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Tolbatov I, Marrone A, Shepard W, Chiaverini L, Upadhyay Kahaly M, La Mendola D, Marzo T, Ciccone L. Inorganic Drugs as a Tool for Protein Structure Solving and Studies on Conformational Changes. Chemistry 2023; 29:e202202937. [PMID: 36477932 DOI: 10.1002/chem.202202937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022]
Abstract
Inorganic drugs are capable of tight interactions with proteins through coordination towards aminoacidic residues, and this feature is recognized as a key aspect for their pharmacological action. However, the "protein metalation process" is exploitable for solving the phase problem and structural resolution. In fact, the use of inorganic drugs bearing specific metal centers and ligands capable to drive the binding towards the desired portions of the protein target could represent a very intriguing and fruitful strategy. In this context, a theoretical approach may further contribute to solve protein structures and their refinement. Here, we delineate the main features of a reliable experimental-theoretical integrated approach, based on the use of metallodrugs, for protein structure solving.
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Affiliation(s)
- Iogann Tolbatov
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Alessandro Marrone
- Department of Pharmacy, University "G. D'Annunzio" Chieti-Pescara, Via dei Vestini, 31, 66100, Chieti, Italy
| | - William Shepard
- Department PROXIMA2 A, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France
| | - Lorenzo Chiaverini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | | | - Diego La Mendola
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Tiziano Marzo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Lidia Ciccone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
- Department PROXIMA2 A, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France
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2
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Crans DC, Sánchez-Lombardo I, McLauchlan CC. Exploring Wells-Dawson Clusters Associated With the Small Ribosomal Subunit. Front Chem 2019; 7:462. [PMID: 31334216 PMCID: PMC6624422 DOI: 10.3389/fchem.2019.00462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/11/2019] [Indexed: 01/23/2023] Open
Abstract
The polyoxometalate P2W18O626-, the Wells-Dawson cluster, stabilized the ribosome sufficiently for the crystallographers to solve the phase problem and improve the structural resolution. In the following we characterize the interaction of the Wells-Dawson cluster with the ribosome small subunit. There are 14 different P2W18O626- clusters interacting with the ribosome, and the types of interactions range from one simple residue interaction to complex association of multiple sites including backbone interactions with a Wells-Dawson cluster. Although well-documented that bridging oxygen atoms are the main basic sites on other polyoxometalate interaction with most proteins reported, the W=O groups are the main sites of the Wells-Dawson cluster interacting with the ribosome. Furthermore, the peptide chain backbone on the ribosome host constitutes the main sites that associate with the Wells-Dawson cluster. In this work we investigate the potential of one representative pair of closely-located Wells-Dawson clusters being a genuine Double Wells-Dawson cluster. We found that the Double Wells-Dawson structure on the ribosome is geometrically sound and in line with other Double Wells-Dawson clusters previously observed in the solid state and solution. This information suggests that the Double Wells-Dawson structure on the ribosome is real and contribute to characterization of this particular structure of the ribosome.
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Affiliation(s)
- Debbie C Crans
- Department Chemistry and the Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, United States
| | - Irma Sánchez-Lombardo
- Department Chemistry and the Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, United States.,División Académica de Ciencias Básicas, Universidad Juárez Autónoma de Tabasco, Cunduacán, Mexico
| | - Craig C McLauchlan
- Department of Chemistry, Illinois State University, Normal, IL, United States
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3
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Bijelic A, Rompel A. Polyoxometalates: more than a phasing tool in protein crystallography. CHEMTEXTS 2018; 4:10. [PMID: 30596006 PMCID: PMC6294228 DOI: 10.1007/s40828-018-0064-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/06/2018] [Indexed: 01/18/2023]
Abstract
Protein crystallography is the most widely used method for determining the molecular structure of proteins and obtaining structural information on protein–ligand complexes at the atomic level. As the structure determines the functions and properties of a protein, crystallography is of immense importance for nearly all research fields related to biochemistry. However, protein crystallography suffers from some major drawbacks, whereby the unpredictability of the crystallization process represents the main bottleneck. Crystallization is still more or less a ‘trial and error’ based procedure, and therefore, very time and resource consuming. Many strategies have been developed in the past decades to improve or enable the crystallization of proteins, whereby the use of so-called additives, which are mostly small molecules that make proteins more amenable to crystallization, is one of the most convenient and successful methods. Most of the commonly used additives are, however, restricted to particular crystallization conditions or groups of proteins. Therefore, a more universal additive addressing a wider range of proteins and being applicable to a broad spectrum of crystallization conditions would represent a significant advance in the field of protein crystallography. In recent years, polyoxometalates (POMs) emerged as a promising group of crystallization additives due to their unique structures and properties. In this regard, the tellurium-centered Anderson–Evans polyoxotungstate [TeW6O24]6− (TEW) showed its high potential as crystallization additive. In this lecture text, the development of POMs as tools in protein crystallography are discussed with a special focus on the so far most successful cluster TEW.
