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

---

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

A surfactant/polymer wall coating consisting of the doubly chained cationic surfactant dimethyldioctadecylammonium bromide (DODAB) and polyoxyethylene (POE) 40 stearate is investigated. The coating is formed by simply rinsing a capillary with a solution containing DODAB and POE 40 stearate. The resultant coating is semi-permanent--demonstrating stable electroosmotic flow (EOF) even after a 60 min high pressure rinse with buffer. The EOF (-0.45+/-(0.23) x 10(-4) cm(2) V(-1) s(-1) at pH 7.4) is suppressed by more than a factor of ten compared to that observed for DODAB alone. Model protein mixtures were separated over a pH range of 3-10 with efficiencies of up to greater than 1 million plates/m for the basic proteins cytochrome c, lysozyme, ribonuclease A and alpha-lactalbumin, and the acidic proteins insulin chain A, trypsin inhibitor, and alpha-chymotrypsinogen A. Migration time reproducibility was 0.5-4.0% from run to run and 0.6-4.3% from day to day. Protein recoveries with this coating ranged from 84% to 97%.
...
PMID:Highly efficient protein separations in capillary electrophoresis using a supported bilayer/diblock copolymer coating. 1677 17

The triple-quantum filtered (TQF) spin-echo signal of (17)O-water, in the presence of proteins, was analysed to yield estimates of the number of weakly, and strongly bound water molecules. The analysis used a constrained direct iterative regression procedure with a three-state model of fast-exchange. Thus, the population size of free, weakly, and strongly bound water were determined simultaneously. The two fractions of the bound water were estimated by using correlation time(s) estimated in other studies. Bovine serum albumin (BSA), basic pancreatic trypsin inhibitor (BPTI), lysozyme and oxyhaemoglobin were studied. Of the four proteins, BSA contained the largest number of strongly and weakly bound water molecules, there being approximately 30 of the former and approximately 3000 of the latter under conditions of high protein concentration. The correlation time of the proteins increases with their concentration in solution, and when this was taken into account for BSA the estimated number of strongly bound water molecules did not change significantly. This NMR technique, and data analysis, will probably also be useful in studies of water binding and mobility in various systems including hydrogels, protein networks, membranes, cells and tissues.
...
PMID:Strong and weak binding of water to proteins studied by NMR triple-quantum filtered relaxation spectroscopy of (17)O-water. 1702 97

A recombinant gelatin (HU4) containing part of the amino acid sequence of the alpha1-chain of human type I collagen was used for preparing hydrogels for the sustained release of proteins. HU4 gelatin was modified with methacrylate residues for chemical crosslinking and gel formation. Methacrylated gelatins with degrees of substitution (DS; defined as fraction of methacrylate residues with respect to the total number of primary amines) of 0.24, 0.67, 0.82, and 0.97 were synthesized, and hydrogels with polymer volume fractions in the swollen state (upsilon(2,s)) between 0.01 and 0.14 were formed by radical polymerization. Mesh size (xi) was > or =26 nm, as determined by dynamic mechanical analysis. Release of the incorporated model proteins lysozyme and trypsin inhibitor occurred by diffusion and was nearly complete. Protein diffusion coefficients in the gel were between 5.0 x 10(-7) and 4.0 x 10(-8) cm(2) s(-1), up to 100 fold lower than in water. Release under physiological conditions was effectively controlled by varying hydrogel mesh size and protein-gelatin charge interactions, which demonstrates that recombinant gelatins are a versatile class of biopolymers for the preparation of hydrogels for protein delivery. HU4 hydrogels were enzymatically degradable by human matrix metalloproteinase 1, which is an indication of their in vivo biodegradability.
...
PMID:Recombinant gelatin hydrogels for the sustained release of proteins. 1746 99

