162 research outputs found
Electrostatic Interactions between Janus Particles
In this paper we study the electrostatic properties of `Janus' spheres with
unequal charge densities on both hemispheres. We introduce a method to compare
primitive-model Monte Carlo simulations of the ionic double layer with
predictions of (mean-field) nonlinear Poisson-Boltzmann theory. We also derive
practical DLVO-like expressions that describe the Janus-particle pair
interactions by mean-field theory. Using a large set of parameters, we are able
to probe the range of validity of the Poisson-Boltzmann approximation, and thus
of DLVO-like theories, for such particles. For homogeneously charged spheres
this range corresponds well to the range that was predicted by
field-theoretical studies of homogeneously charged flat surfaces. Moreover, we
find similar ranges for colloids with a Janus-type charge distribution. The
techniques and parameters we introduce show promise for future studies of an
even wider class of charged-patterned particles.Comment: 14 pages, 6 figure
Dense Regular Packings of Irregular Non-Convex Particles
We present a new numerical scheme to study systems of non-convex, irregular,
and punctured particles in an efficient manner. We employ this method to
analyze regular packings of odd-shaped bodies, not only from a nanoparticle but
also both from a computational geometry perspective. Besides determining
close-packed structures for many shapes, we also discover a new denser
configuration for Truncated Tetrahedra. Moreover, we consider recently
synthesized nanoparticles and colloids, where we focus on the excluded volume
interactions, to show the applicability of our method in the investigation of
their crystal structures and phase behavior. Extensions to the presented scheme
include the incorporation of soft particle-particle interactions, the study of
quasicrystalline systems, and random packings.Comment: 4 pages, 3 figure
Trapping and Characterization of the Reaction Intermediate in Cyclodextrin Glycosyltransferase by Use of Activated Substrates and a Mutant Enzyme
Cyclodextrin glycosyltransferases (CGTases) catalyze the degradation of starch into linear or cyclic oligosaccharides via a glycosyl transfer reaction occurring with retention of anomeric configuration. They are also shown to catalyze the coupling of maltooligosaccharyl fluorides. Reaction is thought to proceed via a double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. This intermediate can be trapped by use of 4-deoxymaltotriosyl α-fluoride (4DG3αF). This substrate contains a good leaving group, fluoride, thus facilitating formation of the intermediate, but cannot undergo the transglycosylation step since the nucleophilic hydroxyl group at the 4-position is missing. When 4DG3αF was reacted with wild-type CGTase (Bacillus circulans 251), it was found to be a slow substrate (kcat = 2 s-1) compared with the parent glycosyl fluoride, maltotriosyl R-fluoride (kcat = 275 s-1). Unfortunately, a competing hydrolysis reaction reduces the lifetime of the intermediate precluding its trapping and identification. However, when 4DG3αF was used in the presence of the presumed acid/base catalyst mutant Glu257Gln, the intermediate could be trapped and analyzed because the first step remained fast while the second step was further slowed (kcat = 0.6 s-1). Two glycosylated peptides were identified in a proteolytic digest of the inhibited enzyme by means of neutral loss tandem mass spectrometry. Edman sequencing of these labeled peptides allowed identification of Asp229 as the catalytic nucleophile and provided evidence for a covalent intermediate in CGTase. Asp229 is found to be conserved in all members of the family 13 glycosyl transferases.
Reassessment of Acarbose as a Transition State Analogue Inhibitor of Cyclodextrin Glycosyltransferase
The binding of several different active site mutants of Bacillus circulans cyclodextrin glycosyltransferase to the inhibitor acarbose has been investigated through measurement of Ki values. The mutations represent several key amino acid positions, most of which are believed to play important roles in governing the product specificity of cyclodextrin glycosyltransferase. Michaelis-Menten parameters for the substrates α-maltotriosyl fluoride (αG3F) and α-glucosyl fluoride (αGF) with each mutant have been determined by following the enzyme-catalyzed release of fluoride with an ion-selective fluoride electrode. In both cases, reasonable correlations are observed in logarithmic plots relating the Ki value for acarbose with each mutant and both kcat/Km and Km for the hydrolysis of either substrate by the corresponding mutants. This indicates that acarbose, as an inhibitor, is mimicking aspects of both the ground state and the transition state. A better correlation is observed for αGF (r = 0.98) than αG3F (r = 0.90), which can be explained in terms of the modes of binding of these substrates and acarbose. Re-refinement of the previously determined crystal structure of wild-type CGTase complexed with acarbose reveals a binding mode consistent with the transition state analogue character of this inhibitor.
