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)

To determine the effects of different amino acids on the structure and stability of an alpha-helix in the context of a globular protein, all 19 naturally-occurring amino acids were substituted for Ser44 in phage T4 lysozyme. A more restricted set of nine replacements was also made for Val131. Ser44 and Val131 are two of a very limited number of possible sites in T4 lysozyme that are well within alpha-helices, are solvent-exposed and relatively free of interactions with neighboring residues, and are not involved in crystal contacts. High resolution structures for the majority of the mutants, some of which crystallized non-isomorphously with wild-type, were determined. With the exception of proline, the amino acid substitutions caused little if any perturbation of the alpha-helix backbone. Also the beta-branched residues Thr, Val and Ile show no indication of either side-chain or backbone distortion. Therefore, other than proline, there is no evidence that differences in helix propensities are associated with different amounts of strain introduced into the helix. For reference, and also to allow estimates of side-chain entropy, a survey was made of side-chain conformations in 100 well-refined protein structures. As noted previously all side-chains within alpha-helices strongly avoid the g- conformation (chi 1 approximately 60 degrees). This restricts the beta-branched residues Thr, Val and Ile to a single conformer (g+, chi 1 approximately -60 degrees). Asp, Asn, Met and Ser within helices also overwhelmingly prefer the g+ conformation. For Arg, Cys, Gln, Glu, Leu and Lys the t (chi 1 approximately 180 degrees) and g+ conformers are populated roughly equally. Only the aromatic residues, His, Tyr, Trp and Phe prefer the t conformation. These preferences are the same whether the side-chain is buried or solvent-exposed. In general, the side-chain conformations adopted by the residues substituted at positions 44 and 131 correspond to the most commonly observed conformation for the same amino acid in helices in known protein structures. The changes in protein stability for the replacements at site 131 in general agree well with those at site 44 (correlation r = 0.97), suggesting that these may be representative of substitutions at fully solvent-exposed sites in the middle of alpha-helices. The free energy values also agree quite well with those observed for equivalent replacements in a number of soluble alpha-helical model peptides and with data from "host-guest" studies and statistical surveys (r = 0.69 to 0.93).(ABSTRACT TRUNCATED AT 400 WORDS)
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PMID:Determination of alpha-helix propensity within the context of a folded protein. Sites 44 and 131 in bacteriophage T4 lysozyme. 828 84

Using the catalytic mechanism of lysozyme as a paradigm for the mechanism of other enzymes that catalyze the hydrolysis of beta-1,4-glycosidic linkages, including chitinase, we have examined the effect of chemical modification with 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) on the reaction catalyzed by Zea mays chitinase. Inactivation with EDC did not result in derivatization of essential carboxylic acid residues, but resulted in the selective modification of a single essential tyrosine residue (Verburg, J. G., Smith, C. E., Lisek, C. A., and Huynh, Q. K., 1991, J. Biol. Chem. 267, 3886-3893). Here, we examine the role of the homologous tyrosine residue in the catalytic mechanism of the Arabidopsis thaliana chitinase. Tyrosine-174 of the Arabidopsis chitinase was replaced, with phenylalanine, alanine, histidine, and methionine by site-directed mutagenesis, and the variant chitinases were expressed in insect cells using baculovirus transfer vectors. A comparison of the reaction catalyzed by each of the variant enzymes indicates that substitution of another amino acid for Tyr-174 alters, but does not eliminate, enzymatic activity. Estimates of the specific activities of the variant chitinases reveal that substitution of His for Tyr-174 has a minimal effect on catalysis, the specific activities of the Phe and Met variants are approximately equivalent to each other, but are 60% the specific activity of wild-type Arabidopsis chitinase, and the specific activity of the Ala variant is only 40% that of wild-type. The observation that the Arabidopsis chitinase is tolerant to mutagenesis at this position suggests that Tyr-174 does not participate directly in catalysis.
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PMID:Examination of the role of tyrosine-174 in the catalytic mechanism of the Arabidopsis thaliana chitinase: comparison of variant chitinases generated by site-directed mutagenesis and expressed in insect cells using baculovirus vectors. 842 56

Two bulky amino acids within the core of phage T4 lysozyme have each been replaced in turn with a series of hydrophobic amino acids. In one set of experiments, Leu99 was replaced with Phe, Met, Ile, Val and Ala. In the second series, Phe153 was replaced with Leu, Met, Ile, Val and Ala. The double mutant in which both Leu99 and Phe153 were replaced with alanine was also constructed. The change in stability of the protein associated with each substitution and the crystal structure of each variant have been determined. In the case of replacements at position 99 the protein behaves in a relatively rigid manner, and changes very little in response to substitutions. In contrast, the protein is more flexible and adjusts much more in response to substitutions of Phe153. In both cases there is a roughly linear dependence between the stability of the mutant protein relative to wild-type (delta delta G) and the difference in the hydrophobic strength of the amino acids involved in the substitution based on solvent transfer measurements (delta delta Gtr). The change in delta delta G is, however, much greater than delta delta Gtr. For the Phe153 replacements the discrepancy is about 1.9-fold, while for the Leu99 series it is about 2.6-fold. Mutants such as Leu99-->Ala, for which the protein remains essentially rigid, tend to create larger cavities and so incur a larger energy of destabilization. Mutants such as Phe153-->Ala, for which the protein structure tends to relax, result in smaller cavities and so are less destabilized. Mutants L99I and L99V are less stable than expected from considerations of transfer free energy and cavity formation due to introduced strain caused by the replacement of Leu99 with a residue of different shape. Mutant F153L is more stable than the reference wild-type, even though the transfer free energy of Leu is less than that of Phe. The increase in stability is apparently due to torsional strain in the side-chain of Phe153 that is present in wild-type lysozyme, but is relieved in the mutant structure.
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PMID:Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences. 843 69