We describe the stacking and separation of proteins by CE under discontinuous conditions in conjunction with light-emitting diode induced fluorescence (LEDIF) detection using a violet LED at 405 nm. The proteins were derivatized with naphthalene-2,3-dicarboxaldehyde (NDA) to form NDA-protein derivatives prior to CE-LEDIF analysis. During the separation, poly(ethylene oxide) (PEO) solution containing CTAB enters from the cathodic inlet to the capillary via electroosomotic flow (EOF). The optimum conditions are: the capillary was filled with 50 mM glycine buffer (pH 9.0) containing 1.0 mM CTAB, NDA-protein derivatives were prepared in deionized water containing 1.0 mM CTAB, and 0.6% PEO was prepared in 50 mM glycine (pH 9.0) containing 2.0 mM CTAB. The analysis of four NDA-protein derivatives is fast (<3 min), with RSD <1.5% in terms of migration time. In order to improve the sensitivity of NDA-protein derivatives, a stacking approach based on increases in viscosity and electric field, as well as sieving was applied. The efficient stacking approach provides LODs (S/N = 3) of 2.41, 0.59, 0.61, and 4.22 nM for trypsin inhibitor, HSA, beta-lactoglobulin, and lysozyme, respectively. In addition, we also applied the stacking approach to determination of the concentration of HSA in one urine sample, which was determined to be 0.31 +/- 0.05 microM (n = 3).
...
PMID:Stacking and separation of protein derivatives of naphthalene-2,3-dicarboxaldehyde by CE with light-emitting diode induced fluorescence detection. 1806 34

The aggregates and gels commonly observed during protein crystallization have generally been considered disordered phases without further characterization. Here their physical nature is addressed by investigating protein salting-out in ammonium sulfate and sodium chloride for six proteins (ovalbumin, ribonuclease A, soybean trypsin inhibitor, lysozyme, and beta-lactoglobulin A and B) at 4 degrees C, 23 degrees C, and 37 degrees C. When interpreted within the framework of a theoretical phase diagram obtained for colloidal particles displaying short-range attractive interactions, the results show that the formation of aggregates can be interpreted theoretically in terms of a gas-liquid phase separation for aggregates that are amorphous or gel-like. A notable additional feature is the existence of a second aggregation line observed for both ovalbumin and ribonuclease A in ammonium sulfate, interpreted theoretically as the spinodal. Further investigation of ovalbumin and lysozyme reveals that the formation of aggregates can be interpreted, in light of theoretical results from mode-coupling theory, as a kinetically trapped state or a gel phase that occurs through the intermediate of a gas-liquid phase separation. Despite the limitations of simple theoretical models of short-range attractive interactions, such as their inability to reproduce the effect of temperature, they provide a framework useful to describe the main features of protein phase behavior.
...
PMID:Protein phase behavior in aqueous solutions: crystallization, liquid-liquid phase separation, gels, and aggregates. 1816 Jun 63

Myeloperoxidase, released by activated phagocytes, forms reactive oxidants by catalysing the reaction of halide and pseudo-halide ions with H(2)O(2). These oxidants have been linked to tissue damage in a range of inflammatory diseases. With physiological levels of halide and pseudo-halide ions, similar amounts of HOCl (hypochlorous acid) and HOSCN (hypothiocyanous acid) are produced by myeloperoxidase. Although the importance of HOSCN in initiating cellular damage via thiol oxidation is becoming increasingly recognized, there are limited data on the reactions of HOSCN with other targets. In the present study, the products of the reaction of HOSCN with proteins has been studied. With albumin, thiols are oxidized preferentially forming unstable sulfenyl thiocyanate derivatives, as evidenced by the reversible incorporation of (14)C from HOS(14)CN. On consumption of the HSA (human serum albumin) free thiol group, the formation of stable (14)C-containing products and oxidation of tryptophan residues are observed. Oxidation of tryptophan residues is observed on reaction of HOSCN with other proteins (including myoglobin, lysozyme and trypsin inhibitor), but not free tryptophan, or tryptophan-containing peptides. Peptide mass mapping studies with HOSCN-treated myoglobin, showed the addition of two oxygen atoms on either Trp(7) or Trp(14) with equimolar or less oxidant, and the addition of a further two oxygen atoms to the other tryptophan with higher oxidant concentrations (> or = 2-fold). Tryptophan oxidation was observed on treating myoglobin with HOSCN in the presence of glutathione and ascorbate. Thus tryptophan residues are likely to be favourable targets for the reaction in biological systems, and the oxidation products formed may be useful biomarkers of HOSCN-mediated protein oxidation.
...
PMID:Tryptophan residues are targets in hypothiocyanous acid-mediated protein oxidation. 1865 72

