Dynamics of hydration in hen egg white lysozyme

We investigate the hydration dynamics of a small globular protein, hen egg-white lysozyme. Extensive simulations (two trajectories of 9 ns each) were carried out to identify the time-scales and mechanism of water attachment to this protein. The location of the surface and integral water molecules in lysozyme was also investigated. Three peculiar temporal scales of the hydration dynamics can be discerned: two among these, with sub-nanosecond mean residence time, tau(w), are characteristic of surface hydration water; the slower time-scale (tau(w) approximately 2/3 ns) is associated with buried water molecules in hydrophilic pores and in superficial clefts. The computed tau(w) values in the two independent runs fall in a similar range and are consistent with each other, thus adding extra weight to our result. The tau(w) of surface water obtained from the two independent trajectories is 20 and 24 ps. In both simulations only three water molecules are bound to lysozyme for the entire length of the trajectories, in agreement with nuclear magnetic relaxation dispersion estimates. Locations other than those identified in the protein crystal are found to be possible for these long-residing water molecules. The dynamics of the hydration water molecules observed in our simulations implies that each water molecule visits a multitude of residues during the lifetime of its bound with the protein. The number of residues seen by a single water molecule increases with the time-scale of its residence time and, on average, is equal to one only for the water molecules with shorter residence time. Thus, tau(w) values obtained from inelastic neutron scattering and based on jump-diffusion models are likely not to account for the contribution of water molecules with longer residence time.     

The binding of precipitant ions in the tetragonal crystals of hen egg white lysozyme

Abstract

The bonds between lysozyme molecules and precipitant ions in single crystals grown with chlorides of several metals are analysed on the basis of crystal structure data. Crystals of tetragonal hen egg lysozyme (HEWL) were grown with chlorides of several alkali and transition metals (LiCl, NaCl, KCl, NiCl₂ and CuCl₂) as precipitants and the three-dimensional structures were determined at 1.35?Å resolution by X-ray diffraction method. The positions of metal and chloride ions attached to the protein were located, divided into three groups and analysed. Some of them, in accordance with the recently proposed and experimentally confirmed crystal growth model, provide connections in protein dimers and octamers that are precursor clusters in the crystallization lysozyme solution. The first group, including Cu⁺², Ni⁺² and Na⁺¹ cations, binds specifically to the protein molecule. The second group consists of metal and chloride ions bound inside the dimers and octamers. The third group of ions can participate in connections between the octamers that are suggested as building units during the crystal growth. The arrangement of chloride and metal ions associated with lysozyme molecule at all stages of the crystallization solution formation and crystal growth is discussed.

Communicated by Ramaswamy H. Sarma     

The stability curve of hen egg white lysozyme

The physiological stability curve--a plot of the free energy of unfolding versus temperature--is calculated for hen egg white lysozyme from a combination of extrapolated unfolding thermodynamic data from reversible conditions and isothermal titrations with guanidine hydrochloride. The shape of the curve suggests the existence of only one folded conformation.     

Organic cosolvents and hen egg white lysozyme folding

Studies on the influence of organic cosolvents on lysozyme folding have been reported. As most of the researches are confined to a few specific molecules and focus on equilibrium states, less is known about the effect on folding dynamics. We have studied the influence of six soluble organic cosolvents on hen egg white lysozyme heat induced denaturation and refolding dynamics. It was found that trifluoroethanol (TFE) can change the folding pathway significantly. With the presence of TFE, the overshot phenomenon generally observed in lysozyme folding at 222 nm disappears. The common mechanism of how organic cosolvents influence folding is analyzed. The heat induced denaturation temperature was found to have a quantitative relationship with the slow phase rate constant during folding. We discuss this finding and hypothesize that it is due to the similar influence of organic cosolvent on the transition state of heat denaturation and refolding.     

Molecular dynamics simulation of thionated hen egg white lysozyme

Understanding of the driving forces of protein folding is a complex challenge because different types of interactions play a varying role. To investigate the role of hydrogen bonding involving the backbone, the effect of thio substitutions in a protein, hen egg white lysozyme (HEWL), was investigated through molecular dynamics simulations of native as well as partly (only residues in loops) and fully thionated HEWL using the GROMOS 54A7 force field. The results of the three simulations show that the structural properties of fully thionated HEWL clearly differ from those of the native protein, while for partly thionated HEWL they only changed slightly compared with native HEWL. The analysis of the torsional-angle distributions and hydrogen bonds in the backbone suggests that the α-helical segments of native HEWL tend to show a propensity to convert to 3(10)-helical geometry in fully thionated HEWL. A comparison of the simulated quantities with experimental NMR data such as nuclear overhauser effect (NOE) atom-atom distance bounds and (3)J((H)(N)(H)(α))-couplings measured for native HEWL illustrates that the information content of these quantities with respect to the structural changes induced by thionation of the protein backbone is rather limited.     

