Use of TSAR as a new tool to analyze the molecular dynamics trajectories of proteins

There is a lack of tools to analyze simulations of protein molecular dynamics quantitatively. Our aim is to use calmodulin, a prototypical calcium-binding protein, to describe a strategy and some tools for extracting relevant information from dynamics calculations. Our main conclusions are as follows:

• •• Autocorrelation vectors may be used to represent a 3D conformation in an n-dimensional space, where n is variable (n ⩽ 20–30).
• •• On such a transformation, classic statistical tools (PCA, clustering, etc.) may be used to differentiate or characterize dynamics trajectories quantitatively.
• •• TSAR, an integrated package used for quantitative structure-activity relationships, is well suited (after minor modifications) for such a purpose.

Finally, this type of strategy is able to point out the effects of the solvent screening parameters of the Amber software on the dynamics trajectories of calmodulin.     

Changes in serum immunoglobulin M (IgM) concentrations during early development of chum salmon (Oncorhynchus keta) as determined by sensitive elisa technique

• 1.1. A specific and sensitive sandwich enzyme-linked immunosorbent assay (ELISA) was developed for the measurement of low levels of serum immunoglobulin M (IgM) of chum salmon Oncorhynchus keta.
• 2.2. In this assay, 5 μl serum was enough to measure the concentration of IgM and the minimum detectable concentration of serum IgM was about 5 ng/ml.
• 3.3. Coefficients of variation within and between assays ranged from 2.90 to 9.61%.
• 4.4. IgM concentrations remained at low level (< 300 ng/ml) until 40 days after hatching and then increased rapidly at the period of emergence (48 days after hatching).

     

A Robust and Versatile Automated Glycoanalytical Technology for Serum Antibodies and Acute Phase Proteins: Ovarian Cancer Case Study

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Highlights

• •Quantitative high-throughput glycoanalytical technology as a diagnostic tool for ovarian cancer detection.
• •Multiplexed approach harnessing N-glycan data for six glycoproteins from a single biological sample.
• •Detailed characterization of human serum N-glycans from antibodies IgG, IgM and IgA and acute phase proteins transferrin, haptoglobin and alpha-1-antitrypsin.
• •Structural differences in antibody and acute phase protein glycosylation for mechanistic insights.

     

Induction of autoantibodies against spermatozoa by injection of allogeneic sperm in the Nile Tilapia,Oreochromis niloticus

• 1.1. The sperm-agglutinating factor (SAF) could be induced in the serum of male Nile tilapias, Oreochromis niloticus, by injection of allogeneic sperm.
• 2.2. Only one class of molecules was demonstrated to be SAF in the serum.
• 3.3. Analysis on purified SAF revealed it to be a tetrameric molecule of IgM with a mol. wt of 760kD.
• 4.4. Cross reaction of the IgM with sperm of other teleost species suggests that sperm-specific surface antigens may be in evolution.

     

Company news

• Daon
• Musicrypt
• EMI Music Canada
• Digital Broadband Networks
• FaceKey Corporation
• Eystar Media Inc (EMI)
• Temasya Wira
• Animated Electronic Industries
• BIO-key International
• Entryport Corporation

     

Monoclonal antibodies prepared against heparin lyase I and their reactivity toward heparin lyase I,II and III

• 1.1. Six different monoclonal IgG mouse antibodies to heparin lyase I from Flavobacterium heparinum were prepared.
• 2.2. The monoclonal antibodies were used to detect heparin lyases I, II and III by dot-blotting immunoassay and by Western blotting.
• 3.3. Individual antibodies showed different reactivity toward the three heparin lyases.
• 4.4. The reactivity of two of the monoclonal antibodies was destroyed by exposing heparin lyases to sodium dodecyl sulfate.
• 5.5. The antibodies can be used to rapidly distinguish between the three heparin lyases.

     

Endoglycosidase S Enables a Highly Simplified Clinical Chemistry Procedure for Direct Assessment of Serum IgG Undergalactosylation in Chronic Inflammatory Disease

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Highlights

• •Selective release of IgG Fc glycans in crude serum by endoglycosidase S.
• •CE-LIF-based measurements of IgG undergalactosylation levels (UGS).
• •UGS as a biomarker: Stratification of non-alcoholic steatohepatitis patients and controls.