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Affiliation(s)
- Aleksandar Bijelic
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Vienna, Austria
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Vienna, Austria
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Abstract
Due to the availability of many macromolecular models in the Protein Data Bank, the majority of crystal structures are currently solved by molecular replacement. However, truly novel structures can only be solved by one of the versions of the special-atom method. The special atoms such as sulfur, phosphorus or metals could be naturally present in the macromolecules, or could be intentionally introduced in a derivatization process. The isomorphous and/or anomalous scattering of X-rays by these special atoms is then utilized for phasing. There are many ways to obtain potentially useful derivatives, ranging from the introduction of special atoms to proteins or nucleic acids by genetic engineering or by chemical synthesis, to soaking native crystals in solutions of appropriate compounds with heavy and/or anomalously scattering atoms. No approach guarantees the ultimate success and derivatization remains largely a trial-and-error process. In practice, however, there is a very good chance that one of a wide variety of the available procedures will lead to successful structure solution.
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5
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Abstract
Experimental methods for the characterization of protein complexes have been instrumental in achieving our current understanding of the protein universe and continue to progress with each year that passes. In this chapter, we review some of the most important tools and techniques in the field, covering the important points in X-ray crystallography, cryo-electron microscopy, NMR spectroscopy, and mass spectrometry. Novel developments are making it possible to study large protein complexes at near-atomic resolutions, and we also now have the ability to study the dynamics and assembly pathways of protein complexes across a range of sizes.
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Affiliation(s)
- Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK.
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
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6
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Bijelic A, Rompel A. Ten Good Reasons for the Use of the Tellurium-Centered Anderson-Evans Polyoxotungstate in Protein Crystallography. Acc Chem Res 2017; 50:1441-1448. [PMID: 28562014 PMCID: PMC5480232 DOI: 10.1021/acs.accounts.7b00109] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Protein
crystallography represents at present the most productive
and most widely used method to obtain structural information on target
proteins and protein–ligand complexes within the atomic resolution
range. The knowledge obtained in this way is essential for understanding
the biology, chemistry, and biochemistry of proteins and their functions
but also for the development of compounds of high pharmacological
and medicinal interest. Here, we address the very central problem
in protein crystallography: the unpredictability of the crystallization
process. Obtaining protein crystals that diffract to high resolutions
represents the essential step to perform any structural study by X-ray
crystallography; however, this method still depends basically on trial
and error making it a very time- and resource-consuming process. The
use of additives is an established process to enable or improve the
crystallization of proteins in order to obtain high quality crystals.
Therefore, a more universal additive addressing a wider range of proteins
is desirable as it would represent a huge advance in protein crystallography
and at the same time drastically impact multiple research fields.
This in turn could add an overall benefit for the entire society as
it profits from the faster development of novel or improved drugs
and from a deeper understanding of biological, biochemical, and pharmacological
phenomena. With this aim in view, we have tested several compounds
belonging
to the emerging class of polyoxometalates (POMs) for their suitability
as crystallization additives and revealed that the tellurium-centered
Anderson–Evans polyoxotungstate [TeW6O24]6– (TEW) was the most suitable POM-archetype.
