Solid-Phase Cross-Linking (SPCL): a new tool for protein structure studies

A wide range of chemical reagents are available to study the protein-protein interactions or protein structures. After reaction with such chemicals, covalently modified proteins are digested, resulting in shorter peptides that are analyzed by mass spectrometry (MS). Used especially when NMR of X-ray data are lacking, this methodology requires the identification of modified species carrying relevant information, among the unmodified peptides. To overcome the drawbacks of existing methods, we propose a more direct strategy relying on the synthesis of solid-supported cleavable monofunctional reagents and cross-linkers that react with proteins and that selectively release, after protein digestion and washings, the modified peptide fragments ready for MS analysis. Using this Solid-Phase Cross-Linking (SPCL) strategy, only modified sequences are analyzed and consistent data can be easily obtained since the signals of interest are not masked or suppressed by over-represented unmodified materials.     

PROMPT: a protein mapping and comparison tool

Background  

Comparison of large protein datasets has become a standard task in bioinformatics. Typically researchers wish to know whether one group of proteins is significantly enriched in certain annotation attributes or sequence properties compared to another group, and whether this enrichment is statistically significant. In order to conduct such comparisons it is often required to integrate molecular sequence data and experimental information from disparate incompatible sources. While many specialized programs exist for comparisons of this kind in individual problem domains, such as expression data analysis, no generic software solution capable of addressing a wide spectrum of routine tasks in comparative proteomics is currently available.     

Affinity chromatography: a useful tool in proteomics studies

Separation or fractionation of a biological sample in order to reduce its complexity is often a prerequisite to qualitative or quantitative proteomic approaches. Affinity chromatography is an efficient protein separation method based on the interaction between target proteins and specific immobilized ligands. The large range of available ligands allows to separate a complex biological extract in different protein classes or to isolate the low abundance species such as post-translationally modified proteins. This method plays an essential role in the isolation of protein complexes and in the identification of protein-protein interaction networks. Affinity chromatography is also required for quantification of protein expression by using isotope-coded affinity tags.     

Ketorolac tromethamine liposomes: encapsulation and release studies

Liposomes loaded with ketorolac tromethamine salt were prepared by using a thin layer evaporation method. The physical properties of liposomes were studied by using atomic force microscopy (AFM) and transmission electron microscopy (TEM). The relationship between lipid composition, encapsulation efficiency, vesicle size, and the release of ketorolac tromethamine-loaded liposomes was studied. The drug content was found to be dependent on the lipidic composition used in the preparations and, in particular, vesicles containing both cationic lipids (dimethyldioctadecylammonium bromide and N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethylammonium chloride), and phosphatidylcholine had a higher entrapped efficiency than liposomes with phosphatidylcholine alone or in the presence of cholesterol. Finally, the cationic liposomes appear to be useful as carriers for ketorolac tromethamine to control its in vitro release.     

Double quantum filtering homonuclear MAS NMR correlation spectra: a tool for membrane protein studies

13C homonuclear correlation spectra based on proton driven spin diffusion (PDSD) are becoming increasingly important for obtaining distance constraints from multiply labeled biomolecules by MAS NMR. One particular challenging situation arises when such constraints are to be obtained from spectra with a large natural abundance signal background which causes detrimental diagonal peak intensities. They obscure cross peaks, and furthermore impede the calculation of a buildup rates matrix which may be used to derive distance constraints, as carried out in "NMR crystallography". Here, we combine double quantum (DQ) filtering with 13C-13C dipolar assisted rotational resonance (DARR) experiments to yield correlation spectra free of natural abundance contributions. Two experimental schemes, using DQ filtering prior to evolution (DOPE), and after mixing (DOAM), have been evaluated. Diagonal peak intensities along the spectrum diagonal are removed completely, and crosspeaks close to the diagonal are easily identifiable. For DOAM spectra with negligible mixing times, it is possible to carry out 'assignment walks' which simplify peak identification substantially. The method is demonstrated on 13C-cys labeled proteorhodopsin, a 27 kDa membrane protein. The magnetization transfer characteristics were studied using buildup curves obtained on uniformly 13C labelled crystalline tripeptide MLF. Our data show that DQ filtered DARR experiments pave the way for obtaining through space constraints for structural studies on ligands, bound to membrane receptors, or on small fragments within large proteins.     

SitesIdentify: a protein functional site prediction tool

Background  

The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application.     

DNA Pooling: a tool for large-scale association studies

DNA pooling is a practical way to reduce the cost of large-scale association studies to identify susceptibility loci for common diseases. Pooling allows allele frequencies in groups of individuals to be measured using far fewer PCR reactions and genotyping assays than are used when genotyping individuals. Here, we discuss recent developments in quantitative genotyping assays and in the design and analysis of pooling studies. Sophisticated pooling designs are being developed that can take account of hidden population stratification, confounders and inter-loci interactions, and that allow the analysis of haplotypes.     

