1
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Aggarwal S, Wachenfeldt CV, Fisher SZ, Oksanen E. A protocol for production of perdeuterated OmpF porin for neutron crystallography. Protein Expr Purif 2021; 188:105954. [PMID: 34416360 DOI: 10.1016/j.pep.2021.105954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/31/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
Hydrogen atoms are at the limit of visibility in X-ray structures even at high resolution. Neutron macromolecular crystallography (NMX) is an unambiguous method to locate hydrogens and study the significance of hydrogen bonding interactions in biological systems. Since NMX requires very large crystals, very few neutron structures of proteins have been determined yet. In addition, the most common hydrogen isotope 1H gives rise to significant background due to its large incoherent scattering cross-section. Therefore, it is advantageous to substitute as many hydrogens as possible with the heavier isotope 2H (deuterium) to reduce the sample volume requirement. While the solvent exchangeable hydrogens can be substituted by dissolving the protein in heavy water, complete deuterium labelling - perdeuteration - requires the protein to be expressed in heavy water with a deuterated carbon source. In this work, we developed an optimized method for large scale production of deuterium-labelled bacterial outer membrane protein F (OmpF) for NMX. OmpF was produced using deuterated media with different carbon sources. Mass spectrometry verified the integrity and level of deuteration of purified OmpF. Perdeuterated OmpF crystals diffracted X-rays to a resolution of 1.9 Å. This work lays the foundation for structural studies of membrane protein by neutron diffraction in future.
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Affiliation(s)
- Swati Aggarwal
- European Spallation Source ERIC, Odarslövsvägen 113, SE-225 92, Lund, Sweden; University Grenoble Alpes, CEA, CNRS, IBS, FR-380 00, Grenoble, France
| | | | - Suzanne Zoë Fisher
- European Spallation Source ERIC, Odarslövsvägen 113, SE-225 92, Lund, Sweden; Department of Biology, Lund University, Sölvegatan 35, Lund, SE-22 362, Sweden
| | - Esko Oksanen
- European Spallation Source ERIC, Odarslövsvägen 113, SE-225 92, Lund, Sweden.
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2
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Bergmann J, Oksanen E, Ryde U. An automated hydrogen orientation procedure for neutron protein crystallography. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s010876732109303x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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3
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Bergmann J, Oksanen E, Ryde U. Combining crystallography with quantum mechanics. Curr Opin Struct Biol 2021; 72:18-26. [PMID: 34392061 DOI: 10.1016/j.sbi.2021.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 11/19/2022]
Abstract
In standard crystallographic refinement of biomacromolecules, the crystallographic raw data are supplemented by empirical restraints that ensure that the structure makes chemical sense. These restraints are typically accurate for amino acids and nucleic acids, but less so for cofactors, substrates, inhibitors, ligands and metal sites. In quantum refinement, this potential is replaced by more accurate quantum mechanical (QM) calculations. Several implementations have been presented, differing in the level of QM and whether it is used for the entire structure or only for a site of particular interest. It has been shown that the method can improve and correct errors in crystal structures and that it can be used to determine protonation and tautomeric states of various ligands and to decide what is really seen in the structure by refining different interpretations and using standard crystallographic and QM quality measures to decide which fits the structure best.
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Affiliation(s)
- Justin Bergmann
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC, P. O. Box 176, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
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4
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Caldararu O, Ekberg V, Logan DT, Oksanen E, Ryde U. Exploring ligand dynamics in protein crystal structures with ensemble refinement. Acta Crystallogr D Struct Biol 2021; 77:1099-1115. [PMID: 34342282 PMCID: PMC8329865 DOI: 10.1107/s2059798321006513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein-ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein-ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and Rfree values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Vilhelm Ekberg
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Derek T. Logan
- Biochemistry and Structural Biology, Centre for Molecular Protein Science, Department of Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source Consortium ESS ERIC, PO Box 176, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
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5
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Kelpšas V, Caldararu O, Blakeley MP, Coquelle N, Wierenga RK, Ryde U, von Wachenfeldt C, Oksanen E. Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps. IUCrJ 2021; 8:633-643. [PMID: 34258011 PMCID: PMC8256706 DOI: 10.1107/s2052252521004619] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/30/2021] [Indexed: 06/13/2023]
Abstract
Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxy-acetone phosphate. This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem from its ability to facilitate the deprotonation of a carbon next to a carbonyl group to generate an enediolate intermediate. The enediolate intermediate is believed to be mimicked by the inhibitor 2-phosphoglycolate (PGA) and the subsequent enediol intermediate by phosphoglycolohydroxamate (PGH). Here, neutron structures of Leishmania mexicana TIM have been determined with both inhibitors, and joint neutron/X-ray refinement followed by quantum refinement has been performed. The structures show that in the PGA complex the postulated general base Glu167 is protonated, while in the PGH complex it remains deprotonated. The deuteron is clearly localized on Glu167 in the PGA-TIM structure, suggesting an asymmetric hydrogen bond instead of a low-barrier hydrogen bond. The full picture of the active-site protonation states allowed an investigation of the reaction mechanism using density-functional theory calculations.
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Affiliation(s)
- Vinardas Kelpšas
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - Octav Caldararu
- Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Nicolas Coquelle
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Rikkert K. Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Pentti Kaiteran katu 1, 90570 Oulu, Finland
| | - Ulf Ryde
- Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | | | - Esko Oksanen
- European Spallation Source Consortium ESS ERIC, Odarslövsvägen 113, 224 84 Lund, Sweden
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6
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Possen BJHM, Rousi M, Keski‐Saari S, Silfver T, Kontunen‐Soppela S, Oksanen E, Mikola J. New evidence for the importance of soil nitrogen on the survival and adaptation of silver birch to climate warming. Ecosphere 2021. [DOI: 10.1002/ecs2.3520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- B. J. H. M. Possen
- Ecology Section Royal HaskoningDHV Larixplein 1 Eindhoven5616 VBThe Netherlands
| | - M. Rousi
- Vantaa Research Unit Natural Resources Institute Finland P.O. Box 18 Vantaa01301Finland
| | - S. Keski‐Saari
- Department of Environmental and Biological Sciences University of Eastern Finland P.O. Box 111 Joensuu80101Finland
| | - T. Silfver
- Faculty of Biological and Environmental Sciences Ecosystems and Environment Research Programme University of Helsinki Niemenkatu 73 Lahti15140Finland
| | - S. Kontunen‐Soppela
- Department of Environmental and Biological Sciences University of Eastern Finland P.O. Box 111 Joensuu80101Finland
| | - E. Oksanen
- Department of Environmental and Biological Sciences University of Eastern Finland P.O. Box 111 Joensuu80101Finland
| | - J. Mikola
- Faculty of Biological and Environmental Sciences Ecosystems and Environment Research Programme University of Helsinki Niemenkatu 73 Lahti15140Finland
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7
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Wallerstein J, Ekberg V, Ignjatović MM, Kumar R, Caldararu O, Peterson K, Wernersson S, Brath U, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C. JACS Au 2021; 1:484-500. [PMID: 34467311 PMCID: PMC8395690 DOI: 10.1021/jacsau.0c00094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 06/13/2023]
Abstract
Molecular recognition is fundamental to biological signaling. A central question is how individual interactions between molecular moieties affect the thermodynamics of ligand binding to proteins and how these effects might propagate beyond the immediate neighborhood of the binding site. Here, we investigate this question by introducing minor changes in ligand structure and characterizing the effects of these on ligand affinity to the carbohydrate recognition domain of galectin-3, using a combination of isothermal titration calorimetry, X-ray crystallography, NMR relaxation, and computational approaches including molecular dynamics (MD) simulations and grid inhomogeneous solvation theory (GIST). We studied a congeneric series of ligands with a fluorophenyl-triazole moiety, where the fluorine substituent varies between the ortho, meta, and para positions (denoted O, M, and P). The M and P ligands have similar affinities, whereas the O ligand has 3-fold lower affinity, reflecting differences in binding enthalpy and entropy. The results reveal surprising differences in conformational and solvation entropy among the three complexes. NMR backbone order parameters show that the O-bound protein has reduced conformational entropy compared to the M and P complexes. By contrast, the bound ligand is more flexible in the O complex, as determined by 19F NMR relaxation, ensemble-refined X-ray diffraction data, and MD simulations. Furthermore, GIST calculations indicate that the O-bound complex has less unfavorable solvation entropy compared to the other two complexes. Thus, the results indicate compensatory effects from ligand conformational entropy and water entropy, on the one hand, and protein conformational entropy, on the other hand. Taken together, these different contributions amount to entropy-entropy compensation among the system components involved in ligand binding to a target protein.
