Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.2.1.17 (lysozyme)
21,489 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A method is presented that generates random protein structures that fulfil a set of upper and lower interatomic distance limits. These limits depend on distances measured in experimental structures and the strength of the interatomic interaction. Structural differences between generated structures are similar to those obtained from experiment and from MD simulation. Although detailed aspects of dynamical mechanisms are not covered and the extent of variations are only estimated in a relative sense, applications to an IgG-binding domain, an SH3 binding domain, HPr, calmodulin, and lysozyme are presented which illustrate the use of the method as a fast and simple way to predict structural variability in proteins. The method may be used to support the design of mutants, when structural fluctuations for a large number of mutants are to be screened. The results suggest that motional freedom in proteins is ruled largely by a set of simple geometric constraints.
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PMID:Prediction of protein conformational freedom from distance constraints. 932 88

A relatively simple protein solvent-accessible surface triangulation method for continuum electrostatics applications employing the boundary element method is presented. First, the protein is placed onto a three-dimensional lattice with a specified lattice spacing. To each lattice point, a box is assigned. Boxes located in the solvent region and in the interior of the protein are removed from the set. Improper connections between boxes and the possible existence of cavities in the interior of the protein which would destroy the proper connectivity of the triangulated surface are taken care of. The remaining set of boxes define the outer contour of the protein. Each free face exposed to the solvent of the remaining set of boxes is triangulated after the surface defined by the free faces has been smoothed to follow the shape of the macromolecule more accurately. The final step consists of a mapping of triangle vertices onto a set of surface points which define the solvent-accessible surface. Normal vectors at triangle vertices are obtained also from the free faces which define the orientation of the surface. The algorithm was tested for six molecules including four proteins; a dipeptide, a helical peptide consisting of 25 residues, calbindin, lysozyme, calmodulin and cutinase. For each molecule, total areas have been calculated and compared with the result computed from a dotted solvent-accessible surface. Since the boundary element method requires a low number of vertices and triangles to reduce the number of unknowns for reasons of efficiency, the number of triangles should not be too high. Nevertheless, credible results are obtained for the total area with relative errors not exceeding 12% for a large lattice spacing (0.30 nm) while close to zero for a smaller lattice spacing (down to 0.16 nm). The output of the triangulation computer program (written in C++) is rather simple so that it can be easily converted to any format acceptable for any molecular graphics programs.
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PMID:A flexible triangulation method to describe the solvent-accessible surface of biopolymers. 974 71

One of the major challenges of molecular allergy is to predict the allergenic potential of a protein, particularly in novel foods. Two aspects have to be distinguished: immunogenicity and cross-reactivity. Immunogenicity reflects the potential of a protein to induce IgE antibodies, whereas cross-reactivity is the reactivity of (usually preexisting) IgE antibodies with the target protein. In addition to these two issues, the relation between IgE-binding potential and clinical symptoms is of interest. This is influenced by physical properties (eg, stability and size) and immunologic properties (affinity and epitope valence). Discussions on immunogenicity and cross-reactivity of allergens rely on the establishment of structural similarities and differences among allergens and between allergens and nonallergens. For comparisons between the 3-dimensional protein folds, the representation as 2-dimensional proximity plots provides a convenient visual aid. Analysis of approximately 40 allergenic proteins (or parts of these proteins), of which the protein folds are either known or can be predicted on the basis of homology, indicates that most of these can be classified into 4 structural families: (1) antiparallel beta-strands: the immunoglobulin-fold family (grass group 2, mite group 2), serine proteases (mite group 3, 6, and 9), and soybean-type trypsin inhibitor (Ole e 1, grass group 11); (2) antiparallel beta-sheets intimately associated with one or more alpha-helices: tree group 1, lipocalin, profilin, aspartate protease (cockroach group 2); (3) (alpha+beta) structures, in which the alpha- and beta-structural elements are not intimately associated: mite group 1, lysozyme/lactalbumin, vespid group 5; and (4) alpha-helical: nonspecific lipid transfer protein, seed 2S protein, insect hemoglobin, fish parvalbumin, pollen calmodulin, mellitin from bee venom, Fel d 1 chain 1, serum albumin. Allergens with parallel beta-strands (in combination with an alpha-helix linking the two strands, a motif commonly found in, for example, nucleotide-binding proteins) seem to be underrepresented. The conclusion is that allergens have no characteristic structural features other than that they need to be able to reach (and stimulate) immune cells and mast cells. Within this constraint, any antigen may be allergenic, particularly if it avoids activation of T(H)2-suppressive mechanisms (CD8 cells and T(H)1 cells).
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PMID:Structural biology of allergens. 1093 64