Measurement of skin protein breakdown in a rat model

Whereas skin protein synthesis can be measured with different approaches, no method potentially applicable in humans is available for measurement of skin protein breakdown. To that end, we measured mixed skin fractional protein breakdown (FBR) in a rat model by use of a stable isotope method (tracee release method) originally developed to measure muscle protein breakdown. Skin mixed protein and collagen fractional synthesis rates (FSR) were also measured. A primed continuous infusion of L-[ring-(2)H(5)]phenylalanine and alpha-[5,5,5-(2)H(3)]ketoisocaproate (KIC) was given for 6 h. Arterial and skin phenylalanine and leucine free enrichments were measured at plateau (5-6 h) and during the decay that followed after the infusion was stopped. Skin FBR (%/h) was 0.260 +/- 0.011 with phenylalanine and 0.201 +/- 0.032 with KIC/leucine [P = not significant (NS)]. Mixed skin FSR (%/h) was 0.169 +/- 0.055 with phenylalanine and 0.146 +/- 0.020 with KIC/leucine (P = NS). Collagen FSR was 0.124 +/- 0.023%/h (P = NS vs. mixed protein FSR). The tracee release method is a sensitive method for measurement of skin protein breakdown; however, given the high intersubject variability of FSR, the calculation of skin net balance is not advisable.     

ProSup: a refined tool for protein structure alignment

We investigated and optimized a method for structure comparison which is based on rigid body superimposition. The method maximizes the number of structurally equivalent residues while keeping the root mean square deviation constant. The resulting number of equivalent residues then provides an adequate similarity measure, which is easy to interpret. We demonstrate that the approach is able to detect remote structural similarity. We show that the number of equivalent residues is a suitable measure for ranking database searches and that the results are in good agreement with expert knowledge protein structure classification. Structure comparison frequently has multiple solutions. The approach that we use provides a range of alternative alignments rather a single solution. We discuss the nature of alternative solutions on several examples.     

Immuno-enzymatic evaluation of the recombinant TSSA-II protein of Trypanosoma cruzi in dogs and human sera: a tool for epidemiological studies

The rTSSA-II (recombinant Trypomastigote Small Surface II) antigen was evaluated by ELISA to detect anti-Trypanosoma cruzi antibodies in sera from naturally infected dogs and humans. For this evaluation ELISA-rTSSA-II was standardized and groups were classified according to the results obtained through xenodiagnosis, ELISA and PCR. Sensitivity (Se), Specificity (Sp), Kappa index (KI) and area under curve (AUC) were determined. The Se was determined by using 14 sera from dogs infected with T. cruzi VI (TcVI) whereas Sp was determined by using 95 non-chagasic sera by xenodiagnosis, ELISA-Homogenate and PCR. The performance of ELISA-rTSSA-II in dog sera was high (AUC=0·93 and KI=0·91). The Se was 92·85% (1 false negative) and Sp was 100%. Two sera from dogs infected with TcI and 1 with TcIII were negative. For patients infected with T. cruzi, reactivity was 87·8% (36/41), there was only 1 indeterminate, and Sp was 100%. Fifty-four sera from non-chagasic and 68 sera from patients with cutaneous leishmaniasis did not react with rTSS-II. ELISA-rTSSA-II showed a high performance when studying sera from naturally infected dogs and it also presented 100% Sp. This assay could be an important tool to carry out sero-epidemiological surveys on the prevalence of T. cruzi circulating lineages in the region.     

Mitochondrial DNA: a tool for populational genetics studies.

Mitochondria are cellular organelles that have the function of the oxidative phosphorilation and the formation of ATP. In humans, the mtDNA is a double-stranded, circular, covalent closed molecule of 16.5 kb. The mtDNA is inherited as a haploid from the mother and heteroplasmy has been found rarely. From a populational perspective, it could be considered as a system of small, sexually isolated demes, or clonal lineages, with an evolutionary rate 5 to 10 times faster than the nuclear genome. All these characteristics make this molecule ideal for evolutionary studies. We present two applications of this molecule in genetical studies. One of these is referred to the Balearic Islands populations, Majorca, Minorca, Ibiza, and Chuetas. The other example is the populational dynamics of the different mitochondrial haplotypes in Drosophila subobscura. We also discuss the importance of nuclear markers to complete these studies as well as the study of the Y chromosome to compensate the bias produced by the study of only the mtDNA.     

