Lysozyme and

A detailed examination of LN behavior is available [88] for the blocked alanine model, the proteins BPTI and lysozyme, and a large water system, compared to reference Langevin trajectories, in terms of energetic, geometric, and dynamic behavior. The middle timestep in LN can be considered an adjustable quantity (when force splitting is used), whose value does not significantly affect performance but does affect accuracy with respect to the reference trajectories. For example, we have used Atm = 3 fs for the proteins in vacuum, but 1 fs for the water system, where librational motions are rapid. 

Figure 3 Calculated X-ray diffuse scattering patterns from (a) a full molecular dynamics trajectory of orthorhombic hen egg white lysozyme and (b) a trajectory obtained by fitting to the full trajectory rigid-body side chains and segments of the backbone. A full description is given in Ref. 13.

The shape of the interaction area between lysozyme and the CDR loops of the antibody is easily distinguished from the hapten-binding crevice. The interaction extends over a large area with maximum dimensions of about 20 X 30 A (Figure 15.15). The interaction surface is irregular but relatively flat, with small protuberances and depressions that are complementary in the antigen and the antibody. Residues from all six CDR loops contribute to the... 

The structure of lysozyme in the complex is the same as that in crystals of free lysozyme, and no conformational changes are seen even in the regions... 

Since there are so few direct packing interactions between protein molecules in a crystal, small changes in, for example, the pH of the solution can cause the molecules to pack in different ways to produce different crystal forms. The structures of some protein molecules such as lysozyme and myoglobin have been determined in different crystal forms and found to be essentially similar, except for a few side chains involved in packing interactions. Because they are so few, these interactions between protein molecules in a crystal do not change the overall structure of the protein. However,... 

At best, van der Waals interactions are weak and individually contribute 0.4 to 4.0 kj/mol of stabilization energy. ITowever, the sum of many such interactions within a macromolecule or between macromolecules can be substantial. For example, model studies of heats of sublimation show that each methylene group in a crystalline hydrocarbon accounts for 8 k[, and each C—IT group in a benzene crystal contributes 7 k[ of van der Waals energy per mole. Calculations indicate that the attractive van der Waals energy between the enzyme lysozyme and a sugar substrate that it binds is about 60 k[/mol. 

FIGURE 5.32 The tertiary structures of heii egg white lysozyme and human o -lactal-bumin are very similar. (Adapted from Acharya, K K, ct at., 7996. Journal of Protein Chemistry 9 549-563 and Acharya, K R., ct at., 1997. Journal of Molecular Biology 221 571—581. 

Hen egg-white lysozyme catalyzes the hydrolysis of various oligosaccharides, especially those of bacterial cell walls. The elucidation of the X-ray structure of this enzyme by David Phillips and co-workers (Ref. 1) provided the first glimpse of the structure of an enzyme-active site. The determination of the structure of this enzyme with trisaccharide competitive inhibitors and biochemical studies led to a detailed model for lysozyme and its hexa N-acetyl glucoseamine (hexa-NAG) substrate (Fig. 6.1). These studies identified the C-O bond between the D and E residues of the substrate as the bond which is being specifically cleaved by the enzyme and located the residues Glu 37 and Asp 52 as the major catalytic residues. The initial structural studies led to various proposals of how catalysis might take place. Here we consider these proposals and show how to examine their validity by computer modeling approaches. 

In concentrated NaOH, chitin becomes alkali chitin which reacts with 2-chloroethanol to yield 0-(2-hydroxyethyl) chitin, known as glycol chitin this compoimd was probably the first derivative to find practical use (as the recommended substrate for lysozyme). Alkali chitin with sodium monochloroacetate yields the widely used water-soluble 0-carboxymethyl chitin sodium salt [118]. The latter is also particularly susceptible to lysozyme, and its oUgomers are degraded by N-acetylglucosaminidase, thus it is convenient for medical appHcations, including bone regeneration. 

The entrapment of a-chymotrypsin, lysozyme, and myehn in AOT-reversed micelles is accompanied by an increase in the micellar water content and in the size of the micelle. As a consequence of the redistribution of water among reversed micelles, the micellar solution results in being constituted by large protein-containing micelles and small unfilled ones [169],... 

From crystal-structure analysis of hen-egg lysozyme and of its complex with the competitive inhibitor tri-Af-acetylchitotriose, the following conclusions were drawn the active site consists of a cleft containing six sub-sites, A to F, of which each could accommodate a) -( 1 — 4)-linked A-acetylglucosa-... 

Separations in hydrophobic interaction chromatography have been modeled as a function of the ionic strength of the buffer and of the hydrophobicity of the column, and tested using the elution of lysozyme and ovalbumin from octyl-, butyl- and phenyl-Sepharose phases.2 The theoretical framework used preferential interaction analysis, a theory competitive to solvophobic theory. Solvophobic theory views protein-surface interaction as a two-step process. In this model, the protein appears in a cavity in the water formed above the adsorption site and then adsorbs to the phase, with the free energy change... 

Enzymes modified with N -carbonyldiimidazole (CDI) include horseradish peroxidase 761 /1-lactamase after nitration and reduction,[771 lysozyme, and urease.[781 Ref. [77] describes how the tyrosine side chain of a protein was nitrated, reduced with dithionite to an amino group, and then treated with CDI or A/-(2,2,2-trifluoro-ethoxycarbonyl)imidazole to give the benzoxazolinonyl alanine moiety ... 

Figure 11.6 Positive ion electrospray mass spectra of an equimolar mixture of five standard proteins, under different instrumental settings, showing cases where prominent signals for the different charge states of (A) insulin, (B) ubiquitin, (C) cytochrome c, (D) lysozyme, and (E) myoglobin were preferentially observed, and (F) where signals for all the proteins were more uniformly detected.

The ROA spectra of partially unfolded denatured hen lysozyme and bovine ribonuclease A, prepared by reducing all the disulfide bonds and keeping the sample at low pH, together with the ROA spectra of the corresponding native proteins, are displayed in Figure 5. As pointed out in Section II,B, the short time scale of the Raman scattering event means that the ROA spectrum of a disordered system is a superposition of snapshot ROA spectra from all the distinct conformations present at equilibrium. Because of the reduced ROA intensities and large... 

Fig. 5. Backscattered Raman and ROA spectra of native (top pair) and reduced (second pair) hen lysozyme, and of native (third pair) and reduced (bottom pair) bovine ri-bonuclease A, together with MOLSCRIPT diagrams of the crystal structures (PDB codes llse and lrbx) showing the native disulfide links. The native proteins were in acetate buffer at pH 5.4 and the reduced proteins in citrate buffer at pH 2.4. The spectra were recorded at 20°C. 

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