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Affiliation(s)
- Johan Wallerstein
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Vilhelm Ekberg
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | | | - Rohit Kumar
- Biochemistry
and Structural Biology, Center for Molecular Protein Science, Department
of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Octav Caldararu
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | - Kristoffer Peterson
- Centre
for Analysis and Synthesis, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Sven Wernersson
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulrika Brath
- The
Swedish NMR Center, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Hakon Leffler
- Microbiology,
Immunology, and Glycobiology, Department of Experimental Medicine, Lund University, 221 00 Lund, Sweden
| | - Esko Oksanen
- European
Spallation Source ESS ERIC, 225 92 Lund, Sweden
| | - Derek T. Logan
- Biochemistry
and Structural Biology, Center for Molecular Protein Science, Department
of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulf J. Nilsson
- Centre
for Analysis and Synthesis, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Ulf Ryde
- Theoretical
Chemistry, Department of Chemistry, Lund
University, 221 00 Lund, Sweden
| | - Mikael Akke
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
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8
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Bergmann J, Oksanen E, Ryde U. Critical evaluation of a crystal structure of nitrogenase with bound N 2 ligands. J Biol Inorg Chem 2021; 26:341-353. [PMID: 33713183 PMCID: PMC8068654 DOI: 10.1007/s00775-021-01858-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/10/2021] [Indexed: 12/19/2022]
Abstract
Recently, a 1.83 Å crystallographic structure of nitrogenase was suggested to show N2-derived ligands at three sites in the catalytic FeMo cluster, replacing the three [Formula: see text] bridging sulfide ligands (two in one subunit and the third in the other subunit) (Kang et al. in Science 368: 1381-1385, 2020). Naturally, such a structure is sensational, having strong bearings on the reaction mechanism of the enzyme. Therefore, it is highly important to ensure that the interpretation of the structure is correct. Here, we use standard crystallographic refinement and quantum refinement to evaluate the structure. We show that the original crystallographic raw data are strongly anisotropic, with a much lower resolution in certain directions than others. This, together with the questionable use of anisotropic B factors, give atoms an elongated shape, which may look like diatomic atoms. In terms of standard electron-density maps and real-space Z scores, a resting-state structure with no dissociated sulfide ligands fits the raw data better than the interpretation suggested by the crystallographers. The anomalous electron density at 7100 eV is weaker for the putative N2 ligands, but not lower than for several of the [Formula: see text] bridging sulfide ions and not lower than what can be expected from a statistical analysis of the densities. Therefore, we find no convincing evidence for any N2 binding to the FeMo cluster. Instead, a standard resting state without any dissociated ligands seems to be the most likely interpretation of the structure. Likewise, we find no support that the homocitrate ligand should show monodentate binding.
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Affiliation(s)
- Justin Bergmann
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
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9
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Bergmann J, Oksanen E, Ryde U. Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase. J Inorg Biochem 2021; 219:111426. [PMID: 33756394 DOI: 10.1016/j.jinorgbio.2021.111426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/19/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to plants (although the enzyme itself is strictly microbial). It has been studied extensively with both experimental and computational methods, but many details of the reaction mechanism are still unclear. X-ray crystallography is the main source of structural information for biomacromolecules, but it has problems to discern hydrogen atoms or to distinguish between elements with the same number of electrons. These problems can sometimes be alleviated by introducing quantum chemical calculations in the refinement, providing information about the ideal structure (in the same way as the empirical restraints used in standard crystallographic refinement) and comparing different interpretations of the structure with normal crystallographic and quantum mechanical quality measures. We have performed such quantum-refinement calculations to address two important issues for nitrogenase. First, we show that the bidentate ligand of the active-site FeV cluster in V‑nitrogenase is carbonate, rather than bicarbonate or nitrate. Second, we study the CO-inhibited structure of Mo‑nitrogenase. CO binds to a reduced and protonated state of the enzyme by replacing one of the sulfide ions (S2B) in the active-site FeMo cluster. We examined if it is possible to deduce from the crystal structure the location of the protons. Our results indicates that the crystal structure is best modelled as fully deprotonated.
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Affiliation(s)
- Justin Bergmann
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden.
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10
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Eriksson A, Caldararu O, Ryde U, Oksanen E. Automated orientation of water molecules in neutron crystallographic structures of proteins. Acta Crystallogr D Struct Biol 2020; 76:1025-1032. [PMID: 33021504 DOI: 10.1107/s2059798320011729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/26/2020] [Indexed: 11/10/2022] Open
Abstract
The structure and function of proteins are strongly affected by the surrounding solvent water, for example through hydrogen bonds and the hydrophobic effect. These interactions depend not only on the position, but also on the orientation, of the water molecules around the protein. Therefore, it is often vital to know the detailed orientations of the surrounding ordered water molecules. Such information can be obtained by neutron crystallography. However, it is tedious and time-consuming to determine the correct orientation of every water molecule in a structure (there are typically several hundred of them), which is presently performed by manual evaluation. Here, a method has been developed that reliably automates the orientation of a water molecules in a simple and relatively fast way. Firstly, a quantitative quality measure, the real-space correlation coefficient, was selected, together with a threshold that allows the identification of water molecules that are oriented. Secondly, the refinement procedure was optimized by varying the refinement method and parameters, thus finding settings that yielded the best results in terms of time and performance. It turned out to be favourable to employ only the neutron data and a fixed protein structure when reorienting the water molecules. Thirdly, a method has been developed that identifies and reorients inadequately oriented water molecules systematically and automatically. The method has been tested on three proteins, galectin-3C, rubredoxin and inorganic pyrophosphatase, and it is shown that it yields improved orientations of the water molecules for all three proteins in a shorter time than manual model building. It also led to an increased number of hydrogen bonds involving water molecules for all proteins.
