Special Issue "Crystallization Under Special and Physical Environments"

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

Deadline for manuscript submissions: closed (1 August 2020).

Special Issue Editor

Prof. Dr. Abel Moreno
Website
Guest Editor
Instituto de Química, Universidad Nacional Autónoma de México. Av. Universidad 3000, Cd.Mx. 04510, Mexico
Interests: protein crystals; biocrystals; crystal growth; protein crystallography; crystal chemistry; biomineralization; biomimetics; biological macromolecules
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Special Issue Information

Dear Colleagues,

Currently, there are powerful experimental techniques for the 3D structure determination of biological macromolecules (proteins, nucleic acids, polysaccharides and their macromolecular complexes). Particularly, X-ray crystallography is one of the most important techniques in this field. This technique can reach quasi-atomic resolution in the most favorable cases. For this approach, the size and complexity of the system are not a priori limitations and this only requires high-quality single crystals.

This Special Issue on “Crystallization Under Special and Physical Environments” will not only include fundamentals for understanding the physical or chemical aspects of the crystallization process, but will also include advanced techniques for controlling the size and orientation through the utilization of electric and magnetic fields and other special environments (hydrogels, organogels, lipid cubic phases, etc.). The third part will include the crystallization of inorganic and organic compounds and proteins grown in special biological conditions, where the use of microorganisms produce crystals inside specialized cells (idioblast) that contains biforine cells that form crystals. Finally, the new trends in crystallography using techniques recently coined as the serial crystallography of macromolecular complexes (Free-lectron Lasers, XFEL) will be shortly discussed in terms of preparing nanocrystals for injection into the XFEL facilities.

Prof. Dr. Abel Moreno
Guest Editor

Manuscript Submission Information

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Published Papers (7 papers)

