Lysozyme mutants

The active site is in a cleft between a large domain with a nonpolar core and a smaller (3-sheet domain that contains many hydrogen-bonded polar side chains (Figs. 12-3,12-4). Human lysozyme has a similar structure and properties.57-59 The T4 lysozyme has an additional C-terminal domain whose function may be to bind the crosslinking peptide of the E. coli peptidoglycan. Goose lysozyme is similar in part to both hen lysozyme and T4 lysozyme. All three enzymes, as well as that of our own tears, may have evolved from a common ancestral protein.60 On the other hand, Streptomyces erythaeus has developed its own lysozyme with a completely different structure.61 An extensive series of T4 lysozyme mutants have been studied in efforts to understand protein folding and stability.61-63... 

Protein Production, Isolation, and Purification. The expression and purification of chicken lysozyme mutant proteins in yeast are performed as described by Malcolm et al. with the following modifications. The 50-ml minimal medium second seed yeast culture is used to inoculate a 2.8-liter Fembach flask containing 500 ml of 1% yeast extract/2% Bacto-peptone/ 8% glucose (w/v) medium and is then incubated for 7 - 9 days at 30°. Cells are harvested, washed twice with 60 ml of 0.5 M NaCl, and collected by centrifugation. The supernatants are pooled, diluted 5-fold with deionized water, and loaded onto a 20-ml column of CM Sepharose Fast Flow (Pharmacia, Piscataway, NJ) equilibrated with 0.1 M potassium phosphate, pH 6.24. The column is washed with the same buffer, and lysozyme is eluted with 0.5 M NaCl/0.1 M potassium phosphate, pH 6.24. Fractions are assayed by activity (decrease in A450 of Micrococcus lysodeikticus cell wall suspensions per minute). Fractions containing lysozyme are concentrated in Centricon-10 (Amicon, Danvers, MA) filter units, washed with 0.1 M potassium phosphate buffer, pH 6.24, and stored at 4°. The protein concentration is determined from e 1 = 26.4.15... 

The neutral corridor test therefore provides a criterion but not a proof of nonneutiality. If an evolutionary intermediate lies outside the corridor, it becomes a candidate for a nonneutral pathway. The lysozyme mutants described in this chapter have already provided such candidates.2 The stage is now set for identifying additional cases and for finding out how often evolutionary intermediates lie within the neutral corridor. 

Hilser, V. J. Freire, E. (1996b). Structure based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J. Mol. Biol In Press. Hilser, V. J. Freire, E. (1996c). Structure-Based Statistical Thermodynamic Analysis of T4 Lysozyme Mutants Structural Mapping of Cooperative Interactions. Biophysical Chem.. ... 

Fig. 5). This almost certainly excludes the recruitment of tran-sientiy populated PrP folding intermediates as precursors of PrP , which would be expected to cause significantly slower folding. Kinetic folding intermediates have been proposed for amyloid formation of human lysozyme mutants (Booth et al, 1997). 

Fangen R, Oh KJ, Cascio D, Hubbell WF (2000) Crystal structures of spin labeled T4 lysozyme mutants implications for the interpretation of EPR spectra in terms of structure. Biochemistry 39 8396-8405... 

Following the methodological developments in CS-only based structure determination and experiments able to obtain shift, RDC and amide temperature coefficient data in transiently populated species in exchange with the ground state, last year saw the first structural characterisation of a so-called invisible protein state. This year, two further publications demonstrate how NMR is capable of studying these states at atomic resolution. Bouvignies and colleagues have determined the structure of an exeited state of a T4 lysozyme mutant present at 3% population and with... 

Extraction of Bound Xenon from Mutant T4-Lysozyme... 

Hermans, J., Wang, L. Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4-lysozyme. J. Am. Chem. Soc. 119 (1997) 2707-2714... 

Mann, G., Prins, J., Hermans, J. Energetics of forced extraction of ligand Simulation studies of Xe in mutant T4 lysozyme as a simple test system. Bioohys. J., in preparation (1998)... 

The critical factor for any method involving an approximation or an extrapolation is its range of application. Liu et al. [15] demonstrated that the approach performed well for mutations involving the creation or deletion of single atoms. The method has also been successfully applied to the prediction of the relative binding affinities of benzene, toluene and o-, p-, and m-xylene to a mutant of T4-lysozyme [16]. In both cases, however, the perturbation to the system was small. To investigate range over which the extrapolation may... 

C Lee. Testing homology modeling on mutant proteins Pi edictmg stiaictural and thermodynamic effects m the Ala98 Val mutants of T4 lysozyme. Folding Des 1 1-12, 1995. 

