Special Issue "Biological Crystallization"

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

Deadline for manuscript submissions: 15 February 2019

Special Issue Editors

Guest Editor
Dr. Jaime Gómez Morales

Laboratorio de Estudios Cristalográficos (IACT, CSIC-UGR), Spain
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Interests: nanocrystallization; bio-inspired crystallization; biominerals; biomaterials
Guest Editor
Prof. Giuseppe Falini

Department of Chemistry "G. Ciamician", University of Bologna, Italy
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Interests: biomineralization; coral; bio-inspired crystallization; biopolymeric substrates
Guest Editor
Prof. Juan Manuel García Ruiz

Laboratorio de Estudios Cristalográficos (IACT, CSIC-UGR), Spain
Website | E-Mail
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 (9 papers)

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Research

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Open AccessArticle Synthesis and Adsorbing Properties of Tabular {001} Calcite Crystals
Crystals 2019, 9(1), 16; https://doi.org/10.3390/cryst9010016
Received: 12 November 2018 / Revised: 20 December 2018 / Accepted: 22 December 2018 / Published: 27 December 2018
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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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Open AccessArticle A Simple Technique to Improve Microcrystals Using Gel Exclusion of Nucleation Inducing Elements
Crystals 2018, 8(12), 464; https://doi.org/10.3390/cryst8120464
Received: 14 November 2018 / Revised: 7 December 2018 / Accepted: 10 December 2018 / Published: 12 December 2018
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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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Open AccessArticle From Initial Hit to Crystal Optimization with Microseeding of Human Carbonic Anhydrase IX—A Case Study for Neutron Protein Crystallography
Crystals 2018, 8(11), 434; https://doi.org/10.3390/cryst8110434
Received: 22 October 2018 / Revised: 16 November 2018 / Accepted: 17 November 2018 / Published: 20 November 2018
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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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Open AccessCommunication Over-Expression, Secondary Structure Characterization, and Preliminary X-ray Crystallographic Analysis of Xenopus tropicalis Ependymin
Crystals 2018, 8(7), 284; https://doi.org/10.3390/cryst8070284
Received: 19 June 2018 / Revised: 6 July 2018 / Accepted: 9 July 2018 / Published: 11 July 2018
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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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Open AccessArticle Recent Insights into Protein Crystal Nucleation
Crystals 2018, 8(5), 219; https://doi.org/10.3390/cryst8050219
Received: 27 April 2018 / Revised: 9 May 2018 / Accepted: 12 May 2018 / Published: 17 May 2018
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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,
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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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Open AccessCommunication Crystal Structure of the Catalytic Domain of MCR-1 (cMCR-1) in Complex with d-Xylose
Crystals 2018, 8(4), 172; https://doi.org/10.3390/cryst8040172
Received: 4 March 2018 / Revised: 12 April 2018 / Accepted: 14 April 2018 / Published: 17 April 2018
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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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Open AccessReview Can Microbially Induced Calcite Precipitation (MICP) through a Ureolytic Pathway Be Successfully Applied for Removing Heavy Metals from Wastewaters?
Crystals 2018, 8(11), 438; https://doi.org/10.3390/cryst8110438
Received: 11 October 2018 / Revised: 31 October 2018 / Accepted: 2 November 2018 / Published: 21 November 2018
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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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Open AccessReview Peculiarities of Protein Crystal Nucleation and Growth
Crystals 2018, 8(11), 422; https://doi.org/10.3390/cryst8110422
Received: 18 October 2018 / Revised: 31 October 2018 / Accepted: 5 November 2018 / Published: 8 November 2018
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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
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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

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Open AccessBrief Report Refolding, Characterization, and Preliminary X-ray Crystallographic Studies on the Campylobacter concisus Plasmid-Encoded Secreted Protein Csep1p Associated with Crohn’s Disease
Crystals 2018, 8(10), 391; https://doi.org/10.3390/cryst8100391
Received: 19 September 2018 / Revised: 9 October 2018 / Accepted: 14 October 2018 / Published: 16 October 2018
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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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