Research Interests:

The long term goal is to understand and manipulate the metabolism of cells through the interactions of their constituent proteins.  One goal is to be able to infer functional linkages of proteins, on the basis of genome sequences and protein expression data. Computational methods have been developed for establishing these relationships, including the phylogenetic profile and Rosetta Stone methods.  To benchmark these computational methods, a large Database of Interacting Proteins has been built up. X-ray crystallography remains a powerful tool for exploring protein structure and interactions. Our X-ray projects are of two types. The first are on amyloids and prions, pathologically interacting proteins. The goal is to understand the structures that underlie the pathologies. The other projects are on the structural biology of Mycobacterium tuberculosis, as part of the TB Structural Genomics Consortium.

To the right is the crystal structure of glutamine sythetase studied by our X-ray crystollagraphic methods.

3D domain swapping is a mechanism for proteins to form oligomers by exchanging identical domains. To date, there are more than 30 domain-swapped proteins with reported structures. Here, we have chosen bovine pancreatic ribonuclease (RNase A) to study 3D domain swapping.
	When concentrated in mild acid solutions, bovine pancreatic ribonuclease (RNase A) forms long-lived oligomers including two types of dimer, two types of trimer, and higher oligomers. We have determined the structures of the two dimers and one trimer and built a model for the other trimer, shown in the picture. In the dimer or trimer, one component is more than the other, thus called major dimer/trimer and minor dimer/trimer, respectively. The major dimeric component forms by a swapping of the C-terminal ß-strands between the monomers, whereas the minor dimeric component forms by swapping the N-terminal alpha helices of the monomers.
	Based on these structures, a linear model for the RNase A major trimer was proposed to form from a central molecule that simultaneously swaps its N-terminal helix with a second RNase A molecule and its C-terminal strand with a third molecule. Studies by dissociation are consistent with this model: the major trimer dissociates into both the major and the minor dimers, as well as monomers. The minor trimer is cyclic, formed from three monomers that each swap their C-terminal ß-strand into an identical molecule, as shown by the crystal structure. This study thus expands the variety of domain-swapped oligomers by revealing the first example of a protein that swaps both N- and C-termini and that can form both a linear and a cyclic domain-swapped oligomer.

As part of a structural genomics pilot project, we have solved the crystal structures of Sm-like archaeal proteins ("SmAPs") from the hyperthermophilic archaea Pyrobaculum aerophilum (PAE) and Methanobacterium thermautotrophicum (MTH), and found that these novel structures provide insights into the central architecture of small nuclear ribonucleoproteins (snRNPs). By forming the cores of snRNP assemblies, eukaryotic Sm and Lsm proteins are key components of several RNA-processing machines, including the 5 x 107 Da spliceosome.
	We determined the PAE SmAP1 crystal structure to 1.75 A-resolution by MAD phasing, and found that SmAP1 monomers assemble into a heptameric ring perforated by a cationic pore (Fig. 1, to the left). In addition to providing direct evidence for such an assembly in eukaryotic snRNPs, our results (i) show that SmAP homodimers are structurally similar to human Sm heterodimers; (ii) show that SmAP is a member of a phylogenetically well-conserved module that likely evolved into modern Sm proteins via gene duplication; and (iii) offer an unconventional model of SmAP1 bound to single stranded RNA that explains the specificity of Sm binding sites found in small nuclear RNAs. The pronounced electrostatic asymmetry of the heptameric disk would impart directionality to putative SmAP-RNA interactions.
The refined PAE SmAP1 model was used to solve the MTH SmAP1 structure to 1.85 A by molecular replacement. As expected, PAE and MTH heptamers are structurally quite similar (Fig. 2, to the right). These results provide an atomic resolution glimpse into the probable structures of eukaryotic snRNPs, and raise a number of interesting questions (which we are currently exploring) regarding the existence of snRNP-like particles in archaeal species. Preliminary biochemical investigation of SmAP suggests that it is dissimilar to human Sm proteins in a number of ways.

Selected Publications:

• Landgraf R, Xenarios I, Eisenberg D, "Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins", J Mol Biol. 307(5), 1487-502 (2001).
• Marcotte EM, Xenarios I, Eisenberg D, "Mining literature for protein-protein interactions", Bioinformatics 17(4), 359-63 (2001).
• Gill HS, Eisenberg D, "The crystal structure of phosphinothricin in the active site of glutamine synthetase illuminates the mechanism of enzymatic inhibition", Biochemistry 40(7), 1903-12 (2001).
• Mura C, Cascio D, Sawaya MR, Eisenberg DS, "The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core", Proc Natl Acad Sci (USA) 98(10), 5532-7 (2001).
• Liu Y, Gotte G, Libonati M, Eisenberg D, "A domain-swapped RNase A dimer with implications for amyloid formation", Nat Struct Biol. 8(3), 211-214 (2001).


Dr. Eisenberg's complete list of publications

Biography: David Eisenberg is currently a Professor of Chemistry & Biochemistry, as well as the Director of the DOE Lab of Structural Biology & Molecular Medicines at UCLA. Before he assumed his role in the UCLA community Mr. Eisenberg received an A.B. in Biochemical Science from Harvard College and preceded to Oxford University where he completed his D.Phil. in Theoretical Chemistry. After completing two Postdoctorales, one at Princeton University regarding water and hydrogen bonding and the other at the California Institute of Technology on protein crystallography, he joined the faculty at UCLA. Currently his research involves the use of x-ray crystallography and the long-term goal of understanding and manipulating the metabolism of cells through the interactions of their constituent proteins. Throughout his career Mr. Eisenberg has published over 200 papers, holds several patents and has presented over 10 lectureships through the University of Michigan, Purdue, Harvard to name a few. Of his many awards some highlights include; Alfred P. Sloan Fellow, UCLA Distinguished Teaching Award, John Simon Guggenheim Fellow, UCLA Faculty Research Lectureship, National Academy of Sciences Member, American Academy of Arts and Sciences Member.