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Research

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Open AccessFeature PaperArticle
On the Quality of Protein Crystals Grown under Diffusion Mass-transport Controlled Regime (I)
Crystals 2020, 10(2), 68; https://doi.org/10.3390/cryst10020068 - 25 Jan 2020
Cited by 2
Abstract
It has been previously shown that the diffraction quality of protein crystals strongly depends on mass transport during their growth. In fact, several studies support the idea that the higher the contribution of the diffusion during mass transport, the better the diffraction quality [...] Read more.
It has been previously shown that the diffraction quality of protein crystals strongly depends on mass transport during their growth. In fact, several studies support the idea that the higher the contribution of the diffusion during mass transport, the better the diffraction quality of the crystals. In this work, we have compared the crystal quality of two model (thaumatin and insulin) and two target (HBII and HBII-III) proteins grown by two different methods to reduce/eliminate convective mass transport: crystal growth in agarose gels and crystal growth in solution under microgravity. In both cases, we used identical counterdiffusion crystallization setups and the same data collection protocols. Additionally, critical parameters such as reactor geometry, stock batches of proteins and other chemicals, temperature, and duration of the experiments were carefully monitored. The diffraction datasets have been analyzed using a principal component analysis (PCA) to determine possible trends in quality indicators. The relevant indicators show that, for the purpose of structural crystallography, there are no obvious differences between crystals grown under reduced convective flow in space and convection-free conditions in agarose gel, indicating that the key factor contributing to crystal quality is the reduced convection environment and not how this reduced convection is achieved. This means that the possible detrimental effect on crystal quality due to the incorporation of gel fibers into the protein crystals is insignificant compared to the positive impact of an optimal convection-free environment provided by gels. Moreover, our results confirm that the counterdiffusion technique optimizes protein crystal quality and validates both environments in order to deliver high quality protein crystals, although other considerations, such as protein/gel interactions, must be considered when defining the optimal crystallization setup. Full article
(This article belongs to the Special Issue Crystallization Under Special and Physical Environments)
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Open AccessArticle
X-ray Single-Crystal Structural Analysis of a Magnetically Oriented Monoclinic Microcrystal Suspension of α-Glycine
Crystals 2019, 9(11), 561; https://doi.org/10.3390/cryst9110561 - 26 Oct 2019
Cited by 1
Abstract
We previously reported on a method for X-ray single-crystal structure determination from a powder sample via a magnetically oriented microcrystal suspension (MOMS). The method was successfully applied to orthorhombic microcrystals (L-alanine, P212121). In this study, we apply [...] Read more.
We previously reported on a method for X-ray single-crystal structure determination from a powder sample via a magnetically oriented microcrystal suspension (MOMS). The method was successfully applied to orthorhombic microcrystals (L-alanine, P212121). In this study, we apply this method to monoclinic microcrystals. Unlike most of the orthorhombic MOMSs, monoclinic MOMSs exhibit two or four orientations with the same magnetic energy (we refer to this as twin orientations), making data processing difficult. In this paper, we perform a MOMS experiment for a powder sample of monoclinic microcrystal (α-glycine, P21/n) to show that our method can also be applied to monoclinic crystals. The single-crystal structure determined in this work is in good agreement with the reported one performed on a real single crystal. Furthermore, the relationship between the crystallographic and magnetic susceptibility axes is determined. Full article
(This article belongs to the Special Issue Crystallization Under Special and Physical Environments)
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Open AccessArticle
The Role of Calcium and Strontium as the Most Dominant Elements during Combinations of Different Alkaline Earth Metals in the Synthesis of Crystalline Silica-Carbonate Biomorphs
Crystals 2019, 9(8), 381; https://doi.org/10.3390/cryst9080381 - 24 Jul 2019
Cited by 2
Abstract
The origin of life from the chemical point of view is an intriguing and fascinating topic, and is of continuous interest. Currently, the chemical elements that are part of the different cellular types from microorganisms to higher organisms have been described. However, although [...] Read more.
The origin of life from the chemical point of view is an intriguing and fascinating topic, and is of continuous interest. Currently, the chemical elements that are part of the different cellular types from microorganisms to higher organisms have been described. However, although science has advanced in this context, it has not been elucidated yet which were the first chemical elements that gave origin to the first primitive cells, nor how evolution eliminated or incorporated other chemical elements to give origin to other types of cells through evolution. Calcium, barium, and strontium silica-carbonates have been obtained in vitro and named biomorphs, because they mimic living organism structures. Therefore, it is considered that these forms can resemble the first structures that were part of primitive organisms. Hence, the objective of this work was to synthesize biomorphs starting with different mixtures of alkaline earth metals—beryllium (Be2+), magnesium (Mg2+), calcium (Ca2+), barium (Ba2+), and strontium (Sr2+)—in the presence of nucleic acids, RNA and genomic DNA (gDNA). Our results allow us to infer that the stability of calcium followed by strontium had played an important role in the evolution of life since the Precambrian era until our current age. In this way, the presence of these two chemical elements as well as silica (in the primitive life) and some organic molecules give origin to a great variety of life forms, in which calcium is the most common dominating element in many living organisms as we know nowadays. Full article
(This article belongs to the Special Issue Crystallization Under Special and Physical Environments)
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Open AccessArticle
Influence of Pyruvic Acid and UV Radiation on the Morphology of Silica-carbonate Crystalline Biomorphs
Crystals 2019, 9(2), 67; https://doi.org/10.3390/cryst9020067 - 28 Jan 2019
Cited by 2
Abstract
In this work we report the effect of introducing pyruvic acid (PA) in the growing process of silica-carbonate biomorphs. Gas-diffusion and single-phase methods were performed, and different concentrations of pyruvic acid were tested. Moreover, influence of UV radiation on the morphogenesis of the [...] Read more.
In this work we report the effect of introducing pyruvic acid (PA) in the growing process of silica-carbonate biomorphs. Gas-diffusion and single-phase methods were performed, and different concentrations of pyruvic acid were tested. Moreover, influence of UV radiation on the morphogenesis of the samples was analyzed. Since PA decomposes in CO2 and other compounds under UV radiation, here we demonstrate that PA decomposition enables a source of carbonate ions to induce the precipitation of silica-carbonate biomorphs in absence of environmental CO2. We also found that high concentrations [0.5 M] of PA inhibit the formation of biomorphs, while lower concentrations [0.01 M] results in common life-like structures. However [0.1 M] of PA provokes the precipitation of carbonates of alkaline earth metals in non-usual crystalline habits, i.e., semi-spherical smoothed shapes sized between 10 and 70 µm and homogeneously growth on a glass substrate. Full article
(This article belongs to the Special Issue Crystallization Under Special and Physical Environments)
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Open AccessArticle
Synthesis of Bimetallic Nanoparticles of Cd4HgS5 by Candida Species
Crystals 2019, 9(2), 61; https://doi.org/10.3390/cryst9020061 - 24 Jan 2019
Abstract
In recent decades, it has been demonstrated that bimetallic nanoparticles (NPs) possess a number of advantages over monometallic NPs, as the combination of metals results in important changes to their physicochemical properties. Synthesis of bimetallic NPs can be achieved through a number of [...] Read more.
In recent decades, it has been demonstrated that bimetallic nanoparticles (NPs) possess a number of advantages over monometallic NPs, as the combination of metals results in important changes to their physicochemical properties. Synthesis of bimetallic NPs can be achieved through a number of methods, yet there are serious difficulties in controlling these protocols. Biological methods based on the use of microorganisms exhibit important advantages over traditional methods, which makes the search for organisms such as bacteria, yeast and fungi endowed with these abilities an important task. In this context, it has been found that Candida species are able to biosynthesize monometallic NPs, but their ability to form bimetallic NPs has not been investigated. CdHgS is a bimetallic NP of special interest, as it has been found useful in a number of applications; however, its preparation by traditional methods poses certain limitations, and the ability to obtain it through biological procedures has never been demonstrated. With this in mind, the major purpose of this study is to evaluate whether several Candida species were able to synthesize bimetallic NPs of CdHgS in a Cd4HgS5 phase. To our knowledge, this is the first report on the biological synthesis of bimetallic NPs in Candida species. Full article
(This article belongs to the Special Issue Crystallization Under Special and Physical Environments)
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Open AccessArticle
Synthesis and Characterization of a Monoclinic Crystalline Phase of Hydroxyapatite by Synchrotron X-ray Powder Diffraction and Piezoresponse Force Microscopy
Crystals 2018, 8(12), 458; https://doi.org/10.3390/cryst8120458 - 08 Dec 2018
Cited by 2
Abstract
In this work, we report the synthesis of a monoclinic hydroxyapatite [Ca10(PO4)6(OH)2] (hereafter called HA) prepared by the sol-gel method assisted by ultrasound radiation at room temperature. The characterization of both the monoclinic and the [...] Read more.
In this work, we report the synthesis of a monoclinic hydroxyapatite [Ca10(PO4)6(OH)2] (hereafter called HA) prepared by the sol-gel method assisted by ultrasound radiation at room temperature. The characterization of both the monoclinic and the hexagonal phases were performed by powder X-ray diffraction (PXRD) and using synchrotron radiation (SR). The measurement of the piezoelectricity was performed by piezoresponse force microscopy (PFM). The synthesis produced a mixture of monoclinic and hexagonal hydroxyapatite (HA). We also discuss the importance of stabilizing the monoclinic phase at room temperature with ultrasound irradiation. The existence of the monoclinic phase has important advantages in terms of showing piezoelectric properties for applications in the new medical rehabilitation therapies. Rietveld refinement of the PXRD data from SR indicated the monoclinic phase to be of about 81%. Finally, piezoelectric force microscopy was used to distinguish the phases of hydroxyapatite by measuring the average piezoelectric coefficient deff = 10.8 pm/V. Full article
(This article belongs to the Special Issue Crystallization Under Special and Physical Environments)
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Review