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Affiliation(s)
- Axl Eriksson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source (ESS) ERIC, PO Box 176, SE-221 00 Lund, Sweden
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11
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Junius N, Vahdatahar E, Oksanen E, Ferrer JL, Budayova-Spano M. Optimization of crystallization of biological macromolecules using dialysis combined with temperature control. J Appl Crystallogr 2020; 53:686-698. [PMID: 32684884 PMCID: PMC7312135 DOI: 10.1107/s1600576720003209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 03/08/2020] [Indexed: 11/10/2022] Open
Abstract
A rational way to find the appropriate conditions to grow crystal samples for bio-crystallography is to determine the crystallization phase diagram, which allows precise control of the parameters affecting the crystal growth process. First, the nucleation is induced at supersaturated conditions close to the solubility boundary between the nucleation and metastable regions. Then, crystal growth is further achieved in the metastable zone - which is the optimal location for slow and ordered crystal expansion - by modulation of specific physical parameters. Recently, a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature-precipitant-concentration phase diagrams has been constructed. Here, it is demonstrated that a thorough knowledge of the phase diagram is vital in any crystallization experiment. The relevance of the selection of the starting position and the kinetic pathway undertaken in controlling most of the final properties of the synthesized crystals is shown. The rational crystallization optimization strategies developed and presented here allow tailoring of crystal size and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.
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Affiliation(s)
- Niels Junius
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Esko Oksanen
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Jean-Luc Ferrer
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
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12
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Bergmann J, Davidson M, Oksanen E, Ryde U, Jayatilaka D. fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins. IUCrJ 2020; 7:158-165. [PMID: 32148844 PMCID: PMC7055371 DOI: 10.1107/s2052252519015975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/27/2019] [Indexed: 05/20/2023]
Abstract
The first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins using a fragmentation approach to break up the protein into residues and solvent, thereby speeding up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations, is described. It it found that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR on the complete unfragmented system when tested on dipeptides, tripeptides and hexapeptides. The largest changes are for the parameters describing H atoms involved in hydrogen-bond interactions, but it is shown that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speed-ups are observed for the larger systems. Using this approach, it is possible to perform a highly parallelized HAR in reasonable times for large systems. The method has been implemented in the TONTO software.
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Affiliation(s)
- Justin Bergmann
- Department of Theoretical Chemistry, Chemical Center, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Max Davidson
- School of Molecular Sciences M310, University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia
| | - Esko Oksanen
- Instruments Division, European Spallation Source ESS ERIC, PO Box 176, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Center, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Dylan Jayatilaka
- School of Molecular Sciences M310, University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia
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13
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Caldararu O, Misini Ignjatović M, Oksanen E, Ryde U. Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures. RSC Adv 2020; 10:8435-8443. [PMID: 35497843 PMCID: PMC9049968 DOI: 10.1039/c9ra09601a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/18/2020] [Indexed: 01/13/2023] Open
Abstract
The function of proteins is influenced not only by the atomic structure but also by the detailed structure of the solvent surrounding it. Computational studies of protein structure also critically depend on the water structure around the protein. Herein we compare the water structure obtained from molecular dynamics (MD) simulations of galectin-3 in complex with two ligands to crystallographic water molecules observed in the corresponding crystal structures. We computed MD trajectories both in a water box, which mimics a protein in solution, and in a crystallographic unit cell, which mimics a protein in a crystal. The calculations were compared to crystal structures obtained at both cryogenic and room temperature. Two types of analyses of the MD simulations were performed. First, the positions of the crystallographic water molecules were compared to peaks in the MD density after alignment of the protein in each snapshot. The results of this analysis indicate that all simulations reproduce the crystallographic water structure rather poorly. However, if we define the crystallographic water sites based on their distances to nearby protein atoms and follow these sites throughout the simulations, the MD simulations reproduce the crystallographic water sites much better. This shows that the failure of MD simulations to reproduce the water structure around proteins in crystal structures observed both in this and previous studies is caused by the problem of identifying water sites for a flexible and dynamic protein (traditionally done by overlaying the structures). Our local clustering approach solves the problem and shows that the MD simulations reasonably reproduce the water structure observed in crystals. Furthermore, analysis of the crystal MD simulations indicates a few water molecules that are close to unmodeled electron density peaks in the crystal structures, suggesting that crystal MD could be used as a complementary tool for identifying and modelling water in protein crystallography. Molecular dynamics simulations can reproduce the water structure around proteins in crystal structure only if a local clustering is performed.![]()
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| | | | - Esko Oksanen
- Instruments Division
- European Spallation Source Consortium ESS ERIC
- SE-221 00 Lund
- Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
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Caldararu O, Manzoni F, Oksanen E, Logan DT, Ryde U. Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Corrigendum. Acta Crystallogr D Struct Biol 2020; 76:85-86. [PMID: 31909746 PMCID: PMC8573741 DOI: 10.1107/s2059798319016383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/04/2019] [Indexed: 11/10/2022] Open
Abstract
Corrections are published for the article by Caldararu et al. [(2019), Acta Cryst. D75, 368–380].
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Caldararu O, Misini Ignjatovic M, Oksanen E, Ryde U. Improving identification and validation of water molecules in protein crystal structures with molecular dynamics simulations. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319093896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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16
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Brockhauser S, Oksanen E, Csankó K, Szegletes Z, Harmat V, Bugris V. Advanced protein crystallisation for neutron macromolecular crystallography. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319088107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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17
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Aprigliano G, Nagy G, Markó M, Ferrer JL, Pfeiffer D, Andersen K, Oksanen E. NMX macromolecular diffractometer at ESS. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319088181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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18
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Kelpsas V, Caldararu O, Kulkarni Y, Wierenga R, Ryde U, Kamerlin L, von Wachenfeldt C, Oksanen E. The neutron structure of Leishmania mexicana triose phosphate isomerase with transition state mimics reveals general base catalyst. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319094427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Kelpšas V, Lafumat B, Blakeley MP, Coquelle N, Oksanen E, von Wachenfeldt C. Perdeuteration, large crystal growth and neutron data collection of Leishmania mexicana triose-phosphate isomerase E65Q variant. Acta Crystallogr F Struct Biol Commun 2019; 75:260-269. [PMID: 30950827 PMCID: PMC6450519 DOI: 10.1107/s2053230x19001882] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/31/2019] [Indexed: 01/07/2023] Open
Abstract
Triose-phosphate isomerase (TIM) catalyses the interconversion of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Two catalytic mechanisms have been proposed based on two reaction-intermediate analogues, 2-phosphoglycolate (2PG) and phosphoglycolohydroxamate (PGH), that have been used as mimics of the cis-enediol(ate) intermediate in several studies of TIM. The protonation states that are critical for the mechanistic interpretation of these structures are generally not visible in the X-ray structures. To resolve these questions, it is necessary to determine the hydrogen positions using neutron crystallography. Neutron crystallography requires large crystals and benefits from replacing all hydrogens with deuterium. Leishmania mexicana triose-phosphate isomerase was therefore perdeuterated and large crystals with 2PG and PGH were produced. Neutron diffraction data collected from two crystals with different volumes highlighted the importance of crystal volume, as smaller crystals required longer exposures and resulted in overall worse statistics.
