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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 25339

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Dr. Blaine Mooers

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Guest Editor

Department of Biochemistry and Physiology, College of Medicine, University of Oklahoma Health Sciences, Oklahoma City, OK 73104-5419, USA
Interests: RNA editing; RNA structure; SAD phasing methods; direct methods phasing; crystal size optimization; molecular modeling
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Jolanta Prywer

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Institute of Physics, Lodz University of Technology, ul. Wólczańska 219, 93-005 Łódź, Poland
Interests: biogenic crystals; crystal growth from solutions; crystal morphology; struvite; carbonate apatite; infectious urinary stones
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The journal Crystals (ISSN: 2073-4352) is pleased to announce the launch of a Special Issue titled “Feature Papers in Biomolecular Crystallography in 2022–2023”.

The Biomolecular Crystallography section facilitates the quick publication of high-quality papers in the field of biomolecular crystals, covering the crystallization, crystallographic research, conventional and nonconventional methods of crystal growth, and the characterization of crystals and crystalline samples.

The scope of this section includes classical methods of structural studies such as X-ray diffraction (single and crystalline powder) and cutting-edge methods such as cryo-electron microscopy (Cryo-EM), as well as those related to the diffraction of electrons, neutrons, and free-electron lasers (XFEL).

We encourage the submission of research articles, reviews, letters, and communications concerning all aspects related to biomolecular crystals from small-molecular-weight biocrystals to biological macromolecules (proteins, nucleic acids, polysaccharides, and membrane proteins).

The topics include, but are not limited to, the following:

Novel methods for the crystallization of biomolecules;
Crystal growth and the design of techniques for the crystallization of biocrystals and biological macromolecules;
Biomolecular crystallography;
Crystallization in vivo for applications in X-ray crystallography;
Single crystal and powder X-ray diffraction;
Crystallo-chemistry and crystallo-physics;
Characterization of biomolecular crystals via X-ray, electron, and neutron diffraction studies;
Nanocrystals production for XFELs and MicroED studies and their 3D characterization;
Crystallization under special and physical environments;
Biomineralization in living organisms.

As a member of the Editorial Board for the Biomolecular Crystallography section and having served as Guest Editor for the Special Issue on Nucleic Acid Crystallography, I accepted the invitation to serve as the Guest Editor of this Special Issue, for which I invite my colleagues and other structural biologists to publish their relevant research in.

Prof. Dr. Blaine Mooers
Prof. Dr. Jolanta Prywer
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 2100 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.

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Published Papers (13 papers)

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Research

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10 pages, 3144 KiB

Open AccessArticle

Endowing Ferroelectric Properties of Tetragonal Lysozyme Crystals through C₆₀ Doping

by Renbin Zhou, Xuejiao Liu, Weihong Guo and Dachuan Yin

Crystals 2024, 14(4), 339; https://doi.org/10.3390/cryst14040339 - 1 Apr 2024

Viewed by 968

Abstract

The inherent nonpolarity of tetragonal lysozyme crystals excludes a ferroelectricity response. Herein, we present a demonstration of achieving measurable ferroelectricity in tetragonal lysozyme crystals through C₆₀ doping. Ferroelectric characterizations revealed that C₆₀-doped tetragonal lysozyme crystals exhibited typical characteristic ferroelectric hysteresis loops. Crystallographic structural analysis suggested that C₆₀ doping may induce a reduction in the overall symmetry of tetragonal Lys@C₆₀, leading to the observed ferroelectricity response. Moreover, the introduction of C₆₀ facilitates efficient electron transport inside the crystal and influences the polarization of Lys@C₆₀, further contributing to the observed ferroelectricity response. This work verifies that C₆₀ doping can serve as a simple strategy to bestow novel ferroelectric properties to non-ferroelectric lysozyme crystals, potentially rendering them suitable for biocompatible and biodegradable application in implantable and wearable bioelectronics. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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16 pages, 4424 KiB

Open AccessArticle

Synthesis and Structure of Unsymmetrical Anthracenyl-Isoxazole Antitumor Agents Via the Diastereoselective Bromination of 3-(9′-Anthryl)-Isoxazole Esters

by Michael J. Campbell, Daniel A. Decato, Chun Li, Matthew J. Weaver and Nicholas R. Natale

