A biophysical model of lysozyme self-association

Exploring exchange processes in proteins by paramagnetic perturbation of NMR spectra

The effect of extrinsic paramagnetic probes on NMR relaxation rates for surface mapping of proteins and other biopolymers is a widely investigated and powerful NMR technique. Here we describe a new application of those probes. It relies on the setting of the relaxation delay to generate magnetization equilibrium and off-equilibrium conditions, in order to tailor the extent of steady state signal recovery with and without the water-soluble nitroxide Tempol. With this approach it is possible to identify signals whose relaxation is affected by exchange processes and, from the relative assignments, to map the protein residues involved in association or conformational interconversion processes on a micro-to-millisecond time scale. This finding is confirmed by the comparison with the results obtained from relaxation dispersion measurements. This simple and convenient method allows preliminary inspection to highlight regions where structural or chemical exchange events are operative, in order to focus on quantitative subsequent determinations by transverse relaxation dispersion experiments or analogous NMR relaxation studies, and/or to gain insights into the predictions of calculations.

The Native Monomer of Bacillus Pumilus Ribonuclease Does Not Exist Extracellularly

Supported by crystallography studies, secreted ribonuclease of Bacillus pumilus (binase) has long been considered to be monomeric in form. Recent evidence obtained using native polyacrylamide gel electrophoresis and size-exclusion chromatography suggests that binase is in fact dimeric. To eliminate ambiguity and contradictions in the data we have measured conformational changes, hypochromic effect, and hydrodynamic radius of binase. The immutability of binase secondary structure upon transition from low to high protein concentration was registered, suggesting the binase dimerization immediately after translocation through the cell membrane and leading to detection of binase dimers only in the culture fluid regardless of ribonuclease concentration. Our results made it necessary to take a fresh look at the binase stability and cytotoxicity towards virus-infected or tumor cells.

Combination of endolysins and high pressure to inactivate Listeria monocytogenes

Outbreaks of listeriosis are often related to the consumption of low-processed ready-to-eat food products (e.g. soft cheeses or smoked fish) contaminated with Listeria monocytogenes. Traditional preservation techniques, such as heat treatment, cannot eliminate Listeria from these products without strongly affecting the quality of the foods. We therefore investigated the use of endolysin (PlyP40, Ply511, or PlyP825) in combination with high hydrostatic pressure processing to kill L. monocytogenes in buffer. The results demonstrated a more than additive effect when both treatments were combined. For example, whereas 0.16 μg/mL PlyP825 or 300 MPa (1 min, 30 °C) applied individually reduced the cell count by 0.2 and 0.3 log cfu, respectively, a combined treatment resulted in a reduction of 5.5 log cfu. Similar results were obtained for the other endolysins combined with high pressure processing. We also showed that the synergistic inactivation of cells by endolysin and HHP is possible at a pressure level of only 200 MPa (2 min, 30 °C). Thus, the application of endolysins did not only substantially increase the bactericidal effect of high pressure, but it also enabled the inactivation of bacterial cells at much lower pressure levels. This shows the potential of using such combined processes for the inactivation of L. monocytogenes and food preservation.

Interaction between lysozyme and poly(acrylic acid) microgels

The interaction between lysozyme and oppositely charged poly(acrylic acid) microgels was investigated by micromanipulator-assisted light microscopy, confocal microscopy and circular dichroism. Lysozyme uptake and distribution within the microgel particles, and its effect on microgel deswelling, was studied regarding effects of pH, ionic strength and lysozyme concentration. For a range of conditions, lysozyme distributes nonuniformly within the microgels, forming a lysozyme/microgel shell in the outer parts of the microgel. This shell formation is associated both with increased lysozyme loading to the microgels and with increased lysozyme-induced microgel deswelling. At high microgel charge density, the shell formation displays nonmonotonic ionic strength dependence. The shells formed are characterized by a net positive charge, and by relatively fast exchange of lysozyme between shell and solution, although the exchange kinetics decreases strongly with decreasing ionic strength. At conditions of slower exchange kinetics, the shells are characterized by an effective pore size of less than about 4 nm.

The stability and formation of native proteins from unfolded monomers is increased through interactions with unrelated proteins

The intracellular concentration of protein may be as high as 400 mg per ml; thus it seems inevitable that within the cell, numerous protein-protein contacts are constantly occurring. A basic biochemical principle states that the equilibrium of an association reaction can be shifted by ligand binding. This indicates that if within the cell many protein-protein interactions are indeed taking place, some fundamental characteristics of proteins would necessarily differ from those observed in traditional biochemical systems. Accordingly, we measured the effect of eight different proteins on the formation of homodimeric triosephosphate isomerase from Trypanosoma brucei (TbTIM) from guanidinium chloride unfolded monomers. The eight proteins at concentrations of micrograms per ml induced an important increase on active dimer formation. Studies on the mechanism of this phenomenon showed that the proteins stabilize the dimeric structure of TbTIM, and that this is the driving force that promotes the formation of active dimers. Similar data were obtained with TIM from three other species. The heat changes that occur when TbTIM is mixed with lysozyme were determined by isothermal titration calorimetry; the results provided direct evidence of the weak interaction between apparently unrelated proteins. The data, therefore, are strongly suggestive that the numerous protein-protein interactions that occur in the intracellular space are an additional control factor in the formation and stability of proteins.

