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)

Although there has been much speculation on the pathways of protein folding, only recently have experimental data on the topic been available. The study of proteins under conditions where species intermediate between the fully folded and unfolded states are stable has provided important information, for example about the disulphide intermediates in BPTI, cis/trans proline isomers of RNase A3 and the molten globule state of alpha-lactalbumin. An alternative approach to investigating folding pathways has involved detection and characterization of transient conformers in refolding studies using stopped-flow methods coupled with NMR measurements of hydrogen exchange. The formation of intermediate structures has been detected in the early stages of folding of cytochrome c, RNaseA and barnase. For alpha-lactalbumin, hydrogen exchange kinetics monitored by NMR proved to be crucial for identifying native-like structural features in the stable molten globule state. An analogous partially folded protein stable under equilibrium conditions has not been observed for the structurally homologous protein hen egg-white lysozyme, although there is evidence that a similar but transient state is formed during refolding. Here we describe NMR experiments based on competition between hydrogen exchange and the refolding process which not only support the existence of such a transient species for lysozyme, but enable its structural characteristics to be defined. The results indicate that the two structural domains of lysozyme are distinct folding domains, in that they differ significantly in the extent to which compact, probably native-like, structure is present in the early stages of folding.
...
PMID:Demonstration by NMR of folding domains in lysozyme. 200 Jan 38

Amide hydrogen/deuterium exchange behaviour has been studied for all of the peptide amides of hen lysozyme by means of two-dimensional n.m.r. spectroscopy. The amides have been grouped into four categories on the basis of their rates of exchange in solution at pH 4.2 and 7.5. The distribution of the amides into the different categories has been examined in the light of the crystallographic structural information, considering the type of secondary structure, the nature of hydrogen bonding and the distance from the protein surface. None of these features was found to determine uniquely the pattern of hydrogen exchange rates within the protein. The exchange behaviour of the individual amides could, however, in general be rationalized by a combination of these features. Hydrogen exchange was also monitored in both tetragonal and triclinic crystals of lysozyme, by allowing exchange to take place in the crystals prior to dissolution and recording of n.m.r. spectra under conditions where further exchange was minimized. This enabled direct comparison to be made of the exchange behaviour in the crystals and solution. A reduction in exchange rate was observed in the crystalline state relative to solution for a substantial number of amides and distinct differences between exchange in the different crystals could be observed. These differences between the solution and the different crystal states do not, however, correlate in a simple manner with proximity to intermolecular contacts in the crystals. However, the existence of these contacts, which are on the surface of the protein molecule, have a profound effect on the exchange of amides in the interior of the protein. The results indicate that the spectrum of fluctuations giving rise to hydrogen exchange may be significantly altered by the intermolecular interactions present within the crystalline state.
...
PMID:A nuclear magnetic resonance study of the hydrogen-exchange behaviour of lysozyme in crystals and solution. 201 Sep 18

