Advances in Protein Crystallization and Crystallography

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 13412

Special Issue Editors


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Guest Editor
University of South Bohemia Ceske Budejovice, Czech Republic
Interests: crystallization of biological macromolecules; conventional; advanced and alternative crystallization techniques; protein crystals; crystal structures; structural and modeling studies

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Guest Editor
Inst of Org Chem and Biochem & Inst of Mol Genetics, Academy of the Science of the Czech Republic, Prague, Czech Republic
Interests: protein crystallization; protein crystallography; enzymes, protein-DNA complexes

Special Issue Information

Dear Colleagues, 

The crystallization of biological macromolecules is still poorly understood and, as a consequence, the success of common trial-and-error experiments is not very predictable. On the other hand, more rational approaches have been developed in the past years, and prospects for the science are in fact good. The topics of the Special Issue are aimed to cover all aspects of biological crystallization and crystallography from basic research on nucleation and crystal growth, to practical developments in crystallization methods and also advanced approaches and new protein crystal structures. New trends and methodologies as well as other structural methods will be encouraged. 

Prof. Ivana Kuta Smatanova
Prof. Pavlína Maloy Řezáčová
Guest Editors

Manuscript Submission Information

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Keywords

  • Crystallization of biological macromolecules
  • Conventional techniques and their modifications
  • Advanced and alternative crystallization methods
  • Crystals of membrane and soluble proteins
  • Crystals of protein–nucleic acid complexes
  • Crystals for XFEL
  • Intracellular protein crystallization
  • Evaluation of crystallization trials
  • Practical crystallography
  • Crystal structures

Published Papers (4 papers)