     

Company news

Including information on:

• ScanSoft
• SpeechWorks International
• Viisage Technology
• Firstec
• BIO-key International
• HP
• ZN Vision Technologies
• Unisys
• US Government’s
• Communication Intelligence Corporation
• Infinity Technologies

     

Oligoclonal β-galactoside-binding immunoglobulins antigenically related to 14kda lectin in human serum and cerebrospinal fluid: Purification and characterization

• 1.1. An antiserum raised against a 14kDa β-galactoside specific lectin from human brain (HBL14) was used to probe blots from samples of serum and cerebrospinal fluid. The only HBL14-immunoreactive material detected was heavy and light chains of a β-galactoside-binding IgG fraction (lectin-like IgG).
• 2.2. Lectin-like IgG, as well as IgG Fab fragments, compete with HBL14 for binding either to anti-HBL14 antibody or to a lactosyl polyacrylamide-based copolymer.
• 3.3. Purification of lectin-like IgG was obtained by affinity chromatography on immobilized rabbit anti-lectin immunoglobulins. The carbohydrate-binding specificity of the purified molecules was restricted to β-Gal-containing structures and close to the HBL14 one.

     

IDentification of a microsomal retinoic acid synthase as a microsomal cytochrome P-450-linked monooxygenase system

• 1.1. To characterize an enzyme which metabolizes retinal in liver microsomes, several properties of the enzymatic reaction from retinal to retinoic acid were investigated using rabbit liver microsomes.
• 2.2. The maximum pH of the reaction in the liver microsomes was 7.6.
• 3.3. The K_m and V_max values for all-trans, 9-cis and 13-cis-retinals were determined.
• 4.4. The reaction proceeded in the presence of NADPH and molecular oxygen.
• 5.5. The incorporation of one atom of molecular oxygen into retinal was confirmed by using oxygen-18, showing that the reaction comprised monooxygenation, not dehydrogenation.
• 6.6. The monooxygenase activity was inhibited by carbon monoxide, phenylisocyanide and antiNADPH-cytochrome P-450 reductase IgG, but not by anti-cytochrome b₅ IgG.
• 7.7. The enzymatic activity inhibited by carbon monoxide was photoreversibly restored by light of a wavelength of around 450 nm.
• 8.8. The retinal-induced spectra of liver microsomes with three isomeric retinals were type I spectra.
• 9.9. The microsomal monooxygenase activity induced by phenobarbital or ethanol were more effective than that by 3-methylcholanthrene, clotrimazole or β-naphthoflavone.
• 10.10. These results showed that the monooxygenase reaction from retinal to retinoic acid in liver microsomes is catalyzed by a cytochrome P-450-linked monooxygenase system.

     

In brief

• Bioscrypt
• Saflink
• Dell
• Fujitsu Microelectronics America
• Identix
• Viisage
• Acsys Biometrics
• US Government

     

Application news

Including information on:

• Martin State Airport
• Bioscrypt
• Saflink
• Office of the Secretary of Defense
• Department of Defense
• Boeing Corporation
• Bell ID, Gemplus
• Siemens
• Foreign Ministry

     

Primary Human Natural Killer Cells Retain Proinflammatory IgG1 at the Cell Surface and Express CD16a Glycoforms with Donor-dependent Variability

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Highlights

• •Enough CD16a from NK cells can be isolated from a single donor following apheresis.
• •NK cell CD16a shows variability between different donors.
• •NK cells preferentially bind IgG1 that lacks core fucosylation.

     

Immunomic Identification of Malaria Antigens Associated With Protection in Mice

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Highlights

• •Production of sera with different levels of protection against rodent Plasmodium.
• •Generation of immunomic and proteomic data sets enriched in protective antigens.
• •Prediction of the most likely protective antigens using a weighted scoring system.

     

Correlation of acid phosphatase but not alkaline phosphatase activity with myelination in the developing mouse brain

• 1.1. Neonatal mice received subcutaneous injections of buffer, thiourea (TU) or propylthiouracil (PTU).
• 2.2. The PTU-treated mice were sacrificed on postnatal day 14 (P14) and the TU-treated mice on P28.
• 3.3. Brain weights of the TU- and PTU-treated mice were not significantly different from the controls.
• 4.4. Acid but not alkaline phosphatase activity in the braistem decreased after TU and PTU treatment.
• 5.5. Myelination as indicated by intensity of luxol fast blue staining was weaker in drug-treated animals.
• 6.6. The level of myelin marker enzyme, 2′,3′-cyclic nucleotide 3′-phosphohydrolase, was lower in the brainstem of PTU-treated animals.
• 7.7. The results suggest a correlation between acid phosphatase but not alkaline phosphatase activity with myelination in the developing mouse brain.

