Biological Crystallization

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Biomolecular Crystals".

Deadline for manuscript submissions: closed (30 June 2019) | Viewed by 69565

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Special Issue Editors

Laboratory of Crystallographic Studies, Analusian Institute of Earth Science (CSIC), University of Granada, Armilla, Spain
Interests: nanocrystallization; bio-inspired crystallization; biomimetic scaffolds; biomaterials
Special Issues, Collections and Topics in MDPI journals
Department of Chemistry "G. Ciamician", University of Bologna, Bologna, Italy
Interests: biomineralization; coral; bio-inspired crystallization; biopolymeric substrates
Laboratorio de Estudios Cristalográficos (IACT, CSIC-UGR), Armilla, Granada, Spain
Interests: crystal growth; pattern formation; self-organization; biominerals

Special Issue Information

Dear Colleagues,

Recently, we have been invited by the journal Crystals to Guest Edit a Special Issue on “Biological Crystallization”. In our opinion, the topic is very broad, as it deals, not only with the formation of inorganic and organic compounds by living organisms, but also with the crystallization of biological materials such as proteins, lipids, keratins, chitins and others.  In the past, many organisms from diverse phyla developed the capability to precipitate various types of crystals, exploring distinctive pathways to use them to build sophisticated structural architectures for different purposes. Functions, such as seeing, hearing, balance, orientation and navigation, colouring, chewing, protecting or supporting the animal bodies, are carried out thanks to these abilities. Understanding the complex strategies that those organisms employ for regulating the nucleation, crystal growth and organization of the crystals to build these sophisticated devices is a source of inspiration in fields as diverse as materials science, nanotechnology or biomedicine. Conversely, knowledge obtained from the synthesis of complex high-tech materials in the laboratory is very useful to understand possible morphogenetic and textural pathways found in biocrystals. In these strategies the interactions between organized biopolymer assemblies and organic molecules with the nascent inorganic solids play a pivotal role in controlling the shape, size distribution, polymorphism, orientation and even assembly of the formed crystals. Considering these different views, the scope of this Special Issue on biological crystallization is intentionally broad. We invite the field specialists to submit original contributions or mini-reviews dealing with the crystallization by organisms at any level of organization, those studies intended to mimic the problem of biological crystallization in vitro and those manuscripts dealing with crystallization of biological materials.

Dr. Jaime Gómez Morales
Prof. Giuseppe Falini
Prof. Juan Manuel García Ruiz
Guest Editors

Manuscript Submission Information

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Keywords

  • Biomineralization
  • Bio-inspired crystallization
  • Crystallization of biological macromolecules
  • Pathological crystallization
  • Characterization of biological crystallization
  • Self-assembly and self-organization

Published Papers (16 papers)

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Editorial

Jump to: Research, Review, Other

3 pages, 185 KiB  
Editorial
Biological Crystallization
by Jaime Gómez-Morales, Giuseppe Falini and Juan Manuel García-Ruiz
Crystals 2019, 9(8), 409; https://doi.org/10.3390/cryst9080409 - 06 Aug 2019
Cited by 2 | Viewed by 2691
Abstract
“Biological Crystallization” is today a very wide topic that includes biomineralization, but also the laboratory crystallization of biological compounds such as macromolecules, carbohydrates or lipids, and the synthesis and fabrication of biomimetic materials by different routes [...] Full article
(This article belongs to the Special Issue Biological Crystallization)