After its first successful application as a crystallization additive,
we repeatedly reported on TEW’s positive effects on the crystallization
behavior of proteins with a particular focus on the protein–TEW
interactions. As electrostatic interactions are the main force for
TEW binding to proteins, TEW with its highly negative charge addresses
in principle all proteins possessing positively charged patches. Furthermore,
due to its high structural and chemical diversity, TEW exhibits major
advantages over some commonly used crystallization additives. Therefore,
we summarized all features of TEW, which are beneficial for protein
crystallization, and present ten good reasons to promote the use of
TEW in protein crystallography as a powerful additive. Our results
demonstrate that TEW is a compound that is, in many respects, predestined
as a crystallization additive. We assume that many crystallographers
and especially researchers, who are not experts in this field but
willing to crystallize their structurally unknown target protein,
could benefit from the use of TEW as it is able to promote both the
crystallization process itself and the subsequent structure elucidation
by providing valuable anomalous signals, which are helpful for the
phasing step.
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Affiliation(s)
- Aleksandar Bijelic
- University of Vienna, Faculty of Chemistry, Department of Biophysical Chemistry, Althanstraße 14, 1090 Vienna, Austria
| | - Annette Rompel
- University of Vienna, Faculty of Chemistry, Department of Biophysical Chemistry, Althanstraße 14, 1090 Vienna, Austria
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Luo Z. Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures. Sci Rep 2016; 6:37123. [PMID: 27841370 PMCID: PMC5107899 DOI: 10.1038/srep37123] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/14/2016] [Indexed: 11/13/2022] Open
Abstract
Majority of novel X-ray crystal structures of proteins are currently solved using the anomalous diffraction signal provided by selenium after incorporation of selenomethionine instead of natural methionine by genetic engineering methods. However, selenium can be inserted into protein crystals in the form of selenourea (SeC(NH2)2), by adding the crystalline powder of selenourea into mother liquor or cryo-solution with native crystals, in analogy to the classic procedure of heavy-atom derivatization. Selenourea is able to bind to reactive groups at the surface of macromolecules primarily through hydrogen bonds, where the selenium atom may serve as acceptor and amide groups as donors. Selenourea has different chemical properties than heavy-atom reagents and halide ions and provides a convenient way of phasing crystal structures of macromolecules.
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Affiliation(s)
- Zhipu Luo
- Synchrotron Radiation Research Section, National Cancer Institute, Argonne National Laboratory, Argonne, 60439, USA
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8
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Wang J, Chai J, Wang H. Structure of the mouse Toll-like receptor 13 ectodomain in complex with a conserved sequence from bacterial 23S ribosomal RNA. FEBS J 2016; 283:1631-5. [PMID: 26676765 DOI: 10.1111/febs.13628] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 11/30/2022]
Abstract
Toll-like receptor 13 (TLR13) recognizes a conserved 10-nucleotide sequence from bacterial 23S ribosomal RNA, and binding of TLR13 to the target rRNA molecule triggers immune responses. Recently, the crystal structure of the TLR13 ectodomain bound by a 13-nucleotide single-stranded RNA (ssRNA13) was determined by using the initial phases provided by a cryo-electron microscopy map of TLR13 in complex with a 25-nucleotide ssRNA (ssRNA25). This structural snapshot describes a unique method for solving the crystal structure of the TLR13-ssRNA13 complex based on medium-resolution reconstruction of TLR13-ssRNA25 cryo-electron microscopy images.
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Affiliation(s)
- Jiawei Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jijie Chai
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongwei Wang
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China
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9
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Bijelic A, Rompel A. The use of polyoxometalates in protein crystallography - An attempt to widen a well-known bottleneck. Coord Chem Rev 2015; 299:22-38. [PMID: 26339074 PMCID: PMC4504029 DOI: 10.1016/j.ccr.2015.03.018] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/23/2015] [Indexed: 02/01/2023]
Abstract
Polyoxometalates (POMs) are discrete polynuclear metal-oxo anions with a fascinating variety of structures and unique chemical and physical properties. Their application in various fields is well covered in the literature, however little information about their usage in protein crystallization is available. This review summarizes the impact of the vast class of POMs on the formation of protein crystals, a well-known (frustrating) bottleneck in macromolecular crystallography, with the associated structure elucidation and a particular emphasis focused on POM's potential as a powerful crystallization additive for future research. The Protein Data Bank (PDB) was scanned for protein structures with incorporated POMs which were assigned a PDB ligand ID resulting in 30 PDB entries. These structures have been analyzed with regard to (i) the structure of POM itself in the immediate protein environment, (ii) the kind of interaction and position of the POM within the protein structure and (iii) the beneficial effects of POM on protein crystallography apparent so far.
