Lysozyme- 6 complex, mechanism

Figure 10.6 (a) Schematic representation of the encapsulation and lysozyme release mechanism from carboxymethyl chitosan-grafted-poly(amidoamine) (CM-chitosan-PAMAM)/ lysozyme polyion complex (PIC) nanoparticles, (b) Schematic representation of synthesis and self-assembling for CM-chitosan-PAMAM dendrimer nanoparticles, and the encapsulation and lysozyme release mechanism from CM-chitosan-PAMAM/lysozyme PIC nanoparticles. Reprinted from X. Zhang, J. Zhao, Y. Wen, C. Zhu.J. Yang, F. Yao, Carboxymethyl chitosan-poly(amidoamme) dendrimer core-shell nanoparticles for intracellular lysozyme dehvery, Carhohydrate Polymers 98 (2013) 1326-1334. Copyright (2013), with permission from Elsevier. 

A pathway (Scheme I) (8.9) for the hydrolysis of oligoglycosides by lysozyme that differs from the previously accepted mechanism (Scheme II) (3,10-12) is described in this section. The alternative pathway, suggested by results of a 55-ps MD simulation of the lysozyme (GlcNAc)e complex (1), is consistent with the available experimental data and with stereoelectronic considerations. Experimental data have demonstrated that Glu 35 and Asp 52 are essential, as shown by recent site-directed mutagenesis results (13.) which corroborate chemical modification studies (3.14 and references cited therein), and that the reaction proceeds with retention of configuration at Ci Q and references cited therein). A fundamental feature of the alternative pathway is that an endocyclic bond is broken in the initial step, in contrast to the exocyclic bond cleavage in the accepted mechanism. 

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. 

Additional studies of the enzyme-substrate complementarity in other complexes along the reaction path are under way. Since the initial report of an alternative pathway for lysozyme hydrolysis (8,9.28) work on the solution hydrolysis of glucosides has demonstrated the existence of a ring opening mechanism (29,30). ... 

T4 lysozyme 33,497 helix stability of 528, 529 hydrophobic core stability of 533, 544 Tanford j8 value 544, 555, 578, 582-Temperature jump 137, 138, 541 protein folding 593 Terminal transferase 408,410 Ternary complex 120 Tertiary structure 22 Theorell-Chance mechanism 120 Thermodynamic cycles 125-131 acid denaturation 516,517 alchemical steps 129 double mutant cycles 129-131, 594 mutant cycles 129 specificity 381, 383 Thermolysin 22, 30,483-486 Thiamine pyrophosphate 62, 83 - 84 Thionesters 478 Thiol proteases 473,482 TNfn3 domain O-value analysis 594 folding kinetics 552 Torsion angle 16-18 Tbs-L-phenylalanine chloromethyl ketone (TPCK) 278, 475 Transaldolase 79 Tyransducin-o 315-317 Transit time 123-125 Transition state 47-49 definition 55... 

It is also safe to say that, because of the great complexity of proteins, even of the simplest, most well-characterized proteins, such as insulin, lysozyme, and myoglobin, and because of the very wide range of proteins present in most physiologic environments, very simplistic hypotheses and mechanisms are generally not very applicable. 

Clementi (1985) described ab initio computational chemistry as a global approach to simulations of complex chemical systems, derived directly from theory without recourse to empirical parametrizations. The intent is to break the computation into steps quantum mechanical computations for the elements of the system, construction of two-body potentials for the interactions between them, statistical mechanical simulations using the above potentials, and, finally, the treatment of higher levels of chemical complexity (e.g., dissipative behavior). This program has been followed for analysis of the hydration of DNA. Early work by Clementi et al. (1977) established intermolecular potentials for the interaction of lysozyme with water, given as maps of the energy of interaction of solvent water with the lysozyme surface. 

It is evident that any detailed mechanism of the catalytic action of lysozyme in the hydrolysis of glycosides would involve the role for proton donors and/or acceptors. The most plausible residues near the cleavage site are Asp-52 and Glu-35. The Asp residue lies in a polar environment, where it is a hydrogen bond acceptor in a complex network of hydrogen bonds. Because of its location, it has virtually a normal pK of 3.5 0.2. At pH 5.0, which is near the optimum pH value of hydrolysis of chitin by lysozyme, Asp-52 is in the ionized form. The Glu residue lies in a nonpolar region, has an increased pK, of 6.3 0.2, and would be largely un-ionized at pH 5.0. 

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