Special Issue "Protein Crystallography"

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

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

Special Issue Editors

Prof. Dr. Xiao-Dong Su
E-Mail Website
Guest Editor
Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
Interests: protein nucleation, crystallization; biological complexes; protein-DNA complex crystals; meso- quasi- or nano-crystals; biomineralization
Prof. Dr. Abel Moreno
E-Mail 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
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein X-ray crystallography has played dominant roles and will continue to contribute greatly to structural biology despite the recent technical revolutions in cryo-EM and XFEL (X-ray free electron laser). Structural biology dissects bio-macromolecules and their complexes at the atomic resolution, thus giving the best mechanistic connections and understanding between physiochemical structures and biological phenomena. Structural biology does not only deal with the well-ordered bio-macromolecules, but also studies flexible and disordered proteins, and phase separation mechanisms caused by some of the disordered proteins. This Special Issue of “Protein Crystallography” will cover all aspects of structural biology relevant to X-ray and electron crystallography. Authors are encouraged to submit their manuscripts covering the topics in the keywords listed below.

Although the static crystal structures have been the major focus in structural biology in the past 60 years, scientists have been paying more and more attention to the dynamic and flexible aspects of bio-macromolecules and their complexes. Therefore, we particularly encourage the submission of manuscripts relevant to bio-macromolecules dynamics and interactions. The additional goals of this issue are to provide the growing community of biological scientists interested in structural biology with good reference material, historical background, and primer references. We will also like to invite manuscripts submissions in those areas.

Prof. Xiao-Dong Su
Prof. Abel Moreno
Guest Editors

Manuscript Submission Information

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Keywords

  • Protein preparation and crystallization
  • X-ray and electron diffraction
  • Structural determination and analyses
  • Structural biology
  • Rational drug design
  • Bio-macromolecule dynamics and interactions
  • Bio-macromolecule design
  • Disordered proteins and phase separation

Published Papers (16 papers)

