New light for science: synchrotron radiation in structural medicine

The influence of the ketogenic diet on the elemental and biochemical compositions of the hippocampal formation

A growing body of evidence demonstrates that dietary therapies, mainly the ketogenic diet, may be highly effective in the reduction of epileptic seizures. All of them share the common characteristic of restricting carbohydrate intake to shift the predominant caloric source of the diet to fat. Catabolism of fats results in the production of ketone bodies which become alternate energy substrates to glucose. Although many mechanisms by which ketone bodies yield its anticonvulsant effect are proposed, the relationships between the brain metabolism of the ketone bodies and their neuroprotective and antiepileptogenic action still remain to be discerned. In the study, X-ray fluorescence microscopy and FTIR microspectroscopy were used to follow ketogenic diet-induced changes in the elemental and biochemical compositions of rat hippocampal formation tissue. The use of synchrotron sources of X-rays and infrared allowed us to examine changes in the accumulation and distribution of selected elements (P, S, K, Ca, Fe, Cu, Zn, and Se) and biomolecules (proteins, lipids, ketone bodies, etc.) with the micrometer spatial resolution. The comparison of rats fed with the ketogenic diet and rats fed with the standard laboratory diet showed changes in the hippocampal accumulation of P, K, Ca, and Zn. The relations obtained for Ca (increased level in CA3, DG, and its internal area) and Zn (decreased areal density in CA3 and DG) were analogous to those that we previously observed for rats in the acute phase of pilocarpine-induced seizures. Biochemical analysis of tissues taken from ketogenic diet-fed rats demonstrated increased intensity of absorption band occurring at 1740 cm(-1), which was probably the result of elevated accumulation of ketone bodies. Moreover, higher absolute and relative (3012 cm(-1)/2924 cm(-1), 3012 cm(-1)/lipid massif, and 3012 cm(-1)/amide I) intensity of the 3012-cm(-1) band resulting from increased unsaturated fatty acids content was found after the treatment with the high-fat diet. This article is part of a Special Issue entitled "Status Epilepticus".

Progress of elemental anomalies of hippocampal formation in the pilocarpine model of temporal lobe epilepsy--an X-ray fluorescence microscopy study

In the present paper, X-ray fluorescence microscopy was applied to follow the processes occurring in rat hippocampal formation during the post-seizure period. In the study, one of the status epilepticus animal models of epilepsy was used, namely the model of temporal lobe epilepsy with pilocarpine-induced seizures. In order to analyze the dynamics of seizure-induced elemental changes, the samples taken from seizure-experiencing animals 3 h and 1, 4, and 7 days after proconvulsive agent administration were analyzed. The obtained results confirmed the utility of X-ray fluorescence microscopy in the research of mechanisms involved in the pathogenesis and progress of epilepsy. The topographic and quantitative elemental analysis of hippocampal formations from different periods of epileptogenesis showed that excitotoxicity, mossy fibers sprouting, and iron-induced oxidative stress may be the processes responsible for seizure-induced neurodegenerative changes and spontaneous recurrent seizures occurring in the chronic phase of the pilocarpine model. The analysis of correlations between the recorded elemental anomalies and quantitative parameters describing animal behavior in the acute period of pilocarpine-induced status epilepticus showed that the areal densities of selected elements measured in the latent period strongly depend on the progress of the acute phase. Especially important seem to be the observations done for Ca and Zn levels which suggest that the intensity of the pathological processes such as excitotoxicity and mossy fibers sprouting depend on the total time of seizure activity. These results as well as dependencies found between the levels of S, K, and Cu and the intensity of maximal seizures clearly confirm how important it is to control the duration and intensity of seizures in clinical practice.

Characterization of wax as a potential diffraction intensity standard for macromolecular crystallography beamlines

A number of commercially available waxes in the form of thin disc samples have been investigated as possible diffraction intensity standards for macromolecular crystallography synchrotron beamlines. Synchrotron X-ray powder diffraction measurements show that beeswax offers the best performance of these waxes owing to its polycrystallinity. Crystallographic lattice parameters and diffraction intensities were examined between 281 and 309 K, and show stable and predictable thermal behaviour. Using an X-ray beam of known incident flux at lambda = 1 A, the diffraction power of two strong Bragg reflections for beeswax were quantified as a function of sample thickness and normalized to 10(10) photons s(-1). To demonstrate its feasibility as a diffraction intensity standard, test measurements were then performed on a new third-generation macromolecular crystallography synchrotron beamline.

Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition

For a long time the structural and molecular features of mammalian histidine decarboxylase (EC 4.1.1.22), the enzyme that produces histamine, have evaded characterization. We overcome the experimental problems for the study of this enzyme by using a computer-based modelling and simulation approach, and have now the conditions to use histidine decarboxylase as a target in histamine pharmacology. In this review, we present the recent (last 5 years) advances in the structure-function relationship of histidine decarboxylase and the strategy for the discovery of new drugs.

Structures of sea anemone toxins

Sea anemones produce a variety of toxic peptides and proteins, including many ion channel blockers and modulators, as well as potent cytolysins. This review describes the structures that have been determined to date for the major classes of peptide and protein toxins. In addition, established and emerging methods for structure determination are summarized and the prospects for modelling newly described toxins are evaluated. In common with most other classes of proteins, toxins display conformational flexibility which may play a role in receptor binding and function. The prospects for obtaining atomic resolution structures of toxins bound to their receptors are also discussed.

Overcoming the inadequacies or limitations of experimental structures as drug targets by using computational modeling tools and molecular dynamics simulations

X-ray crystallography, NMR spectroscopy, and cryoelectron microscopy stand out as powerful tools that enable us to obtain atomic detail about biomolecules that can be potentially targeted by drugs. This knowledge is essential if virtual screening or structure-based ligand-design methods are going to be used in drug discovery. However, the macromolecule of interest is not always amenable to these types of experiment or, as is often the case, the conformation found experimentally cannot be used directly for docking studies because of significant changes between apo and bound forms. Furthermore, sometimes the desired insight into the binding mechanism cannot be gained because the structure of the ligand-receptor complex, not having been time-resolved, represents the endpoint of the binding process and therefore retains little or no information about the intermediate stages that led to its creation. Molecular dynamics (MD) simulations are routinely applied these days to the study of biomolecular systems with the aims of sampling configuration space more efficiently and getting a better understanding of the factors that determine structural stability and relevant biophysical and biochemical processes such as protein folding, ligand binding, and enzymatic reactions. This field has matured significantly in recent years, and strategies have been devised (for example activated, steered, or targeted MD) that allow the calculated trajectories to be biased in attempts to properly shape a ligand binding pocket or simulate large-scale motions involving one or more protein domains. On the other hand, low-frequency motions can be simulated quite inexpensively by calculation of normal modes which allow the investigation of alternative receptor conformations. Selected examples in which these methods have been applied to several medicinal chemistry and in silico pharmacology endeavors are presented.

Structural principles from large RNAs

Since the year 2000 a number of large RNA three-dimensional structures have been determined by X-ray crystallography. Structures composed of more than 100 nucleotide residues include the signal recognition particle RNA, group I intron, the GlmS ribozyme, RNAseP RNA, and ribosomal RNAs from Haloarcula morismortui, Escherichia coli, Thermus thermophilus, and Deinococcus radiodurans. These large RNAs are constructed from the same secondary and tertiary structural motifs identified in smaller RNAs but appear to have a larger organizational architecture. They are dominated by long continuous interhelical base stacking, tend to segregate into domains, and are planar in overall shape as opposed to their globular protein counterparts. These findings have consequences in RNA folding, intermolecular interaction, and packing, in addition to studies of design and engineering and structure prediction.

Protein crystallization in drug design: towards a rational approach

X-ray crystallography is the method of choice for the detailed characterization of stereochemistry of interactions of drug leads and potential chemotherapeutics with their protein targets. The resulting atomic models allow for rational enhancement of the lead properties and consequently for the design of high-affinity inhibitors. However, a major bottleneck of the technique is the requirement for the protein and its complexes to yield high quality single crystals. Furthermore, it is highly desirable that such crystals diffract to high resolution, preferably ≥ 1.2 Å, revealing the structures in atomic detail. Unfortunately, only a small portion of proteins readily crystallize in that fashion. New approaches are being developed to circumvent this problem. One proposed option includes rational protein surface engineering to systematically improve the crystallizability of the protein. This is accomplished by creating surface patches readily mediating weak, but specific, intermolecular interactions that take on the role of crystal contacts during nucleation and crystal growth phase.