Research

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12 pages, 3104 KiB  
Article
Crystallization and Crystallographic Analysis of a Bradyrhizobium Elkanii USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site
by Tatyana Prudnikova, Barbora Kascakova, Jeroen R. Mesters, Pavel Grinkevich, Petra Havlickova, Andrii Mazur, Anastasiia Shaposhnikova, Radka Chaloupkova, Jiri Damborsky, Michal Kuty and Ivana Kuta Smatanova
Crystals 2019, 9(7), 375; https://doi.org/10.3390/cryst9070375 - 23 Jul 2019
Cited by 3 | Viewed by 3747
Abstract
Haloalkane dehalogenases are a very important class of microbial enzymes for environmental detoxification of halogenated pollutants, for biocatalysis, biosensing and molecular tagging. The double mutant (Ile44Leu + Gln102His) of the haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94 (DbeAΔCl) was constructed to study the [...] Read more.
Haloalkane dehalogenases are a very important class of microbial enzymes for environmental detoxification of halogenated pollutants, for biocatalysis, biosensing and molecular tagging. The double mutant (Ile44Leu + Gln102His) of the haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94 (DbeAΔCl) was constructed to study the role of the second halide-binding site previously discovered in the wild-type structure. The variant is less active, less stable in the presence of chloride ions and exhibits significantly altered substrate specificity when compared with the DbeAwt. DbeAΔCl was crystallized using the sitting-drop vapour-diffusion procedure with further optimization by the random microseeding technique. The crystal structure of the DbeAΔCl has been determined and refined to the 1.4 Å resolution. The DbeAΔCl crystals belong to monoclinic space group C121. The DbeAΔCl molecular structure was characterized and compared with five known haloalkane dehalogenases selected from the Protein Data Bank. Full article
(This article belongs to the Special Issue Biological Crystallization)
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12 pages, 2597 KiB  
Article
Induced Nucleation of Biomimetic Nanoapatites on Exfoliated Graphene Biomolecule Flakes by Vapor Diffusion in Microdroplets
by Jaime Gómez-Morales, Luis Antonio González-Ramírez, Cristóbal Verdugo-Escamilla, Raquel Fernández Penas, Francesca Oltolina, Maria Prat and Giuseppe Falini
Crystals 2019, 9(7), 341; https://doi.org/10.3390/cryst9070341 - 03 Jul 2019
Cited by 3 | Viewed by 2794
Abstract
The nucleation of apatite nanoparticles on exfoliated graphene nanoflakes has been successfully carried out by the sitting drop vapor diffusion method, with the aim of producing cytocompatible hybrid nanocomposites of both components. The graphene flakes were prepared by the sonication-assisted, liquid-phase exfoliation technique, [...] Read more.
The nucleation of apatite nanoparticles on exfoliated graphene nanoflakes has been successfully carried out by the sitting drop vapor diffusion method, with the aim of producing cytocompatible hybrid nanocomposites of both components. The graphene flakes were prepared by the sonication-assisted, liquid-phase exfoliation technique, using the following biomolecules as dispersing surfactants: lysozyme, L-tryptophan, N-acetyl-D-glucosamine, and chitosan. Results from mineralogical, spectroscopic, and microscopic characterization (X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Raman, Variable pressure scanning electron microscopy (VPSEM), and transmission electron microscopy (TEM)) indicate that flakes were stacked in multilayers (>5 layers) and most likely intercalated and functionalized with the biomolecules, while the apatite nanoparticles were found forming a coating on the graphene surfaces. It is worthwhile to mention that when using chitosan-exfoliated graphene, the composites were more homogeneous than when using the other biomolecule graphene flakes, suggesting that this polysaccharide, extremely rich in –OH groups, must be arranged on the graphene surface with the –OH groups pointing toward the solution, forming a more regular pattern for apatite nucleation. The findings by XRD and morphological analysis point to the role of “functionalized graphene” as a template, which induces heterogeneous nucleation and favors the growth of apatite on the flakes’ surfaces. The cytocompatibility tests of the resulting composites, evaluated by the 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) colorimetric assay in a dose–dependent manner on GTL-16 cells, a human gastric carcinoma cell line, and on m17.ASC cells, a murine mesenchymal stem cell line with osteogenic potential, reveal that in all cases, full cytocompatibility was found. Full article
(This article belongs to the Special Issue Biological Crystallization)
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8 pages, 3971 KiB  
Article
Cry Protein Crystal-Immobilized Metallothioneins for Bioremediation of Heavy Metals from Water
by Qian Sun, Sze Wan Cheng, Kelton Cheung, Marianne M. Lee and Michael K. Chan
Crystals 2019, 9(6), 287; https://doi.org/10.3390/cryst9060287 - 01 Jun 2019
Cited by 9 | Viewed by 4305
Abstract
Cry proteins have been the subject of intense research due to their ability to form crystals naturally in Bacillus thuringiensis (Bt). In this research we developed a new strategy that allows for the removal of cadmium and chromium from wastewater by using [...] Read more.
Cry proteins have been the subject of intense research due to their ability to form crystals naturally in Bacillus thuringiensis (Bt). In this research we developed a new strategy that allows for the removal of cadmium and chromium from wastewater by using one Cry protein, Cry3Aa, as a framework to immobilize tandem repeats of the cyanobacterial metallothionein SmtA from Synechococcus elongatus (strain PCC 7942). SmtA is a low molecular weight cysteine-rich protein known to bind heavy metals. A series of Cry3Aa-SmtA constructs were produced by the fusion of one, three, or six tandem repeats of SmtA to Cry3Aa. Overexpression of these constructs in Bt resulted in the production of pure Cry3Aa-SmtA fusion crystals that exhibited similar size, crystallinity, and morphology to that of native Cry3Aa protein crystals. All three Cry3Aa-SmtA constructs exhibited efficient binding to cadmium and chromium, with the binding capacity correlated with increasing SmtA copy number. These results suggest the potential use of Cry3Aa-SmtA crystals as a novel biodegradable and cost-effective approach to the removal of toxic heavy metals from the environment. Full article
