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Crystals
Special Issues
Protein Crystallography: The State of the Art
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Protein Crystallography: The State of the Art

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

Deadline for manuscript submissions: 20 February 2025 | Viewed by 3762

Special Issue Editors

Dr. Vasundara Srinivasan

E-Mail Website
Guest Editor
Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Universität Hamburg, Build. 22a, c/o DESY, 22607 Hamburg, Germany
Interests: structural biology; membrane proteins; SARS-CoV-2; mechanistic enzymology; structure-based drug discovery; time-resolved serial crystallography
Special Issues, Collections and Topics in MDPI journals
Dr. Santosh Panjikar

E-Mail Website
Guest Editor
1. ANSTO, Australian Synchrotron, 800 Blackburn Road, Clayton 3168, Australia
2. Department of Molecular Biology and Biochemistry, Monash University, Clayton 3800, Australia
Interests: structural biology; graphene-based biosensors; structural determination of macromolecules; software development in crystallography

Special Issue Information

Dear Colleagues,

X-ray diffraction is a prime technique to reveal the three-dimensional structures of biological molecules (proteins, metallo-enzymes, viruses and nucleic acids) at an atomic resolution of ~1.3 Å. Static structural information has been used to reveal the detailed mechanisms through which these molecules carry out their functions. Recent technical developments have made it possible to observe the structural dynamics of macromolecules and their complexes using various diffraction techniques available in third- or fourth-generation synchrotron sources.

We invite researchers to contribute to this Special Issue on “Protein Crystallography: the State of the Art”, which is intended to serve as a unique forum covering broad aspects of the current status of time-resolved serial crystallography in XFEL and in synchrotrons, pink beam crystallography and its progress and prospects in the field of mechanistic enzymology, structural-based drug discovery, an understanding of macromolecular complexes and membrane proteins as well as future software developments for macromolecular crystallography, and crystallization and complementary techniques (i.e., SAXS, NMR, spectroscopic techniques). We accept research articles, reviews and short communications.

Dr. Vasundara Srinivasan
Dr. Santosh Panjikar
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 submissions that pass pre-check are 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 2100 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

  • time-resolved serial crystallography in XFEL and synchrotrons (TR-SFX, TR-SSX)
  • pink beam crystallography
  • small-angle X-ray scattering (SAXS)
  • structural-based drug discovery
  • mechanistic enzymology
  • membrane proteins
  • macromolecular complexes
  • software developments for macromolecular crystallography
  • deep learning and artificial intelligence

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Published Papers (4 papers)

