Protein flexibility and rigidity predicted from sequence

Structural flexibility has been associated with various biological processes such as molecular recognition and catalytic activity. In silico studies of protein flexibility have attempted to characterize and predict flexible regions based on simple principles. B-values derived from experimental data are widely used to measure residue flexibility. Here, we present the most comprehensive large-scale analysis of B-values. We used this analysis to develop a neural network-based method that predicts flexible-rigid residues from amino acid sequence. The system uses both global and local information (i.e., features from the entire protein such as secondary structure composition, protein length, and fraction of surface residues, and features from a local window of sequence-consecutive residues). The most important local feature was the evolutionary exchange profile reflecting sequence conservation in a family of related proteins. To illustrate its potential, we applied our method to 4 different case studies, each of which related our predictions to aspects of function. The first 2 were the prediction of regions that undergo conformational switches upon environmental changes (switch II region in Ras) and the prediction of surface regions, the rigidity of which is crucial for their function (tunnel in propeller folds). Both were correctly captured by our method. The third study established that residues in active sites of enzymes are predicted by our method to have unexpectedly low B-values. The final study demonstrated how well our predictions correlated with NMR order parameters to reflect motion. Our method had not been set up to address any of the tasks in those 4 case studies. Therefore, we expect that this method will assist in many attempts at inferring aspects of function.     

New PCR-based methods for yeast identification

AIMS: To characterize reference yeast strains and identify indigenous strains isolated from wine fermentations by PCR methods. METHODS AND RESULTS: We compared several PCR techniques for yeast identification. We used oligonucleotide primers that are complementary to (i) intron splice sites, (ii) REP and (iii) ERIC elements to produce PCR fingerprints that display specific patterns between the different yeast species. These three techniques were used to characterize 41 reference yeast strains belonging to 15 different species and to identify 40 indigenous strains isolated from grape must and wine fermentations. Species-specific banding patterns were obtained with the three PCR-techniques with different degrees of intraspecific differentiation depending on the method. By comparing the PCR fingerprints of unknown isolates with those produced by reference strains, we identified yeast strains isolated from an industrial wine fermentation. CONCLUSIONS: All three PCR techniques are rapid, reliable and simple methods of yeast identification. As far as we know, this is the first time that the primers designed for amplifying repetitive elements in bacteria have been successfully used in yeast. SIGNIFICANCE AND IMPACT OF THE STUDY: Industry needs rapid, reliable and simple methods of yeast identification. The proposed PCR techniques will allow to achieve this objective.     

Conserving the Sacred Medicine Mountains: A Vegetation Analysis of Tibetan Sacred Sites in Northwest Yunnan

Mount Kawa Karpo of the Menri ('Medicine Mountains' in Tibetan), in the eastern Himalayas, is one of the most sacred mountains to Tibetan Buddhists. Numerous sacred sites are found between 1900 and 4000 m, and at higher elevations the area as a whole is considered a sacred landscape. Religious beliefs may affect the ecology of these sacred areas, resulting in unique ecological characteristics of importance to conservation; recent studies have demonstrated that sacred areas can often play a major role in conservation. The goal of this study is to preliminarily analyze the vegetation of sacred areas in the Menri region using existing vegetation maps and a Geographical Information System (GIS) for remote assessment. Sacred sites are compared to random points in the landscape, in terms of: elevation, vegetation, and nearness to villages; species composition, diversity, and richness; and frequency of useful and endemic plant species. Detrended correspondence analysis (DCA) ordination reveals that sacred sites differ significantly in both useful species composition (p=0.034) and endemic species composition (p=0.045). Sacred sites are located at lower elevations, and closer to villages, than randomly selected, non-sacred sites (p< 0.0001), and have higher overall species richness (p=0.033) and diversity (p=0.042). In addition, the high-elevation (> 4000 m) areas of the mountain - a sacred landscape - are found to have significantly more endemics than low-elevation areas (p<0.0001). These findings represent an initial analysis of sacred sites and suggest that sacred sites in the Menri region may be ecologically and ethnobotanically unique.     

Solubilization of Peripheral-Type Benzodiazepine Binding Sites from Cat Cerebral Cortex

The present study demonstrates for the first time the solubilization of peripheral-type benzodiazepine binding sites (PBS) from cat cerebral cortex. Of all detergents tested [digitonin, 3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate (CHAPS), Tween 20, deoxycholate, and Triton X-100] in the presence of NaCl, the best solubilization (15% of initial activity) was obtained using 0.5% of the zwitterionic detergent CHAPS plus 2 M NaCl. Specific binding of [3H]PK 11195 to membrane-bound and solubilized PBS was saturable, yielding equilibrium dissociation constants (KD) of 1.3 +/- 0.2 and 1.9 +/- 0.3 nM, respectively, and maximal numbers of binding sites of 1,435 +/- 150 and 980 +/- 126 fmol/mg protein, respectively. The KD value of PK 11195 binding to solubilized PBS obtained from experimental kinetic analysis was 0.95 +/- 0.09 nM. The relative potencies of various compounds (PK 11195, Ro 5-4864, diazepam, flunitrazepam, clonazepam, methyl-beta-carboline-3-carboxylate, and Ro 15-1788) in displacing [3H]PK 11195 specific binding from membrane-bound and solubilized PBS were similar. Most of the solubilized binding activity was destroyed by heating at 60 degrees C for 30 min or by treatment with 2 M guanidinium chloride, which indicates the presence of a protein-binding site in the solubilized preparation. Over 85% of the solubilized binding activity was retained after 1 week at 4 degrees C, which will enable future application of purification procedures without major concern for stability of the material.     