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Affiliation(s)
- Vinardas Kelpšas
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - Bénédicte Lafumat
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
- European Spallation Source ESS ERIC, Odarslövsvägen 113, 224 84 Lund, Sweden
| | | | - Nicolas Coquelle
- Insitut Laue–Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Esko Oksanen
- European Spallation Source ESS ERIC, Odarslövsvägen 113, 224 84 Lund, Sweden
- Department of Biochemistry and Structural Biology, Lund University, Sölvegatan 39A, 221 00 Lund, Sweden
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Caldararu O, Manzoni F, Oksanen E, Logan DT, Ryde U. Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Acta Crystallogr D Struct Biol 2019; 75:368-380. [PMID: 30988254 PMCID: PMC6465982 DOI: 10.1107/s205979831900175x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/30/2019] [Indexed: 11/20/2022]
Abstract
A method has been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. Applications to structures of the galectin-3C–lactose complex and lytic polysaccharide monooxygenase show that it can improve the geometry of hydrogen bonds, particularly those involving water molecules, as well as determine the protonation states of key residues. Neutron crystallography is a powerful method to determine the positions of H atoms in macromolecular structures. However, it is sometimes hard to judge what would constitute a chemically reasonable model, and the geometry of H atoms depends more on the surroundings (for example the formation of hydrogen bonds) than heavy atoms, so that the empirical geometry information for the H atoms used to supplement the experimental data is often less accurate. These problems may be reduced by using quantum-mechanical calculations. A method has therefore been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. A first validation of this method is provided by re-refining the structure of the galectin-3 carbohydrate-recognition domain in complex with lactose. The geometry is improved, in particular for water molecules, for which the method leads to better-resolved hydrogen-bonding interactions. The method has also been applied to the active copper site of lytic polysaccharide monooxygenase and shows that the protonation state of the amino-terminal histidine residue can be determined.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Francesco Manzoni
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
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Verteramo ML, Stenström O, Ignjatović MM, Caldararu O, Olsson MA, Manzoni F, Leffler H, Oksanen E, Logan DT, Nilsson UJ, Ryde U, Akke M. Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding. J Am Chem Soc 2019; 141:2012-2026. [PMID: 30618244 DOI: 10.1021/jacs.8b11099] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding the driving forces underlying molecular recognition is of fundamental importance in chemistry and biology. The challenge is to unravel the binding thermodynamics into separate contributions and to interpret these in molecular terms. Entropic contributions to the free energy of binding are particularly difficult to assess in this regard. Here we pinpoint the molecular determinants underlying differences in ligand affinity to the carbohydrate recognition domain of galectin-3, using a combination of isothermal titration calorimetry, X-ray crystallography, NMR relaxation, and molecular dynamics simulations followed by conformational entropy and grid inhomogeneous solvation theory (GIST) analyses. Using a pair of diastereomeric ligands that have essentially identical chemical potential in the unbound state, we reduced the problem of dissecting the thermodynamics to a comparison of the two protein-ligand complexes. While the free energies of binding are nearly equal for the R and S diastereomers, greater differences are observed for the enthalpy and entropy, which consequently exhibit compensatory behavior, ΔΔ H°(R - S) = -5 ± 1 kJ/mol and - TΔΔ S°(R - S) = 3 ± 1 kJ/mol. NMR relaxation experiments and molecular dynamics simulations indicate that the protein in complex with the S-stereoisomer has greater conformational entropy than in the R-complex. GIST calculations reveal additional, but smaller, contributions from solvation entropy, again in favor of the S-complex. Thus, conformational entropy apparently dominates over solvation entropy in dictating the difference in the overall entropy of binding. This case highlights an interplay between conformational entropy and solvation entropy, pointing to both opportunities and challenges in drug design.
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Affiliation(s)
- Maria Luisa Verteramo
- Centre for Analysis and Synthesis, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Olof Stenström
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | | | - Octav Caldararu
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Martin A Olsson
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Francesco Manzoni
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Hakon Leffler
- Microbiology, Immunology, and Glycobiology, Department of Laboratory Medicine , Lund University , 221 00 Lund , Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC , 225 92 Lund , Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Ulf Ryde
- Theoretical Chemistry, Department of Chemistry , Lund University , 221 00 Lund , Sweden
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry , Lund University , 221 00 Lund , Sweden
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Caldararu O, Oksanen E, Ryde U, Hedegård ED. Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase. Chem Sci 2019; 10:576-586. [PMID: 30746099 PMCID: PMC6334667 DOI: 10.1039/c8sc03980a] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/18/2018] [Indexed: 12/27/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-containing metalloenzymes that can cleave the glycosidic link in polysaccharides. This could become crucial for production of energy-efficient biofuels from recalcitrant polysaccharides. Although LPMOs are considered oxygenases, recent investigations have shown that H2O2 can also act as a co-substrate for LPMOs. Intriguingly, LPMOs generate H2O2 in the absence of a polysaccharide substrate. Here, we elucidate a new mechanism for H2O2 generation starting from an AA10-LPMO crystal structure with an oxygen species bound, using QM/MM calculations. The reduction level and protonation state of this oxygen-bound intermediate has been unclear. However, this information is crucial to the mechanism. We therefore investigate the oxygen-bound intermediate with quantum refinement (crystallographic refinement enhanced with QM calculations), against both X-ray and neutron data. Quantum refinement calculations suggest a Cu(ii)-O-2 system in the active site of the AA10-LPMO and a neutral protonated -NH2 state for the terminal nitrogen atom, the latter in contrast to the original interpretation. Our QM/MM calculations show that H2O2 generation is possible only from a Cu(i) center and that the most favourable reaction pathway is to involve a nearby glutamate residue, adding two electrons and two protons to the Cu(ii)-O-2 system, followed by dissociation of H2O2.
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Affiliation(s)
- Octav Caldararu
- Division of Theoretical Chemistry , Lund University , Chemical Centre , P. O. Box 124 , SE-221 00 Lund , Sweden . ;
| | - Esko Oksanen
- European Spallation Source ESS ERIC , P. O. Box 176 , SE-221 00 Lund , Sweden
- Department of Biochemistry and Structural Biology , Lund University , Chemical Centre , P. O. Box 124 , SE-221 00 Lund , Sweden
| | - Ulf Ryde
- Division of Theoretical Chemistry , Lund University , Chemical Centre , P. O. Box 124 , SE-221 00 Lund , Sweden . ;
| | - Erik D Hedegård
- Division of Theoretical Chemistry , Lund University , Chemical Centre , P. O. Box 124 , SE-221 00 Lund , Sweden . ;
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23
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Abstract
Correction for ‘Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase’ by Octav Caldararu et al., Chem. Sci., 2019, 10, 576–586.
