Crystallization

Author(s):  
Roger G. Harrison ◽  
Paul W. Todd ◽  
Scott R. Rudge ◽  
Demetri P. Petrides

Crystallization is the process of producing crystals from a homogeneous phase. For biochemicals, the homogeneous phase from which crystals are obtained is always a solution. Crystallization is similar to precipitation in that solid particles are obtained from a solution. However, precipitates have poorly defined morphology, while in crystals the constituent molecules are arranged in three-dimensional arrays called space lattices. In comparison to crystallization, precipitation occurs at much higher levels of supersaturation and rates of nucleation but lower solubilities. These and other differences between crystallization and precipitation are highlighted in Table 9.1. Because of these differences and because the theory of crystallization that has been developed is different from that for precipitation, crystallization is considered separately from precipitation. Crystallization is capable of producing bioproducts at very high purity (say, 99.9%) and is considered to be both a polishing step and a purification step. Polishing refers to a process needed to put the bioproduct in its final form for use. For some bioproducts, such as antibiotics, this final form must be crystalline, and sometimes it is even necessary that a specific crystal form be obtained. In some instances, the purification that can be achieved by crystallization is so significant that other more expensive purification steps such as chromatography can be avoided. There are actually two very different applications of crystallization in biotechnology and bioproduct engineering: crystallization for polishing and purification, and crystallization for crystallography. In the latter case, the goal is a small number of crystals with good size (0.2–0.9 mm) and internal quality. Although it has become common to crystallize proteins for characterization of their three-dimensional structure by x-ray diffraction, this is performed only at small scale in the laboratory, and the knowledge about how to crystallize proteins at large scale in a production process is less developed. However, many antibiotics and other small biomolecules are routinely crystallized in production scale processes. This chapter is oriented toward the use of crystallization in processes that can be scaled up.

2014 ◽  
Vol 70 (12) ◽  
pp. 1675-1682 ◽  
Author(s):  
Roie Dann ◽  
Shifra Lansky ◽  
Noa Lavid ◽  
Arie Zehavi ◽  
Valery Belakhov ◽  
...  

Geobacillus stearothermophilusT6 is a thermophilic bacterium that possesses an extensive hemicellulolytic system, including over 40 specific genes that are dedicated to this purpose. For the utilization of xylan, the bacterium uses an extracellular xylanase which degrades xylan to decorated xylo-oligomers that are imported into the cell. These oligomers are hydrolyzed by side-chain-cleaving enzymes such as arabinofuranosidases, acetylesterases and a glucuronidase, and finally by an intracellular xylanase and a number of β-xylosidases. One of these β-xylosidases is Xyn52B2, a GH52 enzyme that has already proved to be useful for various glycosynthesis applications. In addition to its demonstrated glycosynthase properties, interest in the structural aspects of Xyn52B2 stems from its special glycoside hydrolase family, GH52, the structures and mechanisms of which are only starting to be resolved. Here, the cloning, overexpression, purification and crystallization of Xyn52B2 are reported. The most suitable crystal form that has been obtained belonged to the orthorhombicP212121space group, with average unit-cell parametersa = 97.7,b= 119.1,c = 242.3 Å. Several X-ray diffraction data sets have been collected from flash-cooled crystals of this form, including the wild-type enzyme (3.70 Å resolution), the E335G catalytic mutant (2.95 Å resolution), a potential mercury derivative (2.15 Å resolution) and a selenomethionine derivative (3.90 Å resolution). These data are currently being used for detailed three-dimensional structure determination of the Xyn52B2 protein.


2020 ◽  
Author(s):  
Joel Dahlin ◽  
Spiro Antiochos ◽  
C. Richard DeVore

<p>In highly conducting plasmas, reconnecting current sheets are often unstable to the generation of plasmoids, small-scale magnetic structures that play an important role in facilitating the rapid release of magnetic energy and channeling that energy into accelerated particles. There is ample evidence for plasmoids throughout the heliosphere, from in situ observations of flux ropes in the solar wind and planetary magnetospheres to remote-sensing imaging of plasma ‘blobs’ associated with explosive solar activity such as eruptive flares and coronal jets. Accurate models for plasmoid formation and dynamics must capture the large-scale self-organization responsible for forming the reconnecting current sheet. However, due to the computational difficulty inherent in the vast separation between the global and current sheet scales, previous numerical studies have typically explored configurations with either reduced dimensionality or pre-formed current sheets. We present new three-dimensional MHD studies of an eruptive flare in which the formation of the current sheet and subsequent reconnection and plasmoid formation are captured within a single simulation. We employ Adaptive Mesh Refinement (AMR) to selectively resolve fine-scale current sheet dynamics. Reconnection in the flare current sheet generates many plasmoids that exhibit highly complex, three-dimensional structure. We show how plasmoid formation and dynamics evolve through the course of the flare, especially in response to the weakening of the reconnection “guide field” linked to the global reduction of magnetic shear. We discuss implications of our results for particle acceleration and transport in eruptive flares as well as for observations by Parker Solar Probe and the forthcoming Solar Orbiter.</p>


