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)

A method is presented for finding particular normal modes for large molecules such as proteins and nucleic acids. The method is based on an iterative approach that extracts eigenvectors of interest from the full second-derivative matrix. Application of the method to the interdomain (hinge-bending) motion of lysozyme yields a frequency of 3.6 cm-1. This is similar to the value obtained from earlier adiabatic-energy-minimization studies. Analysis of the mode shows that the relaxation associated with the hinge bending is highly delocalized; that is, the dihedral angle and energy changes are distributed over many residues, including some (e.g., Trp-28) that are distant from the cleft and hinge region.
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PMID:Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. 386 Aug 38

The purpose of this paper is to present a new approach to the study of mechanical properties of globular proteins and to summarize some of our results. The approach is based on the analysis of mechanical, viscoelastic properties of a protein monocrystal which is used as a probe of mechanical properties of a protein molecule. As a first rough approximation a protein molecule can be considered as a material resembling molecular crystals and glass-like polymers with the Young's modulus E = 2 - 10 GN . m-2. More detailed information concerning the anisotropy of elasticity and that of inhibitor effect strongly suggests that the lysozyme molecule is a construction having a special hinge-bending degree of freedom. The force constant estimated from our data for this degree of freedom is (0,4-1) . 10(13) erg . rad-2 . mol-1.
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PMID:[Mechanical properties of globular proteins]. 687 32

The structures of various mutants of T4 lysozyme have been determined in 25 non-isomorphous crystal forms. This provides an unusually diverse data base to compare the structures and dynamics of a closely related set of proteins in different crystal packing environments. In general, the more tightly packed crystals diffract better than those that are highly hydrated although the wild-type crystal form is an exception. The ability of the protein to form a relatively open but stable lattice may help explain why many of the mutants crystallize in this form. In different crystalline environments, the lysozyme molecules associate with 2-fold, 3-fold, 4-fold, and 5-fold symmetry, as well as with various types of screw associations. A "back-to-back" dimeric association, and a "head-to-tail" 2(1) screw association, are especially common, each occurring in more than half a dozen crystal forms. The 4-fold and 5-fold modes of association are closely related and provide an example of quasi-equivalent association as envisaged by Caspar and Klug. In different crystal environments the lysozyme molecules display a range of over 50 degrees in the hinge-bending angle between the amino and carboxy-terminal domains. Large variations in the hinge-bending angle are observed not only for lysozymes with mutations in the hinge region, but for molecules with mutations far from this site. This suggests that hinge-bending is an intrinsic property of the lysozyme molecule and is not an artifact due to mutation. As the hinge-bending angle increases about 15 degrees beyond that seen in wild-type there is a distinct conformations change in the side-chains of five residues in the hinge-bending region. Changes in the backbone are localized near residues 13, 59 and 80, but do not include significant changes in (phi, psi). Comparison of the different structures indicates that crystal contacts perturb the backbone structure of the protein by 0.2 to 0.5 A. These perturbations are of the same magnitude for helices and beta-sheet strands, suggesting that protein structures can be defined and maintained equally well by hydrogen-bonding (i.e. strand-strand) or by non-hydrogen-bonding (i.e. helix-helix) interactions. The discrepancies between the lysozyme structures in different crystallographic environments are in line with other comparisons of independently determined protein crystal structures. They suggest that protein structures in general are subject to low energy changes in conformation of 0.2 to 0.5 A.(ABSTRACT TRUNCATED AT 400 WORDS)
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PMID:Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. 761 72

Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises an important question: are the different conformers in the unit cell artifacts of crystal packing forces, or do they represent different solution state structures? The objective of this theoretical study is to determine whether domain motions and hinge-bending could be simulated in T4 lysozyme using molecular dynamics. An analysis of a 400 ps molecular dynamics simulation of the 164 amino acid enzyme T4 lysozyme is presented. Molecular dynamics calculations were computed using the Discover software package (Biosym Technologies). All hydrogen atoms were modeled explicitly with the inclusion of all 152 crystallographic waters at a temperature of 300 K. The native T4 lysozyme molecular dynamics simulation demonstrated hinge-bending in the protein. Relative domain motions between the N-terminal and C-terminal domains were evident. The enzyme hinge bending sites resulted from small changes in backbone atom conformations over several residues rather than rotation about a single bound. Two hinge foci were found in the simulation. One locus comprises residues 8-14 near the C-terminal of the A helix; the other site, residues 77-83 near the C-terminal of the C helix. Comparison of several snapshot structures from the dynamics trajectory clearly illustrates domain motions between the two lysozyme lobes. Time correlated atomic motions in the protein were analyzed using a dynamical cross-correlation map. We found a high degree of correlated atomic motions in each of the domains and, to a lesser extent, anticorrelated motions between the two domains. We also found that the hairpin loop in the N-terminal lobe (residues 19-24) acted as a mobile 'flap' and exhibited highly correlated dynamic motions across the cleft of the active site, especially with residue 142.
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PMID:Investigation of domain motions in bacteriophage T4 lysozyme. 770 80