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Affiliation(s)
- Octav Caldararu
- Division of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC
- SE-221 00 Lund
- Sweden
- Department of Biochemistry and Structural Biology
- Lund University
| | - Ulf Ryde
- Division of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| | - Erik D. Hedegård
- Division of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
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Caldararu O, Kumar R, Oksanen E, Logan DT, Ryde U. Are crystallographic B-factors suitable for calculating protein conformational entropy? Phys Chem Chem Phys 2019; 21:18149-18160. [DOI: 10.1039/c9cp02504a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is not possible to obtain reliable entropy estimates from crystallographic B-factors even with re-refined or room-temperature crystal structures.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| | - Rohit Kumar
- Department of Biophysical Chemistry
- Centre for Molecular Protein Science
- Lund University
- Chemical Centre
- SE-221 00 Lund
| | - Esko Oksanen
- Department of Biophysical Chemistry
- Centre for Molecular Protein Science
- Lund University
- Chemical Centre
- SE-221 00 Lund
| | - Derek T. Logan
- Department of Biophysical Chemistry
- Centre for Molecular Protein Science
- Lund University
- Chemical Centre
- SE-221 00 Lund
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
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25
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Sørensen TLM, Hjorth-Jensen SJ, Oksanen E, Andersen JL, Olesen C, Møller JV, Nissen P. Membrane-protein crystals for neutron diffraction. Acta Crystallogr D Struct Biol 2018; 74:1208-1218. [PMID: 30605135 DOI: 10.1107/s2059798318012561] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/05/2018] [Indexed: 11/10/2022]
Abstract
Neutron macromolecular crystallography (NMX) has the potential to provide the experimental input to address unresolved aspects of transport mechanisms and protonation in membrane proteins. However, despite this clear scientific motivation, the practical challenges of obtaining crystals that are large enough to make NMX feasible have so far been prohibitive. Here, the potential impact on feasibility of a more powerful neutron source is reviewed and a strategy for obtaining larger crystals is formulated, exemplified by the calcium-transporting ATPase SERCA1. The challenges encountered at the various steps in the process from crystal nucleation and growth to crystal mounting are explored, and it is demonstrated that NMX-compatible membrane-protein crystals can indeed be obtained.
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Affiliation(s)
- Thomas Lykke Møller Sørensen
- Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Samuel John Hjorth-Jensen
- Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Esko Oksanen
- European Spallation Source ERIC, PO Box 176, 22100 Lund, Sweden
| | | | - Claus Olesen
- Department of Biomedicine, Aarhus University, Ole Worn Alle 3, DK-8000 Aarhus C, Denmark
| | - Jesper Vuust Møller
- Department of Biomedicine, Aarhus University, Ole Worn Alle 3, DK-8000 Aarhus C, Denmark
| | - Poul Nissen
- Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
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26
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Caldararu O, Cao L, Manzoni F, Oksanen E, Logan D, Ryde U. Quantum refinement of X-ray and neutron protein crystal structures. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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27
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Manzoni F, Wallerstein J, Schrader TE, Ostermann A, Coates L, Akke M, Blakeley MP, Oksanen E, Logan DT. Elucidation of Hydrogen Bonding Patterns in Ligand-Free, Lactose- and Glycerol-Bound Galectin-3C by Neutron Crystallography to Guide Drug Design. J Med Chem 2018; 61:4412-4420. [PMID: 29672051 DOI: 10.1021/acs.jmedchem.8b00081] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The medically important drug target galectin-3 binds galactose-containing moieties on glycoproteins through an intricate pattern of hydrogen bonds to a largely polar surface-exposed binding site. All successful inhibitors of galectin-3 to date have been based on mono- or disaccharide cores closely resembling natural ligands. A detailed understanding of the H-bonding networks in these natural ligands will provide an improved foundation for the design of novel inhibitors. Neutron crystallography is an ideal technique to reveal the geometry of hydrogen bonds because the positions of hydrogen atoms are directly detected rather than being inferred from the positions of heavier atoms as in X-ray crystallography. We present three neutron crystal structures of the C-terminal carbohydrate recognition domain of galectin-3: the ligand-free form and the complexes with the natural substrate lactose and with glycerol, which mimics important interactions made by lactose. The neutron crystal structures reveal unambiguously the exquisite fine-tuning of the hydrogen bonding pattern in the binding site to the natural disaccharide ligand. The ligand-free structure shows that most of these hydrogen bonds are preserved even when the polar groups of the ligand are replaced by water molecules. The protonation states of all histidine residues in the protein are also revealed and correlate well with NMR observations. The structures give a solid starting point for molecular dynamics simulations and computational estimates of ligand binding affinity that will inform future drug design.
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Affiliation(s)
- Francesco Manzoni
- Department of Biochemistry & Structural Biology , Lund University , S-221 00 Lund , Sweden
| | - Johan Wallerstein
- Department of Biophysical Chemistry , Lund University , S-221 00 Lund , Sweden
| | - Tobias E Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) , Forschungszentrum Jülich GmbH , Lichtenbergstrasse 1 , 85747 Garching , Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ) , Technische Universität München , Lichtenbergstrasse 1 , 85748 Garching , Germany
| | - Leighton Coates
- Neutron Scattering Division , Oak Ridge National Laboratory , 1 Bethel Valley Road , Oak Ridge , Tennessee 37831 , United States
| | - Mikael Akke
- Department of Biophysical Chemistry , Lund University , S-221 00 Lund , Sweden
| | - Matthew P Blakeley
- Institut Laue-Langevin , 71 avenue des Martyrs , 38000 Grenoble , France
| | - Esko Oksanen
- Department of Biochemistry & Structural Biology , Lund University , S-221 00 Lund , Sweden.,Instrument Division , European Spallation Source ERIC , Box 176, S-221 00 Lund , Sweden
| | - Derek T Logan
- Department of Biochemistry & Structural Biology , Lund University , S-221 00 Lund , Sweden
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Oksanen E, Chen JCH, Fisher SZ. Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules. Molecules 2017; 22:molecules22040596. [PMID: 28387738 PMCID: PMC6154725 DOI: 10.3390/molecules22040596] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/21/2022] Open
Abstract
The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.
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Affiliation(s)
- Esko Oksanen
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biochemistry and Structural Biology, Lund University, Sölvegatan 39, 22362 Lund, Sweden.
| | - Julian C-H Chen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Suzanne Zoë Fisher
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.
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29
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Manzoni F, Saraboji K, Sprenger J, Kumar R, Noresson AL, Nilsson UJ, Leffler H, Fisher SZ, Schrader TE, Ostermann A, Coates L, Blakeley MP, Oksanen E, Logan DT. Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C. Acta Crystallogr D Struct Biol 2016; 72:1194-1202. [PMID: 27841752 PMCID: PMC5108347 DOI: 10.1107/s2059798316015540] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/03/2016] [Indexed: 11/11/2022]
Abstract
Galectin-3 is an important protein in molecular signalling events involving carbohydrate recognition, and an understanding of the hydrogen-bonding patterns in the carbohydrate-binding site of its C-terminal domain (galectin-3C) is important for the development of new potent inhibitors. The authors are studying these patterns using neutron crystallography. Here, the production of perdeuterated human galectin-3C and successive improvement in crystal size by the development of a crystal-growth protocol involving feeding of the crystallization drops are described. The larger crystals resulted in improved data quality and reduced data-collection times. Furthermore, protocols for complete removal of the lactose that is necessary for the production of large crystals of apo galectin-3C suitable for neutron diffraction are described. Five data sets have been collected at three different neutron sources from galectin-3C crystals of various volumes. It was possible to merge two of these to generate an almost complete neutron data set for the galectin-3C-lactose complex. These data sets provide insights into the crystal volumes and data-collection times necessary for the same system at sources with different technologies and data-collection strategies, and these insights are applicable to other systems.