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Research

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Article
Effects of Proline Substitutions on the Thermostable LOV Domain from Chloroflexus aggregans
Crystals 2020, 10(4), 256; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10040256 - 28 Mar 2020
Cited by 8 | Viewed by 1625
Abstract
Light-oxygen-voltage (LOV) domains are ubiquitous photosensory modules found in proteins from bacteria, archaea and eukaryotes. Engineered versions of LOV domains have found widespread use in fluorescence microscopy and optogenetics, with improved versions being continuously developed. Many of the engineering efforts focused on the [...] Read more.
Light-oxygen-voltage (LOV) domains are ubiquitous photosensory modules found in proteins from bacteria, archaea and eukaryotes. Engineered versions of LOV domains have found widespread use in fluorescence microscopy and optogenetics, with improved versions being continuously developed. Many of the engineering efforts focused on the thermal stabilization of LOV domains. Recently, we described a naturally thermostable LOV domain from Chloroflexus aggregans. Here we show that the discovered protein can be further stabilized using proline substitution. We tested the effects of three mutations, and found that the melting temperature of the A95P mutant is raised by approximately 2 °C, whereas mutations A56P and A58P are neutral. To further evaluate the effects of mutations, we crystallized the variants A56P and A95P, while the variant A58P did not crystallize. The obtained crystal structures do not reveal any alterations in the proteins other than the introduced mutations. Molecular dynamics simulations showed that mutation A58P alters the structure of the respective loop (Aβ-Bβ), but does not change the general structure of the protein. We conclude that proline substitution is a viable strategy for the stabilization of the Chloroflexus aggregans LOV domain. Since the sequences and structures of the LOV domains are overall well-conserved, the effects of the reported mutations may be transferable to other proteins belonging to this family. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
Crystal Structure of a Proteolytic Fragment of the Sensor Histidine Kinase NarQ
Crystals 2020, 10(3), 149; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10030149 - 27 Feb 2020
Cited by 5 | Viewed by 1386
Abstract
Two-component signaling systems (TCSs) are a large and important class of sensory systems in bacteria, archaea, and some eukaryotes, yet their mechanism of action is still not fully understood from the structural point of view. Many TCS receptors are elongated flexible proteins with [...] Read more.
Two-component signaling systems (TCSs) are a large and important class of sensory systems in bacteria, archaea, and some eukaryotes, yet their mechanism of action is still not fully understood from the structural point of view. Many TCS receptors are elongated flexible proteins with transmembrane (TM) regions, and are difficult to work with. Consequently, truncated fragments of the receptors are often used in structural studies. However, it is not fully clear whether the structures of the fragments correspond well to their native structures in the context of full-length proteins. Recently, we crystallized a fragment of Escherichia coli nitrate/nitrite sensor histidine kinase, NarQ, encompassing the sensor, TM, and HAMP domains. Here we report that a smaller proteolytic fragment consisting of the sensor and TM domains can also be crystallized using the in meso approach. The structure of the fragment is similar to the previously determined one, with minor differences in the vicinity of the truncation site. The results show that the crystallization of such sensor–TM fragments can be accomplished and can provide information on the packing of transmembrane helices, albeit limited, and that the proteolysis may or may not be a problem during crystallization. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Communication
Be Cautious with Crystal Structures of Membrane Proteins or Complexes Prepared in Detergents
Crystals 2020, 10(2), 86; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10020086 - 03 Feb 2020
Cited by 16 | Viewed by 2228
Abstract
Membrane proteins are an important class of macromolecules found in all living organisms and many of them serve as important drug targets. In order to understand their biological and biochemical functions and to exploit them for structure-based drug design, high-resolution and accurate structures [...] Read more.
Membrane proteins are an important class of macromolecules found in all living organisms and many of them serve as important drug targets. In order to understand their biological and biochemical functions and to exploit them for structure-based drug design, high-resolution and accurate structures of membrane proteins are needed, but are still rarely available, e.g., predominantly from X-ray crystallography, and more recently from single particle cryo-EM — an increasingly powerful tool for membrane protein structure determination. However, while protein-lipid interactions play crucial roles for the structural and functional integrity of membrane proteins, for historical reasons and due to technological limitations, until recently, the primary method for membrane protein crystallization has relied on detergents. Bicelle and lipid cubic phase (LCP) methods have also been used for membrane protein crystallization, but the first step requires detergent extraction of the protein from its native cell membrane. The resulting, crystal structures have been occasionally questioned, but such concerns were generally dismissed as accidents or ignored. However, even a hint of controversy indicates that methodological drawbacks in such structural research may exist. In the absence of caution, structures determined using these methods are often assumed to be correct, which has led to surprising hypotheses for their mechanisms of action. In this communication, several examples of structural studies on membrane proteins or complexes will be discussed: Resistance-Nodulation-Division (RND) family transporters, microbial rhodopsins, Tryptophan-rich Sensory Proteins (TSPO), and Energy-Coupling Factor (ECF) type ABC transporters. These analyses should focus the attention of membrane protein structural biologists on the potential problems in structure determination relying on detergent-based methods. Furthermore, careful examination of membrane proteins in their native cell environments by biochemical and biophysical techniques is warranted, and completely detergent-free systems for membrane protein research are crucially needed. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
TMP-SSurface: A Deep Learning-Based Predictor for Surface Accessibility of Transmembrane Protein Residues
Crystals 2019, 9(12), 640; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9120640 - 01 Dec 2019
Cited by 3 | Viewed by 1504
Abstract
Transmembrane proteins (TMPs) play vital and diverse roles in many biological processes, such as molecular transportation and immune response. Like other proteins, many major interactions with other molecules happen in TMPs’ surface area, which is important for function annotation and drug discovery. Under [...] Read more.