The effect of alpha-NeuAc(2-->6)Gal/GalNAc-specific lectin from Sambucus nigra (SNA) on the release of lysozyme from human neutrophils was studied in vitro. Interaction of cells with the lectin was accompanied by dose-dependent release of lysozyme, which was increased in the presence of cytochalasin B. The involvement of intracellular signaling pathways in the lectin-induced degranulation of neutrophils was determined using a panel of specific inhibitors tested at concentrations in the range of 10-100 microM. Aristolochic acid (a phospholipase A2 inhibitor), indomethacin (a cyclooxygenase inhibitor), neomycin sulfate (a phospholipase C inhibitor), trifluoperazine (a calmodulin antagonist/protein kinase C inhibitor), N-ethylmaleimide (a sulfhydryl reagent), and guanosine-5;-O-(2-thiodiphosphate) (a G-protein inhibitor) were found to reduce SNA-induced lysozyme release from neutrophils by 20-45%. The treatment of cells with bisindolylmaleimide (a protein kinase C inhibitor), H-8 (an inhibitor of protein kinases A, C, G and of myosin light chain kinase), PD 98059 (a MAP kinase inhibitor), and (+/-)-methoxyverapamil (a Ca2+-channel blocker) failed to affect the release of lysozyme. These results indicate that only selective intracellular pathways associated with activation of G-proteins and phospholipid metabolism as well as the thiol-dependent signaling systems are apparently involved in the realization of the SNA-induced degranulation response of human neutrophils.
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PMID:Effect of signaling inhibitors on the release of lysozyme from human neutrophils activated by Sambucus nigra agglutinin. 1100 87

A novel method is proposed to predict whether two domains connected by a helical link can mutually reorient themselves, as well as where the helix can be distorted to allow the domain-domain movements. The method, based on analysis of the variation of the a.d.p. values along the helix link, is applied to three proteins--calmodulin, lysozyme, and hemagglutinin--for which both the domain-domain flexibility and the helix fragment responsible for it are well documented. The helix regions that are variously distorted to permit domain-domain reorientation are well predicted. The method is also applied to colicin Ia and shows that an inter-domain rearrangement can take place as previously postulated. The prediction of the helix breaking point should prove useful in interpreting structural data and in defining the domain borders automatically for proteins built by domains connected by helical links.
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PMID:Detection of breaking points in helices linking separate domains. 1115 Oct 10

The effects of anesthetics on cellular function may result from direct interactions between anesthetic molecules and proteins. These interactions have a low affinity and are difficult to characterize. To identify proteins that bind anesthetics, we used nuclear magnetic resonance saturation transfer difference (STD) spectroscopy. The method is based on the nuclear Overhauser effect between bound anesthetic protons and all protein protons. To establish STD as a method for testing anesthetic binding to proteins, we conducted measurements on a series of protein/anesthetic solutions studied before by other methods. STD was able to identify that volatile anesthetics bind to bovine serum albumin, oleic acid reduces halothane binding to bovine serum albumin, and halothane binds to apomyoglobin but not lysozyme. Using STD, we found that halothane binding to calmodulin is Ca2+ -dependent, which demonstrates anesthetic specificity for a protein conformation. Thus, STD is a powerful tool for investigating anesthetic-protein interactions because of its abilities to detect weak binding, to screen a single protein for binding of multiple anesthetics simultaneously, and to detect a change in anesthetic binding caused by conformational changes or competition with other ligands.
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PMID:Saturation transfer difference nuclear magnetic resonance spectroscopy as a method for screening proteins for anesthetic binding. 1538 43