     

The influences of individual variations in metabolic rate and tidal conditions on the response to hypoxia in Carcinus maenas (L.)

• 1.1. The oxygen consumption of crabs in normoxic and hypoxic (50% O₂) seawater was measured directly after collection.
• 2.2. The influences of size and lunar cycles were removed by scaling the data.
• 3.3. Strong negative correlations between low individual levels of O₂ consumption and the ability to compensate for hypoxia were apparent in Wicklow (subtidal) crabs.
• 4.4. Compensation for hypoxia was much greater on the flood tide than on the ebb.
• 5.5. Crabs from Roscoff (intertidal) had lower levels of compensation than those from Wicklow.
• 6.6. Size, sex and condition had no apparent effect upon these relationships.
• 7.7. Crabs acclimated to laboratory conditions have not shown this tidal variation in compensation for hypoxia.

     

Characterization of Endogenous Human FcγRIII by Mass Spectrometry Reveals Site,Allele and Sequence Specific Glycosylation*

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Highlights

• •Glycosylation of endogenous FcγRIII from neutrophils and matched plasma from more than 40 donors characterized at two sites involved in IgG binding.
• •Glycosylation of soluble FcγRIII glycosylation at N45 can be used to assign FcγRIIIb alleles.
• •FcγRIIIb allele specific differences in glycosylation at N162 may influence differential activity observed for primary cells.

     

Characteristics of Crassostrea virginica crystalline style chitin digestion

• 1.1. Fundamental chitin digestion characteristics of Crassostrea virginica crystalline style were investigated.
• 2.2. Optimum temperature and pH were 34°C and 4.8. respectively.
• 3.3. The colloidal regenerated chitin (0.56mol/0.5 ml: GlcNAc equivalents) was saturating under all enzyme levels encountered.
• 4.4. There was no evidence of end product inhibition, even after 100 hr incubation.
• 5.5. Calculated K_m for the chitinase complex was 1.19mM when determined using a 30 min assay, but was only 0.70 mM when determined using a 4.6 hr assay.
• 6.6. Both K_m values are lower than reported for similar assays in other molluscs and for most bacteria.
• 7.7. Effect of substrate preparation on the kinetics are discussed.
• 8.8. Eight peaks of chitinase activity were resolved by DEAE-Fractogel ion exchange chromatography.

     

Domain structure of the 90-kDa stress protein: Heparin- and antibody-binding domain

• 1.1. To understand the physiological roles of the 90-kDa stress protein (HSP90), we investigated the heparin- and antibody-binding domains of the protein.
• 2.2. For heparin-binding sites, HSP90 was digested completely with trypsin, and the digests were applied to a heparin-Sepharose column and eluted with 1.0 M NaCl, followed by 8.0 M urea.
• 3.3. Each elutant was purified by a reverse-phase C₁₈ column.
• 4.4. Two peptides from the NaCl-eluted fraction and no peptide from the urea-eluted fraction were purified.
• 5.5. The purified peptides were sequenced by an automated peptide sequencer.
• 6.6. One of the heparin-binding sites was present between Leu-362 and Arg-365; another was present between Leu-645 and Lys-648.
• 7.7. These two peptides were basic and considerably hydrophilic.
• 8.8. For antibody-binding sites, HSP90 was mildly digested with trypsin, electrophoresed on SDS-polyacrylamide gels and transferred to PVDF membranes.
• 9.9. The four bound of the trypsin fragments could be sequenced with a peptide sequencer.
• 10.10. There was only one antibody-binding peptide, 38 kDa, starting from Pro-2. The others showed no cross-reactivity with the antibody and started from Leu-283.
• 11.11. Therefore, the epitopes of HSP90 are present between Pro-2 and Leu-282.
• 12.12. The heparin-binding sites are present from the middle region of the HSP90 molecule, and the antigen sites are at the N-terminal domain.