A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent

This study documents the feasibility of switching to an aprotic medium in sugar receptor research. The solvent change offers additional insights into mechanistic details of receptor--carbohydrate ligand interactions. If a receptor retained binding capacity in an aprotic medium, solvent-exchangeable protons of the ligand would not undergo transfer and could act as additional sensors, thus improving the level of reliability in conformational analysis. To probe this possibility, we first focused on hevein, the smallest lectin found in nature. The NMR-spectroscopic measurements verified complexation, albeit with progressively reduced affinity by more than 1.5 orders of magnitude, in mixtures of up to 50% dimethyl sulfoxide (DMSO). Since hevein lacks the compact beta-strand arrangement of other sugar receptors, such a structural motif may confer enhanced resistance to solvent exchange. Two settings of solid-phase activity assays proved this assumption for three types of alpha- and/or beta-galactoside-binding proteins, that is, a human immunoglobulin G (IgG) subfraction, the mistletoe lectin, and a member of the galectin family of animal lectins. Computer-assisted calculations and NMR experiments also revealed no conspicuous impact of the solvent on the conformational properties of the tested ligands. To define all possible nuclear Overhauser effect (NOE) contacts in a certain conformation and to predict involvement of exchangeable protons, we established a new screening protocol applicable during a given molecular dynamics (MD) trajectory and calculated population densities of distinct contacts. Experimentally, transferred NOE (tr-NOE) experiments with IgG molecules and the disaccharide Gal'alpha1-3Galbeta1-R in DMSO as solvent disclosed that such an additional crosspeak, that is, Gal'OH2--GalOH4, was even detectable for the bound ligand under conditions in which spin diffusion effects are suppressed. Further measurements with the plant lectin and galectins confirmed line broadening of ligand signals and gave access to characteristic crosspeaks in the aprotic solvent and its mixtures with water. Our combined biochemical, computational, and NMR-spectroscopical strategy is expected to contribute notably to the precise elucidation of the geometry of ligands bound to compactly folded sugar receptors and of the role of water molecules in protein--ligand (carbohydrate) recognition, with relevance to areas beyond the glycosciences.     

Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase

Penicillin acylase catalyses the condensation of Calpha-substituted phenylacetic acids with beta-lactam nucleophiles, producing semi-synthetic beta-lactam antibiotics. For efficient synthesis a low affinity for phenylacetic acid and a high affinity for Calpha-substituted phenylacetic acid derivatives is desirable. We made three active site mutants, alphaF146Y, betaF24A and alphaF146Y/betaF24A, which all had a 2- to 10-fold higher affinity for Calpha-substituted compounds than wild-type enzyme. In addition, betaF24A had a 20-fold reduced affinity for phenylacetic acid. The molecular basis of the improved properties was investigated by X-ray crystallography. These studies showed that the higher affinity of alphaF146Y for (R)-alpha-methylphenylacetic acid can be explained by van der Waals interactions between alphaY146:OH and the Calpha-substituent. The betaF24A mutation causes an opening of the phenylacetic acid binding site. Only (R)-alpha-methylphenylacetic acid, but not phenylacetic acid, induces a conformation with the ligand tightly bound, explaining the weak binding of phenylacetic acid. A comparison of the betaF24A structure with other open conformations of penicillin acylase showed that betaF24 has a fixed position, whereas alphaF146 acts as a flexible lid on the binding site and reorients its position to achieve optimal substrate binding.     

Ultrastructural investigation of intact orbital implant surfaces using atomic force microscopy

This study examined the surface nanostructures of three orbital implants: nonporous poly(methyl methacrylate) (PMMA), porous aluminum oxide and porous polyethylene. The morphological characteristics of the orbital implants surfaces were observed by atomic force microscopy (AFM). The AFM topography, phase shift and deflection images of the intact implant samples were obtained. The surface of the nonporous PMMA implant showed severe scratches and debris. The surface of the aluminum oxide implant showed a porous structure with varying densities and sizes. The PMMA implant showed nodule nanostructures, 215.56 ± 52.34 nm in size, and the aluminum oxide implant showed crystal structures, 730.22 ± 341.02 nm in size. The nonporous PMMA implant showed the lowest roughness compared with other implant biomaterials, followed by the porous aluminum oxide implant. The porous polyethylene implant showed the highest roughness and severe surface irregularities. Overall, the surface roughness of orbital implants might be associated with the rate of complications and cell adhesion. SCANNING 33: 211–221, 2011. © 2011 Wiley Periodicals, Inc.     