(This article belongs to the Special Issue Biological Crystallization)
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11 pages, 3277 KiB  
Article
Calcium Carbonate Mineralization in a Surface-Tension-Confined Droplets Array
by Zhong He, Zengzilu Xia, Mengying Zhang, Jinbo Wu and Weijia Wen
Crystals 2019, 9(6), 284; https://doi.org/10.3390/cryst9060284 - 30 May 2019
Cited by 4 | Viewed by 3353
Abstract
Calcium carbonate biomimetic crystallization remains a topic of interest with respect to biomineralization areas in recent research. It is not easy to conduct high-throughput experiments with only a few macromolecule reagents using conventional experimental methods. However, the emergence of microdroplet array technology provides [...] Read more.
Calcium carbonate biomimetic crystallization remains a topic of interest with respect to biomineralization areas in recent research. It is not easy to conduct high-throughput experiments with only a few macromolecule reagents using conventional experimental methods. However, the emergence of microdroplet array technology provides the possibility to solve these issues efficiently. In this article, surface-tension-confined droplet arrays were used to fabricate calcium carbonate. It was found that calcium carbonate crystallization can be conducted in surface-tension-confined droplets. Defects were found on the surface of some crystals, which were caused by liquid flow inside the droplet and the rapid drop in droplet height during the evaporation. The diameter and number of crystals were related to the droplet diameter. Polyacrylic acid (PAA), added as a modified organic molecule control, changed the CaCO3 morphology from calcite to vaterite. The material products of the above experiments were compared with bulk-synthesized calcium carbonate by scanning electron microscopy (SEM), Raman spectroscopy and other characterization methods. Our work proves the possibility of performing biomimetic crystallization and biomineralization experiments on surface-tension-confined microdroplet arrays. Full article
(This article belongs to the Special Issue Biological Crystallization)
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8 pages, 2170 KiB  
Communication
Hybrid Biomimetic Materials from Silica/Carbonate Biomorphs
by Julian Opel, Niklas Unglaube, Melissa Wörner, Matthias Kellermeier, Helmut Cölfen and Juan-Manuel García-Ruiz
Crystals 2019, 9(3), 157; https://doi.org/10.3390/cryst9030157 - 18 Mar 2019
Cited by 10 | Viewed by 3745
Abstract
The formation of a polymer protection layer around fragile mineral architectures ensures that structures stay intact even after treatments that would normally destroy them going along with a total loss of textural information. Here we present a strategy to preserve the shape of [...] Read more.
The formation of a polymer protection layer around fragile mineral architectures ensures that structures stay intact even after treatments that would normally destroy them going along with a total loss of textural information. Here we present a strategy to preserve the shape of silica-carbonate biomorphs with polymers. This method converts non-hybrid inorganic-inorganic composite materials such a silica/carbonate biomorphs into hybrid organic/carbonate composite materials similar to biominerals. Full article
(This article belongs to the Special Issue Biological Crystallization)
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13 pages, 8475 KiB  
Article
pH and Redox Induced Color Changes in Protein Crystals Suffused with Dyes
by Alexander McPherson
Crystals 2019, 9(3), 126; https://doi.org/10.3390/cryst9030126 - 01 Mar 2019
Cited by 1 | Viewed by 3171
Abstract
Protein crystals, otherwise usually colorless, can be stained a variety of hues by saturating them with dyes, by diffusion from the mother liquor or co-crystallization. The colors assumed by dyes are a function of chemical factors, particularly pH and redox potential. Protein crystals [...] Read more.
Protein crystals, otherwise usually colorless, can be stained a variety of hues by saturating them with dyes, by diffusion from the mother liquor or co-crystallization. The colors assumed by dyes are a function of chemical factors, particularly pH and redox potential. Protein crystals saturated with a pH sensitive dye, initially at one pH, can be exposed to the mother liquor at a second pH and the crystal will change color over time as H3O+ ions diffuse through the crystal. This allows diffusion rates of H3O+ through the crystal to be measured. Diffusion fronts are often clearly delineated. Similar experiments can be carried out with redox sensitive dyes by adding reductants, such as ascorbic acid or dithionite, or oxidants such as H2O2, to the crystal’s mother liquor. Presented here are a number of experiments using pH or redox sensitive dye-saturated protein crystals, and some experiments using double dye, sequential redox–pH changes. Full article
(This article belongs to the Special Issue Biological Crystallization)
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12 pages, 2986 KiB  
Article
Synthesis and Adsorbing Properties of Tabular {001} Calcite Crystals
by Nives Matijaković, Giulia Magnabosco, Francesco Scarpino, Simona Fermani, Giuseppe Falini and Damir Kralj
Crystals 2019, 9(1), 16; https://doi.org/10.3390/cryst9010016 - 27 Dec 2018
Cited by 9 | Viewed by 4248
Abstract
