For lysozyme

Table 3. Percentage error for LN compared to reference Langevin trajectories (at 0.5 fs) for energy means and associated variances for lysozyme over 60 ps at 7 = 20 ps At = 0.5 fs, Atm = 3 fs, and At = k Atm, where k2 ranges from 1 for LN 1 to 96 for LN 96.

Fig. 11. The Speedup of LN at increasing outer timesteps for BPTI (2712 variables), lysozyme (6090 variables), and a large water system (without nonbonded cutoffs 37179 variables). For lysozyme, the CPU distribution among the fast, medium, and slow forces is shown for LN 3, 24, and 48.

Fig. 13. Preferential iateraction parameter vs lyotropic number for lysozyme on (° ) bovine semm albumin and ( ) Toyopead.

On the basis of the above, the rate acceleration afforded by lysozyme appears to be due to (a) general acid catalysis by Glu (b) distortion of the sugar ring at the D site, which may stabilize the carbonium ion and the transition state) and (c) electrostatic stabilization of the carbonium ion by nearby Asp. The overall for lysozyme is about 0.5/sec, which is quite slow (Table... 

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. 

In this article are discussed the results of those studies which have become available over the past 15 years and which permit some generalizations on the catalytic mechanism of glycoside hydrolases from widely differing sources and with different sugar and aglycon specificities. It will be seen that, with few exceptions, the data support a mechanism almost identical to that proposed by Phillips and his group for lysozyme. ... 

Del Buono GS, Figueirido FE, Levy RM (1994) Intrinsic pKas of ionizable residues in proteins An explicit solvent calculation for lysozyme. Proteins 20 85-97. 

Lavoie, T. B., Drohan, W. N. and Smith-Gill, S. J. (1992), Experimental analysis by site-directed mutagenesis of somatic mutation effects on affinity and fine specificity in antibodies specific for lysozyme , f. Immunol., 148, 503-513. 

The hardness of only one type of protein crystal has been found in the literature. It is for lysozyme. This is an enzyme found in egg whites and tears. It destroys bacterial membranes. It is relatively small for a protein molecule, consisting of a chain of 129 amino acids folded into a globule with the volume = 30,000 A3. Its crystals are aggregates of these globular molecules held together by London forces (Stryer, 1988). 

The most popular model describing small-angle rotational movements of aromatic rings is the model of torsional vibrations around the C —Cp and Cfi—Cy bonds/30,70) This model has been used in simulations of motions by the methods of molecular dynamics/75 76) However, the results are not always satisfactory. In some cases, for example, for lysozyme,(77) the experimental data do not agree well with the results of simulations the observed motions are slower and less extended than predicted. 

Affinity chromatography was carried out on columns prepared with lightly carboxymethylated chitin, which is known to be a poor substrate for lysozyme. Both native lysozyme and regenerated 13-105 were bound to the column at pH 7 and eluted at pH 3. As controls, the basic proteins cytochrome c and pancreatic RNase A, as well as concanavalin A and a-amylase, were not bound from the same solvent at pH 7. These findings constitute a third line of evidence for formation of native-like structure in regenerated 13-105. 

These results suggest that the crystallographic determination of the structure of a productive enzyme-substrate complex is feasible for lysozyme and oligosaccharide substrates. They also provide the information of pH, temperature, and solvent effects on activity which are necessary to choose the best conditions for crystal structure work. The system of choice for human lysozyme is mixed aqueous-organic solvents at -25°C, pH 4.7. Data gathered on the dielectric constant, viscosity, and pH behavior of mixed solvents (Douzou, 1974) enable these conditions to be achieved with precision. 

Fig. 18. The proton spin-lattice relaxation rate recorded as a function of the magnetic field strength plotted as the proton Larmor frequency for lysozyme samples. Dry ( ), hydrated to 8.9% ( ), 15.7% (O). 23.1% (A), and cross-linked in a gel ( ). The solid lines were computed from the theory. The solid lines are fits to the data using Eq. (4) with Rs given by Eq. (6). The two parameters adjusted are Rsl and b (97). The small peaks most apparent in the dry samples are caused by cross-relaxation to the peptide nitrogen spin (90,122).

Note should be made of the fact that all of the mechamsilis for lysozyme in which a carbonium ion intermediate is formed are depicted as proceeding through a cyclic glycosyl oxo-carbonium ion. In the acid-catalysed hydrolysis of glucosides the carbonium ion formed is probably cyclic rather thEin an open-chain ion (Capon, 1969), even though the cyclic ion would necessarily have to adopt a... 

These studies with acetamidoglycosides provide support for the plausibility of mechanisms for lysozyme in which nucleophilic attack by the neighbouring group takes place. The synthetic substrates developed for lysozyme which lack this group (Raftery and Rand-Meir, 1968) render unnecessary any postulate of involvement of the 2-acetamido-group, but, of course, do not rule out the possibility. 

General acid catalysis by glutamic acid-35 represents at present the mechanism for lysozyme best able to explain the kinetic and structural data. For it to occur, however, distortion of the hexose ring in subsite D to a half-chair must take place so that relief of strain in the transition state will make bond breaking sufficiently easy. A question that must be answered for this picture to be tenable is whether relief of strain can so greatly facilitate bond breaking when the carbonium ion is a glycosyl ion [see also the discussion in Fife (1972) and Atkinson and Bruice (1974)]. 

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