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Crystals
Special Issues
Protein Crystallography: Achievements and Challenges (Volume II)
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Protein Crystallography: Achievements and Challenges (Volume II)

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

Deadline for manuscript submissions: closed (1 October 2023) | Viewed by 4436

Special Issue Editors

Dr. Vladimir Timofeev

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Guest Editor
1. A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, 59, Leninskii Prospect, 119333 Moscow, Russia
2. National Research Centre “Kurchatov Institute”, 1, Akademika Kurchatova pl., 123182 Moscow, Russia
Interests: protein structure; structure–function relationship; bioinformatics; computational biology; reverse immunology
Special Issues, Collections and Topics in MDPI journals
Dr. Hiroaki Tanaka

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Guest Editor
Conforcal Science Inc., Fukasawa 5-14-15, Setagaya-ku, Tokyo 158-0081, Japan
Interests: protein crystal growth; in space crystallization
Special Issues, Collections and Topics in MDPI journals
Dr. Yuri Pisarevsky

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Guest Editor
Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, 59, Leninsky pr., 119333 Moscow, Russia
Interests: protein crystal materials; protein crystal growth; protein-precipitant interaction; X-ray;neutron and optical methods
Special Issues, Collections and Topics in MDPI journals
Dr. Margarita Marchenkova

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Guest Editor
1. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, 119333 Moscow, Russia
2. National Research Centre “Kurchatov Institute”, 123098 Moscow, Russia
Interests: interaction of X-rays and neutrons with matter; Langmuir monolayers; protein crystallization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Proteins are the most important biological macromolecules and are involved in almost all aspects of life. Therefore, the study of the structure of proteins is of great practical and fundamental importance. On the one hand, knowledge of the spatial structure is necessary to study the basic principles of protein functioning, for example, the mechanisms of enzymatic reactions. On the other hand, knowledge of the spatial structure of proteins is used, for example, in biotechnology for the design of enzymes with desired properties, as well as in drag design. Today, the main method for determining the spatial structure of a protein is X-ray structural analysis of protein crystals. The main difficulty in applying this method is obtaining a perfect protein crystal. In this Special Issue, articles devoted to the description of the spatial structures of proteins, as well as articles devoted to the practical and theoretical aspects of improving the quality of protein crystals, are welcome.

Dr. Vladimir I. Timofeev
Dr. Hiroaki Tanaka
Dr. Yuri Pisarevsky
Dr. Margarita Marchenkova
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 2600 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 crystal
  • protein structure
  • structure–function relationship
  • nucleation
  • nucleation theory

Published Papers (3 papers)