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Affiliation(s)
| | - Annette Rompel
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität Wien, Althanstraße 14, 1090 Wien, Austria1
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10
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Abstract
Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.
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Affiliation(s)
- Yigong Shi
- Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.
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11
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Blazevic A, Al-Sayed E, Roller A, Giester G, Rompel A. Tris-Functionalized Hybrid Anderson Polyoxometalates: Synthesis, Characterization, Hydrolytic Stability and Inversion of Protein Surface Charge. Chemistry 2015; 21:4762-71. [DOI: 10.1002/chem.201405644] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Indexed: 11/06/2022]
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12
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Bijelic A, Molitor C, Mauracher SG, Al-Oweini R, Kortz U, Rompel A. Hen egg-white lysozyme crystallisation: protein stacking and structure stability enhanced by a Tellurium(VI)-centred polyoxotungstate. Chembiochem 2015; 16:233-41. [PMID: 25521080 PMCID: PMC4498469 DOI: 10.1002/cbic.201402597] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Indexed: 01/24/2023]
Abstract
As synchrotron radiation becomes more intense, detectors become faster and structure-solving software becomes more elaborate, obtaining single crystals suitable for data collection is now the bottleneck in macromolecular crystallography. Hence, there is a need for novel and advanced crystallisation agents with the ability to crystallise proteins that are otherwise challenging. Here, an Anderson-Evans-type polyoxometalate (POM), specifically Na6 [TeW6 O24 ]⋅22 H2 O (TEW), is employed as a crystallisation additive. Its effects on protein crystallisation are demonstrated with hen egg-white lysozyme (HEWL), which co-crystallises with TEW in the vicinity (or within) the liquid-liquid phase separation (LLPS) region. The X-ray structure (PDB ID: 4PHI) determination revealed that TEW molecules are part of the crystal lattice, thus demonstrating specific binding to HEWL with electrostatic interactions and hydrogen bonds. The negatively charged TEW polyoxotungstate binds to sites with a positive electrostatic potential located between two (or more) symmetry-related protein chains. Thus, TEW facilitates the formation of protein-protein interfaces of otherwise repulsive surfaces, and thereby the realisation of a stable crystal lattice. In addition to retaining the isomorphicity of the protein structure, the anomalous scattering of the POMs was used for macromolecular phasing. The results suggest that hexatungstotellurate(VI) has great potential as a crystallisation additive to promote both protein crystallisation and structure elucidation.