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Affiliation(s)
- Francesco Manzoni
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Kadhirvel Saraboji
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Janina Sprenger
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Rohit Kumar
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Ann Louise Noresson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University, S-221 00 Lund, Sweden
| | - S Zoë Fisher
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Tobias E Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Esko Oksanen
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, S-221 00 Lund, Sweden
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30
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Junius N, Oksanen E, Terrien M, Berzin C, Ferrer JL, Budayova-Spano M. A crystallization apparatus for temperature-controlled flow-cell dialysis with real-time visualization. J Appl Crystallogr 2016; 49:806-813. [PMID: 27275137 PMCID: PMC4886980 DOI: 10.1107/s1600576716004635] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/16/2016] [Indexed: 11/10/2022] Open
Abstract
Many instrumentation developments in crystallization have concentrated on massive parallelization assays and reduction of sample volume per experiment to find initial crystallization conditions. Yet improving the size and diffraction quality of the crystals for diffraction studies often requires decoupling of crystal nucleation and growth. This in turn requires the control of variables such as precipitant and protein concentration, equilibration rate, and temperature, which are all difficult parameters to control in the existing setups. The success of the temperature-controlled batch method, originally developed to grow very large crystals for neutron crystallography, demonstrated that the rational optimization of crystal growth has potential in structural biology. A temperature-controlled dialysis button has been developed for our previous device, and a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature-precipitant concentration phase diagrams has been constructed. The presented approach differs from the current paradigm, since it involves serial instead of parallel experiments, exploring multiple crystallization conditions with the same protein sample. The sample is not consumed in the experiment and the conditions can be changed in a reversible fashion, using dialysis with a flowing precipitant reservoir as well as precise temperature control. The control software allows visualization of the crystals, as well as control of the temperature and composition of the crystallization solution. The rational crystallization optimization strategies presented here allow tailoring of crystal size, morphology and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.
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Affiliation(s)
- Niels Junius
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Esko Oksanen
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Maxime Terrien
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Christophe Berzin
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Jean-Luc Ferrer
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Monika Budayova-Spano
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
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Büker P, Feng Z, Uddling J, Briolat A, Alonso R, Braun S, Elvira S, Gerosa G, Karlsson PE, Le Thiec D, Marzuoli R, Mills G, Oksanen E, Wieser G, Wilkinson M, Emberson LD. New flux based dose-response relationships for ozone for European forest tree species. Environ Pollut 2015; 206:163-74. [PMID: 26164201 DOI: 10.1016/j.envpol.2015.06.033] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/30/2015] [Accepted: 06/27/2015] [Indexed: 05/10/2023]
Abstract
To derive O3 dose-response relationships (DRR) for five European forest trees species and broadleaf deciduous and needleleaf tree plant functional types (PFTs), phytotoxic O3 doses (PODy) were related to biomass reductions. PODy was calculated using a stomatal flux model with a range of cut-off thresholds (y) indicative of varying detoxification capacities. Linear regression analysis showed that DRR for PFT and individual tree species differed in their robustness. A simplified parameterisation of the flux model was tested and showed that for most non-Mediterranean tree species, this simplified model led to similarly robust DRR as compared to a species- and climate region-specific parameterisation. Experimentally induced soil water stress was not found to substantially reduce PODy, mainly due to the short duration of soil water stress periods. This study validates the stomatal O3 flux concept and represents a step forward in predicting O3 damage to forests in a spatially and temporally varying climate.
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Affiliation(s)
- P Büker
- Stockholm Environment Institute at York, Environment Department, University of York, Heslington, York, YO10 5DD, United Kingdom.
| | - Z Feng
- Research Centre for Eco-Environmental Science, Chinese Academy of Sciences, 18 Shuangqing Road, Haidan District, 100085 Beijing, China.
| | - J Uddling
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, 40530 Gothenburg, Sweden.
| | - A Briolat
- Stockholm Environment Institute at York, Environment Department, University of York, Heslington, York, YO10 5DD, United Kingdom.
| | - R Alonso
- Ecotoxicology of Air Pollution, CIEMAT, Av. Complutense 40, 28040 Madrid, Spain.
| | - S Braun
- Institut für Angewandte Pflanzenbiologie (IAP), Sandgrubenstraβe 25/27, 4124 Schönenbuch, Switzerland.
| | - S Elvira
- Ecotoxicology of Air Pollution, CIEMAT, Av. Complutense 40, 28040 Madrid, Spain.
| | - G Gerosa
- Dipartimento di Matematica e Fisica "Niccolò Tartaglia", Università Cattolica del Sacro Cuore, via Musei 41, 25121 Brescia, Italy.
| | - P E Karlsson
- Swedish Environmental Research Institute, IVL, Box 5302, 40014 Gothenburg, Sweden.
| | - D Le Thiec
- UMR Ecologie et Ecophysiologie Forestières, INRA, Rue D'Amance, 54280 Champenoux, France.
| | - R Marzuoli
- Dipartimento di Matematica e Fisica "Niccolò Tartaglia", Università Cattolica del Sacro Cuore, via Musei 41, 25121 Brescia, Italy.
| | - G Mills
- Centre for Ecology and Hydrology, Environment Centre Wales, Deiniol Road, Bangor, Gwynedd, LL57 2UW, United Kingdom.
| | - E Oksanen
- Department of Biology, University of Eastern Finland, Post Box 111, 80101 Joensuu, Finland.
| | - G Wieser
- Department for Natural Hazards and Alpine Timberline, Federal Research and Training Centre for Forests, Natural Hazards and Landscape, Hofburg 1, 6020 Innsbruck, Austria.
| | - M Wilkinson
- Centre for Sustainable Forestry & Climate Change, Forest Research, Alice Holt Lodge, Farnham, Surrey, GU10 4LH, United Kingdom.
| | - L D Emberson
- Stockholm Environment Institute at York, Environment Department, University of York, Heslington, York, YO10 5DD, United Kingdom.
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32
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Oksanen E. Dynamics of biological macromolecules by neutron scattering. CRYSTALLOGR REV 2015. [DOI: 10.1080/0889311x.2015.1064117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Oksanen E, Blakeley MP, El-Hajji M, Ryde U, Budayova-Spano M. The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation. PLoS One 2014; 9:e86651. [PMID: 24466188 PMCID: PMC3900588 DOI: 10.1371/journal.pone.0086651] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/16/2013] [Indexed: 12/02/2022] Open
Abstract
Urate oxidase transforms uric acid to 5-hydroxyisourate without the help of cofactors, but the catalytic mechanism has remained enigmatic, as the protonation state of the substrate could not be reliably deduced. We have determined the neutron structure of urate oxidase, providing unique information on the proton positions. A neutron crystal structure inhibited by a chloride anion at 2.3 Å resolution shows that the substrate is in fact 8-hydroxyxanthine, the enol tautomer of urate. We have also determined the neutron structure of the complex with the inhibitor 8-azaxanthine at 1.9 Å resolution, showing the protonation states of the K10–T57–H256 catalytic triad. Together with X-ray data and quantum chemical calculations, these structures allow us to identify the site of the initial substrate protonation and elucidate why the enzyme is inhibited by a chloride anion.
