Results for “Lysozyme” — Page 5

NASA NTRS2000

Preparation and Characterization of Fluorescent Derivatives of Chicken Egg White Lysozyme

Fluorescence is one of the most versatile and powerful tools for the study of macromolecules. While most proteins are intrinsically fluorescent, working at crystallization concentrations require the use of covalently prepared derivatives added as tracers. This approach requires derivatives that do not markedly affect the crystal packing. We have prepared a number of fluorescent derivatives of chicken egg white lysozyme with probes bound to one of two different sites on the protein molecule. Lucifer yellow, cascade blue, and 5-(2-aminoethyl)aminonapthalene-l-sulfonic acid (EDANS) have been attached to the side chain carboxyl of asp101 using a carbodiimide coupling procedure. asp101 lies within the active site cleft, and it is believed that the probes are at least partially "buried" within that cleft. Lucifer yellow and MANS probes with iodoacetamide reactive groups have been bound to hisl5, located on the "back side" of the molecule relative to the active site. The fluorescently labeled protein is readily purified from the starting material by cation exchange chromatography. All the derivatives fluoresce in both the solution and the crystalline states. Fluorescence characterization has focused on determining the bound probe quantum yields, lifetimes, absorption and emission spectra, and quenching by added solutes in comparison to the free probe. No appreciable changes are found in the lifetimes of any of the probes except for cascade blue, where Tau(sub free) = 3.52 ns vrs Tau(sub bound) = 2.8 ns. Spectral shifts are found in most cases. Particularly strong quenching upon binding is found in the case of the cascade blue derivative, likely due to probe interactions with the active site cleft. While none of the asp101 bound probes are well quenched by commonly employed solutes, such as potassium and sodium iodide, acrylamide, primuline, the chloride salts of manganese, cesium, and cobalt, trifluoroacetamide, trichloroethanol, and thallium iodide, in those cases where quenching is observed the bound probe is less efficiently quenched relative to the free probe. This indicates that the bound probes are less accessible to the bulk solution, an expected finding for attachment within the active site cleft. Attempts have been made to bind other molecules to these sites, with varying success. Interestingly, all three probes contain one or more sulfonate ((Ar-S03)-) groups. We have not been successful in binding analogous probes without sulfate groups such as pyrene, or with derivatized sulfonate groups such as dansyl type probes, analogous to MANS but where the sulfonate group is derivatized, Ar-S02-N2C2H7. None of the probes is rigidly bound to the protein, i.e., they all have a probe motion superimposed on that of the protein.

Sumida, John↗

NASA NTRS2001

Preparation and Preliminary Characterization of Crystallizing Fluorescent Derivatives of Chicken Egg White Lysozyme

Fluorescence is one of the most versatile and powerful tools for the study of macromolecules. While most proteins are intrinsically fluorescent, working at crystallization concentrations require the use of covalently prepared derivatives added as tracers. This approach requires derivatives that do not markedly affect the crystal packing. We have prepared fluorescent derivatives of chicken egg white lysozyme with probes bound to one of two different sites on the protein molecule. Lucifer yellow and 5-(2-aminoethyl)aminonapthalene-1-sulfonic acid (EDANS) have been attached to the side chain carboxyl of Asp(sup 101) using a carbodiimide coupling procedure. Asp(sup 101) lies within the active site cleft, and it is believed that the probes are "buried" within that cleft. Lucifer yellow and MANS probes with iodoacetamide reactive groups have been bound to His(sup 15), located on the "back side" of the molecule relative to the active site. All the derivatives fluoresce in the solution and the crystalline states. Fluorescence characterization has focused on determination of binding effects on the probe quantum yield, lifetime, absorption and emission spectra, and quenching by added solutes. Quenching studies show that, as postulated, the Asp(sup 101)-bound probes are partially sheltered from the bulk solution by their location within the active site cleft. Probes bound to His(sup 15) have quenching constants about equal to those for the free probes, indicating that this site is highly exposed to the bulk solution.

