Lysozyme solvation

The absence of slow dynamics in this system can be attributed to the fact that the penta-alanine peptide does not have any polar side-chain atom which can form a strong HB with water. With a higher level of hydration, the rotational dynamics of water approached that of bulk water, again as expected. A QENS study of protein dynamics was also carried out on the picosecond timescale of a protein, lysozyme solvated in glycerol at different water contents, h (g water/g lysozyme). For all h, a well-visible low-frequeney vibrational bump was observed. The quasi-elastic scattering can be decomposed into two Lorentzian components, corresponding to motions with charaeteristic time constants of 15 ps and 0.8 ps. The 15 ps component is the slow component, which is in the same range observed in many other experimental studies. 

Brass, O., J.M. Letoffe, A. Bakkali, J.C. Bureau, C. Corot, and P. Claudy. 1995. Involvement of protein solvation in the interaction between a contrast medium (iopamidol) and fibrinogen or lysozyme. Biophys Chem 54 83-94. 

Kundrot and Richards (1987, 1988) described the solvation shell in the hen egg white lysozyme crystal, in connection with a study of the compressibility of protein and solvent. Mason et al. (1984) carried out a neutron diffraction analysis of triclinic lysozyme at 1.4 A resolution, with 239 water molecules included in the refinement. 

The solvation of the active-site cleft of lysozyme (Blake et al., 1983) does not seem to be different from that of the rest of the protein surface. 

In an investigation of the role of water in enzymic catalysis. Brooks and Karplus (1989) chose lysozyme for their study. Stochastic boundary molecular dynamics methodology was applied, with which it was possible to focus on a small part of the overall system (i.e., the active site, substrate, and surrounding solvent). It was shown that both structure and dynamics are affected by solvent. These effects are mediated through solvation of polar residues, as well as stabilization of like-charged ion pairs. Conversely, the effects of the protein on solvent dynamics and... 

In the active-site simulations of lysozyme108 (this chapter, Sect. B.2 above) similar water networks that stabilize charged groups have been observed. To illustrate the dynamics of the formation of such networks, a sequence of stereo plots showing the formation and evolution of a stable pair of positively charged residues is displayed in Fig. 56. The pair consists of (NH2)+ moieties of Arg-61 and Arg-73. The solvated structure evolved from a conformation obtained in a vacuum simulation of lysozyme.108,192 The sequence of plots shows the formation of the water-bridged pair over a time period from t = 0 ps to t 8 ps, which followed dynamical equilibration of the solvent around the fixed vacuum structure of the protein. After 8 ps, the ion-pair structure is stable, but fluctuations in the pattern of hydrogen bonds do occur typical... 

Figure 56. Formation of like-charged ion" pairs illustrated by the solvation of two arginine sidechains in lysozyme (Arg-61, leftmost residue, and Arg-73). Stereo plots show (a) the "un-solvated structure at t = 0.0 ps (b) the initial formation of the water-bridged structure at t = 8.25 ps (c) and (d) the fully "solvated water-bridged structures fort = 16.5 ps and t = 33.0 ps, respectively. The protein-solvent hydrogen bonds are shown as dotted lines.

Figure 4. (A) Front view (looking into the active site) and (B) back view of human lysozyme colored according to Feldmann s functional color scheme. Front view of (C) human lysozymes colored according to Eisenberg s atomic solvation parameters. Tryptophan residues are additionally colored red. Continued on next page.

Tryptophan (Trp), tyrosine (Tyr), cystine (Cys), and phenylalanine (Phe) moieties play a determinant role regarding UV light-induced chemical alterations in many proteins. After the absorption of light by these moieties, in most cases mainly by Trp and Tyr, they undergo photoionization and participate in energy-and electron-transfer processes. This not only holds for structural proteins such as keratin and fibroin [11], but also for enzymes in aqueous media such as lysozyme, trypsin, papain, ribonuclease A, and insulin [7]. The photoionization of Trp and/or Tyr residues is the major initial photochemical event, which results in inactivation in the case of enzymes. A typical mechanism pertaining to Trp residues (see Scheme 8.3) commences with the absorption of a photon and the subsequent release of an electron. In aqueous media, the latter is rapidly solvated. By the release of a proton, the tryptophan cation radical Trp is converted to the tryptophan radical Trp. ... 

There have been two different interpretations of the slow dynamics observed in the SD of the lysozyme hydration layer. The first attributes the intermediate time-scales (30 0 ps) to slow water. Bagchi and co-workers employed the dynamic exchange model to relate the observed slow dynamics to the timescale of the fluctuation of water in the hydration layer [11]. In an alternative interpretation. Song et al. used the formulation developed by Song and Marcus that relates the solvation time correlation function to the DR of the medium. They attributed the... 

The use of X-ray techniques to elucidate the three-dimensional structure of enzymes shows that many of them possess a characteristic concave cleft at the active site. Concavities of this type have been observed, for example, in the case of lysozyme [8, 9] trypsin [10], yeast hexokinase [11], liver alcohol dehydrogenase [12] and citrate synthase [13]. It is thus reasonable to assume that the interaction between an enzyme and its substrate, inhibitor or cofactor usually occurs not in bulk water but rather in a shielded proteic cleft whose specific microenvironment is induced by the amino acid residues forming the cleft. Hydrophobicity, electrostatics, solvation and a relatively low dielectric constant prevailing within the cleft no doubt play a decisive role in determining the nature and rate of the reaction catalyzed by the enzyme. 

Unfortunately, the extreme sensitivity to environmental effects makes detailed interpretation of fluorescence changes difficult, particularly when several tyrosine and tryptophan residues are present. For example, Pjura et al (1993) reported that large changes in fluorescence and phosphorescence caused by perturbation of a tryptophanyl residue were not always correlated with the three-dimensional structure, stability and solvation properties of mutants of T4 lysozyme. Increases in polar relaxation about the excited state of tryptophan could result from only small increases in local dynamics or solvent exposure. 

Pjura, R McIntosh, L.P. Wozniak, J.A. Matthews, B.W. Perturbation of Trp 138 in T4 lysozyme by mutations at Gin 105 used to correlate changes in structure, stability, solvation and spectroscopic properties. Proteins 1993,15, 401-412. 

This illustrates the fact that the proper positioning of a group (electrophilic or nucleophilic) may accelerate the rate of a reaction. There is thus an analogy to be made with the active site of an enzyme such as lysozyme. Of course the nature of the leaving group is also important in describing the properties. Furthermore, solvation effects can be of paramount importance for the course of the transformation especially in the transition state. Reactions of this type are called assisted hydrolysis and occur by an intramolecular displacement mechanism steric factors may retard the reactions. 

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