Minimotif Miner: a tool for investigating protein function

In addition to large domains, many short motifs mediate functional post-translational modification of proteins as well as protein-protein interactions and protein trafficking functions. We have constructed a motif database comprising 312 unique motifs and a web-based tool for identifying motifs in proteins. Functional motifs predicted by MnM can be ranked by several approaches, and we validated these scores by analyzing thousands of confirmed examples and by confirming prediction of previously unidentified 14-3-3 motifs in EFF-1.     

Protein-calcium carbonate coprecipitation: a tool for protein encapsulation

A new approach of encapsulation of proteins in polyelectrolyte microcapsules has been developed using porous calcium carbonate microparticles as microsupports for layer-by-layer (LbL) polyelectrolyte assembling. Two different ways were used to prepare protein-loaded CaCO3 microparticles: (i) physical adsorption--adsorption of proteins from the solutions onto preformed CaCO3 microparticles, and (ii) coprecipitation--protein capture by CaCO3 microparticles in the process of growth from the mixture of aqueous solutions of CaCl2 and Na2CO3. The latter was found to be about five times more effective than the former (approximately 100 vs approximately 20 mug of captured protein per 1 mg of CaCO3). The procedure is rather mild; the revealed enzymatic activity of alpha-chymotrypsin captured initially by CaCO3 particles during their growth and then recovered after particle dissolution in EDTA was found to be about 85% compared to the native enzyme. Core decomposition and removal after assembly of the required number of polyelectrolyte layers resulted in release of protein into the interior of polyelectrolyte microcapsules (PAH/PSS)5 thus excluding the encapsulated material from direct contact with the surrounding. The advantage of the suggested approach is the possibility to control easily the concentration of protein inside the microcapsules and to minimize the protein immobilization within the capsule walls. Moreover, it is rather universal and may be used for encapsulation of a wide range of macromolecular compounds and bioactive species.     

TRITON: a graphical tool for ligand-binding protein engineering

The new version of the TRITON program provides user-friendly graphical tools for modeling protein mutants using the external program MODELLER and for docking ligands into the mutants using the external program AutoDock. TRITON can now be used to design ligand-binding proteins, to study protein-ligand binding mechanisms or simply to dock any ligand to a protein. Availability: Executable files of TRITON are available free of charge for academic users at http://ncbr.chemi.muni.cz/triton/     

Chemical inhibitors: a tool for plant cell cycle studies

Synchrony provides a large number of cells at defined points of the cell cycle. Highly synchronised cells are powerful and effective tools for molecular analyses and for studying the biochemical events of the cell cycle in plants. Usually, plant cell suspensions can be synchronised by chemical agents, which arrest the cell cycle by acting on the driving forces of the cell cycle engine such as cyclin-dependent kinase activity, enzymes involved in DNA synthesis or proteolysis of cell cycle regulators or by acting on the cell cycle apparatus (mitotic spindle). The specificity, reversibility and efficiency of each type of cell cycle inhibitor are described and related to their mode of action.     

Aging changes in intracellular protein breakdown

Using radioactively labelled cytosol proteins as substrates we were able to exclude the possible accumulation of any specific inhibitor for the lysosomal proteases in rat liver cytosol during the aging process. There were also no gross changes in the molecular weight patterns of these proteins during the aging process. The percentage of more hydrophobic proteins seems to be identical in both the "old" and "young" cytosol proteins. From immunological experiments we suppose a qualitative change in the composition of rat liver cytosol proteins or of their properties during the aging process.     

Utilization of liposomes in vesicular transport studies

Various coated vesicles are implicated in the intracellular transport between different compartments. In vitro reconstitution is a powerful experimental system to study molecular mechanisms involved in assembly of coat proteins from cytosol onto membranes as well as formation of coated vesicles. Liposomes have been recently utilized in the cell-free systems. In this review, we summarize studies on reconstitutions of coated vesicles or coated structures on liposomes. A novel method using dynamic light scattering (DLS) to quantify vesicle formation from liposomes also is described. Our recent study on the role of phospholipids in vesicle formation, where the DSL assay is used in combination with lipid analysis, also is introduced.     

Intracellular protein breakdown in thermophilic and mesophilic fungi

1. The rate of protein breakdown was determined on growing and non-growing cultures of thermophilic and mesophilic fungi. 2. In growing cells protein breakdown was negligible. 3. In non-growing cells the breakdown rate of total protein varied between 5.2%/h and 6.7%/h. These values were found to be dependent on both the temperature of the protein breakdown assay and the temperature of growth of the organism. 4. The rate of breakdown of soluble protein in thermophilic fungi was 9-15%/h whereas the rate in mesophilic fungi for the soluble protein fraction was only 4%/h.