Threading with chemostructural restrictions method for predicting fold and functionally significant residues: application to dipeptidylpeptidase IV (DPP-IV)

We present a new method for more accurate modeling of protein structure, called threading with chemostructural restrictions. This method addresses those cases in which a target sequence has only remote homologues of known structure for which sequence comparison methods cannot provide accurate alignments. Although remote homologues cannot provide an accurate model for the whole chain, they can be used in constructing practically useful models for the most conserved-and often the most interesting-part of the structure. For many proteins of interest, one can suggest certain chemostructural patterns for the native structure based on the available information on the structural superfamily of the protein, the type of activity, the sequence location of the functionally significant residues, and other factors. We use such patterns to restrict (1) a number of possible templates, and (2) a number of allowed chain conformations on a template. The latter restrictions are imposed in the form of additional template potentials (including terms acting as sequence anchors) that act on certain residues. This approach is tested on remote homologues of alpha/beta-hydrolases that have significant structural similarity in the positions of their catalytic triads. The study shows that, in spite of significant deviations between the model and the native structures, the surroundings of the catalytic triad (positions of C(alpha) atoms of 20-30 nearby residues) can be reproduced with accuracy of 2-3 A. We then apply the approach to predict the structure of dipeptidylpeptidase IV (DPP-IV). Using experimentally available data identifying the catalytic triad residues of DPP-IV (David et al., J Biol Chem 1993;268:17247-17252); we predict a model structure of the catalytic domain of DPP-IV based on the 3D fold of prolyl oligopeptidase (Fulop et al., Cell 1998;94:161-170) and use this structure for modeling the interaction of DPP-IV with inhibitor.     

Brain Under Stress and Alzheimer’s Disease

Modern society is characterized by the ubiquity of stressors that affect every individual to different extents. Furthermore, experimental, clinical, and epidemiological data have shown that chronic activation of the stress response may participate in the development of various somatic as well as neuropsychiatric diseases. Surprisingly, the role that stress plays in the etiopathogenesis of Alzheimer’s disease (AD) has not yet been studied in detail and is therefore not well understood. However, accumulated data have shown that neuroendocrine and behavioral changes accompanying the stress response affect neuronal homeostasis and compromise several key neuronal processes. Mediators of the neuroendocrine stress response, if elevated repeatedly or chronically, exert direct detrimental effects on the brain by impairing neuronal metabolism, plasticity, and survival. Stress-induced hormonal and behavioral reactions may also participate in the development of hypertension, atherosclerosis, insulin resistance, and other peripheral disturbances that may indirectly induce neuropathological processes participating in the development and progression of AD. Importantly, stress-induced detrimental effects as etiological factors of AD are attractive because they can be reduced by several approaches including behavioral and pharmacological interventions. These interventions may therefore represent an important strategy for prevention or attenuation of the progression of AD.     

Spatial and temporal variations of meiofaunal communities from the western sector of the Gulf of Batabanó, Cuba: II. Seagrass systems

The meiofauna from seagrass meadows in the western sector of the Gulf of Batabanó, Cuba were studied to describe the spatial and temporal variations in community structure. Replicated cores were taken in three locations (arranged in m- and km-scales) and in two seasons (dry and wet). The meiofauna (metazoans between 500 and 45 microm) were identified to major taxa. Temporal changes in the meiofaunal communities could not be detected and they are not linked to the subtle seasonal changes in the water column. A larger variation in community structure was observed in the spatial m-scale (among cores in a station) probably accredited to heterogeneity of microenvironment and biological processes. A second source of variation in the km-scale (among locations) was identified relating to physical processes affecting seagrass meadows: marine currents and anthropogenic disturbances. Distribution patterns of meiofauna across locations coincide with one study from 20 years ago in seagrass beds (i.e. higher densities in area closer to break-shelf and diminution of fauna at southern of Pinar del Rio); however, cumulative anthropogenic disturbances on seagrass meadows would most likely explain the depletion of communities observed in our survey in comparison with decades ago. Estimates of meiofaunal density and richness of major taxa from our study (and other areas from the Cuban shelf) are consistently lower than other temperate and tropical sites; possibly caused by low primary productivity due to narrow tidal amplitude and oligotrophic waters.     