Thermally induced fibrillar aggregation of hen egg white lysozyme

We study the effect of pH and temperature on fibril formation from hen egg white lysozyme. Fibril formation is promoted by low pH and temperatures close to the midpoint temperature for protein unfolding (detected using far-ultraviolet circular dichroism). At the optimal conditions for fibril formation (pH 2.0, T = 57 degrees C), on-line static light-scattering shows the formation of fibrils after a concentration-independent lag time of approximately 48 h. Nucleation presumably involves a change in the conformation of individual lysozyme molecules. Indeed, long-term circular dichroism measurements at pH 2.0, T = 57 degrees C show a marked change of the secondary structure of lysozyme molecules after approximately 48 h of heating. From atomic force microscopy we find that most of the fibrils have a thickness of approximately 4 nm. These fibrils have a coiled structure with a periodicity of approximately 30 nm and show characteristic defects after every four or five turns.     

Secretion of hen egg white lysozyme from Kluyveromyces lactis

Hen egg white (HEW) lysozyme was correctly processed and efficiently secreted from an alternative yeast, Kluyveromyces lactis. We constructed secretion vectors using PHO5, PGK, and LAC4 promoters, and found that the highest secretion was obtained under the direction of the PGK promoter in non-selective rich medium. K. lactis secreted HEW lysozyme with two-fold higher efficiency than S. cerevisiae, estimated by using a K. lactis-S. cerevisiae shuttle vector.     

Stabilization of hen egg white lysozyme by a cavity-filling mutation

Stabilization of a protein using cavity-filling strategy has hardly been successful because of unfavorable van der Waals contacts. We succeeded in stabilizing lysozymes by cavity-filling mutations. The mutations were checked by a simple energy minimization in advance. It was shown clearly that the sum of free energy change caused by the hydrophobicity and the cavity size was correlated very well with protein stability. We also considered the aromatic-aromatic interaction. It is reconfirmed that the cavity-filling mutation in a hydrophobic core is a very useful method to stabilize a protein when the mutation candidate is selected carefully.     

Production of15N-labelled hen egg white lysozyme usingAspergillus niger

Summary Aspergillus niger has been used as a host organism for the production of¹⁵N-labelled hen egg white lysozyme (HEWL). In order to achieve maximum incorporation of label, strains expressing the HEWL gene were grown in medium containing ammonium¹⁵N chloride as sole nitrogen source. Yields of HEWL protein were reduced relative to those obtained on more complex media. Gains in yield using complex media were offset by reduction in¹⁵N incorporation. No differences in either yield or kinetics of production were observed when ammonium¹⁵N chloride was replaced by unlabelled ammonium chloride as sole nitrogen source. Yields of¹⁵N-HEWL produced in this way are adequate for, and offer considerable advantages to, NMR studies of structure and folding of mutant and wild-type lysozymes.     

Structural details at active site of hen egg white lysozyme with di- and trivalent metal ions

Metal binding to lysozyme has received wide interest. In particular, it is interesting that Ni2+, Mn2+, Co2+, and Yb3+ chloride salts induce an increase in the solubility of the tetragonal form in crystals of hen egg white lysozyme at high salt concentration, but that Mg2+ and Ca2+ chloride salts do not. To investigate the interactions of the di- and trivalent metal ions with the active site of lysozyme and compare the effects of the di- and trivalent metal ions on molecular conformation of lysozyme based on the structural analysis, the crystal structures of hen egg white lysozyme grown at pH 4.6, in the presence of 0.5 M MgCl2, CaCl2, NiCl2, MnCl2, CoCl2, and YbCl3, have been determined by X-ray crystallography at 1.58 A resolution. The crystals grown in these salts have an identical space group, P4(3)2(1)2. The molecules show no conformational changes, irrespective of the salts used. Ni2+ and Co2+ binding to the Odelta atom of Asp52 in the active site at 1.98 and 2.02 A, respectively, and Yb3+ binding to both the Odelta atom of Asp52 and the Odelta1 atom of Asn46 at 2.25 A have been identified. The binding sites of Mn2+, Mg2+, and Ca2+ have not been found from different Fourier electron density maps. The Ni2+ and Co2+ ions bind to the Odelta atom of Asp52 at almost the same position, while the Yb3+ ion takes a different position from the Ni2+ and Co2+ ions. On the other hand, the anion Cl-, interacting with the Oeta atom of Tyr23 at a site of about 2.90 A, has also been determined for each crystal.     

Crystalline monoclonal antibody Fabs complexed to hen egg white lysozyme

The Fab of a monoclonal anti-lysozyme antibody (HyHEL-10) has been crystallized as the free Fab and as the Fab-antigen complex. Crystals have also been grown of the antigen complex of the Fab of another monoclonal anti-lysozyme antibody (HyHEL-9), which recognizes a different binding surface of lysozyme. All three crystals diffract to at least 3 A resolution and are suitable for X-ray diffraction studies.     