Sumida, John↗

NASA NTRS2001

Preparation and Preliminary Characterization of Crystallizing Fluorescent Derivatives of Chicken Egg White Lysozyme

Fluorescence is one of the most versatile and powerful tools for the study of macromolecules. While most proteins are intrinsically fluorescent, working at crystallization concentrations require the use of covalently prepared derivatives added as tracers. This approach requires derivatives that do not markedly affect the crystal packing. We have prepared fluorescent derivatives of chicken egg white lysozyme with probes bound to one of two different sites on the protein molecule. Lucifer yellow and 5-(2-aminoethyl)aminonapthalene-i-sulfonic acid (EDANS) have been attached to the side chain carboxyl of Asp(sup 101) using a carbodiimide coupling procedure. Asp(sup 101) lies within the active site cleft, and it is believed that the probes are 'buried' within that cleft. Lucifer yellow and MANS probes with iodoacetamide reactive five groups have been bound to His(sup 15), located on the 'back side' of the molecule relative to the active site. All the derivatives fluoresce in the solution and the crystalline states. Fluorescence characterization has focused on determination of binding effects on the probe quantum yield, lifetime, absorption and emission spectra, and quenching by added solutes. Quenching studies show that, as postulated, the Asp(sup 101)-bound probes are partially sheltered from the bulk solution by their location within the active site cleft. Probes bound to His(sup 15) have quenching constants about equal to those for the free probes, indicating that this site is highly exposed to the bulk solution.

Sumida, John P.↗

NASA NTRS1999

Buffer Effects in the Solubility, Nucleation and Growth of Chicken Egg White Lysozyme

The growth of protein crystals is important for determination of their three-dimensional structure, which relates to their biochemical functions and to the practical goal of designing pharmaceuticals to modify that function. While many proteins have been successfully crystallized by a variety of methods, there is still limited understanding of the process of nucleation and growth of even the simplest proteins. Chicken egg-white lysozyme (CEWL) is readily crystallized under a variety of conditions, and studies underway at MSFC are designed to elucidate the mechanisms by which the crystals nucleate and grow. We have investigated the effect of buffer choice on the solubility, nucleation and growth of CEWL. CEWL was purified by dialysis against a .05M phosphate buffer and chromatographic separation from contaminants in a sepharose column. Solubility studies were made as a function of buffer concentration for phosphate and formate buffers, and the nucleation and growth of crystals at 10 C was studied as a function of pH for oxalate, succinate, formate, butyrate, carbonate, phosphate and acetate buffer solutions. The solubility data support the conclusion that there is a solubility minimum as a function of buffer concentration for amphiphilic molecules, while no minimum is observed for a phosphate buffer. Nucleation is suppressed at pH greater than pKa for all buffers except phosphate. The aspect ratio of the (110) faces is shown to be a function of crystal size, rather than pH.

Gibson, Ursula J.↗

NASA NTRS2002

A Proposed Pathway for the Nucleation and Crystal Growth of the Tetragonal Form of Lysozyme

A number of factors, the shape and charge distribution anisotropy, multiple components in the solution (buffer + counter ion, precipitant, protein, and water), conformational flexibility, and large numbers of intermolecular contacts, all serve as complicating variables in understanding the nucleation and growth mechanism for macromolecules. Intermolecular contacts include hydrogen bonds, van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and give specificity while the others are weaker, more prevalent, and more promiscuous, i.e., can lead to a range of possible molecular interactions. We propose that for tetragonal lysozyme, and by extension many other monomeric proteins, there is a solution-phase assembly process to form 4(sub 3) helix structures that are the basic unit for nucleation. The formation of these structures is continuous and concentration dependent. They subsequently also servc as growth units, with that process then being a recapitulation of the nucleation process. The advantages of solution phase assembly are the immediate burying of the strongest interactions, removing them from subsequent participation in the nucleation and growth process, and the introduction of symmetry into the system, which also assists in the assembly process.

Pusey, Marc L.↗

NASA NTRS2002

A Model for Tetragonal Lysozyme Crystal Nucleation and Growth

Macromolecular crystallization is a complex process, involving a system that typically has 5 or more components (macromolecule, water, buffer + counter ion, and precipitant). Whereas small molecules have only a few contacts in the crystal lattice, macromolecules generally have 10's or even 100's of contacts between molecules. These can range from hydrogen bonds (direct or water-mediated), through van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and require some specificity in the molecular alignment, while the others are weaker, more prevalent, and more promiscuous, i.e., can be readily broken and reformed between other sites. Formation of a consistent, ordered, 3D structure may be difficult or impossible in the absence of any or presence of too many strong interactions. Further complicating the process is the inherent structural asymmetry of monomeric (single chain) macromolecules. The process of crystal nucleation and growth involves the ordered assembly of growth units into a defined 3D lattice. We suggest that for many macromolecules, particularly those that are monomeric, this involves a preliminary solution-phase assembly process into a growth unit having some symmetry prior to addition to the lattice, recapitulating the initial stages of the nucleation process. If this model is correct then fluids and crystal growth models assuming a strictly monodisperse nutrient solution need to be revised. This model has been developed from experimental evidence based upon face growth rate, AFM, and fluorescence energy transfer data for the nucleation and growth of tetragonal lysozyme crystals.