Crystals 2024, 14(3), 256; https://doi.org/10.3390/cryst14030256 - 5 Mar 2024

Cited by 1 | Viewed by 1358

Abstract

In pursuit of unsymmetrical precursors for the novel series of anthracenyl-isoxazole amide (AIM) antitumor agents, a series of substituted anthracenes were subjected to bromination and re-aromatization in our study, during which we solved four single crystal X-ray diffractometry (Sc-xrd) structures which we report herein. The C-9 nitrile oxide, after its reaction with bromine, was isolated, but when subjected to re-aromatization, it returned to the starting 10-bromo nitrile oxide 1, which did provide an accurate crystal structure, with R = 0.018. The 10-halogenated 3-(9’-anthryl)-isoxazole esters were subjected to bromination and re-aromatization. Surprisingly, the yields obtained in the presence of the isoxazole were reasonably good (62–68% isolated yields), and the major diastereomers allowed for the characterization using Sc-xrd. The penta bromo product 2 showed a trans, trans, cis relationship for the four bromines on the A-ring of the anthracene, and we observed that for the unit cell, the atropisomers displayed a 1:1 ratio at the chiral axis between the isoxazole and anthrancene rings. Similarly, the 10-chloro 3 indicated a ratio of 1:1 at the chiral axis in the crystal structure. A base-induced re-aromatization afforded 3,10-dihalogenated analogues selectively in very good yields (X = Cl, 89%; X = Br 92%), of which the dibromo 4 was characterized using Sc-xrd. The improved yields of the unique diastereomeric bromination products suggested the consideration of a novel electrophilic aromatic substitution mechanism driven by the stereo-electronic environment, imposed by the isoxazole ester substituent. The promise of the application of this chemistry in the future development of AIM antitumor agents is suggested. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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12 pages, 2641 KiB

Open AccessArticle

Titanium Dioxide Promotes the Growth and Aggregation of Calcium Phosphate and Monosodium Urate Mixed Crystals

by Onyebuchi C. Ukaeje and Bidhan C. Bandyopadhyay

Crystals 2024, 14(1), 11; https://doi.org/10.3390/cryst14010011 - 22 Dec 2023

Viewed by 1541

Abstract

The increased utilization of titanium dioxide (TiO₂) nanoparticles (TNPs) in various industrial and consumer products has raised concerns regarding its harmful effect due to its accumulation within the different systems of the human body. Here, we focused on the influence of TNPs on the growth and aggregation of two crucial crystalline substances, calcium phosphate (CaP) and monosodium urate (MSU), particularly its implications in gout disease. In this study, we adopted microscopic techniques and generated kinetic models to examine the interactions between TNPs, CaP and MSU, and crystallization, under controlled laboratory conditions. Our findings reveal that TNPs not only facilitate the growth of these crystals but also promote their co-aggregations. Crystal dissolution kinetics also exhibit that an increase in TNPs concentration corresponds to a reduction in the dissolution rate of CaP and MSU crystals in presence of the dissoluting agent hydroxycitrate (Hcit). These observations suggest that TNPs can stabilize CaP+MSU mixed crystals, which underscores the significance of TNPs’ exposure in the pathogenesis of gout disease. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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9 pages, 630 KiB

Open AccessArticle

pLDDT Values in AlphaFold2 Protein Models Are Unrelated to Globular Protein Local Flexibility

by Oliviero Carugo

Crystals 2023, 13(11), 1560; https://doi.org/10.3390/cryst13111560 - 1 Nov 2023

Cited by 5 | Viewed by 4581

Abstract

Two non-redundant, high-quality sets of protein X-ray crystal structures from the Protein Data Bank (room temperature, 288–298 K, and low temperature, 95–105 K) were compared to structural predictions conducted using ColabFold/AlphaFold2. In particular, the relationship between B-factors and pLDDT values, which estimate the degree of prediction confidence, was investigated. It was observed that there is basically no correlation between these two quantities and, consequently, that the level of confidence in predictions does not provide information about the degree of local structural flexibility of globular proteins. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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13 pages, 1895 KiB

Open AccessArticle

Variations in the Structural and Colloidal Stability of Magnetoferritin under the Impact of Technological Process Modulations

by Lucia Balejcikova, Kristyna Zolochevska, Natalia Tomasovicova, Anatolii Nagornyi, Oleksandr Tomchuk, Viktor I. Petrenko, Vasil M. Garamus, Laszlo Almasy, Milan Timko and Peter Kopcansky

