-als.lbl.gov/als/science/sci_archive/Mjann.html.) The crystal structure was solved and refined within a few days after data collection was completed. The set of high-quality experimental phases from MAD measurements at the MCF has proven to be the key factor for interpreting and modeling the structures of the protein and ligands. For example, MJ0577 was identified as an ATP-binding protein after examination of the electron density map showed bound ATP.

The discovery of the ATP immediately narrowed down the possible biochemical function of this protein. Biochemical experiments showed that MJ0577 has no appreciable ATPase activity by itself. However, when M. jannaschii cell extract was added to the reaction mixture, 50% of the ATP was hydrolyzed to ADP in 1 hour at 80 degrees C. This result indicates that MJ0577 requires one or more soluble components specific to M. jannaschii to stimulate ATP hydrolysis, suggesting that this is an ATP-mediated molecular switch analogous to Ras, a GTP-mediated molecular switch that requires GAP to hydrolyze GTP.

Research conducted by T. Zarembinski, L.-W. Hung, J. Mueller-Dieckmann, K.-K. Kim, H. Yokota, R. Kim, and S.-H. Kim (Berkeley Lab and University of California at Berkeley) using Beamline 5.0.2.

Publication about this experiment: T. Zarembinski, L.-W. Hung, J. Mueller-Dieckmann, K.-K. Kim, H. Yokota, R. Kim, and S.-H. Kim, Proc. Natl. Acad. Sci. 15 (1998), 15189.

Funding: U. S. Department of Energy, Office of Biological and Environmental Research; Deutsche Forshungsgemeinshaft.

2. REVISED SCHEDULE FOR APRIL-SEPTEMBER 1999 POSTED ON WEB
Contact: GFKrebs@lbl.gov

The operating schedule for running time between April and September 1999 has been updated. Several additional shifts were added for the users by trimming down the ALS maintenance time. This reduction of maintenance shifts was possible because some Center for X-Ray Optics (CXRO) technicians will now work with ALS staff to help carry out maintenance work. The agreement between CXRO and the ALS is documented in a memorandum of understanding signed by Ben Feinberg, ALS Head of Operations, and David Attwood, Head of CXRO. The revised schedule can be viewed on the Web at http://www-als.lbl.gov/als/schedules/aprsep99.html. You can also download a copy as a Microsoft Excel file, as a Microsoft Word file, or in Portable Document Format (PDF).

3. ALS EXPERIMENT FORM STREAMLINED, ON LINE
Contact: alsuser@lbl.gov

ALS experimenters, are you tired of writer's cramp, licking stamps, or shoving pages into the fax machine in order to turn in your experiment form? The ALS hopes to ease your burden by introducing a shorter, online version of the ALS Experiment Form at http://www-als.lbl.gov/als/quickguide/expform.html. To complete the form on the Web, simply fill out the necessary contact information for all experimenters involved, then check off the categories on the Safety Checklist page that apply to your experiment. Only those pages that are relevant to your experiment will be provided for you to complete. (Be sure to have your experiment proposal number handy when filling out the form!) When all the pages are filled out, you can submit the completed form with the click of a mouse.

For those of you who still prefer to fill out the form manually, a Portable Document Format (PDF) version of the form is also available on the Web page noted above. The completed form can be mailed or faxed to the ALS User Services Office, Berkeley Lab, MS 6-2100, Berkeley, CA, 94720; Fax: 510-486-4773.

4. USER APARTMENTS NOW OFFER SHORT STAYS, NEW DISCOUNTS
Contact: alsrooms@lbl.gov

ALS users requiring lodging can now reserve space in the ALS User Apartments for both short- and longer-term stays. The two-bedroom furnished apartments, conveniently located near the Berkeley Lab shuttle stop at Hearst and Oxford Streets, are available on a short-term basis for $40.00 per night (two-night minimum). Special discounted rates are available for persons staying two weeks or longer and for groups of three or more. The cost includes linens, cookware, and cleaning services. Contact Barbara Phillips in the ALS User Services Office (tel.: 510-486-7666; email alsrooms@lbl.gov) for more information or to make reservations. Additional information about other kinds of housing available in the Bay Area is available in the ALS User Guide at http://www-als.lbl.gov/als/quickguide/housing.html.

5. WHO'S IN TOWN: A SAMPLING OF ALS USERS

To highlight the richness of our user community and help introduce recent arrivals, we offer this listing of some of the experimenters who will be collecting data during the next two weeks at the ALS.

Beamline 1.4.3: Ted Raab (Univ. of Colorado, Boulder) will continue infrared spectromicroscopic studies of rhizosphere plants and soils. Ron Simms and Karl Neiman (Utah State Univ.) will investigate pyrene degradation and bound residue formation in contaminated soil. Hoi-Ying Holman (Berkeley Lab) will study biological responses to mixed contaminants. Felicia Hendrickson and Robert Glaeser (Univ. of California, Berkeley) will study FTIR spectra of bacteriorhodopsin microcrystals. Regine Goth-Goldstein (Berkeley Lab) will monitor and map human cell responses to environmental toxins.

Beamline 7.0.1: Roy Willis (Pennsylvania State Univ.) will conduct photoemission studies of magnetic alloys, Jeffrey Kortright (Berkeley Lab) will be imaging magnetic interactions in magnetic multilayers, and Ed Rightor (Dow Chemical Company) will conduct spectromicroscopy studies of polymers and ceramics.

Beamline 8.0.1: Eberhard Umbach (Universitaet Wuerzburg) will study buried interfaces in CdS/Cu(In,Ga)Se2 and related compounds and investigate the electronic and interface properties of beryllium-based II-VI semiconductors.

Beamline 9.0.2.2: Marcus Malow (Freie Universitaet Berlin) and Tom Baer (Univ. of North Carolina, Chapel Hill) will be continuing their pulsed-field ionized photoelectron-photoion experiments on various molecules.

Beamline 9.3.2: Satish Myneni (Berkeley Lab) will work on the characterization of transition-metal organic and inorganic complexes from L-edge spectra, and David Shuh (Berkeley Lab) will perform soft x-ray emission spectroscopy to determine metal ion speciation in environmental materials.

Beamline 10.3.1: Christoph Flink (Berkeley Lab) will be studying copper solubility in silicon and copper precipitation at oxygen precipitates in silicon.

6. OPERATIONS UPDATE
Contact: RMMiller@lbl.gov

Beam reliability for the last two weeks (March 1-14) was 94.2% for user shifts. Beam delivered was 2-bunch at 1.9 GeV. There were no significant outages.

Long-term and weekly operations schedules are available on the Web (http://www-als.lbl.gov/als/accelinfo.html). Weekly operations scheduling meetings are held on Fridays at 3:30 p.m. in the Building 6 conference room. The Accelerator Status Hotline at (510) 486-6766 (ext. 6766 from Lab phones) features a recorded message giving up-to-date information on the operational status of the accelerator.