Transmembrane proteins (TMPs) play vital and diverse roles in many biological processes, such as molecular transportation and immune response. Like other proteins, many major interactions with other molecules happen in TMPs’ surface area, which is important for function annotation and drug discovery. Under the condition that the structure of TMP is hard to derive from experiment and prediction, it is a practical way to predict the TMP residues’ surface area, measured by the relative accessible surface area (rASA), based on computational methods. In this study, we presented a novel deep learning-based predictor TMP-SSurface for both alpha-helical and beta-barrel transmembrane proteins (α-TMP and β-TMP), where convolutional neural network (CNN), inception blocks, and CapsuleNet were combined to construct a network framework, simply accepting one-hot code and position-specific score matrix (PSSM) of protein fragment as inputs. TMP-SSurface was tested against an independent dataset achieving appreciable performance with 0.584 Pearson correlation coefficients (CC) value. As the first TMP’s rASA predictor utilizing the deep neural network, our method provided a referenceable sample for the community, as well as a practical step to discover the interaction sites of TMPs based on their sequence. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
A Novel Substrate-Binding Site in the X-ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion
Crystals 2019, 9(12), 622; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9120622 - 26 Nov 2019
Cited by 1 | Viewed by 1175
Abstract
Escherichia coli (E. coli), one of the most frequently used host for the expression of recombinant proteins, is often affected by the toxic effect of the exogenous proteins that is required to express. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a multi-functional protein [...] Read more.
Escherichia coli (E. coli), one of the most frequently used host for the expression of recombinant proteins, is often affected by the toxic effect of the exogenous proteins that is required to express. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a multi-functional protein that has been used as a control marker for basal function and it is known to undergo cysteine oxidation under different types of cellular stress. Here, we report the 3D structure of the endogenous GAPDH purified from stressed E. coli cells expressing a eukaryotic protein. The structure was solved at 1.64 Å using single-wavelength anomalous dispersion (SAD) phasing with a selenium-modified enzyme. Interestingly, each GAPDH monomer contains a molecule of glyceraldehyde-3 phosphate in a non-previously identified site. Furthermore, the catalytic Cys149 is covalently attached to a ~300 Da molecule, possibly glutathione. This modification alters the conformation of an adjacent alpha helix in the catalytic domain, right opposite to the NAD+ binding site. The conformation of the alpha helix is stabilized after soaking the crystals with NAD+. These results exemplify the effects that the overexpression of an exogenous protein has over the host proteins and sheds light on the structural changes that large oxidant molecules on the catalytic cysteine produce for the GAPDH enzyme. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
Trial Direct Phasing Calculation of A Thyroid Hormone Receptor Alpha Structure (4LNW)
Crystals 2019, 9(10), 533; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9100533 - 16 Oct 2019
Viewed by 820
Abstract
A thyroid receptor alpha structure (PDB ID: 4LNW) was studied for ab initio phasing. With the diffraction intensity data, protein sequence, and ligand structure as the only input, a high-resolution structure was successfully reconstructed by using an iterative projective method based on the [...] Read more.
A thyroid receptor alpha structure (PDB ID: 4LNW) was studied for ab initio phasing. With the diffraction intensity data, protein sequence, and ligand structure as the only input, a high-resolution structure was successfully reconstructed by using an iterative projective method based on the hybrid input–output (HIO) algorithm. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
Comparison of the Quality of Protein Crystals Grown by CLPC Seeds Method
Crystals 2019, 9(10), 501; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9100501 - 26 Sep 2019
Cited by 1 | Viewed by 1030
Abstract
We present a systematic quality comparison of protein crystals obtained with and without cross-linked protein crystal (CLPC) seeds. Four proteins were used to conduct the experiments, and the results showed that crystals obtained in the presence of CLPC seeds exhibited a better morphology. [...] Read more.
We present a systematic quality comparison of protein crystals obtained with and without cross-linked protein crystal (CLPC) seeds. Four proteins were used to conduct the experiments, and the results showed that crystals obtained in the presence of CLPC seeds exhibited a better morphology. In addition, the X-ray diffraction data showed that the CLPC seeds method is a powerful tool to obtain high-quality protein crystals. Therefore, we recommend the use of CLPC seeds in preparing high-quality diffracting protein crystals. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
Protein Crystallization in Ionic-Liquid Hydrogel Composite Membranes
Crystals 2019, 9(5), 253; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9050253 - 17 May 2019
Cited by 7 | Viewed by 1686
Abstract
Protein crystallization is a powerful purification tool. It is the first step for crystallographic structural investigations, and can be preparatory for biotechnological applications. However, crystallizing proteins is challenging and methods to control the crystallization process are needed. Ionic-liquid hydrogel composite membranes (IL-HCMs) have [...] Read more.
Protein crystallization is a powerful purification tool. It is the first step for crystallographic structural investigations, and can be preparatory for biotechnological applications. However, crystallizing proteins is challenging and methods to control the crystallization process are needed. Ionic-liquid hydrogel composite membranes (IL-HCMs) have been used here as material capable of supporting protein crystallization and hosting grown crystals. We found that IL-HCMs affect the selection mechanism of glucose isomerase (GI) polymorphs and make GI crystals grow completely immersed into the hydrogel layer. X-ray diffraction studies show that IL ions do not bind to the protein, likely because IL molecules are constrained in the polymeric framework. Our GI crystal structures have been compared with many existing GI crystal structures using multivariate analysis tools, allowing a comprehensive overview of factors determining structural similarities, i.e., temperature variations and external stresses exerted during or after crystal growth, such as dehydration or presence of hydrogel of a different nature. GI crystals grown on IL-HCM fit perfectly in this framework, showing typical features induced by external forces. Overall, protein crystallization by IL-HCMs show potential for biotechnological applications, as it could constitute a natural means for containing crystallized enzymes in working conditions. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
Optimization of Vapor Diffusion Conditions for Anti-CD20 Crystallization and Scale-Up to Meso Batch
Crystals 2019, 9(5), 230; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9050230 - 29 Apr 2019
Cited by 7 | Viewed by 2271
Abstract
