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)

Acid carboxypeptidase (EC 3.4.12.-) crystallized from culture filtrate of Penicillium janthinellum has been investigated for its use in carboxy-terminal sequence determination of Z-Gly-Pro-Leu-Gly, Z-Gly-Pro-Leu-Gly-Pro, angiotensin I, native lysozyme, native ribonuclease T1, and reduced S-carboxy-methyl-lysozyme. The examination indicated that proline and glycine were liberated from Z-Gly-Pro-Leu-Gly-Pro. At high enzyme concentration, the enzyme catalyzed complete sequential release of amino acids from the carboxy-terminal leucine to the amino-terminal aspartic acid of angiotensin I. The enzyme released the carboxy-terminal leucine from native lysozyme, however, no release of the threonine from native ribonuclease T1 was observed after a prolonged period of incubation with the enzyme. The sequence of the first nine carboxy-terminal residues of denatured lysozyme, leucine, arginine, S-carboxymethyl-cysteine, glycine, arginine, isoleucine, tryptophane, alanine, and glutamine, could be deduced unequivocally from a time release plot of an incubation mixture with the enzyme.
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PMID:Action of crystalline acid carboxypeptidase from Penicillium janthinellum. 23 51

The role of tryptophan residues in the stability of proteins was studied by ozone oxidation, which causes a small change in the tryptophan side chain. Trp 187 of the constant fragment of a type lambda immunoglobulin light chain, Trp 59 of ribonuclease T1, and Trp 62 of hen egg white lysozyme were oxidized specifically by ozone to N'-formylkynurenine or kynurenine. Judging from their circular dichroic and fluorescence spectra, these modified proteins were found to be the same as those of the respective intact proteins. However, even the slight modification of a single tryptophan residue produced a large decrease in the stability of these proteins to guanidine hydrochloride and heat. The smaller the extent of exposure of the tryptophan residue, the greater the effect of the modification on the stability. The formal kinetic mechanism of unfolding and refolding by guanidine hydrochloride of the CL fragment was not altered by tryptophan oxidation, but the rate constants for unfolding and refolding changed. The thermal unfolding transitions were analyzed to obtain the thermodynamic parameters. The enthalpy and entropy changes for the modified proteins were larger than the respective values for the intact proteins.
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PMID:Chemical modification of tryptophan residues and stability changes in proteins. 212 74

Incubation of crude estrogen receptor preparations from mammary tumor cytosol with RNase A increases the sedimentation coefficient of the receptor from 9.7 S to 10.4 S. The effect is not obtained with other low molecular weight basic proteins (lysozyme, cytochrome c, or histone H2B). Nonenzymically active RNase A derivatives such as performic acid oxidized RNase A, fully reductively methylated RNase A, carboxymethyl-His-119-RNase A, and RNase S-protein were ineffective. RNase T1, an acidic endoribonuclease, was also without effect. However, enzymically active RNase S', prepared from a mixture of RNase S-protein and S-peptide, shifted the sedimentation to 10.4 S. The increased sedimentation is not accompanied by a change in the Stokes radius of the receptor (74 A) or buoyant density in metrizamide (1.24 g/ml). The effect of RNase A on the sedimentation of the receptor can be reversed by subsequent incubation with human placental RNase inhibitor or with rabbit anti-RNase A antibodies. Direct interaction was shown by chromatography of the receptor on RNase A Sepharose. Thus, the shift in sedimentation results from binding of RNase A to the receptor and, although this requires that the enzyme active site be available, enzymic activity is not responsible for the effect. The interaction of RNase A with the receptor occurs at low ionic strength; it does not occur at elevated ionic strength or after activation of the receptor by precipitation with ammonium sulfate.
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PMID:Interaction of ribonuclease A with estrogen receptor from rat mammary tumor MTW9. 683 88

alpha-Helical secondary structure occurs widely in globular proteins and its formation is a key step in their folding. As a consequence, understanding the energetics of helix formation is crucial to understanding protein folding and stability. We have measured the helix propensities of the nonpolar amino acids for an alpha-helix in an intact protein, ribonuclease T1, and for a 17-residue peptide with a sequence identical to that of the alpha-helix in the protein. The helix propensities are in excellent agreement. This shows that when compared in the same sequence context, the helix propensities of the nonpolar amino acids are identical in helical peptides and intact proteins, and that conclusions based on studies of the helix-to-coil transitions of peptides may, in favorable cases, be directly applicable to proteins. Our helix propensities based on ribonuclease T1 are in good agreement with those from similar studies of barnase and T4 lysozyme. In contrast, our helix propensities differ substantially from those derived from studies of alanine-stabilized or salt bridge-stabilized model alpha-helical peptides.
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PMID:A direct comparison of helix propensity in proteins and peptides. 909 98

The heat capacities (DeltaC(p,f)) for the temperature-induced folding of proteins: barnase, lysozyme T4, papain, trypsin, ribonuclease T1, chymotrypsin, lysozyme and ribonuclease A have been calculated from the change in solvent accessible surface area between the native state and extended polypeptide chain. To visualize the effect of disulfide cross-links on molar heat capacity, loops of varying number of alanine residues and extended alanine chains with terminal cystein are modeled. The difference in DeltaC(p) values between the extended state and the loop conformation of proteins is linearly related to the number of residues in the loop. Corrections to the heat capacity of folding (DeltaC(p,f)) are applied for proteins with cross-links based on this observation. There is good correlation between corrected values of DeltaC(p,f) and experimental values.
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PMID:Heat capacity of folding of proteins corrected for disulfide cross-links. 1205 96