A fast and accurate method to compute the total solvation free energies of proteins as a function of pH is presented. The method makes use of a combination of approaches, some of which have already appeared in the literature; (i) the Poisson equation is solved with an optimized fast adaptive multigrid boundary element (FAMBE) method; (ii) the electrostatic free energies of the ionizable sites are calculated for their neutral and charged states by using a detailed model of atomic charges; (iii) a set of optimal atomic radii is used to define a precise dielectric surface interface; (iv) a multilevel adaptive tessellation of this dielectric surface interface is achieved by using multisized boundary elements; and (v) 1:1 salt effects are included. The equilibrium proton binding/release is calculated with the Tanford-Schellman integral if the proteins contain more than approximately 20-25 ionizable groups; for a smaller number of ionizable groups, the ionization partition function is calculated directly. The FAMBE method is tested as a function of pH (FAMBE-pH) with three proteins, namely, bovine pancreatic trypsin inhibitor (BPTI), hen egg white lysozyme (HEWL), and bovine pancreatic ribonuclease A (RNaseA). The results are (a) the FAMBE-pH method reproduces the observed pK a's of the ionizable groups of these proteins within an average absolute value of 0.4 p K units and a maximum error of 1.2 p K units and (b) comparison of the calculated total pH-dependent solvation free energy for BPTI, between the exact calculation of the ionization partition function and the Tanford-Schellman integral method, shows agreement within 1.2 kcal/mol. These results indicate that calculation of total solvation free energies with the FAMBE-pH method can provide an accurate prediction of protein conformational stability at a given fixed pH and, if coupled with molecular mechanics or molecular dynamics methods, can also be used for more realistic studies of protein folding, unfolding, and dynamics, as a function of pH.
...
PMID:FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins. 1868 66

Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for proper computational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting different types of QM/MM calculations of electrostatic energies (and related properties) here, our focus will be on pKa calculations. This reflects the fact that pKa's of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor and a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that, by using this approach, we are able to reproduce the relevant side chain pKa's with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an overall perspective of the potential of QM/MM calculations in general evaluations of electrostatic free energies, pointing out that our approach should provide a very powerful and accurate tool to predict the electrostatics of not only solution but also enzymatic reactions, as well as the solvation free energies of even larger systems, such as nucleic acid bases incorporated into DNA.
...
PMID:Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies. 1905 5

Transglutaminases (TGs) are known to exhibit remarkable specificities not only for the Q (or Gln) sites but also for the K (or Lys) sites of proteins with which they react. To gain further insight into K-site specificity, we examined the reactions of dansyl-epsilon-aminocaproyl-GlnGlnIleVal with three chemically and structurally well-characterized proteins (bovine pancreatic ribonuclease A, bovine pancreatic trypsin inhibitor, and chicken egg white lysozyme), as catalyzed by TG2, a biologically important post-translational enzyme. The substrates represent a total of 20 potential surface sites for acylation by the fluorescent Gln probe, yet only two of the lysine side chains reacted with TG2. While the K1 site of ribonuclease and the K15 site of the trypsin inhibitor could be readily acylated by the enzyme, none of the lysines in lysozyme were modified. The findings lead us to suggest that the selection of lysine residues by TG2 is not encoded in the primary amino acid sequence surrounding the target side chain but depends primarily on its being positioned in an accessible segment of the protein structure.
...
PMID:Selectivity in the post-translational, transglutaminase-dependent acylation of lysine residues. 1922 23

The release kinetics for a variety of proteins of a wide range of molecular mass, hydrodynamic radii, and isoelectric points through a nanofiber hydrogel scaffold consisting of designer self-assembling peptides were studied by using single-molecule fluorescence correlation spectroscopy (FCS). In contrast to classical diffusion experiments, the single-molecule approach allowed for the direct determination of diffusion coefficients for lysozyme, trypsin inhibitor, BSA, and IgG both inside the hydrogel and after being released into the solution. The results of the FCS analyses and the calculated pristine in-gel diffusion coefficients were compared with the values obtained from the Stokes-Einstein equation, Fickian diffusion models, and the literature. The release kinetics suggested that protein diffusion through nanofiber hydrogels depended primarily on the size of the protein. Protein diffusivities decreased, with increasing hydrogel nanofiber density providing a means of controlling the release kinetics. Secondary and tertiary structure analyses and biological assays of the released proteins showed that encapsulation and release did not affect the protein conformation and functionality. Our results show that this biocompatible and injectable designer self-assembling peptide hydrogel system may be useful as a carrier for therapeutic proteins for sustained release applications.
...
PMID:Controlled release of functional proteins through designer self-assembling peptide nanofiber hydrogel scaffold. 1927 53


<< Previous 1 2 3 4 5 6 7 8 9 Next >>

---