Author(s):  
T.D. Pollard ◽  
P. Maupin

In this paper we review some of the contributions that electron microscopy has made to the analysis of actin and myosin from nonmuscle cells. We place particular emphasis upon the limitations of the ultrastructural techniques used to study these cytoplasmic contractile proteins, because it is not widely recognized how difficult it is to preserve these elements of the cytoplasmic matrix for electron microscopy. The structure of actin filaments is well preserved for electron microscope observation by negative staining with uranyl acetate (Figure 1). In fact, to a resolution of about 3nm the three-dimensional structure of actin filaments determined by computer image processing of electron micrographs of negatively stained specimens (Moore et al., 1970) is indistinguishable from the structure revealed by X-ray diffraction of living muscle.


2008 ◽  
Vol 615 ◽  
pp. 371-399 ◽  
Author(s):  
S. DONG

We report three-dimensional direct numerical simulations of the turbulent flow between counter-rotating concentric cylinders with a radius ratio 0.5. The inner- and outer-cylinder Reynolds numbers have the same magnitude, which ranges from 500 to 4000 in the simulations. We show that with the increase of Reynolds number, the prevailing structures in the flow are azimuthal vortices with scales much smaller than the cylinder gap. At high Reynolds numbers, while the instantaneous small-scale vortices permeate the entire domain, the large-scale Taylor vortex motions manifested by the time-averaged field do not penetrate a layer of fluid near the outer cylinder. Comparisons between the standard Taylor–Couette system (rotating inner cylinder, fixed outer cylinder) and the counter-rotating system demonstrate the profound effects of the Coriolis force on the mean flow and other statistical quantities. The dynamical and statistical features of the flow have been investigated in detail.


1999 ◽  
Vol 382 ◽  
pp. 307-329 ◽  
Author(s):  
JUDITH K. FOSS ◽  
K. B. M. Q. ZAMAN

The large- and small-scale vortical motions produced by ‘delta tabs’ in a two-stream shear layer have been studied experimentally. An increase in mixing was observed when the base of the triangular shaped tab was affixed to the trailing edge of the splitter plate and the apex was pitched at some angle with respect to the flow axis. Such an arrangement produced a pair of counter-rotating streamwise vortices. Hot-wire measurements detailed the velocity, time-averaged vorticity (Ωx) and small-scale turbulence features in the three-dimensional space downstream of the tabs. The small-scale structures, whose scale corresponds to that of the peak in the dissipation spectrum, were identified and counted using the peak-valley-counting technique. The optimal pitch angle, θ, for a single tab and the optimal spanwise spacing, S, for a multiple tab array were identified. Since the goal was to increase mixing, the optimal tab configuration was determined from two properties of the flow field: (i) the large-scale motions with the maximum Ωx, and (ii) the largest number of small-scale motions in a given time period. The peak streamwise vorticity magnitude [mid ]Ωx−max[mid ] was found to have a unique relationship with the tab pitch angle. Furthermore, for all cases examined, the overall small-scale population was found to correlate directly with [mid ]Ωx−max[mid ]. Both quantities peaked at θ≈±45°. It is interesting to note that the peak magnitude of the corresponding circulation in the cross-sectional plane occurred for θ≈±90°. For an array of tabs, the two quantities also depended on the tab spacing. An array of contiguous tabs acted as a solid deflector producing the weakest streamwise vortices and the least small-scale population. For the measurement range covered, the optimal spacing was found to be S≈1.5 tab widths.


1999 ◽  
Vol 32 (3) ◽  
pp. 241-284 ◽  
Author(s):  
William G. Scott

1. How do ribozymes work? 2412. The hammerhead RNA as a prototype ribozyme 2422.1 RNA enzymes 2422.2 Satellite self-cleaving RNAs 2422.3 Hammerhead RNAs and hammerhead ribozymes 2443. The chemical mechanism of hammerhead RNA self-cleavage 2463.1 Phosphodiester isomerization via an SN2(P) reaction 2473.2 The canonical role of divalent metal ions in the hammerhead ribozyme reaction 2513.3 The hammerhead ribozyme does not actually require metal ions for catalysis 2543.4 Hammerhead RNA enzyme kinetics 2574. Sequence requirements for hammerhead RNA self-cleavage 2604.1 The conserved core, mutagenesis and functional group modifications 2604.2 Ground-state vs. transition-state effects 2615. The three-dimensional structure of the hammerhead ribozyme 2625.1 Enzyme–inhibitor complexes 2625.2 Enzyme–substrate complex in the initial state 2645.3 Hammerhead ribozyme self-cleavage in the crystal 2645.4 The requirement for a conformational change 2655.5 Capture of conformational intermediates using crystallographic freeze-trapping 2665.6 The structure of a hammerhead ribozyme ‘early’ conformational intermediate 2675.7 The structure of a hammerhead ribozyme ‘later’ conformational intermediate 2685.8 Is the conformational change pH dependent? 2695.9 Isolating the structure of the cleavage product 2715.10 Evidence for and against additional large-scale conformation changes 2745.11 NMR spectroscopic studies of the hammerhead ribozyme 2786. Concluding remarks 2807. Acknowledgements 2818. References 2811. How do ribozymes work? 241The discovery that RNA can be an enzyme (Guerrier-Takada et al. 1983; Zaug & Cech, 1986) has created the fundamental question of how RNA enzymes work. Before this discovery, it was generally assumed that proteins were the only biopolymers that had sufficient complexity and chemical heterogeneity to catalyze biochemical reactions. Clearly, RNA can adopt sufficiently complex tertiary structures that make catalysis possible. How does the three- dimensional structure of an RNA endow it with catalytic activity? What structural and functional principles are unique to RNA enzymes (or ribozymes), and what principles are so fundamental that they are shared with protein enzymes?