Demonstration of an imaging technique for the measurement of PSF elongation caused by Atmospheric Dispersion
Elongation of the point spread function due to atmospheric dispersion becomes
a severe problem for high resolution imaging instruments, if an atmospheric
dispersion corrector is not present. In this work we report on a novel
technique to measure this elongation, corrected or uncorrected, from imaging
data. By employing a simple diffraction mask it is possible to magnify the
chromatic elongation caused by the atmosphere and thus make it easier to
measure. We discuss the theory and design of such a mask and report on two
proof of concept observations using the 40 cm Gratama telescope at the
University of Groningen. We evaluate the acquired images using a geometric
approach, a forward modelling approach and from a direct measurement of the
length of the point spread function. For the first two methods we report
measurements consistent with atmospheric dispersion models to within 0.5
arcsec. Direct measurements of the elongation do not prove suitable for the
characterisation of atmospheric dispersion. We conclude that the addition of
this type of diffraction mask can be valuable for measurements of PSF
elongation. This can enable high precision correction of atmospheric dispersion
on future instruments.Comment: Accepted for publication in the Monthly Notices of the Royal
Astronomical Society. Contains 11 pages, 11 figures, 2 table
A Triangular Tessellation Scheme for the Adsorption Free Energy at the Liquid-Liquid Interface: Towards Non-Convex Patterned Colloids
We introduce a new numerical technique, namely triangular tessellation, to
calculate the free energy associated with the adsorption of a colloidal
particle at a flat interface. The theory and numerical scheme presented here
are sufficiently general to handle non-convex patchy colloids with arbitrary
surface patterns characterized by a wetting angle, e.g., amphiphilicity. We
ignore interfacial deformation due to capillary, electrostatic, or
gravitational forces, but the method can be extended to take such effects into
account. It is verified that the numerical method presented is accurate and
sufficiently stable to be applied to more general situations than presented in
this paper. The merits of the tessellation method prove to outweigh those of
traditionally used semi-analytic approaches, especially when it comes to
generality and applicability.Comment: 21 pages, 11 figures, 0 table
Kinetic Characterization and X-ray Structure of a Mutant of Haloalkane Dehalogenase with Higher Catalytic Activity and Modified Substrate Range
Conversion of halogenated aliphatics by haloalkane dehalogenase proceeds via the formation of a covalent alkyl-enzyme intermediate which is subsequently hydrolyzed by water. In the wild type enzyme, the slowest step for both 1,2-dichloroethane and 1,2-dibromoethane conversion is a unimolecular enzyme isomerization preceding rapid halide dissociation. Phenylalanine 172 is located in a helix-loop-helix structure that covers the active site cavity of the enzyme, interacts with the Clβ of 1,2-dichloroethane during catalysis, and could be involved in stabilization of this helix-loop-helix region of the cap domain of the enzyme. To obtain more information about the role of this residue in dehalogenase function, we performed a mutational analysis of position 172 and studied the kinetics and X-ray structure of the Phe172Trp enzyme. The Phe172Trp mutant had a 10-fold higher kcat/Km for 1-chlorohexane and a 2-fold higher kcat for 1,2-dibromoethane than the wild-type enzyme. The X-ray structure of the Phe172Trp enzyme showed a local conformational change in the helix-loop-helix region that covers the active site. This could explain the elevated activity for 1-chlorohexane of the Phe172Trp enzyme, since it allows this large substrate to bind more easily in the active site cavity. Pre-steady-state kinetic analysis showed that the increase in kcat found for 1,2-dibromoethane conversion could be attributed to an increase in the rate of an enzyme isomerization step that preceeds halide release. The observed conformational difference between the helix-loop-helix structures of the wild-type enzyme and the faster mutant suggests that the isomerization required for halide release could be a conformational change that takes place in this region of the cap domain of the dehalogenase. It is proposed that Phe172 is involved in stabilization of the helix-loop-helix structure that covers the active site of the enzyme and creates a rigid hydrophobic cavity for small apolar halogenated alkanes.
Self-assembly of "Mickey Mouse" shaped colloids into tube-like structures: experiments and simulations
The self-assembly of anisotropic patchy particles with triangular shape was
studied by experiments and computer simulations. The colloidal particles were
synthesized in a two-step seeded emulsion polymerization process, and consist
of a central smooth lobe connected to two rough lobes at an angle of
90, resembling the shape of a "Mickey Mouse" head. Due to the
difference in overlap volume, adding an appropriate depletant induces an
attractive interaction between the smooth lobes of the colloids only, while the
two rough lobes act as steric constraints. The essentially planar geometry of
the "Mickey Mouse" particles is a first geometric deviation of dumbbell shaped
patchy particles. This new geometry is expected to form one-dimensional
tube-like structures rather than spherical, essentially zero-dimensional
micelles. At sufficiently strong attractions, we indeed find tube-like
structures with the sticky lobes at the core and the non-sticky lobes pointing
out as steric constraints that limit the growth to one direction, providing the
tubes with a well-defined diameter but variable length both in experiments and
simulations. In the simulations, we found that the internal structure of the
tubular fragments could either be straight or twisted into so-called Bernal
spirals
- …