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Affiliation(s)
- Esko Oksanen
- Institut de Biologie Structurale (IBS), Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives, Grenoble, France, IBS, Centre National de la Recherche Scientifique, Grenoble, France, IBS, Université Grenoble Alpes, Grenoble, France
| | | | | | - Ulf Ryde
- Department of Theoretical Chemistry Lund University, Lund, Sweden
| | - Monika Budayova-Spano
- Institut de Biologie Structurale (IBS), Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives, Grenoble, France, IBS, Centre National de la Recherche Scientifique, Grenoble, France, IBS, Université Grenoble Alpes, Grenoble, France
- * E-mail:
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Repo H, Kuokkanen E, Oksanen E, Goldman A, Heikinheimo P. Is the bovine lysosomal phospholipase B-like protein an amidase? Proteins 2013; 82:300-11. [PMID: 23934913 DOI: 10.1002/prot.24388] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/17/2013] [Accepted: 07/26/2013] [Indexed: 12/17/2022]
Abstract
The main function of lysosomal proteins is to degrade cellular macromolecules. We purified a novel lysosomal protein to homogeneity from bovine kidneys. By gene annotation, this protein is defined as a bovine phospholipase B-like protein 1 (bPLBD1) and, to better understand its biological function, we solved its structure at 1.9 Å resolution. We showed that bPLBD1 has uniform noncomplex-type N-glycosylation and that it localized to the lysosome. The first step in lysosomal protein transport, the initiation of mannose-6-phosphorylation by a N-acetylglucosamine-1-phosphotransferase, requires recognition of at least two distinct lysines on the protein surface. We identified candidate lysines by analyzing the structural and sequentially conserved N-glycosylation sites and lysines in bPLBD1 and in the homologous mouse PLBD2. Our model suggests that N408 is the primarily phosphorylated glycan, and K358 a key residue for N-acetylglucosamine-1-phosphotransferase recognition. Two other lysines, K334 and K342, provide the required second site for N-acetylglucosamine-1-phosphotransferase recognition. bPLBD1 is an N-terminal nucleophile (Ntn) hydrolase. By comparison with other Ntn-hydrolases, we conclude that the acyl moiety of PLBD1 substrate must be small to fit the putative binding pocket, whereas the space for the rest of the substrate is a large open cleft. Finally, as all the known substrates of Ntn-hydrolases have amide bonds, we suggest that bPLBD1 may be an amidase or peptidase instead of lipase, explaining the difficulty in finding a good substrate for any members of the PLBD family.
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Affiliation(s)
- Heidi Repo
- Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland; Department of Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
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Oksanen E, Pandey V, Pandey AK, Keski-Saari S, Kontunen-Soppela S, Sharma C. Impacts of increasing ozone on Indian plants. Environ Pollut 2013; 177:189-200. [PMID: 23466168 DOI: 10.1016/j.envpol.2013.02.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 01/25/2013] [Accepted: 02/08/2013] [Indexed: 05/22/2023]
Abstract
Increasing anthropogenic and biogenic emissions of precursor compounds have led to high tropospheric ozone concentrations in India particularly in Indo-Gangetic Plains, which is the most fertile and cultivated area of this rapidly developing country. Current ozone risk models, based on European and North American data, provide inaccurate estimations for crop losses in India. During the past decade, several ozone experiments have been conducted with the most important Indian crop species (e.g. wheat, rice, mustard, mung bean). Experimental work started in natural field conditions around Varanasi area in early 2000's, and the use of open top chambers and EDU (ethylene diurea) applications has now facilitated more advanced studies e.g. for intra-species sensitivity screening and mechanisms of tolerance. In this review, we identify and discuss the most important gaps of knowledge and future needs of action, e.g. more systematic nationwide monitoring for precursor and ozone formation over Indian region.
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Affiliation(s)
- E Oksanen
- University of Eastern Finland, Department of Biology, POB 111, 80101 Joensuu, Finland.
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36
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Mäenpää M, Ossipov V, Kontunen-Soppela S, Keinänen M, Rousi M, Oksanen E. Biochemical and growth acclimation of birch to night temperatures: genotypic similarities and differences. Plant Biol (Stuttg) 2013; 15 Suppl 1:36-43. [PMID: 22612878 DOI: 10.1111/j.1438-8677.2012.00609.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The responses of plants to environmental factors are connected to the time of day. In this study, silver birch (Betula pendula) was grown in growth chambers at five different night temperatures (6-22 °C), using gradual changes during the evening and morning hours. Despite the increased night respiration and unaffected daytime net photosynthesis (per square metre), the carbon uptake (biomass) of birch did not decrease, probably due to enhanced biochemical processes on warmer nights and the advantage of higher temperatures during the evening and morning hours. The plant stem height, internode length, stem dry weight (DW), stem mass fraction and specific leaf area increased with warmer night temperatures. Changes in growth and metabolite concentrations were partly nonlinear along the temperature gradient. Thus, the temperature effect depends on the temperature window considered. Genotypes had both common and genotype-specific biochemical responses to night temperatures. The common responses among genotypes were related to growth responses, whereas the unique responses may indicate genotype-specific differences in acclimation. The differences in genotypic growth and metabolite levels are valuable for assessing genotype qualities and understanding the connections between the metabolome and growth.
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Affiliation(s)
- M Mäenpää
- Department of Biology, University of Eastern Finland, Joensuu, Finland.
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37
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Oksanen E, Blakeley MP, El-Hajji M, Ryde U, Castro B, Budayova-Spano M. Surprising protonation states in urate oxidase – combining X-ray and neutron crystallography with QM/MM. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312098248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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38
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Butcher SJ, Happonen LJ, Oksanen E, Liljeroos L, Goldman AG, Kajander T. Packaging of the membrane-containing thermophilic virus STIV2. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312099412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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39
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Kaila VRI, Oksanen E, Goldman A, Bloch DA, Verkhovsky MI, Sundholm D, Wikström M. A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase. Biochim Biophys Acta 2011; 1807:769-78. [PMID: 21211513 DOI: 10.1016/j.bbabio.2010.12.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 12/20/2010] [Accepted: 12/26/2010] [Indexed: 01/12/2023]
Abstract
Cytochrome c oxidase (CcO) is the terminal enzyme of the respiratory chain. By reducing oxygen to water, it generates a proton gradient across the mitochondrial or bacterial membrane. Recently, two independent X-ray crystallographic studies ((Aoyama et al. Proc. Natl. Acad. Sci. USA 106 (2009) 2165-2169) and (Koepke et al. Biochim. Biophys. Acta 1787 (2009) 635-645)), suggested that a peroxide dianion might be bound to the active site of oxidized CcO. We have investigated this hypothesis by combining quantum chemical calculations with a re-refinement of the X-ray crystallographic data and optical spectroscopic measurements. Our data suggest that dianionic peroxide, superoxide, and dioxygen all form a similar superoxide species when inserted into a fully oxidized ferric/cupric binuclear site (BNC). We argue that stable peroxides are unlikely to be confined within the oxidized BNC since that would be expected to lead to bond splitting and formation of the catalytic P intermediate. Somewhat surprisingly, we find that binding of dioxygen to the oxidized binuclear site is weakly exergonic, and hence, the observed structure might have resulted from dioxygen itself or from superoxide generated from O(2) by the X-ray beam. We show that the presence of O(2) is consistent with the X-ray data. We also discuss how other structures, such as a mixture of the aqueous species (H(2)O+OH(-) and H(2)O) and chloride fit the experimental data.
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Affiliation(s)
- Ville R I Kaila
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland.
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40
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Oksanen E, Dauvergne F, Goldman A, Budayova-Spano M. Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810027111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.