One of the most common crystal habits of the thermodynamically stable polymorph of calcium carbonate, calcite, is the rhombohedral one, which exposes {10.4} faces. When calcite is precipitated in the presence of Li+ ions, dominantly {00.1} faces appear together with the {10.4}, [...] Read more.
One of the most common crystal habits of the thermodynamically stable polymorph of calcium carbonate, calcite, is the rhombohedral one, which exposes {10.4} faces. When calcite is precipitated in the presence of Li+ ions, dominantly {00.1} faces appear together with the {10.4}, thus generating truncated rhombohedrons. This well-known phenomenon is explored in this work, with the aim of obtaining calcite crystals with smooth {00.1} faces. In order to achieve this objective, the formation of calcite was examined in precipitation systems with different c(Ca2+)/c(Li+) ratios and by performing an initial high-power sonication. At the optimal conditions, a precipitate consisting of thin, tabular {001} calcite crystals and very low content of incorporated Li+ has been obtained. The adsorption properties of the tabular crystals, in which the energetically unstable {00.1} faces represent almost all of the exposed surface, were tested with model dye molecules, calcein and crystal violet, and compared to predominantly rhombohedral crystals. It was found that the {00.1} crystals showed a lower adsorption capability when compared to the {10.4} crystals for calcein, while the adsorption of crystal violet was similar for both crystal morphologies. The obtained results open new routes for the usage of calcite as adsorbing substrates and are relevant for the understanding of biomineralization processes in which the {00.1} faces often interact with organic macromolecules. Full article
(This article belongs to the Special Issue Biological Crystallization)
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13 pages, 5269 KiB  
Article
A Simple Technique to Improve Microcrystals Using Gel Exclusion of Nucleation Inducing Elements
by Adafih Blackburn, Shahla H. Partowmah, Haley M. Brennan, Kimberly E. Mestizo, Cristina D. Stivala, Julia Petreczky, Aleida Perez, Amanda Horn, Sean McSweeney and Alexei S. Soares
Crystals 2018, 8(12), 464; https://doi.org/10.3390/cryst8120464 - 12 Dec 2018
Cited by 3 | Viewed by 3917
Abstract
A technique is described for generating large well diffracting crystals from conditions that yield microcrystals. Crystallization using this technique is both rapid (crystals appear in <1 h) and robust (48 out of 48 co-crystallized with a fragment library, compared with 26 out of [...] Read more.
A technique is described for generating large well diffracting crystals from conditions that yield microcrystals. Crystallization using this technique is both rapid (crystals appear in <1 h) and robust (48 out of 48 co-crystallized with a fragment library, compared with 26 out of 48 using conventional hanging drop). Agarose gel is used to exclude nucleation inducing elements from the remaining crystallization cocktail. The chemicals in the crystallization cocktail are partitioned into high concentration components (presumed to induce aggregation by reducing water activity) and low concentration nucleation agents (presumed to induce nucleation through direct interaction). The nucleation agents are then combined with 2% agarose gel and deposited on the crystallization shelf of a conventional vapor diffusion plate. The remaining components are mixed with the protein and placed in contact with the agarose drop. This technique yielded well diffracting crystals of lysozyme, cubic insulin, proteinase k, and ferritin (ferritin crystals diffracted to 1.43 Å). The crystals grew rapidly, reaching large size in less than one hour (maximum size was achieved in 1–12 h). This technique is not suitable for poorly expressing proteins because small protein volumes diffuse out of the agarose gel too quickly. However, it is a useful technique for situations where crystals must grow rapidly (such as educational applications and preparation of beamline test specimens) and in situations where crystals must grow robustly (such as co-crystallization with a fragment library). Full article
(This article belongs to the Special Issue Biological Crystallization)
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11 pages, 3436 KiB  
Article
From Initial Hit to Crystal Optimization with Microseeding of Human Carbonic Anhydrase IX—A Case Study for Neutron Protein Crystallography
by Katarina Koruza, Bénédicte Lafumat, Maria Nyblom, Wolfgang Knecht and Zoë Fisher
Crystals 2018, 8(11), 434; https://doi.org/10.3390/cryst8110434 - 20 Nov 2018
Cited by 5 | Viewed by 7293
Abstract
Human carbonic anhydrase IX (CA IX) is a multi-domain membrane protein that is therefore difficult to express or crystalize. To prepare crystals that are suitable for neutron studies, we are using only the catalytic domain of CA IX with six surface mutations, named [...] Read more.
Human carbonic anhydrase IX (CA IX) is a multi-domain membrane protein that is therefore difficult to express or crystalize. To prepare crystals that are suitable for neutron studies, we are using only the catalytic domain of CA IX with six surface mutations, named surface variant (SV). The crystallization of CA IX SV, and also partly deuterated CA IX SV, was enabled by the use of microseed matrix screening (MMS). Only three drops with crystals were obtained after initial sparse matrix screening, and these were used as seeds in subsequent crystallization trials. Application of MMS, commercial screens, and refinement resulted in consistent crystallization and diffraction-quality crystals. The crystallization protocols and strategies that resulted in consistent crystallization are presented. These results demonstrate not only the use of MMS in the growth of large single crystals for neutron studies with defined conditions, but also that MMS enabled re-screening to find new conditions and consistent crystallization success. Full article
