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)

The change in free energy of binding of hen egg white lysozyme (HEL) to the antibody HyHel-10 arising from ten point mutations in HEL (D101K, D101G, K96M, K97D, K97G, K97G, R21E, R21K, W62Y, and W63Y) was calculated using a combination of the finite difference Poisson-Boltzmann method for the electrostatic contribution, a solvent accessible surface area term for the non-polar contribution, and rotamer counting for the sidechain entropy contribution. Comparison of experimental and calculated results indicate that because of pKa shifts in some of the mutated residues, primarily those involving Aspartate or Glutamate, proton uptake or release occurs in binding. When this effect was incorporated into the binding free energy calculations, the agreement with experiment improved significantly, and resulted in a mean error of about 1.9 kcal/mole. Thus these calculations predict that there should be a significant pH dependence to the change in binding caused by these mutations. The other major contributions to binding energy changes comes from solvation and charge charge interactions, which tend to oppose each other. Smaller contributions come from nonpolar interactions and sidechain entropy changes. The structures of the HyHel-10-HEL complexes with mutant HEL were obtained by modeling, and the effect of the modeled structure on the calculations was also examined. "Knowledge based" modeling and automatic generation of models using molecular mechanics produced comparable results.
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PMID:Calculation of HyHel10-lysozyme binding free energy changes: effect of ten point mutations. 974 43

In an earlier publication by Chattoraj et al. [Biophysical Chemistry 63 (1996) 37], a generalized equation for standard free energy of (delta G0) interaction of surfactant, inorganic salts and aqueous solvent with protein, forming a single phase has been deduced on strict thermodynamic grounds. In the present paper, this equation has been utilized to calculate delta G0 in kilojoules per kilogram of different proteins for the change of bulk surfactant activity from zero to unity in the mole fraction scale. Values of binding interactions of CTAB, MTAB, DTAB and SDS to BSA, beta-lactoglobulin, gelatin, casein, myosin, lysozyme and their binary and ternary mixtures had already been determined in this laboratory at different surfactant concentrations, pH, ionic strength and temperature using an equilibrium dialysis technique. Values of delta G0 for saturated protein-surfactant complexes as well as unsaturated complexes are found to be equal. delta G0 is also found to vary linearly with maximum moles of surfactants bound to a kilogram of protein or protein mixture and the slope of this linear plot represents standard free energy delta G0B for the transfer of 1 mol of surfactant from the bulk for binding reaction with protein; -delta G0 values for different systems vary widely and the order of their magnitudes represents relative affinities of surfactants to proteins. Magnitude of -delta G0B on the other hand varies within a narrow range of 32-37 kJ/mol of surfactant. For interaction of SDS with BSA, close to the CMC, values of delta G0 are very high due to the formation of micelles of protein-bound surfactants. Values of delta G0 for negative binding of inorganic salts to proteins and protein mixtures have been evaluated using our generalized equation in which excess binding values of water and salts have been calculated from the data obtained from our previous isopiestic experiments. delta G0 values in these cases are positive due to the excess hydration of proteins. Negative values of delta G0 in surfactant interaction and positive values of delta G0 for hydration of proteins in the presence of neutral salts represent relative affinities of proteins for solute and solvent since in all cases, the reference state for delta G0 is the unit mole fraction of solute in the aqueous phase.
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PMID:Standard free energies of binding of solute to proteins in aqueous medium. Part 2. Analysis of data obtained from equilibrium dialysis and isopiestic experiments. 1020 94

Stability of hen lysozyme in the presence of acetonitrile (MeCN) at different pH values of the medium was studied by scanning microcalorimetry with a special emphasis on determination of reliable values of the denaturational heat capacity change. It was found that the temperature of denaturation decreases on addition of MeCN. However, the free energy extrapolation showed that below room temperature the thermodynamic stability increases at low concentrations of MeCN in spite of the general destabilizing effect at higher concentrations and temperatures. Charge-induced contribution to this stabilization was shown to be negligible (no pH-dependence was found); therefore, the most probable cause for the phenomenon is an increase of hydrophobic interactions at low temperatures in aqueous solutions containing small amounts of the organic additive. The difference in preferential solvation of native and denatured states of lysozyme was calculated from the stabilization free energy data. It was found that the change in preferential solvation strongly depends on the temperature in the water-rich region. At the higher MeCN content this dependence decreases until, at 0.06 mole fractions of MeCN, the difference in the preferential solvation between native and denatured lysozyme becomes independent of the temperature over a range of 60 K. The importance of taking into account non-ideality of a mixed solution, when analyzing preferential solvation phenomena was emphasized.
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PMID:On the stabilizing action of protein denaturants: acetonitrile effect on stability of lysozyme in aqueous solutions. 1063 79