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Research

14 pages, 3730 KiB  
Article
Self-Assembly and Conformational Change in the Oligomeric Structure of the Ectodomain of the TBEV E Protein Studied via X-ray, Small-Angle X-ray Scattering, and Molecular Dynamics
by Petr V. Konarev, Anna V. Vlaskina, Dmitry Korzhenevskiy, Tatiana V. Rakitina, Dmitry Petrenko, Yulia Agapova, Yulia Kordonskaya and Valeriya R. Samygina
Crystals 2023, 13(12), 1676; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst13121676 - 12 Dec 2023
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Abstract
The determination of the three-dimensional structures of viral proteins is a necessary step both for understanding the mechanisms of virus pathogenicity and for developing methods to combat viral infections. This study aimed to explore the folding and oligomeric state of the major component [...] Read more.
The determination of the three-dimensional structures of viral proteins is a necessary step both for understanding the mechanisms of virus pathogenicity and for developing methods to combat viral infections. This study aimed to explore the folding and oligomeric state of the major component of the virion surface of the tick-borne encephalitis virus (TBEV), the ectodomain of the envelope E protein (ectoE), which was expressed in E. coli in a soluble form and purified from inclusion bodies as a mixture of dimeric and monomeric forms. The time-dependent assembly of monomers into dimers was detected using size-exclusion chromatography. An X-ray diffraction study of the ectoE crystals grown at pH 4.5 confirmed the dimeric folding of the recombinant protein typical for ectoE. The ability of ectoE dimers to self-assemble into tetramers was detected via small-angle X-ray scattering (SAXS) in combination with molecular dynamics. Such self-assembly occurred at protein concentrations above 4 mg/mL and depended on the pH of the solution. In contrast to stable, specific dimers, we observed that tetramers were stabilized with weak intermolecular contacts and were sensitive to environmental conditions. We discovered the ability of ectoE tetramers to change conformation under crystallization conditions. These results are important for understanding the crystallization process of viral proteins and may be of interest for the development of virus-like particles. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges (Volume II))
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12 pages, 2842 KiB  
Article
QM/MM Study of a Nucleophilic Substitution Reaction Catalyzed by Uridine Phosphorylase from Vibrio cholerae
by Alexander A. Lashkov, Polina A. Eistrich-Geller, Valeriya R. Samygina and Sergey V. Rubinsky
Crystals 2023, 13(5), 803; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst13050803 - 11 May 2023
Viewed by 1360
Abstract
Uridine phosphorylases are used for biotechnological synthesis of pyrimidine derivatives and, moreover, their substrates and inhibitors are used in medicine. Therefore, studies of the mechanisms of the chemical reaction catalyzed by the enzyme and its specificity for various substrates are relevant. The research [...] Read more.
Uridine phosphorylases are used for biotechnological synthesis of pyrimidine derivatives and, moreover, their substrates and inhibitors are used in medicine. Therefore, studies of the mechanisms of the chemical reaction catalyzed by the enzyme and its specificity for various substrates are relevant. The research into the enzymatic reaction main stage—nucleophilic substitution of the nitrogenous base in uridine with an orthophosphate or orthovanadate group by hybrid QM/MM methods—was carried out. A comparison of various levels of theory and calculation schemes showed that preliminary optimization of the reactants’s geometry, as well as calculation of the initial trajectory of the minimum energy path, can be achieved by semi-empirical methods. At the same time, for the minimum energy path clarification, transition state geometry optimization, and calculation of the thermochemical parameters, it is preferable to use density functional theory in combination with modern ab initio methods. In comparison with the calculations of the activation barrier carried out in a solvent without an enzyme, differences in the kinetics of the enzymatic reaction due to the orientation and concentration actions of amino acid residues of the enzyme were revealed. This led to lowering the activation barrier by 20 kcal/mol and contributed to the reaction under physiologically acceptable conditions. It was shown that the free activation energy during the nucleophilic attack for uridine with hydrovanadate ion is 2 kcal/mol lower than for the hydrophosphate ion and this is consistent with the literature data. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges (Volume II))
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9 pages, 1900 KiB  
Article
Probing the Role of a Conserved Phenylalanine in the Active Site of Thiocyanate Dehydrogenase
by Larisa A. Varfolomeeva, Anastasia Yu. Solovieva, Nikolai S. Shipkov, Olga G. Kulikova, Natalia I. Dergousova, Tatiana V. Rakitina, Konstantin M. Boyko, Tamara V. Tikhonova and Vladimir O. Popov
Crystals 2022, 12(12), 1787; https://doi.org/10.3390/cryst12121787 - 8 Dec 2022
Viewed by 1283
Abstract
Copper-containing enzymes catalyze a broad spectrum of redox reactions. Thiocyanate dehydrogenase (TcDH) from Thioalkalivibrio paradoxus Arh1 enables the bacterium to use thiocyanate as a unique source of energy and nitrogen. Oxidation of thiocyanate takes place in the trinuclear copper center of TcDH with [...] Read more.
Copper-containing enzymes catalyze a broad spectrum of redox reactions. Thiocyanate dehydrogenase (TcDH) from Thioalkalivibrio paradoxus Arh1 enables the bacterium to use thiocyanate as a unique source of energy and nitrogen. Oxidation of thiocyanate takes place in the trinuclear copper center of TcDH with peculiar organization. Despite the TcDH crystal structure being established, a role of some residues in the enzyme active site has yet to be obscured. F436 residue is located in the enzyme active site and conserved among a number of TcDH homologs, however, its role in the copper center formation or the catalytic process is still not clear. To address this question, a mutant form of the enzyme with F436Q substitution (TcDHF436Q) was obtained, biochemically characterized, and its crystal structure was determined. The TcDHF436Q had an unaltered protein fold but did not possess enzymatic activity, whereas it contained all three copper ions, according to ICP-MS data. The structural data showed that the F436Q substitution resulted in a disturbance of hydrophobic interactions within the active site crucial for a correct transition between open/closed forms of the enzyme–substrate channel. Thus, we demonstrated that F436 does not participate in copper ion binding, but rather possesses a structural role in the TcDH active site. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges (Volume II))
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