Synchrotron radiation applications to macromolecular crystallography

Large-Scale Structural Biology of the Human Proteome

The large-scale structural biology projects that target human proteins focus predominantly on the catalytic domains of potential therapeutic targets and the domains of human proteins that mediate protein-protein and protein-small-molecule interactions. Their main scientific objective is to elucidate the molecular basis for specificity and selectivity of function within large protein families of therapeutic interest, such as kinases, phosphatases, and proteins involved in epigenetic regulation. Half of the unique human protein structures determined in the past three years derive from these initiatives.

Calcium/calmodulin-dependent protein kinase activates serum response factor transcription activity by its dissociation from histone deacetylase, HDAC4. Implications in cardiac muscle gene regulation during hypertrophy

Serum response factor (SRF) plays a pivotal role in cardiac myocyte development, muscle gene transcription, and hypertrophy. Previously, elevation of intracellular levels of Ca2+ was shown to activate SRF function without involving the Ets family of tertiary complex factors through an unknown regulatory mechanism. Here, we tested the hypothesis that the chromatin remodeling enzymes of class II histone deacetylases (HDAC4) regulate SRF activity in a Ca2+-sensitive manner. Expression of HDAC4 profoundly repressed SRF-mediated transcription in both muscle and nonmuscle cells. Protein interaction studies demonstrated physical association of HDAC4 with SRF in living cells. The SRF/HDAC4 co-association was disrupted by treatment of cells with hypertrophic agonists such as angiotensin-II and a Ca2+ ionophore, ionomycin. Furthermore, activation of Ca2+/calmodulin-dependent protein kinase (CaMK)-IV prevented SRF/HDAC4 interaction and derepressed SRF-dependent transcription activity. The SRF.HDAC4 complex was localized to the cell nucleus, and the activated CaMK-IV disrupted HDAC4/SRF association, leading to export of HDAC4 from the nucleus and stimulation of SRF transcription activity. Thus, these results identify SRF as a functional interacting target of HDAC4 and define a novel tertiary complex factor-independent mechanism for SRF activation by Ca2+/CaMK-mediated signaling.

Trapping reaction intermediates in macromolecular crystals for structural analyses

The development of "time-resolved" crystallographic methods, including trapping of reaction intermediates and rapid data collection, allows the comparative study of discrete structural species formed during a macromolecular reaction, such as enzymatic catalysis, ribozyme cleavage, or a protein photocycle. The primary technical details that must be addressed in such studies are the reaction initiation, the accumulation of a specific reaction species throughout the crystal, the lifetime of that species and of the crystal under the experimental conditions, and the method used to collect X-ray data. Methods of reaction initiation range from substrate diffusion, which is appropriate for the visualization of very long-lived intermediates, to photolysis, which is appropriate for the accumulation of rate-limited species with half-lives ranging from milliseconds to nanoseconds. This review discusses various methods for initiating turnover in crystals and trapping rate-limiting species for structural studies.

Methodologies for target selection in structural genomics

As the number of complete genomes that have been sequenced keeps growing, unknown areas of the protein space are revealed and new horizons open up. Most of this information will be fully appreciated only when the structural information about the encoded proteins becomes available. The goal of structural genomics is to direct large-scale efforts of protein structure determination, so as to increase the impact of these efforts. This review focuses on current approaches in structural genomics aimed at selecting representative proteins as targets for structure determination. We will discuss the concept of representative structures/folds, the current methodologies for identifying those proteins, and computational techniques for identifying proteins which are expected to adopt new structural folds.

Experimental evidence for the correlation of bond distances in peptide groups detected in ultrahigh-resolution protein structures

The structural analysis of a deamidated derivative of ribonuclease A, determined at 0.87 A resolution, reveals a highly significant negative correlation between CN and CO bond distances in peptide groups. This trend, i.e. the CO bond lengthens when the CN bond shortens, is also found in seven out of eight protein structures, determined at ultrahigh resolution (<0.95 A). In five of them the linear correlation is statistically significant at the 95% confidence level. The present findings are consistent with the traditional view of amide resonance and, although already found in small peptide structures, they represent a new and important result. In fact, in a protein structure the fine details of the peptide geometry are only marginally affected by the crystal field and they are mostly produced by intramolecular and solvent interactions. The analysis of very high-resolution protein structures can reveal subtle information about local electronic features of proteins which may be critical to folding, function or ligand binding.

New results using Laue diffraction and time-resolved crystallography

Several time-resolved crystallographic structures were determined over the past year, using a variety of trapping protocols and several data collection methods. A significant theme of recent time-resolved work is the importance of parallel comparative studies on the same protein, using different experimental protocols, in order to fully characterize the structural variation of the intermediates formed in the reaction pathway.

Millisecond Laue structures of an enzyme-product complex using photocaged substrate analogs

The structure of a rate-limited product complex formed during a single initial round of turnover by isocitrate dehydrogenase has been determined. Photolytic liberation of either caged substrate or caged cofactor and Laue X-ray data collection were used to visualize the complex, which has a minimum half-life of approximately 10 milliseconds. The experiment was conducted with three different photoreactive compounds, each possessing a unique mechanism leading to the formation of the enzyme-substrate (ES) complex. Photoreaction efficiency and subsequent substrate affinities and binding rates in the crystal are critical parameters for these experiments. The structure suggests that CO2 dissociation is a rapid event that may help drive product formation, and that small conformational changes may contribute to slow product release.