Effect of phosphorus concentration on phosphorus removal and biomass

Membrane bioreactor (MBR) process was employed to study the effect of biological phosphorus removal (bio-P removal) and P-content in treated sludge with increased phosphorus concentration present in the wastewater. Further, the following four test fractions of raw wastewaters was obtained having different P-concentrations viz., run 1: P-20 mg/L, run 2: P-40 mg/L, run 3: P-60 mg/L, run 4: P-80 mg/L. The effective P-removal obtained for these four test fractions were found to be 23.07 mg/L (98.17%), 41.35 mg/L (88.16%), 45.75 mg/L (72.04%) and 55.80 mg/L (66.82%) respectively for run 1, 2, 3 and 4 fractions. Moreover, the similar increase in phosphorous concentration i.e., from 20 to 80 mg/L caused an apparent increase in total solid (TS) values from 7 to 8.3 g TS/L, whereas the total volatile solid (TVS) content remained constant (i.e. 4.5 g TVS/L). These results inferred that the proportion of TVS in the TS decreased from 70 to 55%. Moreover, by increasing the initial P-concentration from 20 to 80 mg/L, the corresponding P-proportion of excess sludge was increased from 2 to 6.2%.     

E(6) diffraction catastrophe of the primary rainbow of oblate water drops: observations with white-light and laser illumination

Oblate drops of water illuminated perpendicular to their symmetry axis exhibit catastrophe patterns near the primary-rainbow scattering angle. Previous patterns include the hyperbolic umbilic focal section and separate lips events [see, e.g., H. J. Simpson and P. L. Marston, Appl. Opt. 30, 3468 (1991)]. The present observations concern a much higher-order singularity analyzed by J. F. Nye [Proc. R. Soc. London Ser. A 438, 397 (1992)], the E(6) or symbolic umbilic, in the scattering by levitated drops with monochromatic and collimated white-light illumination. Photographs show the colors produced when the drop is illuminated by white light. The E(6) occurs when the Gaussian curvature of the scattered wave front vanishes in both principal directions, resulting in a high degree of directional focusing. This type of focusing, although only slightly explored, is applicable to the more general problem of scattering from penetrable spheroids.     

Absolute interferometric distance measurement using a FM-demodulation technique

We propose an interferometric method for measuring absolute distances larger than the wavelength. A laser diode is used as a light source. The principle of operation is based on multiple-wavelength interferometry that uses a modulated light source. This method uses the fact that the wavelength of light emitted by the laser diode can be varied by means of the injection current. The modulation of the injection current in combination with the optical heterodyne technique causes a high-frequency phase-modulated detector signal. The phase deviation of the signal is a measure of the optical path difference in the interferometer. By FM demodulation of the detector output with a phase-locked loop demodulator, the optical path difference can be determined directly without the classical ambiguity problem of interferometry. The measuring range in the experiments was limited to 50 mm by the maximum travel range of the used specimen translation stage. Because of the inherent light sensitivity of the method described, the rangefinder can be used for three-dimensional profile measurements on a wide variety of objects, even on diffuse scattering surfaces.     

Resolution and intensity distribution of output images reconstructed by sampled computer-generated holograms

We address reconstruction abilities of computer-generated holograms that are fabricated in a sampled form and designed for spherical-wave illumination. Our approach enables one to define the limit of resolution of the object reconstruction and the light-intensity distribution in an output plane. The analysis takes into account a hologram aperture, a sampling aperture, and a curvature radius of spherical illumination. Theoretical results are confirmed by experimental verification.     

Fluid jet polishing of optical surfaces

We present a new finishing process that is capable of locally shaping and polishing optical surfaces of complex shapes. A fluid jet system is used to guide a premixed slurry at pressures less than 6 bars to the optical surface. We used a slurry comprising water and 10% #800 SiC abrasives (21.8 mum) to reduce the surface roughness of a BK7 sample from 350 to 25 nm rms and to vary the shape of a polished sample BK7, maintaining its surface roughness of 1.6 nm rms, thereby proving both the shaping and polishing possibilities of the presented method.     

Rectangular surface-relief transmission gratings with a very large first-order diffraction efficiency (~95%) for unpolarized light

Computer optimization shows that the first-order diffraction efficiency of a lossless-transmission surface-relief grating with a rectangular surface profile can be made very large (~95%) simultaneously for light of TE and TM polarizations incident near the Bragg angle by the proper choice of the fill factor. The case for visible light incident close to the Bragg angle on unslanted gratings with periodicities corresponding to Bragg angles of 30 degrees , 37.5 degrees , and 45 degrees is presented. The refractive index of the grating material was chosen in the range between 1.2 and 2.     

Low-coherence fiber-optic sensor with a large numerical aperture for topographic measurements

We describe a compact fiber-optic setup for three-dimensional topometry. The measuring principle is based on low-coherence interferometry in combination with a confocal microscope. Integrating an optical arrangement based on compact disk optics together with fiber optics into one sensor yields a compact unit. The sensor has a numerical aperture of 0.45 and is suitable for measuring large surface slopes with high spatial resolution. Further, a depth measuring range of more than 1 mm can be achieved. The capabilities of our setup for three-dimensional measurements are demonstrated.