Transition-state structure, lysozyme

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)]. 

The mechanism of action of lysozyme has been suggested to involve strain in the substrate as a result of binding to the protein.31 The protein requires that the substrate binds to the protein in a distorted state that is close to the transition state of the reaction. The energy for this distortion can arise from the substrate binding energy. This example differs from the entatic state hypothesis because this strain arises from substrate binding and is not a feature of the protein structure. However, the entatic state... 

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... 

Despite the above generalizations, hydration water likely participates in the transition state for certain reactions. X-Ray diffraction results have identihed, for some enzymes, bound solvent that may enter into the transition state, for example, lysozyme (Blake et al., 1983), DNase I (Oefner and Suck, 1986), and the aspartic proteinase from Rhizoptts chi-nensis (Suguna et al., 1987). Meyer et al. (1988) suggested the participation of water organized in a network or tunnellike structure in the... 

The elucidation of the X-ray structure of lysozyme provided the first direct information about the structure of an enzyme-substrate complex (Blake et al., 1967). This and other biochemical studies led to the proposal of three major catalytic factors general acid catalysis, steric strain and electrostatic stabilisation. It was found that the effect of steric strain is unlikely to be important because it can be relaxed by small shifts in the substrate and enzyme geometries (Warshel and Levitt, 1976 Pincus et al., 1977). This point was further established by quantitative FEP calculations (Warshel, 1991). On the other hand, it was found that electrostatic interactions play a very important role in the enzymatic reaction. The total electrostatic stabilisation of the carbonium transition state, relative to the corresponding stabilisation in solution, was found to be 29 kJ/mol (cf. Figure 12., Warshel, 1978). This value appears to account... 

Selected examples of apparent free energies of interaction attributable to single amino acid side chains are summarized for three enzymes, T4 lysozyme, dihydrofolate reductase (DHFR), and tyrosyl-tRNA synthetase (TRS) (see Figs. 1,5, and 12, respectively, for structural information). In each case, the thermodynamic effect of the substitution was quantitated in terms of reduced binding affinity for the substrate or transition state, or reduced thermostability in the case of T4 lysozyme. 

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