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Affiliation(s)
- Aleksandar Bijelic
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität WienAlthanstrasse 14, 1090 Wien (Austria) E-mail:
| | - Christian Molitor
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität WienAlthanstrasse 14, 1090 Wien (Austria) E-mail:
| | - Stephan G Mauracher
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität WienAlthanstrasse 14, 1090 Wien (Austria) E-mail:
| | - Rami Al-Oweini
- School of Engineering and Science, Jacobs UniversityP. O. Box 750 561, 28725 Bremen (Germany)
| | - Ulrich Kortz
- School of Engineering and Science, Jacobs UniversityP. O. Box 750 561, 28725 Bremen (Germany)
| | - Annette Rompel
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität WienAlthanstrasse 14, 1090 Wien (Austria) E-mail:
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Mauracher SG, Molitor C, Al-Oweini R, Kortz U, Rompel A. Latent and active abPPO4 mushroom tyrosinase cocrystallized with hexatungstotellurate(VI) in a single crystal. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2301-15. [PMID: 25195745 PMCID: PMC4157443 DOI: 10.1107/s1399004714013777] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/12/2014] [Indexed: 01/08/2023]
Abstract
Tyrosinases, bifunctional metalloenzymes, catalyze the oxidation of monophenols and o-diphenols to o-quinones, the precursor compounds of the brown-coloured pigment melanin. In eukaryotic organisms, tyrosinases are expressed as latent zymogens that have to be proteolytically cleaved in order to form highly active enzymes. This activation mechanism, known as the tyrosinase maturation process, has scientific and industrial significance with respect to biochemical and technical applications of the enzyme. Here, not only the first crystal structure of the mushroom tyrosinase abPPO4 is presented in its active form (Ser2-Ser383) and in its 21 kDa heavier latent form (Ser2-Thr545), but furthermore the simultaneous presence of both forms within one single-crystal structure is shown. This allows for a simple approach to investigate the transition between these two forms. Isoform abPPO4 was isolated and extensively purified from the natural source (Agaricus bisporus), which contains a total of six polyphenol oxidases (PPOs). The enzyme formed crystals (diffracting to a resolution of 2.76 Å) owing to the employment of the 6-tungstotellurate(VI) salt (Na6[TeW6O24]·22H2O) as a cocrystallization agent. Two of these disc-shaped Anderson-type polyoxoanions [TeW6O24](6-) separate two asymmetric units comprising one crystallographic heterodimer of abPPO4, thus resulting in very interesting crystal packing.
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Affiliation(s)
- Stephan Gerhard Mauracher
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität Wien, Althanstrasse 14, 1090 Wien, Austria
| | - Christian Molitor
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität Wien, Althanstrasse 14, 1090 Wien, Austria
| | - Rami Al-Oweini
- School of Engineering and Science, Jacobs University, PO Box 750 561, 28725 Bremen, Germany
| | - Ulrich Kortz
- School of Engineering and Science, Jacobs University, PO Box 750 561, 28725 Bremen, Germany
| | - Annette Rompel
- Institut für Biophysikalische Chemie, Fakultät für Chemie, Universität Wien, Althanstrasse 14, 1090 Wien, Austria
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14
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Data collection for crystallographic structure determination. Methods Mol Biol 2014. [PMID: 24590721 DOI: 10.1007/978-1-4939-0354-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Diffraction data measurement is the final experimental step of crystal structure analysis; all subsequent stages are computational. Good-quality data, optimized for a particular application, make the structure solution and refinement easier and enhance the accuracy of the final models. This chapter describes the principles of the rotation method of data collection and discusses various scenarios that are useful for different types of applications, such as anomalous phasing, molecular replacement, ligand identification, etc. Some typical problems encountered in practice are also discussed.
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15
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Mauracher SG, Molitor C, Al-Oweini R, Kortz U, Rompel A. Crystallization and preliminary X-ray crystallographic analysis of latent isoform PPO4 mushroom (Agaricus bisporus) tyrosinase. Acta Crystallogr F Struct Biol Commun 2014; 70:263-6. [PMID: 24637771 PMCID: PMC3936457 DOI: 10.1107/s2053230x14000582] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/09/2014] [Indexed: 11/11/2023] Open
Abstract
Tyrosinase exhibits catalytic activity for the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones. Owing to polymerization of these quinones, brown-coloured high-molecular-weight compounds called melanins are generated. The latent precursor form of polyphenol oxidase 4, one of the six tyrosinase isoforms from Agaricus bisporus, was purified to homogeneity and crystallized. The obtained crystals belonged to space group C121 (two molecules per asymmetric unit) and diffracted to 2.78 Å resolution. The protein only formed crystals under low-salt conditions using the 6-tungstotellurate(VI) salt Na6[TeW6O24] · 22H2O as a co-crystallization agent.