The crystal form is one of the preferred formulations for biotherapeutics, especially thanks to its ability to ensure high stability of the active ingredient. In addition, crystallization allows the recovery of a very pure drug, thus facilitating the manufacturing process. However, in many [...] Read more.
The crystal form is one of the preferred formulations for biotherapeutics, especially thanks to its ability to ensure high stability of the active ingredient. In addition, crystallization allows the recovery of a very pure drug, thus facilitating the manufacturing process. However, in many cases, crystallization is not trivial, and other formulations, such as the concentrate solution, represent the only choice. This is the case of anti-cluster of differentiation 20 (anti-CD20), which is one of the most sold antibodies for therapeutic uses. Here, we propose a set of optimized crystallization conditions for producing anti-CD20 needle-shaped crystals within 24 h in a very reproducible manner with high yield. High crystallization yield was obtained with high reproducibility using both hanging drop vapor diffusion and meso batch, which is a major step forward toward further scaling up the crystallization of anti-CD20. The influence of anti-CD20 storage conditions and the effect of different ions on the crystallization processes were also assessed. The crystal quality and the high yield allowed the first crystallographic investigation on anti-CD20, which positively confirmed the presence of the antibody in the crystals. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
Enhancement of Lysozyme Crystallization Using DNA as a Polymeric Additive
Crystals 2019, 9(4), 186; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9040186 - 01 Apr 2019
Cited by 6 | Viewed by 1432
Abstract
This study reports the first experimental evidence of using DNA as a polymeric additive to enhance protein crystallization. Using three kinds of DNA with different molecular weights—calf DNA, salmon DNA, and herring DNA—this study showed an improvement in the success rate of lysozyme [...] Read more.
This study reports the first experimental evidence of using DNA as a polymeric additive to enhance protein crystallization. Using three kinds of DNA with different molecular weights—calf DNA, salmon DNA, and herring DNA—this study showed an improvement in the success rate of lysozyme crystallization, as compared to control experiments, especially at low lysozyme concentration. The improvement of crystallization is particularly significant in the presence of calf DNA with the highest molecular weight. Calf DNA also speeds up the induction time of lysozyme crystallization and increases the number of crystals per drop. We hypothesized the effect of DNA on protein crystallization may be due to the combination of excluded volume effect, change of water’s surface tension, and the water competition effect. This work confirms predications of the potential use of DNA as a polymeric additive to enhance protein crystallization, potentially applied to systems with limited protein available or difficult to crystallize. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
Fab Fragment of VHH-Based Antibody Netakimab: Crystal Structure and Modeling Interaction with Cytokine IL-17A
Crystals 2019, 9(3), 177; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9030177 - 26 Mar 2019
Cited by 4 | Viewed by 2282
Abstract
Interleukin 17A (IL-17A) is a proinflammatory cytokine produced by Th17 cells. Antibody BCD-085 (netakimab) against human IL-17A is one of the new inhibitors of this cytokine. In netakimab, the VH domain is replaced by the VHH domain of Lama glama [...] Read more.
Interleukin 17A (IL-17A) is a proinflammatory cytokine produced by Th17 cells. Antibody BCD-085 (netakimab) against human IL-17A is one of the new inhibitors of this cytokine. In netakimab, the VH domain is replaced by the VHH domain of Lama glama possessing a long complementarity determining region (CDR-H3) in its heavy chain. Here we demonstrate the high affinity of IL-17A to the Fab fragment of netakimab and to its integral part, the VHH domain. We have determined the crystal structure of the Fab fragment of netakimab at 1.9 Å resolution. High variability in the orientation of light and heavy chains of the Fab fragment of netakimab was shown, which is determined by the peculiarity of the structural organization of the CDR-H3. As the high conformational plasticity of the molecule hampers modeling the Fab fragment of netakimab complexed to IL-17A, we have carried out modeling the complex between the antigen and the integral part of the Fab fragment, the VHH domain. We explain the high netakimab Fab fragment affinity for IL-17A by a large number of protein–protein contacts due to additional interactions between CDR-H3 and the cytokine dimer. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
Very Low Nucleation Rates of Glucose Isomerase Crystals under Microgravity in the International Space Station
Crystals 2019, 9(2), 90; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9020090 - 11 Feb 2019
Cited by 1 | Viewed by 1255
Abstract
In situ observation of the nucleation and growth of glucose isomerase (GI) crystals under microgravity was conducted using an optical microscope during the first flight of the Advanced Nano Step project undertaken in the International Space Station (ISS). Very low apparent nucleation rates [...] Read more.
In situ observation of the nucleation and growth of glucose isomerase (GI) crystals under microgravity was conducted using an optical microscope during the first flight of the Advanced Nano Step project undertaken in the International Space Station (ISS). Very low apparent nucleation rates (J’) of GI crystals in the solution and on the substrate of the growth container were confirmed compared with those on the ground. In particular, J’ of GI crystals in the solution were a few times lower than that on the substrate. The growth rates (R) of the {101} faces of GI crystals on the substrate and the apparent growth rates (R’) in the solution were measured. The very low nucleation rates allowed us to successfully measure R at a very high supersaturation region (up to ln(C/Ce) = 6), at which R cannot be measured on the ground. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Article
Direct Phasing of Protein Crystals with Non-Crystallographic Symmetry
Crystals 2019, 9(1), 55; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9010055 - 18 Jan 2019
Viewed by 1954
Abstract
An iterative projection algorithm proposed previously for direct phasing of high-solvent-content protein crystals is extended to include non-crystallographic symmetry (NCS) averaging. For proper NCS, when the NCS axis is positioned, the molecular envelope can be automatically rebuilt. For improper NCS, when the NCS [...] Read more.
An iterative projection algorithm proposed previously for direct phasing of high-solvent-content protein crystals is extended to include non-crystallographic symmetry (NCS) averaging. For proper NCS, when the NCS axis is positioned, the molecular envelope can be automatically rebuilt. For improper NCS, when the NCS axis and the translation vector are known, the molecular envelope can also be automatically reconstructed. Some structures with a solvent content of around 50% could be directly solved using this ab initio phasing method. Trial calculations are described to illustrate the methodology. Real diffraction data are used and the calculated phases are good for automatic model building. The refinement of approximate NCS parameters is discussed. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Review

