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Crystals
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Protein Crystallography: Achievements and Challenges
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Protein Crystallography: Achievements and Challenges

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

Deadline for manuscript submissions: closed (20 April 2022) | Viewed by 12933

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 highly 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 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 (5 papers)

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Research

14 pages, 3891 KiB  
Article
A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine
by Konstantin M. Boyko, Ilya O. Matyuta, Alena Y. Nikolaeva, Tatiana V. Rakitina, Vladimir O. Popov, Ekaterina Yu. Bezsudnova and Maria G. Khrenova
Crystals 2022, 12(5), 619; https://doi.org/10.3390/cryst12050619 - 26 Apr 2022
Viewed by 2289
Abstract
Effective biocatalysts for the synthesis of optically pure amines from keto precursors are highly required in organic synthesis. Transaminases are a large group of PLP-dependent enzymes, which can be utilized for production of chiral amines or amino acids. The bioinformatic approach previously made [...] Read more.
Effective biocatalysts for the synthesis of optically pure amines from keto precursors are highly required in organic synthesis. Transaminases are a large group of PLP-dependent enzymes, which can be utilized for production of chiral amines or amino acids. The bioinformatic approach previously made to search for promising transaminases with unusual characteristics surprisingly revealed mysterious genes in some Gram-negative bacteria, which products were annotated as aminotransferases, but they lacked the key catalytic lysine residue required for covalent binding of the PLP-cofactor. To address the question of which products these genes encode, we obtained the first structure of such a type of protein from the bacterium Variovorax paradoxus (VP5454) and provided its comprehensive analysis. We demonstrated that VP5454 has a typical aminotransferase fold and architecture of the active site, where substitution of the catalytic lysine with asparagine was observed. Despite that no covalent adduct can be formed between PLP and asparagine residue, using X-ray analysis and molecular dynamic (MD) simulation, we demonstrated that VP5454 is able to bind the PLP molecule in the transaminase in a specific manner, with PLP coordinated via its phosphate moiety. Taking into account a number of sequences homologous to VP5454 with a substituted catalytic lysine found in the genomes of various bacteria, we speculate that the proteins encoded by these sequences may have hidden functional roles. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges)
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16 pages, 1442 KiB  
Article
Deconvolution of the MBP-Bri2 Interaction by a Yeast Two Hybrid System and Synergy of the AlphaFold2 and High Ambiguity Driven Protein-Protein Docking
by Evgeniya V. Smirnova, Tatiana V. Rakitina, George A. Saratov, Anna A. Kudriaeva and Alexey A. Belogurov, Jr.
Crystals 2022, 12(2), 197; https://doi.org/10.3390/cryst12020197 - 28 Jan 2022
Cited by 4 | Viewed by 2734
Abstract
Myelin basic protein (MBP) is one of the key proteins in the development of multiple sclerosis (MS). However, very few intracellular MBP partners have been identified up to now. In order to find proteins interacting with MBP in the brain, an expression library [...] Read more.
Myelin basic protein (MBP) is one of the key proteins in the development of multiple sclerosis (MS). However, very few intracellular MBP partners have been identified up to now. In order to find proteins interacting with MBP in the brain, an expression library from the human brain was screened using a yeast two-hybrid system. Here we showed that MBP interacts with the C-terminal 24-residue peptide of Integral transmembrane protein II associated with familial British and Danish dementia (ITM2B/Bri2 or Bri2). This peptide (Bri23R) was one residue longer than the known Bri23 peptide, which is cleaved from the C-terminus of Bri2 during its maturation in the Golgi and has physiological activity as a modulator of amyloid precursor protein processing. Since the spatial structures for both MBP and Bri2 were not known, we used computational methods of structural biology including an artificial intelligence system AlphaFold2 and high ambiguity driven protein-protein docking (HADDOCK 2.1) to gain a mechanistic explanation of the found protein-protein interaction and elucidate a possible structure of the complex of MBP with Bri23R peptide. As expected, MBP was mostly unstructured, although it has well-defined α-helical regions, while Bri23R forms a stable β-hairpin. Simulation of the interaction between MBP and Bri23R in two different environments, as parts of the two-hybrid system fusion proteins and in the form of single polypeptides, showed that MBP twists around Bri23R. The observed interaction results in the adjustment of the size of the internal space between MBP α-helices to the size of the β-hairpin of Bri23R. Since Bri23 is known to inhibit aggregation of amyloid oligomers, and the association of MBP to the inner leaflet of the membrane bilayer shares features with amyloid fibril formation, Bri23 may serve as a peptide chaperon for MBP, thus participating in myelin membrane assembly. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges)
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8 pages, 994 KiB  
Article
Precipitant-Free Crystallization of Lysozyme and Glucose Isomerase by Drying
by Yoshihisa Suzuki, Shiori Fujiwara, Shoko Ueta and Takashi Sakai
Crystals 2022, 12(2), 129; https://doi.org/10.3390/cryst12020129 - 18 Jan 2022