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Affiliation(s)
| | - Christian Molitor
- Institut für Biophysikalische Chemie, Universität Wien, Althanstrasse 14, 1090 Wien, Austria
| | - Rami Al-Oweini
- School of Engineering and Science, Jacobs University, PO Box 750 561, 28759 Bremen, Germany
| | - Ulrich Kortz
- School of Engineering and Science, Jacobs University, PO Box 750 561, 28759 Bremen, Germany
| | - Annette Rompel
- Institut für Biophysikalische Chemie, Universität Wien, Althanstrasse 14, 1090 Wien, Austria
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16
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Demont A, Prestipino C, Hernandez O, Elkaïm E, Paofai S, Naumov N, Fontaine B, Gautier R, Cordier S. Unprecedented electron-poor octahedral Ta(6) clusters in a solid-state compound: synthesis, characterisations and theoretical investigations of Cs(2)BaTa(6)Br(15)O(3). Chemistry 2013; 19:12711-9. [PMID: 23918625 DOI: 10.1002/chem.201300777] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Indexed: 11/09/2022]
Abstract
The crystal structure of Cs2BaTa6Br15O3 has been elucidated by using synchrotron X-ray powder diffraction and absorption experiments. It is built from edge-bridged octahedral [(Ta6Bri9Oi3)Bra6]4− cluster units with a singular poor metallic electron (ME) count equal to thirteen. This leads to a paramagnetic behaviour related to one unpaired electron. The arrangement of the Ta6 clusters is similar to that of Cs2LaTa6Br15O3 exhibiting 14-MEs per [(Ta6Bri9Oi3)Bra6]5− motif. The poorer electron-count cluster presents longer metal–metal distances as foreseen according to the electronic structure of edge-bridged hexanuclear cluster. Density functional theory (DFT) calculations on molecular models were used to rationalise the structural properties of 13- and 14-ME clusters. Periodic DFT calculations demonstrate that the electronic structure of these solid-state compounds is related to those of the discrete octahedral units. Oxygen–barium interactions seem to prevent the geometry of the octahedral cluster to strongly distort, allowing stabilisation of this unprecedented electron-poor Ta6 cluster in the solid state.
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Affiliation(s)
- Antoine Demont
- Institut des Sciences Chimiques de Rennes, UMR 6226, CNRS, Université de Rennes 1-ENSC Rennes, Avenue du Général Leclerc, 35042 Rennes Cedex (France), Fax: (+33) 223-236-799
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Dahms SO, Kuester M, Streb C, Roth C, Sträter N, Than ME. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:284-97. [PMID: 23385464 PMCID: PMC3565441 DOI: 10.1107/s0907444912046008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 11/07/2012] [Indexed: 01/17/2023]
Abstract
Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome.
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Affiliation(s)
- Sven O. Dahms
- Protein Crystallography Group, Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Miriam Kuester
- Protein Crystallography Group, Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Carsten Streb
- Institute of Inorganic Chemistry II, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Egerlandstrasse 1, D-91058 Erlangen, Germany
| | - Christian Roth
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Universität Leipzig, D-04103 Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Universität Leipzig, D-04103 Leipzig, Germany
| | - Manuel E. Than
- Protein Crystallography Group, Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, D-07745 Jena, Germany
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Abstract
In all organisms, fatty acid synthesis is achieved in variations of a common cyclic reaction pathway by stepwise, iterative elongation of precursors with two-carbon extender units. In bacteria, all individual reaction steps are carried out by monofunctional dissociated enzymes, whereas in eukaryotes the fatty acid synthases (FASs) have evolved into large multifunctional enzymes that integrate the whole process of fatty acid synthesis. During the last few years, important advances in understanding the structural and functional organization of eukaryotic FASs have been made through a combination of biochemical, electron microscopic and X-ray crystallographic approaches. They have revealed the strikingly different architectures of the two distinct types of eukaryotic FASs, the fungal and the animal enzyme system. Fungal FAS is a 2·6 MDa α₆β₆ heterododecamer with a barrel shape enclosing two large chambers, each containing three sets of active sites separated by a central wheel-like structure. It represents a highly specialized micro-compartment strictly optimized for the production of saturated fatty acids. In contrast, the animal FAS is a 540 kDa X-shaped homodimer with two lateral reaction clefts characterized by a modular domain architecture and large extent of conformational flexibility that appears to contribute to catalytic efficiency.
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Pilet G, Perrin A. Octahedral rhenium cluster chemistry: from high-temperature syntheses to the elaboration of new inorganic/molecular hybrid compounds via solution route. CR CHIM 2005. [DOI: 10.1016/j.crci.2005.03.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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