Pusey, Marc L.↗

NASA NTRS2002

Tetragonal Lysozyme Nucleation and Crystal Growth: The Role of the Solution Phase

Experimental evidence indicates a dominant role of solution phase interactions in nucleating and growing tetragonal lysozyme crystals. These interactions are extensive, even at saturation, and may be a primary cause of misoriented regions in crystals grown on Earth. Microgravity, by limiting interfacial concentrations to diffusion-controlled levels, may benefit crystal quality by also reducing the extent of associated species present at the interface.

Pusey, Marc L.↗

NASA NTRS2003

X-Ray Diffraction and Imaging Study of Imperfections of Crystallized Lysozyme with Coherent X-Rays

Phase-sensitive x-ray diffraction imaging and high angular-resolution diffraction combined with phase contrast radiographic imaging are employed to characterize defects and perfection of a uniformly grown tetragonal lysozyme crystal in symmetric Laue case. The fill width at half-maximum (FWHM) of a 4 4 0 rocking curve measured from the original crystal is approximately 16.7 arcseconds, and defects, which include point defects, line defects, and microscopic domains, have been clearly observed in the diffraction images of the crystal. The observed line defects carry distinct dislocation features running approximately along the <110> growth front, and they have been found to originate mostly at a central growth area and occasionally at outer growth regions. Individual point defects trapped at a crystal nucleus are resolved in the images of high sensitivity to defects. Slow dehydration has led to the broadening of the 4 4 0 rocking curve by a factor of approximately 2.4. A significant change of the defect structure and configuration with drying has been revealed, which suggests the dehydration induced migration and evolution of dislocations and lattice rearrangements to reduce overall strain energy. The sufficient details of the observed defects shed light upon perfection, nucleation and growth, and properties of protein crystals.

Hu, Zheng-Wei↗

NASA NTRS2003

Modeling Tetragonal Lysozyme Crystal Growth Rates

Tetragonal lysozyme 110 face crystal growth rates, measured over 5 orders of magnitude in range, can be described using a model where growth occurs by 2D nucleation on the crystal surface for solution supersaturations of c/c(sub eq) less than or equal to 7 +/- 2. Based upon the model, the step energy per unit length, beta was estimated to be approx. 5.3 +/- 0.4 x 10(exp -7) erg/mol-cm, which for a step height of 56 A corresponds to barrier of approx. 7 +/- 1 k(sub B)T at 300 K. For supersaturations of c/c(sub eq) > 8, the model emphasizing crystal growth by 2D nucleation not only could not predict, but also consistently overestimated, the highest observable crystal growth rates. Kinetic roughening is hypothesized to occur at a cross-over supersaturation of c/c(sub eq) > 8, where crystal growth is postulated to occur by a different process such as adsorption. Under this assumption, all growth rate data indicated that a kinetic roughening transition and subsequent crystal growth by adsorption for all solution conditions, varying in buffer pH, temperature and precipitant concentration, occurs for c/c(sub eq)(T, pH, NaCl) in the range between 5 and 10, with an energy barrier for adsorption estimated to be approx. 20 k(sub B)T at 300 K. Based upon these and other estimates, we determined the size of the critical surface nucleate, at the crossover supersaturation and higher concentrations, to range from 4 to 10 molecules.

Gorti, Sridhar↗

NASA NTRS2003

Kinetic Roughening and Energetics of Tetragonal Lysozyme Crystal Growth

Lysozyme crystal growth rates over 5 orders of magnitude in range can be described using a layer-by-layer model where growth occurs by 2D nucleation on the crystal surface. Based upon the 2D nucleation model of layer growth, the effective barrier for growth was determined to be gamma = 1.3 plus or minus 0.3 x 10(exp -13) erg/molecule, corresponding to a barrier of 3.2 plus or minus 0.7 k(sub B)T, at 22 C. For solution supersaturation, In c/c(sub eq) greater than or equal to 1.9 plus or minus 0.2, the nucleation model would not predict or consistently estimate the highest observable crystal growth rates. As such, a kinetic roughening hypothesis where crystal growth occurs by a continuous mode was implemented for all growth rate data obtained above In c(sub r)/c(sub eq) greater than or equal to 2. That is, independent of the solution conditions that vary with either buffer pH, temperature or precipitant concentration, crystal growth occurs by the continuous addition of molecules anywhere on the crystal surface, above a roughening solution supersaturation. The energy barrier, E(sub c), for the continuous growth process is determined as 6.1 plus or minus 0.4 x 10(exp -13) erg/molecule or 15 plus or minus 1 k(sub B)T at 22 C.