The crystal structures of HCO-Met-Leu-Phe-OC(CH3)3, (CH25H39N3O5S), fMLP-OtBu, and HCO-Met psi [CSNH]-Leu-Phe-OCH3, (C22H33N3O4S2), fMS LP-OMe, have been determined by single crystal X-ray diffraction, and their conformational properties investigated by molecular mechanics energy calculations. Crystals of fMLP-OtBu are monoclinic, space group P2(1), a = 12.027(4), b = 9.492(3), c = 12.660(4) A, beta = 101.99(3) degrees, Z = 2; those of fMS LP-OMe are orthorhombic, space group P2(1)2(1)2(1), a = 7.130(1), b = 12.097(2), c = 31.060(5) A, Z = 4. The first compounds fMLP-OtBu is the t-butyl ester of the tripeptide fMLP that represents one of the most potent compounds in inducing the lysozyme release from human neutrophils that reflects the chemotactic activity. From the crystal structure, it is shown that the orientation of the phenylalanine side chain is largely affected by the presence of the bulky group. fMSLP-OMe was shown to be inactive after thionation of the methionine residue in the original tripeptide. Nevertheless, the crystal structure does not reveal any influence of the presence of the thionated peptidic bond on the backbone conformation. The X-ray results have been used to generate parameters for empirical energy calculations. Subsequently, a strategy based on random generation of conformations followed by energy-minimization was applied to investigate the conformational space of thiopeptides, in comparison with normal peptides. From molecular free energy calculations, it is shown that the main influence of the introduction of a thioamide bond on the molecular structure is to prevent the existence of C7(eq) conformations involving the thiomethionine residue. Consequently, a larger number of conformers are found to form intramolecular hydrogen bonds involving the formyl group, reducing its availability to interact with the receptor. For the first time, the theoretical prediction of the existence of C7eq conformations for fMLP is made. The resulting conformers are compared to previously active structures of these chemotactic agents.
...
PMID:Crystal and molecular structure of two geometrically restricted chemotactic tripeptides, analogues of formyl-methionine-leucine-phenylalanine. 209 Jun 40

Escherichia coli DNA photolyase contains a stable flavin radical that is readily photoreduced in the presence of added electron donors. Picosecond, nanosecond, and conventional flash photolysis technique have been employed to investigate the events leading to photoreduction from 40 ps to tens of milliseconds following flash excitation. Direct light absorption by the flavin radical produces the first excited doublet state which undergoes rapid (within 100 ps) intersystem crossing to yield the lowest excited quartet (n pi*) state. In contrast, light absorption by the folate chromophore produces a new intermediate state via interaction of the folate excited singlet state with the ground-state flavin radical, leading to an enhanced yield of the excited radical doublet state and hence quartet state. Subsequent reaction of the excited quartet state involves hydrogen atom abstraction from a tryptophan residue. Secondary electron transfer from added electron donors occurs to the oxidized tryptophan radical with rate constants ranging from 10(4) (dithiothreitol) to 4 x 10(6) M-1 s-1 (n-propyl gallate). The low value of the latter rate compared to reduction of the tryptophan radical in lysozyme suggests that the reactive tryptophan is highly buried in photolyase. A redox potential diagram has been constructed for the ground and excited states involved. It is concluded that the one-electron reduction potential of the excited quartet state of the flavin radical must be at least 1.23 V more positive than the ground state, in agreement with the value of delta E greater than 1.77 V calculated from spectroscopic data.
...
PMID:Excited-state properties of Escherichia coli DNA photolyase in the picosecond to millisecond time scale. 220 May 10

Complete main-chain (NH and alpha CH) 1H NMR assignments are reported for the 130 residues of human lysozyme, along with extensive assignments for side-chain protons. Analysis of 2-D NOESY experiments shows that the regions of secondary structure for human lysozyme in solution are essentially identical with those found previously in a similar study of hen lysozyme and are in close accord with the structure of the protein reported previously from X-ray diffraction studies in the crystalline state. Comparison of the chemical shifts, spin-spin coupling constants, and hydrogen exchange behavior are also consistent with closely similar structures for the two proteins in solution. In a number of cases specific differences in the NMR parameters between hen and human lysozymes can be correlated with specific differences observed in the crystal structures.
...
PMID:1H NMR studies of human lysozyme: spectral assignment and comparison with hen lysozyme. 220 98