Mixed macromolecular crowding inhibits amyloid formation of hen egg white lysozyme

The effects of two single macromolecular crowding agents, Ficoll 70 and bovine serum albumin (BSA), and one mixed macromolecular crowding agent containing both BSA and Ficoll 70, on amyloid formation of hen egg white lysozyme have been examined by thioflavin T binding, Congo red binding, transmission electron microscopy, and activity assay, as a function of crowder concentration and composition. Both the mixed crowding agent and the protein crowding agent BSA at 100 g/l almost completely inhibit amyloid formation of lysozyme and stabilize lysozyme activity on the investigated time scale, but Ficoll 70 at the same concentration neither impedes amyloid formation of lysozyme effectively nor stabilizes lysozyme activity. Further kinetic and isothermal titration calorimetry analyses indicate that a mixture of 5 g/l BSA and 95 g/l Ficoll 70 inhibits amyloid formation of lysozyme and maintains lysozyme activity via mixed macromolecular crowding as well as weak, nonspecific interactions between BSA and nonnative lysozyme. Our data demonstrate that BSA and Ficoll 70 cooperatively contribute to both the inhibitory effect and the stabilization effect of the mixed crowding agent, suggesting that mixed macromolecular crowding inside the cell may play a role in posttranslational quality control mechanism.     

Formation of amyloid fibrils from fully reduced hen egg white lysozyme

The fully reduced hen egg white lysozyme (HEWL), which is a good model of random coil structure, has been converted to highly organized amyloid fibrils at low pH by adding ethanol. In the presence of 90% (v/v) ethanol, the fully reduced HEWL adopts beta-sheet secondary structure at pH 4.5 and 5.0, and an alpha-to-beta transition is observed at pH 4.0. A red shift of the Congo red absorption spectrum caused by the precipitation of the fully reduced HEWL in the presence of 90% (v/v) ethanol is typical of the presence of amyloid aggregation. EM reveals unbranched fibrils with a diameter of 2-5 nm and as long as 1-2 microm. The pH dependence of the initial structure of the fully reduced HEWL in the presence of 90% (v/v) ethanol suggests that Asp and His residues may play an important role.     

Pressure effect on denaturant-induced unfolding of hen egg white lysozyme.

The influence of hydrostatic pressure (< or =100 MPa) on denaturant-induced unfolding of hen egg white lysozyme was investigated by means of ultraviolet spectroscopy at various temperatures. Assuming a two-state transition model, the dependence of Gibbs free-energy change of unfolding on the denaturant concentration was calculated. Under applied hydrostatic pressure, these data were interpreted as suggesting that a two-state model is not applicable in a restricted temperature range; the dominant effect of hydrostatic pressure is to affect the cooperativity in protein unfolding due to a chemical equilibrium shift in the direction of the reduction in the system volume. The deviation from the two-state transition model appears to be rationalized by assuming that applied pressure induces an intermediate conformation between the native and unfolded states of the protein. The implication of the thermodynamic stability of protein under pressure was discussed.     

Type I collagen prevents amyloid aggregation of hen egg white lysozyme

Both collagen and amyloidogenic proteins have an inherent ability to undergo a self-assembly process leading to formation of supramolecular structures. Though our understanding of collagen–amyloid link is very poor, a few experimental evidences have indicated the protective nature of collagen against amyloid fibril formation. To further our understanding of collagen–amyloid relationship, we have explored the role of type I collagen on amyloid-aggregation of lysozyme. Thioflavin-T assay data indicated strong inhibition of both spontaneous and seeded aggregation of lysozyme by collagen. Both chemical and thermal denaturation experiments have showed increased lysozyme stability in the presence of collagen. However, the presence of collagen did not alter lysozyme activity. These findings confirm that type I collagen is capable of blocking or interfering with the amyloid aggregation of lysozyme, and the results may have significant implications for the design of collagen based therapeutics against aggregation of disease linked amyloidogenic proteins.     