Viewed by 1781
Abstract
Protein crystallization is usually conducted by using precipitants, although the “salting-out” phenomenon is still unclear and complex. Moreover, the addition of precipitants sometimes results in irreversible disordered precipitation of protein molecules. Although precipitant-free lysozyme crystals obtained by centrifugal concentration showed significant changes in [...] Read more.
Protein crystallization is usually conducted by using precipitants, although the “salting-out” phenomenon is still unclear and complex. Moreover, the addition of precipitants sometimes results in irreversible disordered precipitation of protein molecules. Although precipitant-free lysozyme crystals obtained by centrifugal concentration showed significant changes in three-dimensional structure compared to the structure of salted-out crystals, it was rather difficult to mount crystals from a viscous dense liquid phase after centrifugal concentration, and the quality of the crystals often deteriorated during the mounting process. Here we present novel precipitant-free crystallization methods, which were effective for lysozyme and glucose isomerase. Tetragonal lysozyme crystals were successfully crystallized in a glass capillary simply by drying highly concentrated lysozyme solution in the presence of 0.01 M hydrochloric acid without using any precipitants. Glucose isomerase dissolved in ultra-pure water was also successfully crystallized in hanging drops by drying highly concentrated solution under low-humidity conditions. Oscillation images of the obtained crystals were safely collected without handling; they clearly indicated the crystals had a tetragonal form for lysozyme and an orthorhombic form for glucose isomerase, and their lattice parameters are similar to those of previously reported crystals obtained by salting-out methods. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges)
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13 pages, 5727 KiB  
Article
The Role of Cations of the Precipitant in the Interaction of Protein Molecules in the Lysozyme Oligomers in Crystallization Solutions
by Yuliya V. Kordonskaya, Vladimir I. Timofeev, Yulia A. Dyakova, Margarita A. Marchenkova, Yury V. Pisarevsky and Mikhail V. Kovalchuk
Crystals 2021, 11(12), 1534; https://doi.org/10.3390/cryst11121534 - 9 Dec 2021
Cited by 5 | Viewed by 2039
Abstract
At the moment, the main opinion is that protein crystallization depends mainly on the the precipitant anions, therefore, there have been only few works devoted to the problem of the influence of its cations. Using the molecular dynamics method, we investigated the stability, [...] Read more.
At the moment, the main opinion is that protein crystallization depends mainly on the the precipitant anions, therefore, there have been only few works devoted to the problem of the influence of its cations. Using the molecular dynamics method, we investigated the stability, changes in the compactness and structural transformations of lysozyme dimers and octamers in solutions with different precipitants (LiCl, NaCl, KCl and CuCl2) in order to study the contribution of cations during crystal formation in more detail. As a result, we found that cations have a rather noticeable effect on the behavior of oligomers: the higher the atomic mass of the cation, the greater the changes in the dimers structures during its dynamics and, according to the data of SAXS experiments, the lower the concentration of dimers. However, for octamers, this dependence is more complicated. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges)
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14 pages, 5993 KiB  
Article
Novel Device and Strategy for Growing Large, High-Quality Protein Crystals by Controlling Crystallization Conditions
by Naoki Tanigawa, Sachiko Takahashi, Bin Yan, Masayuki Kamo, Naoki Furubayashi, Koji Kubota, Koji Inaka and Hiroaki Tanaka
Crystals 2021, 11(11), 1311; https://doi.org/10.3390/cryst11111311 - 27 Oct 2021
Cited by 1 | Viewed by 2041
Abstract
Neutron diffraction experiments are informative for determining the locations of hydrogen atoms in protein molecules; however, much larger crystals are needed than those required for X-ray diffraction. Thus, additional techniques are required to grow larger crystals. Here, a unique crystallization device and strategy [...] Read more.
Neutron diffraction experiments are informative for determining the locations of hydrogen atoms in protein molecules; however, much larger crystals are needed than those required for X-ray diffraction. Thus, additional techniques are required to grow larger crystals. Here, a unique crystallization device and strategy for growing large protein crystals are introduced. The device uses two micropumps to control crystal growth by altering the precipitant concentration and regulating the pinpoint injection of dry air flow to the crystallization cell. Furthermore, the crystal growth can be observed in real time. Preliminary microbatch crystallization experiments at various concentration ranges of polyethylene glycol (PEG) 4000 and sodium chloride were first performed to elucidate optimized crystallization conditions. Based on these results, a device to precisely control the sodium chloride and PEG concentrations and the supply of dry air to the crystallization cell was used, and 1.8 mm lysozyme and 1.5 mm alpha-amylase crystals with good reproducibility were obtained. X-ray data sets of both crystals were collected at room temperature at BL2S1 of the Aichi Synchrotron Radiation Center and confirmed that these crystals were of high quality. Therefore, this crystallization device and strategy were effective for growing large, high-quality protein crystals. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges)
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