(This article belongs to the Special Issue Biological Crystallization)
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8 pages, 1833 KiB  
Communication
Over-Expression, Secondary Structure Characterization, and Preliminary X-ray Crystallographic Analysis of Xenopus tropicalis Ependymin
by Jeong Kuk Park, Yeo Won Sim and SangYoun Park
Crystals 2018, 8(7), 284; https://doi.org/10.3390/cryst8070284 - 11 Jul 2018
Cited by 4 | Viewed by 2673
Abstract
The gene encoding frog (Xenopus tropicalis) ependymin without the signaling sequence was gene-synthesized, and the protein successfully over-expressed in ~mg quantities adequate for crystallization using insect cell expression. Circular dichroism (CD) analysis of the protein purified with >95% homogeneity indicated that [...] Read more.
The gene encoding frog (Xenopus tropicalis) ependymin without the signaling sequence was gene-synthesized, and the protein successfully over-expressed in ~mg quantities adequate for crystallization using insect cell expression. Circular dichroism (CD) analysis of the protein purified with >95% homogeneity indicated that ependymin contains both α-helix and β-strand among the secondary structure elements. The protein was further crystallized using polyethylene glycol 8000 as the precipitating reagent, and X-ray diffraction data were collected to 2.7 Å resolution under cryo-condition at a synchrotron facility. The crystal belongs to a hexagonal space group P6122 (or P6522) having unit cell parameters of a = b = 61.05 Å, c = 234.33 Å. Matthews coefficient analysis indicated a crystal volume per protein mass (VM) of 2.76 Å3 Da−1 and 55.4% solvent content in the crystal when the calculated molecular mass of the protein only was used. However, the apparent SDS-PAGE molecular mass of ~33 kDa (likely resulting from N-glycosylation) suggested VM of 1.90 Å3 Da−1 and 35.4% solvent content instead. In both cases, the asymmetric unit of the crystal likely contains only one subunit of the protein. Full article
(This article belongs to the Special Issue Biological Crystallization)
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12 pages, 2002 KiB  
Article
Recent Insights into Protein Crystal Nucleation
by Christo N. Nanev
Crystals 2018, 8(5), 219; https://doi.org/10.3390/cryst8050219 - 17 May 2018
Cited by 14 | Viewed by 3464
Abstract
Homogeneous nucleation of protein crystals in solution is tackled from both thermodynamic and energetic perspectives. The entropic contribution to the destructive action of water molecules which tend to tear up the crystals and to their bond energy is considered. It is argued that, [...] Read more.
Homogeneous nucleation of protein crystals in solution is tackled from both thermodynamic and energetic perspectives. The entropic contribution to the destructive action of water molecules which tend to tear up the crystals and to their bond energy is considered. It is argued that, in contrast to the crystals’ bond energy, the magnitude of destructive energy depends on the imposed supersaturation. The rationale behind the consideration presented is that the critical nucleus size is determined by the balance between destructive and bond energies. By summing up all intra-crystal bonds, the breaking of which is needed to disintegrate a crystal into its constituting molecules, and using a crystallographic computer program, the bond energy of the closest-packed crystals is calculated (hexagonal closest-packed crystals are given as an example). This approach is compared to the classical mean work of separation (MWS) method of Stranski and Kaischew. While the latter is applied merely for the so-called Kossel-crystal and vapor grown crystals, the approach presented can be used to establish the supersaturation dependence of the protein crystal nucleus size of arbitrary lattice structures. Full article
(This article belongs to the Special Issue Biological Crystallization)
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9 pages, 32084 KiB  
Communication
Crystal Structure of the Catalytic Domain of MCR-1 (cMCR-1) in Complex with d-Xylose
by Zhao-Xin Liu, Zhenggang Han, Xiao-Li Yu, Guoyuan Wen and Chi Zeng
Crystals 2018, 8(4), 172; https://doi.org/10.3390/cryst8040172 - 17 Apr 2018
Cited by 10 | Viewed by 4018
Abstract
The polymyxin colistin is known as a “last resort” antibacterial drug toward pandrug-resistant enterobacteria. The recently discovered plasmid-encoded mcr-1 gene spreads rapidly across pathogenic strains and confers resistance to colistin, which has emerged as a global threat. The mcr-1 gene encodes a phosphoethanolamine [...] Read more.
The polymyxin colistin is known as a “last resort” antibacterial drug toward pandrug-resistant enterobacteria. The recently discovered plasmid-encoded mcr-1 gene spreads rapidly across pathogenic strains and confers resistance to colistin, which has emerged as a global threat. The mcr-1 gene encodes a phosphoethanolamine transferase (MCR-1) that catalyzes the transference of phosphoethanolamine to lipid A moiety of lipopolysaccharide, resulting in resistance to colistin. Development of effective MCR-1 inhibitors is crucial for combating MCR-1-mediated colistin resistance. In this study, MCR-1 catalytic domain (namely cMCR-1) was expressed and co-crystallized together with d-xylose. X-ray crystallographic study at a resolution of 1.8 Å found that cMCR-1-d-xylose co-crystals fell under space group P212121, with unit-cell parameters a = 51.6 Å, b = 73.1 Å, c = 82.2 Å, α = 90°, β = 90°, γ = 90°. The asymmetric unit contained a single cMCR-1 molecule complexed with d-xylose and had a solvent content of 29.13%. The structural model of cMCR-1-d-xylose complex showed that a d-xylose molecule bound in the putative lipid A-binding pocket of cMCR-1, which might provide a clue for MCR-1 inhibitor development. Full article
(This article belongs to the Special Issue Biological Crystallization)
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Review