The early stage products of the Maillard reaction of egg white lysozyme with D-glucose were studied. Incubation with D-glucose at 50 degrees C for 20 days caused reaction on the Lys and Arg residues of lysozyme as follows: all of the six Lys residues and 10 of the 11 Arg residues in lysozyme reacted with D-glucose; Arg 61 did not react with D-glucose. The Lys residues reacted with D-glucose with 1 mol of dehydration per mole of residue, and the Arg residues reacted with 2 mol of dehydration per mole of residue. The major constituent of the Amadori product with the epsilon-amino group of the Lys residue and the D-glucose was found to be the beta-pyranose form. The structure of the early stage product of the Maillard reaction of a protein with a sugar is the same as that of an amino acid with a sugar.
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PMID:Structural studies of the Maillard reaction products of a protein using ion trap mass spectrometry. 1067 72

The uptake of water vapour by 20 different polyaminoacids have been evaluated by an isopiestic vapour pressure technique in absence of solute at three different temperatures (22 degrees C, 30 degrees C and 37 degrees C). The water vapour adsorption isotherm for different polyaminoacids in the range of water activity varying between zero and unity apparently agreed with that expected from a type III BET isotherm. From the linear BET plots, obeyed in the lower range of water activity, the BET constants n(m) and Qm for different polyamines have been evaluated. The amount of water vapour adsorbed (n1) was calculated in moles/kg of polyaminoacids as well as in moles/mole of amino acid residue. Its value at unit water activity (deltan(o)1) has been evaluated by an extrapolation method and the results support that the multilayer adsorption of water vapour at the interface of polyaminoacids takes place. Values of deltan(o)1 are strictly comparable in terms of moles per kg rather than mole per mole unit. In case of beta lactoglobulin (betalg), lysozyme and BSA, theoretically obtained deltan(o)1 values were observed to be considerably larger than experimental values of deltan(o)1. This indicated that amino acid residues in the polypeptide release a large amount of water due to the formation of a globular structure. Using the Bull equation in the integrated form, standard free energies, deltaGo(w) for water-polyamino acid binding interaction at two different temperatures have been evaluated. Based on the Clausius-Clapeyron equation in an integrated form, the integral enthalpy for water-polyamino acid interaction has also been evaluated.
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PMID:Thermodynamics of interaction of water vapour with 20 different poly-L-amino acids. 1125 13

Extent of binding (gammap) of globular proteins to calf-thymus DNA have been measured in mole per mole of nucleotide as function of equilibrium protein concentration. We have exploited measurement of the surface tension of the protein solution in the presence and absence of DNA to calculate the binding ration (gammap). Interaction of bovine serum albumin with DNA has been studied at different pH. Interaction of bovine serum albumin with DNA has been studied at different pH, ionic strength and in presence of Ca2+. Interaction of BSA with denatured DNA has also been investigated. Binding isotherms for other globular proteins like beta-lactoglobulin, alpha-lactalbumin and lysozyme have been compared under identical physicochemical condition. It has been noted with considerable interest that globular form of protein is important to some extent in protein-DNA interaction. An attempt has been made to explain the significance of difference in binding ratios of these two biopolymers in aqueous medium for different systems in the light of electrostatic and hydrophobic effects. Values of maximum binding ration (gammap(m)) at saturated level for different systems have been also presented. The Gibb's free energy decrease (-deltaG0) of the binding of proteins to DNA has been compared more precisely for the saturation of binding sites in the DNA with the change of activity of protein in solution from zero to unity in the rational mole fraction scale.
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PMID:Binding of globular proteins to DNA from surface tension measurement. 1188 79

A comparative study was performed on lysozyme modification after exposure to Fenton reagent (Fe(II)/H2 O2) or hydroxyl radicals produced by y radiation. The conditions were adjusted to obtain, with both systems, a 50% loss of activity of the modified ensemble. Gamma radiation modified almost all types of amino acid residues in the enzyme, with little specificity. The modification order was Tyr > Met = Cys > Lys > Ile + Leu > Gly > Pro = Phe > Thr + Ala > Trp = Ser > Arg > Asp + Glu, with 42 mol of modified residues per initial mole of native enzyme. In contrast, when the enzyme was exposed to the Fenton reaction, only some types of amino acids were modified. Furthermore, a smaller number of residues (13.5) were damaged per initial mole of enzyme. The order of the modified residues was Tyr > Cys > Trp > Met His > Ile + Leu > Val > Arg. These results demonstrate that the modifications elicited by these two free radical sources follow different mechanisms. An intramolecular free radical chain reaction is proposed to play a dominant role in the oxidative modification of the protein promoted by gamma radiation.
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PMID:Lysozyme modification by the fenton reaction and gamma radiation. 1207 46