FIR Faber, BW Matthews. A mutant T4 lysozyme displays five different crystal conformations. Nature 348 263-266, 1990. 

Lysozyme from bacteriophage T4 is a 164 amino acid polypeptide chain that folds into two domains (Figure 17.3) There are no disulfide bridges the two cysteine residues in the amino acid sequence, Cys 54 and Cys 97, are far apart in the folded structure. The stability of both the wild-type and mutant proteins is expressed as the melting temperature, Tm, which is the temperature at which 50% of the enzyme is inactivated during reversible beat denat-uration. For the wild-type T4 lysozyme the Tm is 41.9 °C. 

Figure 17.4 Melting temperatures, Tm, of engineered single-, double-, and tripledisulfide-containing mutants of T4 lysozyme relative to wild-type lysozyme. The red bars show the differences in Tm values of the oxidized and reduced forms of the mutant lysozymes. The green bars for the multiple-bridged proteins correspond to the sum of the differences in Tm values for the constituent single-bridged lysozymes. (Adapted from M. Matsumura et al.. Nature 342 291-293, 1989.)...

Both types of mutations have been made in T4 lysozyme. The chosen mutations were Gly 77-Ala, which caused an increase in Tm of 1 °C, and Ala 82-Pro, which increased Tm by 2 °C. The three-dimensional structures of these mutant enzymes were also determined the Ala 82-Pro mutant had a structure essentially identical to the wild type except for the side chain of residue 82 this strongly indicates that the effect on Tm of Ala 82-Pro is indeed due to entropy changes. Such effects are expected to be additive, so even though each mutation makes only a small contribution to increased stability, the combined effect of a number of such mutations should significantly increase a protein s stability. 

Mutants that fill cavities in hydrophobic cores do not stabilize T4 lysozyme... 

T4 lysozyme has two such cavities in the hydrophobic core of its a helical domain. From a careful analysis of the side chains that form the walls of the cavities and from building models of different possible mutations, it was found that the best mutations to make would be Leu 133-Phe for one cavity and Ala 129-Val for the other. These specific mutants were chosen because the new side chains were hydrophobic and large enough to fill the cavities without making too close contacts with surrounding atoms. 

Karpusas, M., et al. Hydrophobic packing in T4 lysozyme probed by cavity-filling mutants. Proc. Natl. Acad. Sci. USA 86 8237-8241, 1989. 

Anderson DE, Hurley JH, Nicholson H, Baase WA, Mathews BW Hydro-phobic core repacking and aromatic-aromatic interaction in the thermostable mutant of T4 lysozyme Ser 117-Phe. Protein Sci 1993 2 1285-1290. 

The conformational plasticity supported by mobile regions within native proteins, partially denatured protein states such as molten globules, and natively unfolded proteins underlies many of the conformational (protein misfolding) diseases (Carrell and Lomas, 1997 Dobson et al., 2001). Many of these diseases involve amyloid fibril formation, as in amyloidosis from mutant human lysozymes, neurodegenerative diseases such as Parkinson s and Alzheimer s due to the hbrillogenic propensities of a -synuclein and tau, and the prion encephalopathies such as scrapie, BSE, and new variant Creutzfeldt-Jacob disease (CJD) where amyloid fibril formation is triggered by exposure to the amyloid form of the prion protein. In addition, aggregation of serine protease inhibitors such as a j-antitrypsin is responsible for diseases such as emphysema and cirrhosis. 

Exit of the virus from the cell occurs as a result of cell lysis. The phage codes for a lytic enzyme, the T4 lysozyme, which causes an attack on the peptidoglycan of the host cell. The burst size of the virus (the average number of phage particies per cell) depends upon how rapidly lysis occurs. If lysis occurs early, then a smaller burst size occurs, whereas slower lysis leads to a higher burst size. The wild type phage exhibits the phenomenon of lysis inhibition, and therefore has a large burst size, but rapid lysis mutants, in which lysis occurs early, show smaller burst sizes. 

Pons, J. Rajpal, A. Kirsch, J.F., Energetic analysis of an antibody/antigen interface alanine scanning mutagenesis and double mutant cycles on the HyHEL-10/lysozyme interaction, Prot. Sci. 1999, 8, 958-968. 

Fields, B.A., F.A. Goldbaum, W. Dall Acqua, E.L. Malchiodi, A. Cauerhff, F.P. Schwarz, X. Ysem, R.J. Poljak, and R.A. Mariuzza. 1996. Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme. Biochemistry 35 15494-15503. 

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