A plasmid-borne gene encoding bacteriophage T4 lysozyme with a structural mutation, Tyr161-Ala, was mutagenized by by the use of polymerase chain reaction. The mutagenized gene was inserted into a specialized bacteriophage lambda cloning vector that must acquire a functional lysozyme gene in order to form plaques. Functional variants of the mutant lysozyme were selected. Three compensatory second-site revertants were obtained: Thr152-Met, Lys43-Ile, and Thr151-Ala. The effects of these mutations are interpreted in light of previous structural and genetic studies of T4 lysozyme.
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PMID:Second-site reversion of a structural defect in bacteriophage T4 lysozyme. 856 37

Previous analysis of randomly generated multiple mutations within the core of bacteriophage T4 lysozyme suggested that the "large-to-small" substitution Leu121 to Ala (L121A) and the spatially adjacent "small-to-large" substitution Ala129 to Met (A129M) might be mutually compensating. To test this hypothesis, the individual variants L121A and A129M were generated, as well as the double "size-switch" mutant L121A/A129M. To make the interchange symmetrical, the combination of L121A with A129L to give L121A/A129L was also constructed. The single mutations were all destabilizing. Somewhat surprisingly, the small-to-large substitutions, which increase hydrophobic stabilization but can also introduce strain, were less deleterious than the large-to-small replacements. Both Ala129 --> Leu and Ala129 --> Met offset the destabilization of L121A by about 50%. Also, in contrast to typical Leu --> Ala core substitutions, which destabilize by 2 to 5 kcal/mol, Leu121 --> Ala slightly stabilized A129L and A129M. Crystal structure analysis showed that a combination of side-chain and backbone adjustments partially accommodated changes in side-chain volume, but only to a limited degree. For example, the cavity that was created by the Leu121 to Ala replacement actually became larger in L121A/A129L. The results demonstrate that the destabilization associated with a change in volume of one core residue can be specifically compensated by an offsetting volume change in an adjacent residue. It appears, however, that complete compensation is unlikely because it is difficult to reconstitute an equivalent set of interactions. The relatively slow evolution of core relative to surface residues appears, therefore, to be due to two factors. First, a mutation in a single core residue that results in a substantial change in size will normally lead to a significant loss in stability. Such mutations will presumably be selected against. Second, if a change in bulk does occur in a buried residue, it cannot normally be fully compensated by a mutation of an adjacent residue. Thus, the most probable response will tend to be reversion to the parent protein.
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PMID:Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme. 867 87

Eighteen synthetic xanthone derivatives were tested for their inhibitory effects on the activation of mast cells and neutrophils. 1,3- and 3,5-Dihydroxyxanthone showed strong inhibitory effects on the release of beta-glucuronidase and histamine from rat peritoneal mast cells stimulated with compound 48/80. 1,6-Dihydroxyxanthone and 1,3,8-trihydroxyxanthone showed strong inhibitory effects on the release of beta-glucuronidase, and beta-glucuronidase and lysozyme, respectively, from rat neutrophils stimulated with formyl-Met-Leu-Phe (fMLP). 1,3- and 1,6-Dihydroxyxanthone, 1,3,7-trihydroxyxanthone, and 1,3,5,6-, 2,3,6,7-, and 3,4,5,6-tetrahydroxyxanthone showed potent inhibitory effects on superoxide formation of rat neutrophils stimulated with fMLP. 1,6- and 3,5-Dihydroxyxanthone showed remarkable inhibitory effects on hind-paw oedema induced by polymyxin B in normal as well as in adrenalectomized mice. These data indicated that the anti-inflammatory effect of these compounds is mediated through the suppression of chemical mediators released from mast cell and neutrophil degranulation.
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PMID:Synthesis and anti-inflammatory effects of xanthone derivatives. 879 82

The synthesis and biological activity on human neutrophils of for-Met-(gamma-lactam)-Leu-Phe-OMe [fM(gamma l)LP-OMe], an analogue of the chemotactic fMLP-OMe, are reported. The tetrapeptide evidences chemotactic activity as well as superoxide anion production and lysozyme release, although with lower efficacy when compared with the parent tripeptide.
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PMID:Synthesis and biological activity of a conformationally constrained chemotactic gamma-lactam formyl tetrapeptide. 893 89