Lysozyme dimerization: Brownian dynamics simulation

The lysozyme dimerization reaction has been studied within the framework of encounter-complex (EC) formation theory using the MacroDox software package. Two types of energetically favorite ECs were determined. In the first of them, active-center amino acids of lysozyme take part in the complex formation or the second molecule blocks accessibility to active center sterically. Epitope amino-acid residues are involved in the complex of type II. The existence of both types of complexes does not contradict experimental data. Dimer-formation rate constants for different kinds of EC were calculated. Increasing the pH from 2.0 to 10.0 decreases the total positive lysozyme charge and eliminates the unfavorable repulsive electrostatic interaction. The rate constant of EC formation is inversely proportional to the protein total charge. The association rate constant was also enhanced by an increase of ionic strength that screened repulsive electrostatic interaction between positively charged proteins.

Multilayers of a Globular Protein and a Weak Polyacid: Role of Polyacid Ionization in Growth and Decomposition in Salt Solutions

Thin films obtained from a layer-by-layer deposition of a weak polycarboxylic acid and a positively charged globular protein were studied by in situ ATR-FTIR. The system was chicken egg lysozyme (Lys), bovine pancrease ribonuclease A (RNase), or bovine gamma-globulin (IgG) self-assembled with polycarboxylic acids. When the pH value was lowered below a critical point, the growth of films and their tolerance to decomposition by added sodium chloride improved dramatically. Stabilization of protein/polyacid films in salt solutions at lower pH values occurred due to the onset of nonelectrostatic interactions to intermolecular binding within protein/polyacid multilayers and was controlled by polyacid ionization within the film rather than the pH of the external solution. A fractional ionization of polyacid in the pH-stabilization region was lower with protein-containing films than for polyacid/linear polycation films, reflecting hindrance of the inter-association of protonated carboxylic groups by protein globules. Practical ramifications of the pH-stabilization effect might extend to areas of biotechnology and biomaterials.

Identification of amino acid residues participating in intermolecular salt bridges between self-associating proteins

Salt bridges between self-associating hen egg white (HEW) lysozyme and bovine insulin molecules were converted to covalent links by ethanedinitrile (cyanogen) and identified using mass spectrometry. Peptides resulting from cyanogen-mediated intermolecular cross-linking of HEW lysozyme were detected using in-gel digestion and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Sequence data from electrospray ionization-quadrupole-time of flight mass spectrometry (ESI-Q-TOF MS) revealed that one of the peptides has a covalent bond between Asp 66 and Arg 14. The self-assembly of bovine insulin was also investigated using cyanogen. Using high-performance liquid chromatography (HPLC) coupled with ESI-Q-TOF MS, an intermolecular salt bridge association was identified by covalently linking the B chain C-terminal carboxyl group of Ala 30 and the charged imidazole of His 5 (B chain). A method was developed incorporating cyanogen, enzymatic digestion, one-dimensional gel electrophoresis, MALDI-TOF MS, and HPLC ESI-Q-TOF MS to identify amino acid residues participating in salt bridge formations at protein-protein interfaces. The novelty of this approach is the ease with which cyanogen can be administered to a protein sample and the apparent lack of nonspecific cross-linking side reactions interfering with the analysis.

Monomer concentrations and dimerization constants in crystallizing lysozyme solutions by dialysis kinetics

Dialysis kinetics measurements have been made to study the effect of ionic strength on the dimerization of lysozyme in acidic solutions that lead to the growth of tetragonal lysozyme crystals. Using glutaraldehyde cross-linked dimers of lysozyme, we have determined that both monomers and dimers can escape from 25,000 molecular weight cutoff dialysis membranes with velocity constants of 5.1 x 10(-7) and 1.0 x 10(-7) s(-1) for the monomer and dimer species, respectively. The flux from 25K MWCO membranes has been measured for lysozyme in pH 4.0 buffered solutions of 1, 3, 4, 5, and 7% NaCl over a wide range of protein concentrations. Assuming that dimerization is the first step in crystallization, a simple monomer to dimer equilibrium was used to model the flux rates. Dimerization constants calculated at low protein concentrations were 265, 750, 1212, and 7879 M(-1) for 3, 4, 5, and 7% NaCl, respectively. These values indicate that dimerization increases with the ionic strength of the solution suggesting that aggregation is moderated by electrostatic interactions. At high protein concentrations and high supersaturation, the dimerization model does not describe the data well. However, the Li model that uses a pathway of monomer <-> dimer <-> tetramer <-> octamer <-> 16-mer fits the measured flux data remarkably well suggesting the presence of higher order aggregates in crystallizing solutions.