Author(s):  
Bo Li ◽  
Ruihong Qiao ◽  
Zhizhi Wang ◽  
Weihong Zhou ◽  
Xin Li ◽  
...  

Telomere repeat factor 1 (TRF1) is a subunit of shelterin (also known as the telosome) and plays a critical role in inhibiting telomere elongation by telomerase. Tankyrase 1 (TNKS1) is a poly(ADP-ribose) polymerase that regulates the activity of TRF1 through poly(ADP-ribosyl)ation (PARylation). PARylation of TRF1 by TNKS1 leads to the release of TRF1 from telomeres and allows telomerase to access telomeres. The interaction between TRF1 and TNKS1 is thus important for telomere stability and the mitotic cell cycle. Here, the crystal structure of a complex between the N-terminal acidic domain of TRF1 (residues 1–55) and a fragment of TNKS1 covering the second and third ankyrin-repeat clusters (ARC2-3) is presented at 2.2 Å resolution. The TNKS1–TRF1 complex crystals were optimized using an `oriented rescreening' strategy, in which the initial crystallization condition was used as a guide for a second round of large-scale sparse-matrix screening. This crystallographic and biochemical analysis provides a better understanding of the TRF1–TNKS1 interaction and the three-dimensional structure of the ankyrin-repeat domain of TNKS.


2005 ◽  
Vol 62 (10) ◽  
pp. 3758-3774 ◽  
Author(s):  
Daniel J. Kirshbaum ◽  
Dale R. Durran

Abstract The three-dimensional structure of shallow orographic convection is investigated through simulations performed with a cloud-resolving numerical model. In moist flows that overcome a given topographic barrier to form statically unstable cap clouds, the organization of the convection depends on both the atmospheric structure and the mechanism by which the convection is initiated. Convection initiated by background thermal fluctuations embedded in the flow over a smooth mountain (without any small-scale topographic features) tends to be cellular and disorganized except that shear-parallel bands may form in flows with strong unidirectional vertical shear. The development of well-organized bands is favored when there is weak static instability inside the cloud and when the dry air surrounding the cloud is strongly stable. These bands move with the flow and distribute their cumulative precipitation evenly over the mountain upslope. Similar shear-parallel bands also develop in flows where convection is initiated by small-scale topographic noise superimposed onto the main mountain profile, but in this case stronger circulations are also triggered that create stationary rainbands parallel to the low-level flow. This second dominant mode, which is less sensitive to the atmospheric structure and the strength of forcing, is triggered by lee waves that form over small-scale topographic bumps near the upstream edge of the main orographic cloud. Due to their stationarity, these flow-parallel bands can produce locally heavy precipitation amounts.


Author(s):  
Feng Jie Zheng ◽  
Fu Zheng Qu ◽  
Xue Guan Song

Reservoir-pipe-valve (RPV) systems are widely used in many industrial process. The pressure in an RPV system plays an important role in the safe operation of the system, especially during the sudden operation such as rapid valve opening/closing. To investigate the pressure especially the pressure fluctuation in an RPV system, a multidimensional and multiscale model combining the method of characteristics (MOC) and computational fluid dynamics (CFD) method is proposed. In the model, the reservoir is modeled by a zero-dimensional virtual point, the pipe is modeled by a one-dimensional MOC, and the valve is modeled by a three-dimensional CFD model. An interface model is used to connect the multidimensional and multiscale model. Based on the model, a transient simulation of the turbulent flow in an RPV system is conducted, in which not only the pressure fluctuation in the pipe but also the detailed pressure distribution in the valve are obtained. The results show that the proposed model is in good agreement with the full CFD model in both large-scale and small-scale spaces. Moreover, the proposed model is more computationally efficient than the CFD model, which provides a feasibility in the analysis of complex RPV system within an affordable computational time.


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