Neutrophils contain various antibacterial polypeptides and proteins in the granules. Defensins have been known as the major antimicrobial granular components. Recently, we have purified a novel cationic antibacterial polypeptide of 11 kDa (CAP11) from guinea pig neutrophil granules. In this study, we have examined the extracellular release and biological activity of CAP11, and compared with defensins. CAP11 was extracellularly released from neutrophils by N-formyl Met-Leu-Phe, phorbol 12-myristate 13-acetate, accompanied by the release of lysozyme, a specific and azurophil granule component, without release of beta-glucuronidase, an azurophil granule component, whereas defensins were released by phagocytosis, accompanied by the release of beta-glucuronidase, suggesting that the localization of CAP11 and defensins is different among neutrophil granules. Defensins increased neutrophil adhesion, and inhibited phagocytosis of opsonized zymosan particles and phagocytosis-associated superoxide anion generation. In contrast, CAP11 did not affect these neutrophil functions. Both CAP11 and defensins possessed the histamine-releasing activities for mast cells, but CAP11 was 10-fold less potent than defensins. CAP11 and defensins showed the antibacterial activities against both Escherichia coli and Staphylococcus aureus. However, the antibacterial activity of defensins was completely lost in the presence of physiological concentration of NaCl (0.15 M), although CAP11 retained the antibacterial activity even in the presence of NaCl. Furthermore, CAP11 exhibited the 10-fold more potent antiretroviral activity than defensins against Moloney murine leukemia viruses. Together these observations indicate that when released from neutrophils, CAP11 likely functions as an antimicrobial molecule in the extracellular milieu, whereas defensins may participate in the modulation of neutrophil function and mast cell histamine release.
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PMID:Comparative studies on the extracellular release and biological activity of guinea pig neutrophil cationic antibacterial polypeptide of 11 kDa (CAP11) and defensins. 908 Jun 67

Much interest is currently focused on understanding the detailed contribution that particular amino acid residues make in protein structure and function. Although the use of site-directed mutagenesis has greatly contributed to this goal, the approach is limited to the standard repertoire of twenty amino acids. Fluorinated amino acids have been utilized successfully to probe protein structure and dynamics as well as point to the importance of specific residues to biological function. In our continuing investigations on the importance of the amino acid methionine in biological systems, the successful incorporation of L-S-(trifluoromethyl)homocysteine (L-trifluoromethionine; L-TFM) into bacteriophage lambda lysozyme (LaL), an enzyme containing three methionine residues, is reported. The L isomer of TFM was synthesized in an overall yield of 33% from N-acetyl-D,L-homocysteine thiolactone and trifluoromethyl iodide. An expression plasmid giving strong overproduction of LaL was prepared and transformed into an Escherichia coli strain auxotrophic for methionine permitting the expression of LaL in the presence of L-TFM. The analogue would not support growth of the auxotroph and was found to be inhibitory to cell growth. However, cells that were initially grown in a Met-rich media followed by protein induction under careful control of the respective concentrations of L-Met and L-TFM in the media, were able to overexpress TFM-labeled LaL (TFM-LaL) at both high (70%) and low (31%) levels of TFM incorporation. TFM-LaL at both levels of incorporation exhibited analogous activity to the wild type enzyme and were inhibited by chitooligosaccharides indicating that incorporation of the analogue did not hinder enzyme function. Interestingly, the 19F solution NMR spectra of the TFM-labeled enzymes consisted of four sharp resonances spanning a chemical shift range of 0.9 ppm, with three of the resonances showing very modest shielding changes on binding of chitopentaose. The 19F NMR analysis of TFM-LaL at both high and low levels of incorporation suggested that one of the methionine positions gives rise to two separate resonances. The intensities of these two resonances were influenced by the extent of incorporation which was interpreted as an indication that subtle conformational changes in protein structure are induced by incorporated TFM. The similarities and differences between Met and TFM were analyzed using ab initio molecular orbital calculations. The methodology presented offers promise as a new approach to the study of protein-ligand interactions as well as for future investigations into the functional importance of methionine in proteins.
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PMID:Incorporation of trifluoromethionine into a phage lysozyme: implications and a new marker for use in protein 19F NMR. 911 20

The new C alpha-tetrasubstituted alpha-amino acid residue 2-[2'-(methylthio)ethyl]methionine (Dmt) has been introduced into the reference chemotactic tripeptide HCO-Met-Leu-Phe-OMe (fMLP-OMe) in place of the leucine or methionine, respectively. The biological activity of the new analogues [Dmt2]fMLP-OMe (2) and [Dmt1]fMLP-OMe (3) has been determined; whereas 2 is active toward human neutrophils, stimulating directed migration, superoxide anion generation, and lysozyme release, 3 results practically inactive in all tested assays. A conformational analysis on 2 and 3 has been performed in solution by using ir absorption and 1H-nmr. The conformation of 2 was also examined in the crystal by x-ray diffraction methods. Both 2 and 3 adopt fully extended conformation in correspondence with the Dmt residue. Biological and conformational results are discussed and compared with related previously studied models.
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PMID:Synthesis, conformation, and biological activity of two fMLP-OMe analogues containing the new 2-[2'-(methylthio)ethyl]methionine residue. 928 91


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