In an attempt to facilitate crystallization, engineered cysteines were used to promote formation of a 'back-to-back' dimer that occurs in different crystal forms of wild-type and mutant T4 lysozymes. The designed double mutant, N68C/A93C, in which the surface residues Asn68 and Ala93 were replaced by cysteines, formed dimers in solution and crystallized isomorphously to wild-type, but at a much faster rate. Overall, the mutant structure remained very similar to wild-type despite the formation of two intermolecular disulfide bridges. The crystals of cross-linked dimers ahd thermal factors somewhat lower than wild-type, indicating reduced mobility, but did not diffract to noticeably higher resolution. Introduction of the same cross-links was also used to obtain crystals in a different space group of a T4 lysozyme mutant that could not be crystallized previously. The results suggest that the formation of the lysozyme dimer is a critical intermediate in the formation of more than one crystal form and that covalent cross-linking of the intermediate accelerates nucleation and facilitates crystal growth. The disulfide cross-links are located on the 'back' of the molecule and formation of the cross-linked dimer appears to leave the active sites completely unobstructed. Nevertheless, the cross-linked dimer is completely inactive. One explanation for this behavior is that the disulfide bridges prevent hinge-bending motion that may be required for catalysis. Another possibility is that the formation of the dimer increases the overall bulk of the enzyme and prevents its access to the susceptible glycosidic bonds within the cell wall substrate.
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PMID:Rapid crystallization of T4 lysozyme by intermolecular disulfide cross-linking. 817 78

A new aspect of the internal protein motion is pointed-- the electrostatic charges of the titratable groups fixed on the protein structure are combined with the hinge binding motion of lysozyme domain. Then the lysozyme molecule is examined as a system having charges that oscillate with the parameters of the mechanical motion. So, from such point of view, the lysozyme molecule becomes infrared and radiofrequency active. This model is applied for the case of a triclinic lysozyme crystal and the direction of the external electromagnetic flux in respect to the main crystal axes is found that corresponds to the best conditions for maximal absorption. For the purpose of the experimental measurement of the space dependence of the absorption, the direction of the incident wave and its polarization are calculated in respect to the main crystal planes in case of maximal efficiency of the absorption.
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PMID:Selective absorption of radio frequency energy due to collective motion of charged domains: case of lysozyme crystal. 857 83

The effect of Vibrio cholerae non-O1 protease on host defense proteins (lysozyme, secretory immunoglobulin A and lactoferrin) was studied in relation to its virulence mechanism. The proteins treated with the protease were analysed by SDS-PAGE. There was no influence of the protease on lysozyme. The protease cleaved lactoferrin into two fragments of 50 kDa and 34 kDa. N-terminal amino acid sequencing of these fragments revealed that the cleavage site was near the hinge region, between serine 420 and serine 421. This cleavage could affect the transition from open to closed configuration which is involved in iron binding and release. The anti-bacterial activity of lactoferrin was not affected by protease treatment. Secretory immunoglobulin A yielded a 42-kDa protein as the cleavage product. The susceptibility of secretory immunoglobulin A to V. cholerae non-O1 protease suggests a mechanism by which bacteria might evade the effect of this immunoglobulin.
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PMID:Effect of Vibrio cholerae non-O1 protease on lysozyme, lactoferrin and secretory immunoglobulin A. 859 71

A normal mode analysis of the closed form of dimeric citrate synthase has been performed. The largest-amplitude collective motion predicted by this method compares well with the crystallographically observed hinge-bending motion. Such a result supports those obtained previously in the case of hinge-bending motions of smaller systems, such as lysozyme or hexokinase. Taken together, all these results suggest that low-frequency normal modes may become useful for determining a first approximation of the conformational path between the closed and open forms of these proteins.
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PMID:Hinge-bending motion in citrate synthase arising from normal mode calculations. 874 51

Simulations of lysozyme by molecular dynamics have greatly increased our understanding of this enzyme. It has been shown how the internal motions are related to the structural elements (helices, sheets and loops) of the molecule. Comparisons of the motions in the free and substrate-bound form reveal that most are similar but that there are significant differences. Comparisons of the theoretical results with X-ray and nuclear magnetic resource data show good agreement. The hinge-bending motion, which opens and closes the binding site cleft between the two domains, is correlated with substrate binding. From analysis of simulations with bound substrate, an alternative mechanism for oligoglycoside hydrolysis was proposed. It involves cleavage of an endocyclic C-O bond, instead of the exocyclic cleavage proposed in the standard mechanism. Both mechanisms have been demonstrated in solution, but it is still unclear which is prevalent in lysozyme.
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PMID:Simulations of lysozyme: internal motions and the reaction mechanism. 876 98

T4 lysozyme and mutants thereof crystallize in different conformations that are related to each other by a bend about a hinge in the molecule. This observation suggests that the wild type protein may undergo a hinge-bending motion in solution to allow substrate access to an otherwise closed active site cleft [Faber, H.R., & Matthews, B.W. (1990) Nature 348, 263-266]. To test this hypothesis, either single or pairs of nitroxide side chains were introduced into the protein to monitor tertiary contact interactions and inter-residue distances, respectively, in solution. A set of constraints for these structural parameters was derived from a reference state, a covalent enzyme-substrate adduct where the enzyme is locked in the closed state. In the absence of substrate, differences in both inter-residue distances and tertiary contact interactions relative to this reference state are consistent with a hinge-bending motion that opens the active site cleft. Quantitative analysis of spin-spin interactions between nitroxide pairs reveals an 8 A relative domain movement upon substrate binding. In addition, it is demonstrated that the I3P mutation, which produces a large hinge-bending angle in the crystal, has no effect on the solution conformation. Thus, the hinge motion is not the result of the mutation but is an integral part of T4 lysozyme catalysis in solution, as suggested recently [Zhang, X.J., Wozniak, J.A., & Matthews, B.W. (1995) J. Mol. Biol. 250, 527-552]. The strategy employed here, based on site-directed spin labeling, should be generally applicable to the study of protein conformation and conformational changes in solution.
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PMID:Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling. 900 82


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