The effect of tri-N-acetylglucosamine on hydrogen exchange in hen egg white lysozyme

Tritium-hydrogen isotope exchange techniques have been employed to study the effect of tri-N-acetylglucosamine binding on the conformational dynamics of hen egg white lysozyme. Numerical Laplace inversion of the data provides exchange rate probability density functions that reveal three overlapping peaks for both the free enzyme and (GlcNAc)3-enzyme complex. Binding of (GlcNAc)3 decreases the exchange rates of all protons to some extent with by far the largest effect being observed for the slow exchanging protons. These have been located, by comparison with neutron diffraction results (Mason, S. A., Bentley, G. A., and McIntyre, G. J. (1984) in Neutrons in Biology (Schoenborn, B. P., ed) pp. 323-334, Plenum Press, New York), within the beta-sheet structure and on helices (8-13), (28-34), and (89-97), that define the edges of the so-called "hydrophobic box" in lysozyme. The regions of the protein that are most affected by binding (GlcNAc)3, as revealed by hydrogen exchange, are found to be quite distinct from the regions observed to undergo conformational changes by x-ray diffraction. Most of these segments of the protein are located at some distance from the (GlcNAc)3-binding site itself. Two segments (the beta-sheet and helix (28-34)) are closely associated with the two active-site carboxylate groups. These results suggest that exchange-stable regions having strong, highly organized hydrogen bonding may have an important role in catalytic function and the differential propagation of conformational and dynamic perturbations caused by ligand binding at distant sites on the protein.     

Relation between hen egg white lysozyme and bacteriophage T4 lysozyme: Evolutionary implications

Hen egg white lysozyme and T4 bacteriophage lysozyme have the same catalytic function, but have non-homologous amino acid sequences. Notwithstanding the differences in their primary structures, the two lysozymes have similarities in their overall backbone conformations, in their modes of binding substrates and probably in their mechanisms of action.By different criteria, the similarity between the folding of the two enzymes can be shown to be statistically significant. Also the transformation which optimizes the agreement between the backbones of the two molecules is shown to accurately align their active site clefts, so that saccharide units bound in the A, B, C and D subsites of hen egg white lysozyme coincide within 1 to 2 Å with analogous saccharides bound to phage lysozyme. Furthermore, a number of the specific interactions between enzyme and substrate which were observed for hen egg white lysozyme, and thought to be important for catalysis, are found to occur in a structurally analogous way in the phage enzyme. Fifty-four atoms from the respective active sites which appear to be equivalent, including saccharides bound in the B and C sites, superimpose with a root-mean-square discrepancy of 1.35 Å.These structural and functional similarities suggest that the two lysozymes have arisen by divergent evolution from a common precursor. This is the first case in which two proteins of completely different amino acid sequence have been shown, with high probability, to have evolved by divergent rather than convergent evolution.     

L-Arginine increases the solubility of unfolded species of hen egg white lysozyme

L-Arginine (L-Arg) has been widely used as an enhancer of protein renaturation. The mechanism behind its action is still not fully understood. Using hen egg white lysozyme as a model protein, we present data that clearly demonstrate the suppression of the aggregation of denatured protein by L-Arg. By chemical modification of free cysteines, a series of unfolded lysozyme species were obtained that served as models for unfolded and intermediate states during the process of oxidative refolding. An increased equilibrium solubility of unfolded species and intermediates in the presence of L-Arg seems to be its major mechanism of action.     

Tolerance of point substitution of methionine for isoleucine in hen egg white lysozyme

X-ray structure determination of proteins by using the multiple-wavelength anomalous dispersion method targeting selenomethionine is now widely employed. Isoleucine was examined for the second choice of the substitution of methionine next to leucine. We performed a systematic mutational study of the substitutions of methionine for isoleucine. All mutated lysozymes were less stable than the wild-type by about 1 kcal/mol and it is suggested that this instability was caused by the change in residual hydrophobicity from isoleucine to methionine. The X-ray structures of all mutant lysozymes were very similar to that of the wild-type. In addition, both the accessible surface areas and the conformation of the side chain of methionine in all mutant lysozymes were similar to those of the side chain at the respective isoleucine in the wild-type. Therefore, it is suggested that the mutation from isoleucine to methionine in a protein can be considered as a "safe" substitution.     

Recovery of lysozyme from hen egg white by selective magnetic cake filtration

A new concept for the improvement of the downstream processing and purification is the so‐called magnetic separation. By using surface functionalized magnetic substrate particles, which selectively adsorb the target product, it can be directly separated out of a crude bioprocess stream. These methods are already used for analytical purposes, where only small amounts of functionalized particles are necessary. To apply the same concept at a larger scale, effective and economical procedures have to be provided. First, suitable process equipment has to be developed. Second, the magnetic particles have to be manufactured with a stable surface functionalization and long‐term stability for their reuse. Up to now mainly high‐gradient magnetic separation filter devices are applied for selective magnetic separation. They consist of a magnetic matrix in which the magnetic particles are trapped. In this work, a new magnetic filter is introduced that overcomes the capacity limitations of the current high‐gradient magnetic separation technology. The principle is demonstrated by selective recovery of lysozyme from hen egg white. Prior to the separation experiments magnetic beads with a strong acid cation‐exchange surface functionalization are synthesized. The separation procedure is implemented in only one unit operation. With the implementation of the displacement elution sequence lysozyme can be separated out of a hen egg white solution with a purification factor of PF=36 and a purity P=0.83.