The anti-hen egg-white lysozyme (HEWL) antibodies HyHEL-10 and F9.13.7 recognize a common epitope. The structures of the complexes differ, however, in the numbers of electrostatic and hydrogen-bond interactions and in the distributions of contacts between the light and heavy chains. The equilibria and kinetics characterizing the F9.13.7 complex formation were evaluated for both wild-type and mutant derivatives of HEWL to help to understand how the different contacts are effectively used in the complexes with the two antibodies. Three epitope hot spots, Y20, K96, and R73 (destabilization > 4 kcal/mole), were found by alanine scanning mutagenesis. The first two constitute two of the three hot spots in the HyHEL-10 complex. The hot spots of the HyHEL-10 paratope are centered on the HEWL epitope; whereas R73 (HEWL), the only important light-chain-contacting residue, is clearly separated from the other hot spots of the F9.13.7 complex. The larger number of epitope warm plus hot spots found in the F9.13.7 complex compared with that of HyHEL-10 shows that the specificity of the former is greater even though the K(D) value is 20-fold larger. Conservative mutations showed that the specificity enhancement is related to the greater number of functional polar and hydrogen bond interactions in the F9.13.7 complex. Alanine scanning mutagenesis would not have illuminated these distinctions. It is shown that the concept of antigen specificity, as defined by cross-reactivity with natural variant antigens, is flawed by phylogenetic bias, and that specificity can only be defined by the use of unbiased epitopes, which are conveniently accessed by site-directed mutagenesis.
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PMID:How do two unrelated antibodies, HyHEL-10 and F9.13.7, recognize the same epitope of hen egg-white lysozyme? 1223 53

Molecular simulations were performed to study a system consisting of protein (e.g., lysozyme) and self-assembled monolayers (SAMs) terminating with different chemical groups in the presence of explicit water molecules and ions. Mixed SAMs of oligo (ethylene glycol) [S(CH2)4(OCH2CH2)4OH, (OEG)] and hydroxyl-terminated SAMs [S(CH2)4OH] with a mole fraction of OEG at chiOEG = 0.2, 0.5, 0.8, and 1.0 were used in this study. In addition, methyl-terminated SAMs [S(CH2)11CH3] were also studied for comparison. The structural and dynamic behavior of hydration water, the flexibility and conformation state of SAMs, and the orientation and conformation of protein were examined. Simulation results were compared with those of experiments. It appears that there is a correlation between OEG surface resistance to protein adsorption and the surface density of OEG chains, which leads to a large number of tightly bound water molecules around OEG chains and the rapid mobility of hydrated SAM chains.
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PMID:Molecular simulation study of water interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled monolayers. 1537 29

The extent of adsorption (Gamma2(1)) of bovine serum albumin (BSA), beta-lactoglobulin, lysozyme, gelatin, and DNA from aqueous solution onto the hydrophilic surface of cellulose has been measured as function of biopolymer concentration at different temperatures, pHs, and ionic strengths, and in the presence of a high concentration of inorganic salts and denaturants. In all cases, the value of Gamma2(1) increases with the increase of biopolymer concentration (X2) in bulk and it attains a maximum value at a critical mole fraction concentration X2m. The value of Gamma2m depends upon the nature of protein, temperature, pH, and ionic strength, as well as the nature of neutral salts present in excess. Gamma2m for proteins at a fixed physicochemical condition stands in the following order: Gelatin>betalactoglobulin>lysozyme>BSA. The isotherms for adsorption of DNA nucleotides on cellulose surface at pH 4.0 have been compared at different temperatures and ionic strengths, and in the presence of high concentration of inorganic salts LiCl, NaCl, KCl, and Na2SO4. Values of Gamma2m for different systems have been evaluated and critically compared. At pH 6.0 and 8.0, Gamma2(1) values of DNA nucleotides on cellulose are all negative due to the excess positive hydration of cellulose. At pH 4.0, adsorption of nucleotides of acid, alkali, and heat-denatured DNA widely differ from each other and in the presence of excess concentration of urea becomes negative. The probable mechanisms of biopolymer-cellulose adsorption in terms of polymer hydration, steric interaction, London-van der Waals, hydrophobic, and other types of interactions have been discussed qualitatively. The standard free energy change for the adsorption of protein and DNA nucleotides on the cellulose surface at the state of adsorption saturation has been calculated in kJ per kg of cellulose using an integrated form of the Gibbs adsorption equation. The relation between DeltaG degrees and maximum affinities between biopolymers and the polysaccharide interface have been discussed for various systems.
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PMID:Adsorption of biopolymers at hydrophilic cellulose-water interface. 1564 88


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