Crystals 2023, 13(10), 1493; https://doi.org/10.3390/cryst13101493 - 14 Oct 2023

Viewed by 1658

Abstract

Iron-based materials, especially magnetite nanocrystals, have found extensive applications in many fields. Novel challenges focus on a deeper understanding of interactions between magnetite and biological macromolecules for developing further applications in diagnostic and treatment methods in medicine. Inspired by ferritin, the iron storage protein occurring in bacteria, plant, animal, and human cells, we developed an artificial ferritin-like material known as magnetoferritin. We present structural studies of magnetoferritin samples prepared using a controlled in vitro physicochemical synthesis. Considerable structural and size changes were observed by increasing the iron content and post-synthesis treatment. We propose the modulation of colloidal stability by using suitable solvents. Ultraviolet and visible spectroscopy, dynamic light scattering, colloidal stability measurements, infrared spectroscopy, and small-angle X-ray scattering methods were employed. The presented results aid in increasing the effectiveness of the various applications of magnetoferritin according to specific industrial requirements. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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12 pages, 3799 KiB

Open AccessArticle

Crystal Structure and Spectroscopic Analysis of 3-Diethoxyphosphoryl-28-[1-(1-deoxy-β-D-glucopyranosyl)-1H-1,2,3-triazol-4-yl]carbonylbetulin

by Monika Kadela-Tomanek, Ewa Bębenek, Arkadiusz Sokal, Maria Książek and Elwira Chrobak

Crystals 2023, 13(10), 1488; https://doi.org/10.3390/cryst13101488 - 13 Oct 2023

Cited by 2 | Viewed by 1091

Abstract

The molecular structure of 3-diethoxyphosphoryl-28-[1-(1-deoxy-β-D-glucopyranosyl)-1H-1,2,3-triazol-4-yl]carbonylbetulin was investigated through various experimental and theoretical methods. X-ray diffraction, Hirshfeld surface, experimental and calculated FT-IR spectra analysis, molecular electrostatic potential (MEP) and molecular orbital (HOMO and LUMO) were used for the analyses. It was found that the introduction of a triazole substituent affects the arrangement of molecules in the crystal structure and the formation of hydrogen bonds. The Hirshfeld surface analysis shows that the red regions are concentrated near groups, which create hydrogen bonds, which means that the hydrogen bonds are strong. The analysis of HOMO and LUMO orbitals and the chemical reactivity descriptors shows that the compound is kinetically and chemically stable. A molecular electrostatic potential map was used to analyze the electrophilic and nucleophilic area in the molecule. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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12 pages, 3137 KiB

Open AccessArticle

Crystal Packing Differences as a Key Factor for Stabilization of the N-Terminal Fragment of the Human HINT1 Protein

by Rafał Dolot, Aleksandra Mikołajczyk and Barbara Nawrot

Crystals 2023, 13(8), 1197; https://doi.org/10.3390/cryst13081197 - 2 Aug 2023

Viewed by 1167

Abstract

Histidine triad nucleotide-binding protein 1 (HINT1) is the oldest and most widely distributed branch of the histidine triad superfamily of proteins. The HINT1 protein plays an important role in various biological processes and has been found in many species. Here we report the first nearly complete structure of the human HINT1 protein at 1.43 Å resolution obtained from a crystal of the P2₁2₁2₁ orthorhombic space group. The final structure has an R_cryst = 22.4% (R_free = 27.7%) and contains a fragment of the N-terminal part that was not determined in the previously deposited structures. In addition, selective binding of the L-malate ion was detected, which had not been observed previously. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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12 pages, 2553 KiB

Open AccessArticle

Structure of Mycobacterium tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Synthase in Complex with Butylacetylphosphonate

by Victor Oliveira Gawriljuk, Rick Oerlemans, Robin M. Gierse, Riya Jotwani, Anna K. H. Hirsch and Matthew R. Groves