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Review
Biological vs. Crystallographic Protein Interfaces: An Overview of Computational Approaches for Their Classification
Crystals 2020, 10(2), 114; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10020114 - 13 Feb 2020
Cited by 5 | Viewed by 1398
Abstract
Complexes between proteins are at the basis of almost every process in cells. Their study, from a structural perspective, has a pivotal role in understanding biological functions and, importantly, in drug development. X-ray crystallography represents the broadest source for the experimental structural characterization [...] Read more.
Complexes between proteins are at the basis of almost every process in cells. Their study, from a structural perspective, has a pivotal role in understanding biological functions and, importantly, in drug development. X-ray crystallography represents the broadest source for the experimental structural characterization of protein-protein complexes. Correctly identifying the biologically relevant interface from the crystallographic ones is, however, not trivial and can be prone to errors. Over the past two decades, computational methodologies have been developed to study the differences of those interfaces and automatically classify them as biological or crystallographic. Overall, protein-protein interfaces show differences in terms of composition, energetics and evolutionary conservation between biological and crystallographic ones. Based on those observations, a number of computational methods have been developed for this classification problem, which can be grouped into three main categories: Energy-, empirical knowledge- and machine learning-based approaches. In this review, we give a comprehensive overview of the training datasets and methods so far implemented, providing useful links and a brief description of each method. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Review
Methods for Obtaining Better Diffractive Protein Crystals: From Sample Evaluation to Space Crystallization
Crystals 2020, 10(2), 78; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10020078 - 30 Jan 2020
Cited by 2 | Viewed by 1382
Abstract
In this paper, we present a summary on how to obtain protein crystals from which better diffraction images can be produced. In particular, we describe, in detail, quality evaluation of the protein sample, the crystallization conditions and methods, flash-cooling protection of the crystal, [...] Read more.
In this paper, we present a summary on how to obtain protein crystals from which better diffraction images can be produced. In particular, we describe, in detail, quality evaluation of the protein sample, the crystallization conditions and methods, flash-cooling protection of the crystal, and crystallization under a microgravity environment. Our approach to protein crystallization relies on a theoretical understanding of the mechanisms of crystal growth. They are useful not only for space experiments, but also for crystallization in the laboratory. Full article
(This article belongs to the Special Issue Protein Crystallography)
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Other