The effect of a variety of proteins and amino acids was investigated on oxygen free radical activity as assessed by copper/hydrogen peroxide induced benzoate hydroxylation as well as copper-catalysed ascorbate autoxidation. Serum albumins from a variety of species (human, bovine and dog) had both inhibitory and stimulatory effects depending on the molar copper to protein ratio; low ratios were inhibitory and high stimulatory. Some other proteins tested (lysozyme, soybean trypsin inhibitor and conalbumin) also had dual (inhibitory and stimulatory) effects, as did both histidine and polyhistidine, but all effects occurred at different molar ratios presumably dependent on the relative affinities for the copper ions. In contrast, metallothionein and caeruloplasmin, proteins specialised to bind copper in vivo had no stimulatory effects. In this paper we show that in addition to their fairly well documented inhibitory effects, under certain conditions some proteins also stimulate radical reactions. The possible role of this phenomenon in vivo is discussed.
...
PMID:Stimulatory and inhibitory actions of proteins and amino acids on copper-catalysed free radical generation in the bulk phase. 228 96

Association of platelets and neutrophils is frequently observed within thrombi or inflammatory sites. Interactions between these two cell populations have been reported for the production of several mediators of inflammation such as hydrogen peroxides or leukotrienes. Another potential mediator of thrombosis and inflammation is paf-acether, which is synthesized by activated platelets and neutrophils. Since platelets form and release large amounts of the paf-acether precursor lyso paf-acether, platelet and neutrophil cooperation for paf-acether biosynthesis was investigated. Purified human neutrophils (4 x 10(6)/ml) stimulated by opsonized zymosan (ZC, 1 mg/ml) formed 4.5 +/- 2.5 ng/ml paf-acether. Human washed platelets (3 x 10(8)/ml) stimulated with thrombin (1 IU/ml) formed 0.60 +/- 0.43 ng/ml paf-acether. Platelets and neutrophils, incubated together and both stimulated by their specific agonist, formed more than twice as much paf-acether as did platelets and neutrophils separately (10.90 +/- 4.25 ng/ml, n = 6, P less than .001). The formation of lyso paf-acether and the release of lysozyme and LDH were unchanged under the cooperation conditions. The formation of paf-acether almost doubled (10.24 +/- 3.81 ng/ml paf-acether vs. 5.30 +/- 2.23, P less than .05, n = 4) when ZC-stimulated neutrophils were incubated with supernatants from thrombin-stimulated platelets as well as with synthetic lyso paf-acether. Extracted and purified lyso paf-acether from thrombin-stimulated platelets led to an increase of biosynthesis of paf-acether by neutrophils (13.86 +/- 2.26 ng/ml paf-acether vs. 5.76 +/- 0.38, P less than .05, n = 3). These results indicate that a cooperation between platelets and neutrophils exists for paf-acether formation. The phenomenon depends on a platelet-derived soluble factor, possibly lyso paf-acether. This cell-to-cell interaction is of interest since paf-acether is formed by and acting on platelets and neutrophils and represents a molecular basis for potent amplification of inflammatory reactions.
...
PMID:Cooperation between platelets and neutrophils for paf-acether (platelet-activating factor) formation. 230 6

The conformation in solution in methyl sulfoxide of the immunoadjuvant peptidoglycan monomer (PGM), obtained by digestion with lysozyme of the linear peptidoglycan polymer isolated from Brevibacterium divaricatum, was studied by 1H-n.m.r. spectroscopy. The temperature dependence of the chemical shift of the resonances of the amide protons suggested that the amino group of alanine-5 is involved in hydrogen bonding, most probably to the alpha-carbonyl of the isoglutamine which showed restricted rotation, as indicated by the large chemical shift non-equivalence for the resonances of the beta CH2 group. A cyclic structure is proposed for the C-terminal pentapeptide of PGM, which is further supported by various n.O.e. interactions involving the meso-diaminopimelic residue and the N-acetylmuramoyl group.
...
PMID:1H-N.M.R. studies of a natural immunoadjuvant peptidoglycan monomer: proposed structure in solution in methyl sulfoxide. 234 38

