Special Issue "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: 1 May 2022.

Special Issue Editors

Dr. Vladimir Timofeev
E-Mail Website
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 crystallography; X-ray analysis; structure-function relationship; crystallization theory; microgravity protein crystallization
Dr. Hiroaki Tanaka
E-Mail Website
Guest Editor
Confocal Science Inc., 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo, Japan
Interests: protein crystal growth; in space crystallization
Dr. Yuri Pisarevsky
E-Mail Website
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
Dr. Margarita Marchenkova
E-Mail Website
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 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 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 2000 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 (7 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Article
Precipitant-Free Crystallization of Lysozyme and Glucose Isomerase by Drying
Crystals 2022, 12(2), 129; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst12020129 - 18 Jan 2022
Viewed by 91
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)
Show Figures

Figure 1

Article
The Role of Cations of the Precipitant in the Interaction of Protein Molecules in the Lysozyme Oligomers in Crystallization Solutions
Crystals 2021, 11(12), 1534; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst11121534 - 09 Dec 2021
Viewed by 380
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)
Show Figures

Figure 1

Article
The Crystal Structure of Nα-p-tosyl-lysyl Chloromethylketone-Bound Oligopeptidase B from Serratia Proteamaculans Revealed a New Type of Inhibitor Binding
Crystals 2021, 11(11), 1438; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst11111438 - 22 Nov 2021
Viewed by 341
Abstract
A covalent serine protease inhibitor—Na-p-Tosyl-Lysyl Chloromethylketone (TCK) is a modified lysine residue tosylated at the N-terminus and chloromethylated at the C-terminus, one molecule of which is capable of forming two covalent bonds with both Ser and His catalytic residues, was co-crystallized with modified [...] Read more.
A covalent serine protease inhibitor—Na-p-Tosyl-Lysyl Chloromethylketone (TCK) is a modified lysine residue tosylated at the N-terminus and chloromethylated at the C-terminus, one molecule of which is capable of forming two covalent bonds with both Ser and His catalytic residues, was co-crystallized with modified oligopeptidase B (OpB) from Serratia proteomaculans (PSPmod). The kinetics study, which preceded crystallization, shows that the stoichiometry of TCK-dependent inhibition of PSPmod was 1:2 (protein:inhibitor). The crystal structure of the PSPmod-TCK complex, solved at a resolution of 2.3 Å, confirmed a new type of inhibitor binding. Two TCK molecules were bound to one enzyme molecule: one with the catalytic Ser, the other with the catalytic His. Due to this mode of binding, the intermediate state of PSPmod and the disturbed conformation of the catalytic triad were preserved in the PSPmod-TCK complex. Nevertheless, the analysis of the amino acid surroundings of the inhibitor molecule bound to the catalytic Ser and its comparison with that of antipain-bound OpB from Trypanosoma brucei provided an insight in the structure of the PSPmod substrate-binding pocket. Supposedly, the new type of binding is typical for the interaction of chloromethylketone derivatives with two-domain OpBs. In the open conformational state that these enzymes are assumed in solution, the disordered configuration of the catalytic triad prevents simultaneous interaction of one inhibitor molecule with two catalytic residues. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges)
Show Figures

Graphical abstract

Article
Novel Device and Strategy for Growing Large, High-Quality Protein Crystals by Controlling Crystallization Conditions
Crystals 2021, 11(11), 1311; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst11111311 - 27 Oct 2021
Viewed by 435
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)
Show Figures

Figure 1

Article
Comparison of Spatial Structures and Packaging of Phosphorybosil Pyrophosphate Synthetase 2 from Thermus thermophilus HB27 in Rhombohedral and Tetragonal Crystals
Crystals 2021, 11(9), 1128; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst11091128 - 16 Sep 2021
Viewed by 606
Abstract
We report the spatial structure of phosphoribosyl pyrophosphate synthetase 2 from the thermophilic bacterium Thermus thermophilus HB27 (TthPRPPS2) obtained at a 1.85 Å resolution using a diffraction set collected from rhombohedral crystals (space group R32-h), grown with lithium sulfate as [...] Read more.
We report the spatial structure of phosphoribosyl pyrophosphate synthetase 2 from the thermophilic bacterium Thermus thermophilus HB27 (TthPRPPS2) obtained at a 1.85 Å resolution using a diffraction set collected from rhombohedral crystals (space group R32-h), grown with lithium sulfate as a precipitant. This crystal structure was compared with the structure of TthPRPPS2, previously obtained at a 2.2 Å resolution using diffraction sets from the tetragonal crystals (space group P41212), grown with ammonium sulfate as a precipitant. The comparison of these structures allows the study of the differences between protein molecules in both crystalline structures, as well as the packaging of enzyme molecules in crystals of both spatial groups. Our results may contribute to the research of the structural basis of catalytic activity and substrate specificity of this enzyme. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges)
Show Figures

Figure 1

Article
Free Energy Change during the Formation of Crystalline Contact between Lysozyme Monomers under Different Physical and Chemical Conditions
Crystals 2021, 11(9), 1121; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst11091121 - 14 Sep 2021
Viewed by 451
Abstract
We use the MM/GBSA method to calculate the free energies of dimer formation by binding two monomers with different combinations of precipitant ions, both embedded in the structure of monomers and in the crystallization solution. It shows that the largest difference in free [...] Read more.
We use the MM/GBSA method to calculate the free energies of dimer formation by binding two monomers with different combinations of precipitant ions, both embedded in the structure of monomers and in the crystallization solution. It shows that the largest difference in free energy values corresponds to the most accurate dimer model, which considers all precipitant ions in their structure. In addition, it shows that in the absence of precipitant ions in the solution of lysozyme molecules, a monomer is a more energetically favorable state. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges)
Show Figures

Figure 1

Article
Study of the Interaction of Sorption and Catalytic Centers in Carboxypeptidase T by X-ray Analysis
Crystals 2021, 11(9), 1088; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst11091088 - 07 Sep 2021
Viewed by 500
Abstract
Carboxypeptidase T (CPT; EC 3.4.17.18) from Thermoactinomyces vulgaris is a distant homolog of the highly specific pancreatic carboxypeptidase B; but has a broad substrate specificity; the source of which remains unclear. A previous study of the structural bases of the substrate specificity of [...] Read more.
Carboxypeptidase T (CPT; EC 3.4.17.18) from Thermoactinomyces vulgaris is a distant homolog of the highly specific pancreatic carboxypeptidase B; but has a broad substrate specificity; the source of which remains unclear. A previous study of the structural bases of the substrate specificity of CPT using stable sulfamoyl analogs of the transition state of the elimination of leucine; phenylalanine; arginine; and glutamic acid; showed that the binding of the C-terminal residue of the substrate to the primary selectivity pocket of CPT leads to a change in the distance between Zn2+ and the sulfur atom. This value is related to the efficiency of catalysis of the corresponding substrate or the inhibition constant of the corresponding stable analog of the transition state. In this work; we obtained crystallographic and kinetic data of the complex of CPT with N-sulfamoyl-L-valine; confirming the effect of the binding of the ligand’s side group by the primary specificity pocket of CPT on the structure of the catalytic center; which can explain the unusual substrate specificity of CPT. Full article
(This article belongs to the Special Issue Protein Crystallography: Achievements and Challenges)
Show Figures

Figure 1

Back to TopTop