A new method to interpret electrospray mass spectral data based on calculating the ratio of mass-to-charge (m/z) values of multiply charged ions is described. The mass-to-charge ratios of any two multiply charged ions corresponding to a single compound are unique numbers that enable the charge states for each ion to be unequivocally identified. The multiply charged ions in electrospray mass spectra originate from the addition or abstraction of protons, cations, or anions to and from a compound under analysis. In contrast to existing deconvolution processes, the charge ratio analysis method (CRAM), identifies the charge states of multiply charged ions without any prior knowledge of the nature of the charge-carrying species. In the case of high-resolution electrospray mass spectral data, in which multiply charged ions are resolved to their isotopic components, the CRAM is capable of correlating the isotope peaks of different multiply charged ions that share the same isotopic composition. This relative ratio method is illustrated here for electrospray mass spectral data of lysozyme and oxidized ubiquitin recorded at low- to high-mass resolution on quadrupole ion trap and Fourier transform ion cyclotron mass spectrometers, and theoretical data for the protein calmodulin based upon a reported spectrum recorded on the latter.
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PMID:Charge ratio analysis method: approach for the deconvolution of electrospray mass spectra. 1562 85

The fast and accurate prediction of protein flexibility is one of the major challenges in protein science. Enzyme activity, signal transduction, and ligand binding are dynamic processes involving essential conformational changes ranging from small side chain fluctuations to reorientations of entire domains. In the present work, we describe a reimplementation of the CONCOORD approach, termed tCONCOORD, which allows a computationally efficient sampling of conformational transitions of a protein based on geometrical considerations. Moreover, it allows for the extraction of the essential degrees of freedom, which, in general, are the biologically relevant ones. The method rests on a reliable estimate of the stability of interactions observed in a starting structure, in particular those interactions that change during a conformational transition. Applications to adenylate kinase, calmodulin, aldose reductase, T4-lysozyme, staphylococcal nuclease, and ubiquitin show that experimentally known conformational transitions are faithfully predicted.
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PMID:Geometry-based sampling of conformational transitions in proteins. 1799 73

Nonenzymatic deamidation of asparagine residues in proteins generates aspartyl (Asp) and isoaspartyl (isoAsp) residues via a succinimide intermediate in a neutral or basic environment. Electron capture dissociation (ECD) can differentiate and quantify the relative abundance of these isomeric products in the deamidated proteins. This method requires the proteins to be digested, usually by trypsin, into peptides that are amenable to ECD. ECD of these peptides can produce diagnostic ions for each isomer; the c. + 58 and z - 57 fragment ions for the isoAsp residue and the fragment ion ((M + nH)((n-1)+.) - 60) corresponding to the side-chain loss from the Asp residue. However, deamidation can also occur as an artifact during sample preparation, particularly when using typical tryptic digestion protocols. With 18O labeling, it is possible to differentiate deamidation occurring during trypsin digestion which causes a +3 Da (18O1 + 1D) mass shift from the pre-existing deamidation, which leads to a +1-Da mass shift. This paper demonstrates the use of (18)O labeling to monitor three rapidly deamidating peptides released from proteins (calmodulin, ribonuclease A, and lysozyme) during the time course of trypsin digestion processes, and shows that the fast (approximately 4 h) trypsin digestion process generates no additional detectable peptide deamidations.
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PMID:Use of 18O labels to monitor deamidation during protein and peptide sample processing. 1839 20

We compared sensitivity and selectivity of five dyes for detection of 2D PAGE-resolved proteins derived from Escherichia coli and MDCK cells. The sensitivity of these dyes was in the following order: SYPRO Ruby>Deep Purple>CBB-G250>CBB-R250>Colloidal Gold. Also, we report herein for the first time the application of Colloidal Gold (which is commonly used for staining proteins on blotted membranes) for in-gel staining of proteins. For E. coli, most of the dyes preferably detected proteins with pI range of 4.0-6.9, whereas Deep Purple preferably detected proteins with less acidic range (pI 5.0-7.9). For MDCK cells, while other dyes preferably stained proteins at pI range of 5.0-7.9, Colloidal Gold preferably stained more basic proteins (pI 7.0-9.9). This preferential staining property of Colloidal Gold to basic proteins was confirmed in SDS-PAGE-separated lysozyme (pI 9.4), compared to calmodulin (pI 4.0) and albumin (pI 6.0). These data provide useful information to select appropriate dyes for gel-based proteomic analysis of individual samples.
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PMID:A comparative study of different dyes for the detection of proteomes derived from Escherichia coli and MDCK cells: sensitivity and selectivity. 1934 17


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