We have reviewed here the three-dimensional structure of an antigen-Fab complex as determined by X-ray crystallographic studies. The antigen is hen egg-white lysozyme (HEL), a protein whose three-dimensional structure and antigenic properties are well known. The Fab was prepared from a murine monoclonal anti-HEL antibody, IgGl,kappa, obtained by cell-hybridization techniques. The equilibrium association constant for the complex is 4.5 X 10(7) mol-1. The complex was crystallized and its three-dimensional structure was determined at 6-A and 2.8-A resolution. A three-dimensional model of the structure was built based on electron-density maps and the amino-acid sequence [determined from the nucleotide sequence of cDNA clones (M. Verhoeyen, C. Berek, J.M. Jarvis, G. Winter, in preparation)]. The three-dimensional structure of the complex shows that 17 antibody residues make close contacts (less than or equal to 4 A) with 16 antigen residues. Fifteen of the contacting antibody residues belong to the six complementarity-determining regions of the light chain (6 residues) and of the heavy chain (9 residues). The remaining two are located in regions of constant or nearly constant sequence ["framework" regions]. The 16 contacting lysozyme residues form a discontinuous, topographical determinant, since they are widely separated in the linear amino-acid sequence but are brought to relative spatial proximity by the three-dimensional folding of the polypeptide chain. The contacting surfaces are relatively flat, with protruding side chains of antigen and antibody penetrating each other over an area with maximum dimensions of 30 X 20 A. As in several other systems of protein-protein interactions, the contacts are chemically characterized as van der Waals interactions and hydrogen bonds. Detailed analysis of the interactions reveals that the antibody's recognition of the antigen is finely specific and is affected by antigenic variation (as observed in lysozymes from other avian species). The quaternary structure of the complexed Fab is elongated, with the axes of the variable (VH + VL) and constant (CH1 + CL) domains making an angle close to 180 degrees. Comparison of the three-dimensional structure of the complexed lysozyme with that of native lysozyme showed no significant conformational change at the current resolution (2.8 A). Comparison of the Fab moiety of the complex with other Fabs of known three-dimensional structure suggested that upon complexing no conformational change takes place in the tertiary structure of Fab either.(ABSTRACT TRUNCATED AT 400 WORDS)
...
PMID:The structural basis of antigen-antibody recognition. 243 94

Solvent exchange of 18O-labeled buried water in bovine pancreatic trypsin inhibitor (BPTI), trypsin, and trypsin-BPTI complex is measured by high-precision isotope ratio mass spectrometry. Buried water is labeled by equilibration of the protein in 18O-enriched water. Protein samples are then rapidly dialyzed against water of normal isotope composition by gel filtration and stored. The exchangeable 18O label eluting with the protein in 10-300 s is determined by an H2O-CO2 equilibration technique. Exchange of buried waters with solvent water is complete before 10-15 s in BPTI, trypsin, and BPTI-trypsin, as well as in lysozyme and carboxypeptidase measured as controls. When in-exchange dialysis and storage are carried out at pH greater than or equal to 2.5, trypsin-BPTI and trypsin, but not free BPTI, have the equivalent of one 18O atom that exchanges slowly (after 300 s and before several days). This oxygen is probably covalently bound to a specific site in trypsin. When in-exchange dialysis and storage are carried out at pH 1.1, the equivalent of three to seven 18O atoms per molecule is associated with the trypsin-BPTI complex, apparently due to nonspecific covalent 18O labeling of carboxyl groups at low pH. In addition to 18O exchange of buried waters, the hydrogen isotope exchange of buried NH groups H bonded to buried waters was also measured. Their base-catalyzed exchange rate constants are on the order of NH groups that in the crystal are exposed to solvent (static accessibility greater than 0) and hydrogen-bonded main chain O, and their pH min is similar to that for model compounds. The pH dependence of their exchange rate constants suggests that direct exchange with water may significantly contribute to their observed exchange rate.
...
PMID:Solvent exchange of buried water and hydrogen exchange of peptide NH groups hydrogen bonded to buried waters in bovine pancreatic trypsin inhibitor. 244 53


<< Previous 1 2 3 4 5 6 7 8 9 10 Next >>

---