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13 pages, 1030 KiB  
Review
Can Microbially Induced Calcite Precipitation (MICP) through a Ureolytic Pathway Be Successfully Applied for Removing Heavy Metals from Wastewaters?
by Álvaro Esteban Torres-Aravena, Carla Duarte-Nass, Laura Azócar, Rodrigo Mella-Herrera, Mariella Rivas and David Jeison
Crystals 2018, 8(11), 438; https://doi.org/10.3390/cryst8110438 - 21 Nov 2018
Cited by 69 | Viewed by 10362
Abstract
Microbially induced calcite precipitation (MICP) through a ureolytic pathway is a process that promotes calcite precipitation as a result of the urease enzymatic activity of several microorganisms. It has been studied for different technological applications, such as soil bio-consolidation, bio-cementation, CO2 sequestration, [...] Read more.
Microbially induced calcite precipitation (MICP) through a ureolytic pathway is a process that promotes calcite precipitation as a result of the urease enzymatic activity of several microorganisms. It has been studied for different technological applications, such as soil bio-consolidation, bio-cementation, CO2 sequestration, among others. Recently, this process has been proposed as a possible process for removing heavy metals from contaminated soils. However, no research has been reported dealing with the MICP process for heavy metal removal from wastewater/waters. This (re)view proposes to consider to such possibility. The main characteristics of MICP are presented and discussed. The precipitation of heavy metals contained in wastewaters/waters via MICP is exanimated based on process characteristics. Moreover, challenges for its successful implementation are discussed, such as the heavy metal tolerance of inoculum, ammonium release as product of urea hydrolysis, and so on. A semi-continuous operation in two steps (cell growth and bio-precipitation) is proposed. Finally, the wastewater from some typical industries releasing heavy metals are examined, discussing the technical barriers and feasibility. Full article
(This article belongs to the Special Issue Biological Crystallization)
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16 pages, 667 KiB  
Review
Peculiarities of Protein Crystal Nucleation and Growth
by Christo N. Nanev
Crystals 2018, 8(11), 422; https://doi.org/10.3390/cryst8110422 - 08 Nov 2018
Cited by 11 | Viewed by 4449
Abstract
This paper reviews investigations on protein crystallization. It aims to present a comprehensive rather than complete account of recent studies and efforts to elucidate the most intimate mechanisms of protein crystal nucleation. It is emphasized that both physical and biochemical factors are at [...] Read more.
This paper reviews investigations on protein crystallization. It aims to present a comprehensive rather than complete account of recent studies and efforts to elucidate the most intimate mechanisms of protein crystal nucleation. It is emphasized that both physical and biochemical factors are at play during this process. Recently-discovered molecular scale pathways for protein crystal nucleation are considered first. The bond selection during protein crystal lattice formation, which is a typical biochemically-conditioned peculiarity of the crystallization process, is revisited. Novel approaches allow us to quantitatively describe some protein crystallization cases. Additional light is shed on the protein crystal nucleation in pores and crevices by employing the so-called EBDE method (equilibration between crystal bond and destructive energies). Also, protein crystal nucleation in solution flow is considered. Full article
(This article belongs to the Special Issue Biological Crystallization)
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Other