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Matyssek R, Karnosky DF, Wieser G, Percy K, Oksanen E, Grams TEE, Kubiske M, Hanke D, Pretzsch H. Advances in understanding ozone impact on forest trees: messages from novel phytotron and free-air fumigation studies. Environ Pollut 2010; 158:1990-2006. [PMID: 20133031 DOI: 10.1016/j.envpol.2009.11.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 11/29/2009] [Indexed: 05/28/2023]
Abstract
Recent evidence from novel phytotron and free-air ozone (O3) fumigation experiments in Europe and America on forest tree species is highlighted in relation to previous chamber studies. Differences in O3 sensitivity between pioneer and climax species are examined and viewed for trees growing at the harsh alpine timberline ecotone. As O3 apparently counteracts positive effects of elevated CO2 and mitigates productivity increases, response is governed by genotype, competitors, and ontogeny rather than species per se. Complexity in O3 responsiveness increased under the influence of pathogens and herbivores. The new evidence does not conflict in principle with previous findings that, however, pointed to a low ecological significance. This new knowledge on trees' O3 responsiveness beyond the juvenile stage in plantations and forests nevertheless implies limited predictability due to complexity in biotic and abiotic interactions. Unravelling underlying mechanisms is mandatory for assessing O3 risks as an important component of climate change scenarios.
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Affiliation(s)
- R Matyssek
- Ecophysiology of Plants, Technische Universität München, Am Hochanger 13, D-85354 Freising-Weihenstephan, Germany.
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Tuominen H, Salminen A, Oksanen E, Jämsen J, Heikkilä O, Lehtiö L, Magretova NN, Goldman A, Baykov AA, Lahti R. Crystal structures of the CBS and DRTGG domains of the regulatory region of Clostridiumperfringens pyrophosphatase complexed with the inhibitor, AMP, and activator, diadenosine tetraphosphate. J Mol Biol 2010; 398:400-13. [PMID: 20303981 DOI: 10.1016/j.jmb.2010.03.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 03/10/2010] [Accepted: 03/10/2010] [Indexed: 01/01/2023]
Abstract
Nucleotide-binding cystathionine beta-synthase (CBS) domains serve as regulatory units in numerous proteins distributed in all kingdoms of life. However, the underlying regulatory mechanisms remain to be established. Recently, we described a subfamily of CBS domain-containing pyrophosphatases (PPases) within family II PPases. Here, we express a novel CBS-PPase from Clostridium perfringens (CPE2055) and show that the enzyme is inhibited by AMP and activated by a novel effector, diadenosine 5',5-P1,P4-tetraphosphate (AP(4)A). The structures of the AMP and AP(4)A complexes of the regulatory region of C. perfringens PPase (cpCBS), comprising a pair of CBS domains interlinked by a DRTGG domain, were determined at 2.3 A resolution using X-ray crystallography. The structures obtained are the first structures of a DRTGG domain as part of a larger protein structure. The AMP complex contains two AMP molecules per cpCBS dimer, each bound to a single monomer, whereas in the activator-bound complex, one AP(4)A molecule bridges two monomers. In the nucleotide-bound structures, activator binding induces significant opening of the CBS domain interface, compared with the inhibitor complex. These results provide structural insight into the mechanism of CBS-PPase regulation by nucleotides.
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Affiliation(s)
- H Tuominen
- Department of Biochemistry and Food Chemistry, University of Turku, Vatselankatu 2, FI-20014 Turku, Finland
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Ora A, Oksanen E, Kajander T, Goldman A, Butcher SJ. Crystallization and preliminary crystallographic analysis of mouse peroxiredoxin II with significant pseudosymmetry. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:357-60. [PMID: 20208180 DOI: 10.1107/s1744309110003684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 01/29/2010] [Indexed: 11/10/2022]
Abstract
Peroxiredoxin II was cloned from mouse B cells into pCold 1 expression vector and produced as a His-tagged recombinant protein in Escherichia coli. A ring form was isolated by gel filtration. A crystal obtained by the sitting-drop vapour-diffusion method diffracted to 1.77 A resolution at 100 K. The crystal belonged to space group P2(1)2(1)2, with unit-cell parameters a = 117.4, b = 133.9, c = 139.1 A. The asymmetric unit is expected to contain six dimers of peroxiredoxin II, with a corresponding solvent content of 39.3%. Peaks in the native Patterson function together with pseudo-systematic absences suggested that the crystals suffered from severe translational pseudosymmetry.
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Affiliation(s)
- Ari Ora
- Institute of Biotechnology, PO Box 65, 00014 University of Helsinki, Finland
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44
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Oksanen E, Blakeley MP, Bonneté F, Dauvergne MT, Dauvergne F, Budayova-Spano M. Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase. J R Soc Interface 2009; 6 Suppl 5:S599-610. [PMID: 19586953 DOI: 10.1098/rsif.2009.0162.focus] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Urate oxidase (Uox) catalyses the oxidation of urate to allantoin and is used to reduce toxic urate accumulation during chemotherapy. X-ray structures of Uox with various inhibitors have been determined and yet the detailed catalytic mechanism remains unclear. Neutron crystallography can provide complementary information to that from X-ray studies and allows direct determination of the protonation states of the active-site residues and substrate analogues, provided that large, well-ordered deuterated crystals can be grown. Here, we describe a method and apparatus used to grow large crystals of Uox (Aspergillus flavus) with its substrate analogues 8-azaxanthine and 9-methyl urate, and with the natural substrate urate, in the presence and absence of cyanide. High-resolution X-ray (1.05-1.20 A) and neutron diffraction data (1.9-2.5 A) have been collected for the Uox complexes at the European Synchrotron Radiation Facility and the Institut Laue-Langevin, respectively. In addition, room temperature X-ray data were also collected in preparation for joint X-ray and neutron refinement. Preliminary results indicate no major structural differences between crystals grown in H(2)O and D(2)O even though the crystallization process is affected. Moreover, initial nuclear scattering density maps reveal the proton positions clearly, eventually providing important information towards unravelling the mechanism of catalysis.
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Affiliation(s)
- E Oksanen
- Institute of Biotechnology, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
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Parkash V, Lindholm P, Peränen J, Kalkkinen N, Oksanen E, Saarma M, Leppänen VM, Goldman A. The structure of the conserved neurotrophic factors MANF and CDNF explains why they are bifunctional. Protein Eng Des Sel 2009; 22:233-41. [PMID: 19258449 DOI: 10.1093/protein/gzn080] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We have solved the structures of mammalian mesencephalic astrocyte-derived neurotrophic factor (MANF) and conserved dopamine neurotrophic factor (CDNF). CDNF protects and repairs midbrain dopaminergic neurons in vivo; MANF supports their survival in culture and is also cytoprotective against endoplasmic reticulum (ER) stress. Neither protein structure resembles any known growth factor but the N-terminal domain is a saposin-like lipid-binding domain. MANF and CDNF may thus bind lipids or membranes. Consistent with this, there are two patches of conserved lysines and arginines. The natively unfolded MANF C-terminus contains a CKGC disulphide bridge, such as reductases and disulphide isomerases, consistent with a role in ER stress response. The structure thus explains why MANF and CDNF are bifunctional; neurotrophic activity may reside in the N-terminal domain and ER stress response in the C-terminal domain. