Of lysozyme

Hayward, S., Kitao, A., Berendsen, H.J.C. Model-free methods to analyze domain motions in proteins from simulation A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 27 (1997) 425-437. 

In an early study of lysozyme ([McCammon et al. 1976]), the two domains of this protein were assumed to be rigid, and the hinge-bending motion in the presence of solvent was described by the Langevin equation for a damped harmonic oscillator. The angular displacement 0 from the equilibrium position is thus governed by... 

B. R. Brooks and M. Karplus. Normal modes for specific motions of macromolecules Application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA, 82 4995-4999, 1985. 

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

Clinical experience has shown that certain types of lens materials are more prone to deposit problems. In general, lenses with negatively charged moieties at the surface accumulate greater amounts of lysozyme, the principal tear film protein (10). The introduction and use of disposable lenses make these deposits and their clinical problems less significant. 

Equation (8) shows that it is the fluctuations of the lowest frequency modes that contribute most to the overall fluctuation of the molecule. For example, in the case of lysozyme, the lowest frequency nonnal mode (out of a total of 6057) accounts for 13% of the total mass-weighted MSF. It is for this reason that it is common to analyze just the lowest frequency modes for the large-scale functional motions. 

M Totrov, R Abagyan. Detailed ah initio prediction of lysozyme-antibody complex with 1.6 AA accuracy. Nature Struct Biol 1 259-263, 1994. 

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... 

Fremont, D.H., Monnaie, D., Nelson, C.A., Hendrickson, W.A., Unanue, E.R. Crystal structure of I-A in complex with a dominant epitope of lysozyme. Immunity 8 305-317, 1998. 

Figure 17.3 The polypeptide chain of lysozyme fiom hacteiiophage T4 folds into two domains. The N-terminal domain is of the a + P type, built up from two a helices (red) and a four-stranded antiparallel P sheet (green). The C-terminal domain comprises seven short a helices (brown and blue) in a rather irregular arrangement. (The last half of this domain is colored blue for clarity.)...

Theoretical Studies of Enzymic Reactions Dielectric, Electrostatic and Steric Stabilizations of the Carbonium Ion in the Reaction of Lysozyme A. Warshel and M. Levitt Journal of Molecular Biology 103 (1976) 227-249... 

Figure 11.15 also shows that cytochrome C is displaced by lysozyme during extraction, i.e. at longer extraction times (cf. Figure 11.15(b) and (c)) the amount of lysozyme is increased as the amount of cytochrome C is decreased. 

Table 8. Parameters of cooperative bonding of lysozyme, haemoglobin and serum albumin (proteins) by a macroreticular MA-EDMA (2.5 mol%) copolymer...

GENERAL ACID CATALYSIS AND ELECTROSTATIC STABILIZATION IN THE CATALYTIC REACTION OF LYSOZYME... 

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

FIGURE 6.2. A schematic description of the rate-determining steps in the catalytic reaction of lysozyme. 

FIGURE 6.3. The strain hypothesis for the catalytic reaction of lysozyme. The enzyme is assumed to destabilize the chair geometry by pushing the ground state substrate toward the sofa configuration. This ground-state destabilization effect is supposed to reduce Ag M. 

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. 

In order to make an effective use of the VB formulation we have to calibrate the relevant parameters using reliable experimental information. The most important task is to obtain the relevant a-. Since the a s represent the energy of forming the different configurations in the gas phase at infinite separation between the given fragments, it is natural to try to obtain them from gas-phase experiments. In the case of the catalytic reaction of lysozyme one can compile the relevant information from the available gas-phase experiments (Table 6.1) and use it to determine the a s. 

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. 

FIGURE 6.11. Comparison of the environment around the transition state of lysozyme in the enzyme-active site and in the reference solvent cage. 

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