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Research

12 pages, 1198 KiB  
Article
AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement
by Lawrence Chai, Ping Zhu, Jin Chai, Changxu Pang, Babak Andi, Sean McSweeney, John Shanklin and Qun Liu
Crystals 2021, 11(10), 1227; https://doi.org/10.3390/cryst11101227 - 12 Oct 2021
Cited by 10 | Viewed by 4076
Abstract
Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a commonly used phasing method for crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database to [...] Read more.
Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a commonly used phasing method for crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database to find suitable templates for phasing. However, sequence information is not always available, such as when proteins are crystallized with unknown binding partner proteins or when the crystal is of a contaminant. The recent development of AlphaFold published the predicted protein structures for every protein from twenty distinct species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough to enable sequence-independent phasing of diffraction data from two crystallization contaminants of unknown sequence. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained, which allowed the identification and structure determination of YncE and YadF. Our results demonstrate the general utility of the AlphaFold-predicted structure database with respect to sequence-independent crystallographic phasing. Full article
(This article belongs to the Special Issue Advances in Protein Crystallization and Crystallography)
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16 pages, 2759 KiB  
Article
Ionic Liquids as Protein Crystallization Additives
by Crissy L. Tarver, Qunying Yuan and Marc L. Pusey
Crystals 2021, 11(10), 1166; https://doi.org/10.3390/cryst11101166 - 24 Sep 2021
Cited by 9 | Viewed by 2402
Abstract
Among its attributes, the mythical philosopher’s stone is supposedly capable of turning base metals to gold or silver. In an analogous fashion, we are finding that protein crystallization optimization using ionic liquids (ILs) often results in the conversion of base protein precipitate to [...] Read more.
Among its attributes, the mythical philosopher’s stone is supposedly capable of turning base metals to gold or silver. In an analogous fashion, we are finding that protein crystallization optimization using ionic liquids (ILs) often results in the conversion of base protein precipitate to crystals. Recombinant inorganic pyrophosphatases (8 of the 11 proteins) from pathogenic bacteria as well as several other proteins were tested for optimization by 23 ILs, plus a dH2O control, at IL concentrations of 0.1, 0.2, and 0.4 M. The ILs were used as additives, and all proteins were crystallized in the presence of at least one IL. For 9 of the 11 proteins, precipitation conditions were converted to crystals with at least one IL. The ILs could be ranked in order of effectiveness, and it was found that ~83% of the precipitation-derived crystallization conditions could be obtained with a suite of just eight ILs, with the top two ILs accounting for ~50% of the hits. Structural trends were found in the effectiveness of the ILs, with shorter-alkyl-chain ILs being more effective. The two top ILs, accounting for ~50% of the unique crystallization results, were choline dihydrogen phosphate and 1-butyl-3-methylimidazolium tetrafluoroborate. Curiously, however, a butyl group was present on the cation of four of the top eight ILs. Full article
(This article belongs to the Special Issue Advances in Protein Crystallization and Crystallography)
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16 pages, 4128 KiB  
Article
Stabilization of Haloalkane Dehalogenase Structure by Interfacial Interaction with Ionic Liquids
by Anastasiia Shaposhnikova, Michal Kuty, Radka Chaloupkova, Jiri Damborsky, Ivana Kuta Smatanova, Babak Minofar and Tatyana Prudnikova
Crystals 2021, 11(9), 1052; https://doi.org/10.3390/cryst11091052 - 1 Sep 2021
Cited by 4 | Viewed by 2822
Abstract
Ionic liquids attracted interest as green alternatives to replace conventional organic solvents in protein stability studies. They can play an important role in the stabilization of enzymes such as haloalkane dehalogenases that are used for biodegradation of warfare agents and halogenated environmental pollutants. [...] Read more.
Ionic liquids attracted interest as green alternatives to replace conventional organic solvents in protein stability studies. They can play an important role in the stabilization of enzymes such as haloalkane dehalogenases that are used for biodegradation of warfare agents and halogenated environmental pollutants. Three-dimensional crystals of haloalkane dehalogenase variant DhaA80 (T148L+G171Q+A172V+C176F) from Rhodococcus rhodochrous NCIMB 13064 were grown and soaked with the solutions of 2-hydroxyethylammonium acetate and 1-butyl-3-methylimidazolium methyl sulfate. The objective was to study the structural basis of the interactions between the ionic liquids and the protein. The diffraction data were collected for the 1.25 Å resolution for 2-hydroxyethylammonium acetate and 1.75 Å resolution for 1-butyl-3-methylimidazolium methyl sulfate. The structures were used for molecular dynamics simulations to study the interactions of DhaA80 with the ionic liquids. The findings provide coherent evidence that ionic liquids strengthen both the secondary and tertiary protein structure due to extensive hydrogen bond interactions. Full article
(This article belongs to the Special Issue Advances in Protein Crystallization and Crystallography)
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14 pages, 2361 KiB  
Article
Molecular Characterization of the Native (Non-Linked) CD160–HVEM Protein Complex Revealed by Initial Crystallographic Analysis
by Simona Lenhartová, Marek Nemčovič, Radka Šebová, Mário Benko, Dirk M. Zajonc and Ivana Nemčovičová
Crystals 2021, 11(7), 820; https://doi.org/10.3390/cryst11070820 - 15 Jul 2021
Viewed by 2959
Abstract
An increasing number of surface-exposed ligands and receptors acting on immune cells are being considered as a starting point in drug development applications. As they are dedicated to manipulating a wide range of immune responses, accurately predicting their molecular interactions will be necessary [...] Read more.
An increasing number of surface-exposed ligands and receptors acting on immune cells are being considered as a starting point in drug development applications. As they are dedicated to manipulating a wide range of immune responses, accurately predicting their molecular interactions will be necessary for the development of safe and effective therapeutics to enhance immune responses and vaccination. Here, we focused on the characterization of human CD160 and HVEM immune receptors, whose mutual engagement leads to bidirectional signaling (e.g., T cell inhibition, natural killer cell activation or mucosal immunity). In particular, our study reports on the molecule preparation, characterization and initial crystallographic analysis of the CD160–HVEM complex and both HVEM and CD160 in the absence of their binding partner. Despite the importance of the CD160–HVEM immune signaling and its therapeutic relevance, the structural and mechanistic basis underlying CD160–HVEM engagement has some controversial evidence. On one hand, there are studies reporting on the CD160 molecule in monomeric form that was produced by refolding from bacterial cells, or as a covalently linked single-chain complex with its ligand HVEM in insect cells. On the other hand, there are older reports providing evidence on the multimeric form of CD160 that acts directly on immune cells. In our study, the native non-linked CD160–HVEM complex was co-expressed in the baculovirus insect host, purified to homogeneity by anion-exchange chromatography to provide missing evidence of the trimeric form in solution. Its trimeric existence was also confirmed by the initial crystallographic analysis. The native CD160–HVEM complex crystallized in the orthorhombic space group with unit cell parameters that could accommodate one trimeric complex (3:3) in an asymmetric unit, thus providing ample space for the multimeric form. Crystals of the CD160–HVEM complex, CD160 trimer and HVEM monomer (reported in two space groups) diffracted to a minimum Bragg spacing of 2.8, 3.1 and 1.9/2.1 Å resolution, respectively. The obtained data will lead to elucidating the native structure of the complex. Full article
(This article belongs to the Special Issue Advances in Protein Crystallization and Crystallography)
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