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Research

11 pages, 1606 KiB  
Article
Identifications of False Positives Amongst Sodium(I) Cations in Protein Three-Dimensional Structures—A Validation Approach Extendible to Any Alkali or Alkaline Earth Cation and to Any Monoatomic Anion
by Oliviero Carugo
Crystals 2024, 14(11), 918; https://doi.org/10.3390/cryst14110918 - 24 Oct 2024
Viewed by 525
Abstract
Validation of the data deposited in the Protein Data Bank is of the upmost importance, since many other databases, data mining processes, and artificial intelligence tools are strictly grounded on them. The present paper is divided into two parts. The first part describes [...] Read more.
Validation of the data deposited in the Protein Data Bank is of the upmost importance, since many other databases, data mining processes, and artificial intelligence tools are strictly grounded on them. The present paper is divided into two parts. The first part describes and analyzes validation methods that have been designed and used by the structural biology community. Everything began with the Ramachandran plot, with its allowed and disallowed types of backbone conformations, and evolved in different directions, with the inclusion of additional stereochemical features, distributions’ analyses of structural moieties, and scrutiny of structure factor amplitudes across the reciprocal lattice. The second part of the paper is focused on the largely unexplored problem of the high number of false positives amongst the sodium(I) cations observed in protein crystal structures. It is demonstrated that these false positives, which are atoms wrongly identified with sodium, can be identified by using electrostatic considerations and it is anticipated that this approach can be extended to other alkali and alkaline earth cations or to monoatomic anions. In the end, I think a global initiative, accessible to all volunteers and possibly overseen by the Protein Data Bank, should take the place of the numerous web servers and software applications by providing the community with a select few reliable and widely accepted tools. Full article
(This article belongs to the Special Issue Protein Crystallography: The State of the Art)
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13 pages, 5500 KiB  
Article
Predicting X-ray Diffraction Quality of Protein Crystals Using a Deep-Learning Method
by Yujian Shen, Zhongjie Zhu, Qingjie Xiao, Kanglei Ye, Qisheng Wang, Yue Wang and Bo Sun
Crystals 2024, 14(9), 771; https://doi.org/10.3390/cryst14090771 - 29 Aug 2024
Viewed by 851
Abstract
Over the past few decades, significant advancements in protein crystallography have led to a steady increase in the number of determined protein structures. The X-ray diffraction experiment remains one of the primary methods for investigating protein crystal structures. To obtain information about crystal [...] Read more.
Over the past few decades, significant advancements in protein crystallography have led to a steady increase in the number of determined protein structures. The X-ray diffraction experiment remains one of the primary methods for investigating protein crystal structures. To obtain information about crystal structures, a sufficient number of high-quality crystals are typically required. At present, X-ray diffraction experiments on protein crystals primarily rely on manual selection by experimenters. However, each experiment is not only costly but also time-consuming. To address the urgent need for automatic selection of the proper protein crystal candidates for X-ray diffraction experiments, a protein-crystal-quality classification network, leveraging the ConvNeXt network architecture, is proposed. Subsequently, a new database is created, which includes protein crystal images and their corresponding X-ray diffraction images. Additionally, a novel method for categorizing protein quality based on the number of diffraction spots and the resolution is introduced. To further enhance the network’s focus on essential features of protein crystal images, a CBAM (Convolutional Block Attention Module) attention mechanism is incorporated between convolution layers. The experimental results demonstrate that the network achieves significant improvement in performing the prediction task, thereby effectively enhancing the probability of high-quality crystals being selected by experimenters. Full article
(This article belongs to the Special Issue Protein Crystallography: The State of the Art)
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19 pages, 3206 KiB  
Article
Novel Quaternary Ammonium Aldimine Derivatives Featuring 3,4,5-Trimethoxy Phenyl Fragment: Synthesis, Crystal Structure and Evaluation of Antioxidant and Antibacterial Activity
by Rusi Rusew, Mariya Georgieva, Vanya Kurteva and Boris Shivachev
Crystals 2024, 14(6), 486; https://doi.org/10.3390/cryst14060486 - 22 May 2024
Viewed by 889
Abstract
This study demonstrates the synthesis of five novel quaternary ammonium aldimines through a two-step synthetic route involving a condensation reaction between 4-pyridincarboxyaldehyde and 3,4,5-trimethoxyaniline, followed by the quaternization of the pyridine N-atom with various aromatic α-bromo ketones. The newly obtained compounds underwent characterization [...] Read more.
This study demonstrates the synthesis of five novel quaternary ammonium aldimines through a two-step synthetic route involving a condensation reaction between 4-pyridincarboxyaldehyde and 3,4,5-trimethoxyaniline, followed by the quaternization of the pyridine N-atom with various aromatic α-bromo ketones. The newly obtained compounds underwent characterization for both purity and molecular structure, utilizing HR-MS, 1D, and 2D NMR spectroscopy in solution, as well as a comparison between single-crystal and powder X-ray analyses in a solid state. The thermal behavior of the studied compounds was evaluated using differential scanning calorimetry (DSC). The antioxidant properties of the compounds were assessed through DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging and ferric-reducing antioxidant power (FRAP) assays, employing Trolox as a standard. The performed in vitro antibacterial screening indicates a selective antibacterial activity against Gram-negative K. pneumoniae and P. aeruginosa, while no such activity is detected for Gram-negative E. coli and Gram-positive S. aureus. Full article
(This article belongs to the Special Issue Protein Crystallography: The State of the Art)
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15 pages, 3992 KiB  
Article
The Dynamical Properties of Three Different Variants of the Orange Carotenoid Protein: A Quasielastic Neutron Scattering Study
by Mina Hajizadeh, Maksym Golub, Marcus Moldenhauer, Wiebke Lohstroh, Thomas Friedrich and Jörg Pieper
Crystals 2024, 14(4), 361; https://doi.org/10.3390/cryst14040361 - 11 Apr 2024
Viewed by 1050
Abstract
Besides a well-adapted structure, proteins often require a specific dynamical flexibility to undergo conformational changes in order to carry out their function. The latter dynamics can be directly measured by quasielastic neutron scattering as demonstrated here for three variants of the orange carotenoid [...] Read more.
Besides a well-adapted structure, proteins often require a specific dynamical flexibility to undergo conformational changes in order to carry out their function. The latter dynamics can be directly measured by quasielastic neutron scattering as demonstrated here for three variants of the orange carotenoid protein (OCP), which plays a pivotal role in the protection of the cyanobacterial photosynthetic apparatus against photodamage. We investigate the dynamics of the structurally compact, dark-adapted wild type of OCP (OCPwt) in comparison with that of two mutant forms. The latter two mutants differ preferentially in their structures. The orange mutant OCP-W288A is assumed to have a compact structure and to preferentially bind the pigment echinenone, while the pink mutant OCP-W288A appears to represent the more elongated structure of the red active state of OCP binding the carotenoid canthaxanthin, respectively. The study reveals three major findings: (a) the dynamics of the red active state of OCP is significantly enhanced due to a larger number of protein residues being exposed to the solvent at the surface of the protein; (b) the dynamics of all OCP forms appear to be suppressed upon the freezing of the solvent, which is most likely due to an ice-induced aggregation of the proteins; and (c) the wild type and the compact mutant exhibit different dynamics attributed to a missing H-bond between the pigment and protein, resulting a destabilization of the surrounding protein. Full article
(This article belongs to the Special Issue Protein Crystallography: The State of the Art)
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