Gorti, Sridhar↗

NASA NTRS2004

Growth Modes and Energetics of 101 Face Lysozyme Crystal Growth

From analyses of lysozyme 101 face growth rate data using a 2D nucleation model for layer-by-layer growth, we find the effective barrier for crystal growth to be gamma = 1.0 +/- 0.2 x 10(exp -13) erg/molecule. The magnitude of the effective barrier is 2.4 +/- 0.5 k(sub beta)T, at 22 C. We also find that beyond a critical solution supersaturation, sigma(sub c), crystal growth rates are more accurately described by a kinetic roughening hypothesis. Beyond sigma(sub c), crystals grow by the continuous addition of molecules anywhere on the crystal surface rather than layer-by-layer. The magnitude of the critical supersaturation (sigma(sub c), = 1.7 +/- 0.2) for a crossover from a layer-by-layer to continuous growth is found to be statistically independent of the solution conditions that vary with buffer pH, temperature or precipitant concentration. Using the experimentally determined values for gamma and sigma(sub c), we find the crystal growth unit to be comprised of 7 +/- 3 molecules. The energy barrier, E(sub c), for the continuous addition of the growth Units is 6.2 +/- 0.3 x 10(exp -13) erg/molecule or 15 +/1 1 k(sub beta)T at 22C.

Gorti, Sridhar↗

NASA NTRS1999

Growth of (101) faces of tetragonal lysozyme crystals: measured growth-rate trends

Previous extensive measurements of the growth rates of the (110) face of tetragonal lysozyme crystals have shown unexpected dependencies on the supersaturation. In this study, similar growth-rate measurements were performed for the (101) faces of the crystals. The data show a similar dependence on the supersaturation, becoming appreciable only at high supersaturations, reaching a maximum value and then decreasing. The (101) growth rates are larger at low supersaturations than the (110) growth rates under the same conditions and are smaller at high supersaturations. These trends suggest that the growth mechanism of the (101) face is similar to that of the (110) face: both processes involve the addition of multimeric growth units formed in solution, but the average size of the units for the (101) face is likely to be smaller than for the (110) face.

Egg Proteins/chemistry↗

NASA NTRS2004

Diffraction and imaging study of imperfections of crystallized lysozyme with coherent X-rays

Phase-contrast X-ray diffraction imaging and high-angular-resolution diffraction combined with phase-contrast radiographic imaging were employed to characterize defects and perfection of a uniformly grown tetragonal lysozyme crystal in the symmetric Laue case. The full-width at half-maximum (FWHM) of a 4 4 0 rocking curve measured from the original crystal was approximately 16.7 arcsec and imperfections including line defects, inclusions and other microdefects were observed in the diffraction images of the crystal. The observed line defects carry distinct dislocation features running approximately along the <1 1 0> growth front and have been found to originate mostly in a central growth area and occasionally in outer growth regions. Inclusions of impurities or formations of foreign particles in the central growth region are resolved in the images with high sensitivity to defects. Slow dehydration led to the broadening of a fairly symmetric 4 4 0 rocking curve by a factor of approximately 2.6, which was primarily attributed to the dehydration-induced microscopic effects that are clearly shown in X-ray diffraction images. The details of the observed defects and the significant change in the revealed microstructures with drying provide insight into the nature of imperfections, nucleation and growth, and the properties of protein crystals.

Muramidase/chemistry↗

NASA NTRS1997

Growth Mechanism of the (110) Face of Tetragonal Lysozyme Crystals

The measured macroscopic growth rates of the (110) face of tetragonal lysozyme show an unexpectedly complex dependence on the supersaturation. In earlier studies it has been shown that an aggregate growth unit could account for experimental growth-rate trends. In particular molecular packing and interactions in the growth of the crystal were favored by completion of the helices along the 4, axes. In this study the molecular orientations of the possible growth units and the molecular growth mechanism were identified. This indicated that growth was a two-step process: aggregate growth units corresponding to the 4, helix are first formed in the bulk solution by stronger intermolecular bonds and then attached to the crystal face by weaker bonds. A more comprehensive analysis of the measured (110) growth rates was also undertaken. They were compared with the predicted growth rates from several dislocation and two-dimensional nucleation growth models, employing tetramer and Octamer growth units in polydisperse solutions and monomer units in monodisperse solutions. The calculations consistently showed that the measured growth rates followed the expected model relations with octamer growth units, in agreement with the predictions from the molecular level analyses.

Nadarajah, Arunan↗

DOE OSTI2020