Lysozyme, mechanism

The Lysozyme Mechanism Involves General Acid-Base Catalysis... 

MD simulations can aid in the understanding of enzymic reactions by providing new insights into the structures and intermolecular interactions fundamental to the chemical catalysis. By studying the structures from the simulation of the lysozyme-(GlcNAc)g complex, we have proposed an alternative to the accepted mechanism which accounts for the available experimental observations. The proposal of this lysozyme mechanism illustrates one way in which simulations can serve to generate new ideas which can be explored by experiment and computation. 

It is hoped that the analysis and results reported here will stimulate new experiments on the lysozyme mechanism. 

Is the lysozyme mechanism now proven No. A key feature of the scientific method, as Albert Einstein once summarized it, is No amount of experimentation can ever prove me right a single experiment can prove me wrong. In the case of the lysozyme mechanism,... 

Kirby, A.J.(2001) The lysozyme mechanism sorted—after 50 years. Nat. Struct. Biol. 8, 737-739. 

It was emphasized by C. A. Vernon in the initial formulation of the lysozyme mechanism that the electrostatic stabilization of the oxocarbenium ion by Asp-52 is the most important catalytic factor.208 Theoretical calculations suggest that the activation energy for kcat is lowered by 32 kj/mol ( 8 keal/mol) by electrostatic stabilization.221 A high value for this is indicated by experiments show-... 

The lysozyme mechanism (Scheme 11.21) has an acylal intermediate with a decay step which is fast compared with its rate of formation, so it is not normally possible to observe the intermediate. The acylal mechanism has recently been established by modifying both enzyme and substrate so that the intermediate can be isolated in this case, the intermediate was stabilised so much that its X-ray crystallographic structure could be determined. Substrate A in Scheme 11.21 was employed [22 ] in which the 2 -fluoro substituent reduces the reactivity at the Cl position so that any acylal enzyme formed from this substrate would have a... 

Scheme 11.21 Lysozyme mechanism for hydrolysis of the substrate jS-cel lob iosyl fluoride A is a modified reactive substrate which yields a weakly reactive acylal intermediate.

Figure 3. Scheme I and II showing proposed lysozyme mechanisms (from Post and Karplus 1986).

Bottoni A, Miscione GP, De Vivo M (2005) A theoretical DFT investigation of the lysozyme mechanism computational evidence for a covalent intermediate pathway. Proteins, Stmct Funct Genet 59 118-130... 

Most model systems of this sort have tried to mimic the lysozyme mechanism. Anderson and Fife [59] showed many years ago that benzaldehyde disalicyl acetal 3.29 (Scheme 2.29) is hydrolyzed over 10 times faster than its dimethyl ester but that the contribution of the second, carboxylate group (the potential nucleophile) is... 

From the lysozyme mechanism shown in Figure 24.9, we can conclude that Asp 52 is the group with a pAa of 3.8 and Glu 35 is the group with a pAa of 6.7. The pH-activity profile indicates that lysozyme is maximally active when Asp 52 is in its basic form and Glu 35 is in its acidic form. 

Kirby, A. J. (2001).The lysozyme mechanism sorted after 50 yeais.Nature Struct. Mol. Biol, Vol. 8, N0.9, pp. 737-739... 

Dean, K.E.S., Kirby, A.J. Conceted general acid and nucleophilic catalysis of acetal hydrolysis a simple model for the lysozyme mechanism. J. Chem. Soc. Perkin Trans. 2. 2002, 428-132. 

The mechanism of the lysozyme reaction is shown in Figures 16.36 and 16.37. Studies using O-enriched water showed that the Ci—O bond is cleaved on the substrate between the D and E sites. Hydrolysis under these conditions incorporates into the Ci position of the sugar at the D site, not into the oxygen at C4 at the E site (Figure 16.36). Model building studies place the cleaved bond approximately between protein residues Glu and Asp. Glu is in a nonpolar or hydrophobic region of the protein, whereas Asp is located in a much more polar environment. Glu is protonated, but Asp is ionized... 

The commonly accepted mechanism for the catalytic reaction of lysozyme is the so-called general acid catalysis mechanism. 

FIGURE 6.7. The key resonance structures for the catalytic reaction of lysozyme. The e, s include only the solute contributions and the complete expression is given in eqs. (6.4) and (6.5). The quantum mechanical atoms are enclosed within the shaded region. 

FIGURE 6.10. Comparing the energetics of the EVB configurations in solution and in the active site of lysozyme. The calculations were done by using the PDLD and related models (Refs. 6 and 7) and they represent a study of a stepwise mechanism. The energetics of a more concerted pathway (e.g., that of Fig. 6.9) is almost identical to that of the stepwise mechanism and correlated in a similar way with the electrostatic effect of the protein. 

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. ... 

---