10 pages, 1918 KiB  
Brief Report
Refolding, Characterization, and Preliminary X-ray Crystallographic Studies on the Campylobacter concisus Plasmid-Encoded Secreted Protein Csep1p Associated with Crohn’s Disease
by Mohammad Mizanur Rahman, Bradley Goff, Li Zhang and Anna Roujeinikova
Crystals 2018, 8(10), 391; https://doi.org/10.3390/cryst8100391 - 16 Oct 2018
Cited by 1 | Viewed by 3963
Abstract
Colonization of Campylobacter concisus in the gastrointestinal tract can lead to the development of inflammatory bowel disease (IBD). Plasmid-encoded C. concisus-secreted protein 1 (Csep1p) was recently identified as a putative pathogenicity marker associated with active Crohn’s disease, a clinical form [...] Read more.
Colonization of Campylobacter concisus in the gastrointestinal tract can lead to the development of inflammatory bowel disease (IBD). Plasmid-encoded C. concisus-secreted protein 1 (Csep1p) was recently identified as a putative pathogenicity marker associated with active Crohn’s disease, a clinical form of IBD. Csep1p shows no significant full-length sequence similarity to proteins of known structure, and its role in pathogenesis is not yet known. This study reports a method for extraction of recombinantly expressed Csep1p from Escherichia coli inclusion bodies, refolding, and purification to produce crystallizable protein. Purified recombinant Csep1p behaved as a monomer in solution. Crystals of Csep1p were grown by the hanging drop vapour diffusion method, using polyethylene glycol (PEG) 4000 as the precipitating agent. A complete data set has been collected to 1.4 Å resolution, using cryocooling conditions and synchrotron radiation. The crystals belong to space group P62 or P64, with unit cell parameters a = b = 85.8, c = 55.2 Å, α = β = 90, and γ = 120°. The asymmetric unit appears to contain one subunit, corresponding to a packing density of 2.47 Å3 Da−1. Full article
(This article belongs to the Special Issue Biological Crystallization)
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