Crystals 2023, 13(5), 737; https://doi.org/10.3390/cryst13050737 - 27 Apr 2023

Cited by 2 | Viewed by 1826

Abstract

Stagnation in the development of new antibiotics emphasizes the need for the discovery of drugs with novel modes of action that can tackle antibiotic resistance. Contrary to humans, most bacteria use the methylerythritol phosphate (MEP) pathway to synthesize crucial isoprenoid precursors. 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) catalyzes the first and rate-limiting step of the pathway, making it an attractive target. Alkylacetylphosphonates (alkylAPs) are a class of pyruvate mimicking DXPS inhibitors that react with thiamin diphosphate (ThDP) to form a stable phosphonolactyl (PLThDP) adduct. Here, we present the first M. tuberculosis DXPS crystal structure in complex with an inhibitor (butylacetylphosphonate (BAP)) using a construct with improved crystallization properties. The 1.6 Å structure shows that the BAP adduct interacts with catalytically important His40 and several other conserved residues of the active site. In addition, a glycerol molecule, present in the D-glyceraldehyde 3-phosphate (D-GAP) binding site and within 4 Å of the BAP adduct, indicates that there is space to extend and develop more potent alkylAPs. The structure reveals the BAP binding mode and provides insights for enhancing the activity of alkylAPs against M. tuberculosis, aiding in the development of novel antibiotics. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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12 pages, 2078 KiB

Open AccessFeature PaperArticle

Textile Functionalization by Porous Protein Crystal Conjugation and Guest Molecule Loading

by Luke F. Hartje, David A. Andales, Lucas P. Gintner, Lucas B. Johnson, Yan V. Li and Christopher D. Snow

Crystals 2023, 13(2), 352; https://doi.org/10.3390/cryst13020352 - 18 Feb 2023

Cited by 1 | Viewed by 1933

Abstract

Protein crystals are versatile nanostructured materials that can be readily engineered for applications in nanomedicine and nanobiotechnology. Despite their versatility, the small size of typical individual protein crystals (less than one cubic mm) presents challenges for macroscale applications. One way to overcome this limitation is by immobilizing protein crystals onto larger substrates. Cotton is composed primarily of cellulose, the most common natural fiber in the world, and is routinely used in numerous material applications including textiles, explosives, paper, and bookbinding. Here, two types of protein crystals were conjugated to the cellulosic substrate of cotton fabric using a 1,1′-carbonyldiimidazole/aldehyde mediated coupling protocol. The efficacy of this attachment was assessed via accelerated laundering and quantified by fluorescence imaging. The ability to load guest molecules of varying sizes into the scaffold structure of the conjugated protein crystals was also assessed. This work demonstrates the potential to create multifunctional textiles by incorporating diverse protein crystal scaffolds that can be infused with a multiplicity of useful guest molecules. Cargo molecule loading and release kinetics will depend on the size of the guest molecules as well as the protein crystal solvent channel geometry. Here, we demonstrate the loading of a small molecule dye into the small pores of hen egg white lysozyme crystals and a model enzyme into the 13-nm pores delimited by “CJ” crystals composed of an isoprenoid-binding protein from Campylerbacter jejuni. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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16 pages, 3600 KiB

Open AccessArticle

Direct Phasing of Coiled-Coil Protein Crystals

by Ruijiang Fu, Wu-Pei Su and Hongxing He

Crystals 2022, 12(11), 1674; https://doi.org/10.3390/cryst12111674 - 20 Nov 2022

Cited by 2 | Viewed by 1982

Abstract

Coiled-coil proteins consisting of multiple copies of helices take part in transmembrane transportation and oligomerization, and are used for drug delivery. Cross-alpha amyloid-like coiled-coil structures, in which tens of short helices align perpendicular to the fibril axis, often resist molecular replacement due to the uncertainty to position each helix. Eight coiled-coil structures already solved and posted in the protein data bank are reconstructed ab initio to demonstrate the direct phasing results. Non-crystallographic symmetry and intermediate-resolution diffraction data are considered for direct phasing. The retrieved phases have a mean phase error around 30∼40°. The calculated density map is ready for model building, and the reconstructed model agrees with the deposited structure. The results indicate that direct phasing is an efficient approach to construct the protein envelope from scratch, build each helix without model bias which is also used to confirm the prediction of AlphaFold and RosettaFold, and solve the whole structure of coiled-coil proteins. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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19 pages, 10390 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Biological Mineralization of Hydrophilic Intraocular Lenses

by Petros G. Koutsoukos, Panagiota D. Natsi, Sotirios P. Gartaganis and Panos S. Gartaganis