Yeast Nucleosome DNA Pattern: Deconvolution from Genome Sequences of S. cerevisiae

Abstract

Positional correlation analysis for the complete genome of Saccharomyces cerevisiae is performed with the aim to reveal possible chromatin-related sequence features. A strong periodicity with the period 10.4 bases is detected in the distance histograms for the dinucleotides AA and TT, with the characteristic decay distance of approximately 50 base pairs. The oscillations are observed as well in the distributions of other dinucleotides. However, the respective amplitudes are small, consistent with secondary effects, due to dominant periodicity of AA and TT. The observations are in accord with earlier data on the chromatin sequence periodicities and nucleosome DNA sequence patterns. The autocorrelations of AA and TT dinucleotides in yeast include also a counter-phase component. A tentative DNA sequence pattern for the yeast nucleosomes is suggested and verified by comparison of its autocorrelation plots with the respective natural autocorrelations. The nucleosome mapping guided by the pattern is in accord with experimental data on the linker length distribution in yeast.     

Studies on the Nutritional Value of Tempeh

1. The nutritional value of tempeh in comparison with that of unfermented soybeans was studied in rat feeding experiment. It was observed that the PER value of tempeh (fresh or stored) was not significantly different from that of the unfermented soybeans (fresh or stored).

2. The peroxide value of the oil of stored tempeh powder was only 10% of that of stored soybean powder. Red blood cells of rats receiving tempeh were less than 20% in hemolysis by dialuric acid whereas hemolysis was 100% for the rats receiving the unfermented soybeans. Serum tocopherol was 0.14±0.05 mg/dl in the former group, but 0.07±0.05 mg/dl in the latter. Liver TBA values were 0.20±0.05 O. D./g and 0.65±0.13 O. D./g in the tempeh and the unfermented soybeans group, respectively.

3. Subsitution of whole egg for tempeh to supply 30% of protein in the diet improved the quality of the protein as measured by the protein efficiency ratio. An equal improvement was accomplished by supplementation of tempeh with lysine, methionine, and threonine in such amounts as the level of these amino acids equal to that in the tempeh-egg diet.     

A Trypanosoma brucei protein required for maintenance of the flagellum attachment zone and flagellar pocket ER domains

Trypanosomes and Leishmanias are important human parasites whose cellular architecture is centred on the single flagellum. In trypanosomes, this flagellum is attached to the cell along a complex flagellum attachment zone (FAZ), comprising flagellar and cytoplasmic components, the integrity of which is required for correct cell morphogenesis and division. The cytoplasmic FAZ cytoskeleton is conspicuously associated with a sheet of endoplasmic reticulum termed the 'FAZ ER'. In the present work, 3D electron tomography of bloodstream form trypanosomes was used to clarify the nature of the FAZ ER. We also identified TbVAP, a T. brucei protein whose knockdown by RNAi in procyclic form cells leads to a dramatic reduction in the FAZ ER, and in the ER associated with the flagellar pocket. TbVAP is an orthologue of VAMP-associated proteins (VAPs), integral ER membrane proteins whose mutation in humans has been linked to familial motor neuron disease. The localisation of tagged TbVAP and the phenotype of TbVAP RNAi in procyclic form trypanosomes are consistent with a function for TbVAP in the maintenance of sub-populations of the ER associated with the FAZ and the flagellar pocket. Nevertheless, depletion of TbVAP did not affect cell viability or cell cycle progression.     

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Protein-protein interactions mediate most of the processes in the living cell and control homeostasis of the organism. Impaired protein interactions may result in disease, making protein interactions important drug targets. It is thus highly important to understand these interactions at the molecular level. Protein interactions are studied using a variety of techniques ranging from cellular and biochemical assays to quantitative biophysical assays, and these may be performed either with full-length proteins, with protein domains or with peptides. Peptides serve as excellent tools to study protein interactions since peptides can be easily synthesized and allow the focusing on specific interaction sites. Peptide arrays enable the identification of the interaction sites between two proteins as well as screening for peptides that bind the target protein for therapeutic purposes. They also allow high throughput SAR studies. For identification of binding sites, a typical peptide array usually contains partly overlapping 10-20 residues peptides derived from the full sequences of one or more partner proteins of the desired target protein. Screening the array for binding the target protein reveals the binding peptides, corresponding to the binding sites in the partner proteins, in an easy and fast method using only small amount of protein.In this article we describe a protocol for screening peptide arrays for mapping the interaction sites between a target protein and its partners. The peptide array is designed based on the sequences of the partner proteins taking into account their secondary structures. The arrays used in this protocol were Celluspots arrays prepared by INTAVIS Bioanalytical Instruments. The array is blocked to prevent unspecific binding and then incubated with the studied protein. Detection using an antibody reveals the binding peptides corresponding to the specific interaction sites between the proteins.     

Markovian approximation to the finite loci coalescent with recombination along multiple sequences

The coalescent with recombination process has initially been formulated backwards in time, but simulation algorithms and inference procedures often apply along sequences. Therefore it is of major interest to approximate the coalescent with recombination process by a Markov chain along sequences. We consider the finite loci case and two or more sequences. We formulate a natural Markovian approximation for the tree building process along the sequences, and derive simple and analytically tractable formulae for the distribution of the tree at the next locus conditioned on the tree at the present locus. We compare our Markov approximation to other sequential Markov chains and discuss various applications.