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Brief Report
The Crystal Structure of the Plasmodium falciparum PdxK Provides an Experimental Model for Pro-Drug Activation
Crystals 2019, 9(10), 534; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9100534 - 17 Oct 2019
Viewed by 981
Abstract
Pyridoxine/pyridoxal kinase (PdxK), belongs to the ribokinase family and is involved in the vitamin B6 salvage pathway by phosphorylating 5-pyridoxal (PL) into an active form. In the human malaria parasite, Plasmodium falciparum, PfPdxK functions to salvage vitamin B6 from both itself [...] Read more.
Pyridoxine/pyridoxal kinase (PdxK), belongs to the ribokinase family and is involved in the vitamin B6 salvage pathway by phosphorylating 5-pyridoxal (PL) into an active form. In the human malaria parasite, Plasmodium falciparum, PfPdxK functions to salvage vitamin B6 from both itself and its host. Here, we report the crystal structure of PfPdxK from P. falciparum in complex with a non-hydrolyzable ATP analog (AMP-PNP) and PL. As expected, the fold is retained and both AMP-PNP and PL occupy the same binding sites when compared to the human ortholog. However, our model allows us to identify a FIxxIIxL motif at the C terminus of the disordered repeat motif (XNXH)m that is implicated in binding the WD40 domain and may provide temporal control of PfPdxK through an interaction with a E3 ligase complex. Furthermore, molecular docking approaches based on our model allow us to explain differential PfPdxK phosphorylation and activation of a novel class of potent antimalarials (PT3, PT5 and PHME), providing a basis for further development of these compounds. Finally, the structure of PfPdxK provides a high-quality model for a better understanding of vitamin B6 synthesis and salvage in the parasite. Full article
(This article belongs to the Special Issue Protein Crystallography)
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