Crystals 2022, 12(10), 1418; https://doi.org/10.3390/cryst12101418 - 8 Oct 2022

Cited by 2 | Viewed by 2774

Abstract

Biomaterials calcify upon implantation in contact with biological fluids, which are supersaturated with respect to more than one crystalline phase of calcium phosphate. The implantation of intraocular lenses (IOLs) for cataract treatment has been hailed as a major advance. Hydrophilic acrylic IOLs, made of Poly(2-hydroxyethyl methacrylate) (PHEMA), upon contact with aqueous humor, exhibit significant incidence of opacification, due to the formation of calcium phosphate crystals, mainly hydroxyapatite (Ca₅(PO₄)₃OH, HAP) on the surface or in their interior. The aqueous humor is supersaturated with respect to HAP. Clinical findings were duplicated by laboratory experiments through the development of appropriate experimental models which included batch reactors, well stirred operating at constant supersaturation (CCR) and reactors simulating anterior eye chamber (ECSR). In both CCR and ECSR, simulated aqueous humor was used. In ECSR the flow rate was the same as in the eye chamber (2.5 mL per 24 h). HAP formed both on the surface and inside the IOLs tested. Induction times preceding the crystallization of HAP on the surface of the IOLs and crystal growth rates were measured. Surface hydroxyl ionized groups favored the development of locally high supersaturation by surface complexation. In the interior of the IOLs, HAP formed by the diffusion of the calcium and phosphate ions inside the polymeric matrix. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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Review

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12 pages, 2416 KiB

Open AccessReview

Structural Changes as a Tool for Affinity Recognition: Conformational Switch Biosensing

by Viviana Scognamiglio and Amina Antonacci

Crystals 2022, 12(9), 1209; https://doi.org/10.3390/cryst12091209 - 27 Aug 2022

Cited by 3 | Viewed by 1515

Abstract

Biosensors draw inspiration from natural chemosensing based on molecular switches between different bond-induced conformational states. Proteins and nucleic acids can be adapted into switch-based biosensors with a wide plethora of different configurations, taking advantage of the variety of transduction systems, from optical to electrochemical or electrochemiluminescence, as well as from nanomaterials for signal augmentation. This review reports the latest trends in conformational switch biosensors reported in the literature in the last 10 years, focusing on the main representative and recent examples of protein-based switching biosensors, DNA nanomachines, and structure-switched aptamers being applied for the detection of a wide range of target analytes with interest in biomedical and agro-environmental sectors. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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Other

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16 pages, 2517 KiB

Open AccessPerspective

A Short and Practical Overview on Light-Sensing Proteins, Optogenetics, and Fluorescent Biomolecules inside Biomorphs Used as Optical Sensors

by Ulises Galindo-García, María Vanegas-Reza, Roberto Arreguín-Espinosa, Karina Sandra Pérez, Ricardo Pérez-Solis, María Eugenia Mendoza, Karla Yadira Cervantes-Quintero, Selene R. Islas, Mayra Cuéllar-Cruz and Abel Moreno

Crystals 2023, 13(9), 1343; https://doi.org/10.3390/cryst13091343 - 3 Sep 2023

Viewed by 1881

Abstract

In this contribution, we describe a brief overview of the role of different light-signaling proteins in different biochemical processes (mostly in plants) along the electromagnetic spectrum. We also revise, in terms of perspectives, the applications of all these proteins to optogenetics as a new emerging field of research. In the second part, we present some case studies: First, we used two fluorescent proteins showing an optical response in the green- and red-light wavelengths both isolated from marines’ organisms, which were incorporated as light sensors into the silico-carbonate of Ca, Ba, and Sr (usually called biomorphs). The second case study consisted in incorporating phototropins from a plant (Arabidopsis thaliana) into the synthesis of biomorphs. Finally, the last part analyses the influence of these three proteins on the shape and structure in the synthesis of silico-carbonates of calcium, barium, and strontium as optical sensors, in order to detect the location of these biomolecules inside these self-assembly crystalline materials called biomorphs. Full article

(This article belongs to the Special Issue Feature Papers in Biomolecular Crystals in 2022-2023)

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