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Open AccessEditor’s ChoiceReview
Applications of X-ray Powder Diffraction in Protein Crystallography and Drug Screening
Crystals 2020, 10(2), 54; https://doi.org/10.3390/cryst10020054 - 21 Jan 2020
Cited by 4
Abstract
Providing fundamental information on intra/intermolecular interactions and physicochemical properties, the three-dimensional structural characterization of biological macromolecules is of extreme importance towards understanding their mechanism of action. Among other methods, X-ray powder diffraction (XRPD) has proved its applicability and efficiency in numerous studies of [...] Read more.
Providing fundamental information on intra/intermolecular interactions and physicochemical properties, the three-dimensional structural characterization of biological macromolecules is of extreme importance towards understanding their mechanism of action. Among other methods, X-ray powder diffraction (XRPD) has proved its applicability and efficiency in numerous studies of different materials. Owing to recent methodological advances, this method is now considered a respectable tool for identifying macromolecular phase transitions, quantitative analysis, and determining structural modifications of samples ranging from small organics to full-length proteins. An overview of the XRPD applications and recent improvements related to the study of challenging macromolecules and peptides toward structure-based drug design is discussed. This review congregates recent studies in the field of drug formulation and delivery processes, as well as in polymorph identification and the effect of ligands and environmental conditions upon crystal characteristics. These studies further manifest the efficiency of protein XRPD for quick and accurate preliminary structural characterization. Full article
(This article belongs to the Special Issue Crystallization Under Special and Physical Environments)
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