Discovery of [7-(2,6-dichlorophenyl)-5-methylbenzo [1,2,4]triazin-3-yl]-[4-(2-pyrrolidin-1-ylethoxy)phenyl]amine--a potent, orally active Src kinase inhibitor with anti-tumor activity in preclinical assays

We describe the identification of [7-(2,6-dichlorophenyl)-5-methylbenzo [1,2,4]triazin-3-yl]-[4-(2-pyrrolidin-1-ylethoxy)phenyl]amine (3), a potent, orally active Src inhibitor with desirable PK properties, demonstrated activity in human tumor cell lines and in animal models of tumor growth.     

Expression and purification of a two-component flaviviral proteinase resistant to autocleavage at the NS2B-NS3 junction region

Regulated proteolysis of the polyprotein precursor of West Nile virus (WNV) by the essential NS2B–NS3(pro)tease, a promising drug target for WNV inhibitors, is required for the propagation of infectious virions. Structural and drug design studies, however, require pilot-scale quantities of a pure and catalytically active WNV protease that is resistant to self-proteolysis. Autolytic cleavage at the NS2B–NS3 boundary leads to individual, non-covalently associated, NS2B and NS3 domains, together with residual amounts of the intact NS2B–NS3, in the NS2B–NS3pro samples. We modified the cleavage site sequence of the NS2B–NS3 junction region and then developed expression and purification procedures to prepare a covalently linked, single-chain, NS2B–NS3pro K48A mutant construct. This construct exhibits high stability and functional activity and is thus well suited for the follow-up purification and structural and drug design studies.     

Autologous stromal vascular fraction cells: A tool for facilitating tolerance in rheumatic disease

Since the days of Medawar, the goal of therapeutic tolerogenesis has been a “Holy Grail” for immunologists. While knowledge of cellular and molecular mechanisms of this process has been increasing at an exponential rate, clinical progress has been minimal. To provide a mechanistic background of tolerogenesis, we overview common processes in the naturally occurring examples of: pregnancy, cancer, oral tolerance and anterior chamber associated immune deviation. The case is made that an easily accessible byproduct of plastic surgery, the adipose stromal vascular fraction, contains elements directly capable of promoting tolerogenesis such as T regulatory cells and inhibitory macrophages. The high content of mesenchymal and hematopoietic stem cells from this source provides the possibility of trophic/regenerative potential, which would augment tolerogenic processes by decreasing ongoing inflammation. We discuss the application of this autologous cell source in the context of rheumatoid arthritis, concluding with some practical examples of its applications.     

Cell death mechanisms: Cross-talk and role in disease

Multiple cell death mechanisms operate in both uni- and multicellular organisms. Hence, research during the past forty years has revealed that apoptosis is not the only cell death program involved in the regulation of tissue homeostasis and the removal of unwanted cells in biological organisms. While the molecular pathways of apoptosis and necrosis are now relatively well established, the precise mechanisms of other cell death modalities, and their cross-talk, require additional study. This is particularly important, since many human disorders can be attributed, directly or indirectly, to defective cell death mechanisms. In this review we shall discuss the characteristics and cross-talk between various modes of cell death and their role in cell death-related disorders, notably, neurodegenerative disease and cancer.     

Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae

We have devised an approach for analyzing shotgun proteomics datasets based on the normalized spectral abundance factor that can be used for quantitative proteomics analysis. Three biological replicates of samples enriched for plasma membranes were isolated from S. cerevisiae grown in 14N-rich media and 15N-minimal media and analyzed via quantitative multidimensional protein identification technology. The natural log transformation of NSAF values from S. cerevisiae cells grown in 14N YPD media and 15N-minimal media had a normal distribution. The t-test analysis demonstrated 221 of 1316 proteins were significantly overexpressed in one or the other growth conditions with a p value <0.05. Notably, amino acid transporters were among the 14 membrane proteins that were significantly upregulated in cells grown in minimal media, and we functionally validated these increases in protein expression with radioisotope uptake assays for selected proteins.