Awarded papers by Polish crystallographers published in 2021
Biological and medical crystallography
Joanna L. Loch, Barbara Imiołczyk, Joanna Śliwiak, Anna Wantuch, Magdalena Bejger, Mirosław Gilski, Mariusz Jaskólski
Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznań
“Crystal structures of the elusive Rhizobium etli l-asparaginase reveal a peculiar active site”
Nature Communications 12, 6717 (2021)
https://doi.org/10.1038/s41467-021-27105-x
The publication describes the enzymatic function and the spatial structure of a new enzyme (called ReAV) that breaks down a simple amino acid - asparagine - into aspartic acid and ammonia. Enzymes with such a function, called asparaginases, are urgently needed by medicine, because under certain additional conditions, they may turn out to be excellent drugs in the treatment of acute leukemia in children. The enzyme described in the publication does not meet all the criteria of a perfect drug, but getting to know its structure gives a chance for its "improvement" to meet these criteria. The ReAV enzyme is new in the sense that its structure has completely surprised researchers who know the inside out of asparaginases. On the other hand, the battle to understand the structure of the ReAV protein has been going on for almost 20 years. This shows both the scale of the problem and the scale of the achievement. The article was prepared by a team working under the supervision of prof. Mariusz Jaskólski from the Department of Crystallography at the Faculty of Chemistry, AMU. The publication is the result of collaboration between scientists from the University of Adam Mickiewicz, the Institute of Bioorganic Chemistry of the Polish Academy of Sciences in Poznań and the Jagiellonian University in Kraków.
Chemical and pharmaceutical crystallography
Krzysztof A. Konieczny, Julia Bąkowicz, Damian Paliwoda, Mark R. Warren, Arkadiusz Ciesielski, Michał K. Cyrański, Iwona Turowska-Tyrk
Advanced Materials Engineering and Modelling Group, Wrocław University of Science and Technology; ICGM, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier; Diamond Light Source, Harwell Campus, Chilton, Oxfordshire; Faculty of Chemistry, University of Warsaw
"Structural reasons for the formation of multicomponent products and the influence of high pressure"
Acta Crystallographica, 2021, B77, 321-330
https://doi.org/10.1107/S2052520621004492
The interaction between light and crystalline materials is an issue with great application potential. Light can be a carrier of information or energy that can be stored inside the crystal, as well as being a stimulus causing photochemical reactions in the crystal, which can be an ecological alternative to conventional methods used in selective organic synthesis. The high degree of order and translational structure of the crystals provide, in some cases, a certain degree of control over the photoinduced processes taking place in them. In the published studies, an additional external stimulus in the form of high pressure was used to influence the kinetics and selectivity of photochemical reactions in the crystals of 4- (2,4,6-triisopropylbenzoyl) benzoic acid salt with phenylethylamine. At atmospheric pressure, radiation of the appropriate wavelength induces competing photocycling reactions leading to the formation of three different photoproducts. The multidirectional nature of this process gives the appearance that it is completely random, but a careful structural analysis of the crystals at many stages of the reaction made it possible to unequivocally state that it is a deterministic process, and the formation of the next product is correlated with the formation of the previous ones.
The use of high pressure of about 1.0 GPa means that only two of the three products are formed as a result of irradiating the crystal. This means that high pressure may be a factor influencing the selectivity of photochemical reactions in crystals. The reasons for this are cumulative subtle structural changes, such as changes in the intermolecular interactions, the volume of voids in the crystal or the conformation of substrate molecules as a function of pressure.
Physical crystallography
Ireneusz Bugański, Luca Bindi
Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Kraków; Graduate School of Engineering, Hokkaido University, Sapporo; Dipartimento di
Scienze della Terra, Universita` degli Studi di Firenze
"Insight into the structure of decagonite – the extraterrestrial decagonal quasicrystal"
IUCr Journal (2021) 8, 87-101
https://doi.org/10.1107/S2052252520015444
A set of X-ray data collected on a fragment of decagonite, Al71Ni24Fe5, the only known natural decagonal quasicrystal found in a meteorite formed at the beginning of the Solar System, allowed us to determine the first structural model for a natural quasicrystal. It is a two-layer structure with decagonal columnar clusters arranged according to the pentagonal Penrose tiling. The structural model showed peculiarities and slight differences with respect to those obtained for other synthetic decagonal quasicrystals. Interestingly, decagonite is found to exhibit low linear phason strain and a high degree of perfection despite the fact it was formed under conditions very far from those used in the laboratory.
Figure shows two sections of the investigated decagonite crystal..
Tomasz Pawlak, Isaac Sudgen, Grzegorz Bujacz, Dinu Iuga, Steven P. Brown & Marek J. Potrzebowski
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Łódź; Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London; Institute of Molecular and Industrial Biotechnology, Łódź University of Technology; Department of Physics, University of Warwick, Coventry
"Synergy of Solid-State NMR, Single-Crystal X-ray Diffraction, and Crystal Structure Prediction Methods: A Case Study of Teriflunomide (TFM)"
Crystal growth & design, 21(6) (2021) 3328-3343
https://doi.org/10.1021/acs.cgd.1c00123
Awarded work presents the X-ray diffraction crystal structure and spectral properties of a new, room-temperature polymorph of teriflunomide that undergoes a reversible thermal transition, and it is related to the change in Z′ value, from 2 to 1. Our study shows the power of combining experiments with DFT calculations and CSP to understand the solid-state landscape for pharmaceutical molecules.
Theory, methodology and didactics of crystallography
Bartosz Naskręcki, Zbigniew Dauter, Mariusz Jaskólski
Faculty of Mathematics and Computer Science, A. Mickiewicz University, Poznań; Macromolecular Crystallography Laboratory, NCI, Argonne National Laboratory, Argonne; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznań; Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań
“Arithmetic proof of the multiplicity-weighted Euler characteristic for symmetrically arranged space-filling polyhedral”
Acta Crystallographica A77, 2021, 126-129.
https://doi.org/10.1107/S2053273320016186
“A topological proof of the modified Euler characteristic based on the orbifold concept”
Acta Crystallographica A77, 2021, 317-326.
https://doi.org/10.1107/S2053273321004320
The previously discovered modified Euler formula for space-filling polyhedra (such as, for example, unit cells or Dirichlet domains) has been a hypothesis so far. The award-winning papers provide two proofs of this hypothesis, generalized as a modified Euler characteristic of topological spaces. The first proof uses the properties of the parity groups of indexes assigned to the lattice elements and is crowned with a reference to the Whitehead theorem. The second proof is based on the analogy between a translationally filled space, polyhedrons, and a three-dimensional torus. The introduction of the orbifold concept allows us to naturally carry out a topological proof and to generalize it to the space situation of any dimension.
