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: 31 October 2019.

Special Issue Editors

Prof. 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. Abel Moreno
E-Mail Website
Guest Editor

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

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Crystals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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 (8 papers)

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Research

Open AccessArticle
Trial Direct Phasing Calculation of A Thyroid Hormone Receptor Alpha Structure (4LNW)
Crystals 2019, 9(10), 533; https://doi.org/10.3390/cryst9100533 (registering DOI) - 16 Oct 2019
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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Open AccessArticle
Comparison of the Quality of Protein Crystals Grown by CLPC Seeds Method
Crystals 2019, 9(10), 501; https://doi.org/10.3390/cryst9100501 - 26 Sep 2019
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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Open AccessArticle
Protein Crystallization in Ionic-Liquid Hydrogel Composite Membranes
Crystals 2019, 9(5), 253; https://doi.org/10.3390/cryst9050253 - 17 May 2019
Cited by 1
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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Open AccessArticle
Optimization of Vapor Diffusion Conditions for Anti-CD20 Crystallization and Scale-Up to Meso Batch
Crystals 2019, 9(5), 230; https://doi.org/10.3390/cryst9050230 - 29 Apr 2019
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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Open AccessArticle
Enhancement of Lysozyme Crystallization Using DNA as a Polymeric Additive
Crystals 2019, 9(4), 186; https://doi.org/10.3390/cryst9040186 - 01 Apr 2019
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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Open AccessArticle
Fab Fragment of VHH-Based Antibody Netakimab: Crystal Structure and Modeling Interaction with Cytokine IL-17A
Crystals 2019, 9(3), 177; https://doi.org/10.3390/cryst9030177 - 26 Mar 2019
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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Open AccessArticle
Very Low Nucleation Rates of Glucose Isomerase Crystals under Microgravity in the International Space Station
Crystals 2019, 9(2), 90; https://doi.org/10.3390/cryst9020090 - 11 Feb 2019
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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Open AccessArticle
Direct Phasing of Protein Crystals with Non-Crystallographic Symmetry
Crystals 2019, 9(1), 55; https://doi.org/10.3390/cryst9010055 - 18 Jan 2019
Cited by 8
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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