In the present paper a procedure to calculate the properties of proteins in aqueous mixed solvents, particularly the excesses of the constituents of the mixed solvent near the protein molecule and the preferential binding parameters, is suggested. Expressions for the Kirkwood-Buff integrals in ternary mixtures and for the preferential binding parameter were derived and used to calculate various properties of infinitely dilute proteins in aqueous mixed solvents. The derived expressions and experimental information regarding the partial molar volumes and the preferential binding parameters were used to calculate the excesses (deficits) of water and cosolvent (in comparison with the bulk concentrations of protein-free mixed solvent) in the vicinity of ribonuclease A, ribonuclease T1, and lysozyme molecules. The calculations showed that water was in excess in the vicinity of ribonuclease A for water/glycerol and water/trehalose mixtures, and the cosolvent urea was in excess in the vicinity of ribonuclease T1 and lysozyme. The derivative of the activity coefficient of the protein with respect to the mole fraction of water was also calculated. This derivative was negative for the water/glycerol and water/trehalose mixed solvents and positive for the water/urea mixture. The mixture of lysozyme in the water/urea solvent is of particular interest, because the lysozyme at pH 7.0 is in its native state up to 9.3M urea, while at pH 2.0 it is denaturated between 2.5 and 5M and higher concentrations of urea. Our results demonstrated a striking similarity in the hydration of lysozyme at both pHs. It is worthwhile to note that the excesses of urea were only weakly composition dependent on both cases.
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PMID:A protein molecule in an aqueous mixed solvent: fluctuation theory outlook. 1610 95

It is now feasible to carry out molecular dynamics simulations of proteins in water that are long compared to the overall tumbling of the molecule. Here, we examine rotational diffusion in four small, globular proteins (ubiquitin, binase, lysozyme, and fragment B3 of protein G) with the TIP3P, TIP4P/EW, and SPC/E water models, in simulations that are 6 to 60 times as long as the mean rotational tumbling time. We describe a method for extracting diffusion tensors from such simulations and compare the results to experimental values extracted from NMR relaxation measurements. The simulation results accurately follow a diffusion equation, even for spherical harmonic correlation functions with l as large as 8. However, the best-fit tensors are significantly different from experiment, especially for the commonly used TIP3P water model. Simulations that are 20 to 100 times longer than the rotational tumbling times are needed for good statistics. A number of residues exhibit internal motions on the nanosecond time scale, but in all cases examined here, a product of internal and overall time-correlation functions matches the total time-correlation function well.
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PMID:Evaluating rotational diffusion from protein MD simulations. 1805 65

In recent years, a growing number of protein folding studies have focused on the unfolded state, which is now recognized as playing a major role in the folding process. Some of these studies show that interactions occurring in the unfolded state can significantly affect the stability and kinetics of the protein folding reaction. In this study, we modeled the effect of electrostatic interactions, both native and nonnative, on the folding of three protein systems that underwent selective charge neutralization or reversal or complete charge suppression. In the case of the N-terminal L9 protein domain, our results directly attribute the increase in thermodynamic stability to destabilization of the unfolded ensemble, reaffirming the experimental observations. These results provide a deeper structural insight into the ensemble of the unfolded state and predict a new mutation site for increased protein stability. In the second case, charge reversal mutations of RNase Sa affected protein stability, with the destabilizing mutations being less destabilizing at higher salt concentrations, indicating the formation of charge-charge interactions in the unfolded state. In the N-terminal L9 and RNase Sa systems, changes in electrostatic interactions in the unfolded state that cause an increase in free energy had an overall compaction effect that suggests a decrease in entropy. In the third case, in which we compared the beta-lactalbumin and hen egg-white lysozyme protein homologues, we successfully eliminated differences between the folding kinetics of the two systems by suppressing electrostatic interactions, supporting previously reported findings. Our coarse-grained molecular dynamics study not only reproduces experimentally reported findings but also provides a detailed molecular understanding of the elusive unfolded-state ensemble and how charge-charge interactions can modulate the biophysical characteristics of folding.
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PMID:Nonnative electrostatic interactions can modulate protein folding: molecular dynamics with a grain of salt. 1968 7

Estimation of the thermodynamic properties of proteins in mixed solvents is crucial for understanding the effect of cosolvents on rates and equilibrium constants of reactions involving proteins. In this paper, a predictive, molecular level approach for the study of preferential interactions of proteins with either water or cosolvents based on all-atom, statistical mechanical models is used to calculate the preferential interaction coefficient of proteins. Model systems comprised of the cosolvents urea, glycerol, arginine hydrochloride, guanidinium hydrochloride, and glucose with the proteins RNase T1, Hen egg white lysozyme, and alpha-chymotrypsinogen A(alpha-Cgn A) are studied. Trajectories in the range 10-20 ns are analyzed in order to validate this method. From the computational perspective, several key aspects of these simulations are investigated in detail. Protein dynamics and cosolvent dynamics play an important role in the estimation of preferential interaction coefficients, and in determining the length of simulation required to get a reliable estimate of the coefficient. Further, simulation results are found to be sensitive to changes in the cosolvent force field parameters. A comparison of simulated and experimental data is performed for two different force field parameters for glycerol and urea in order to assess the sensitivity of the preferential interaction coefficient to changes in force field parameters. This work highlights the effect of length of simulation, cosolvent force field parameters, and protein structure fluctuations on estimation of the preferential interaction coefficient of proteins in mixed solvents.
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PMID:Molecular computations of preferential interaction coefficients of proteins. 1969 45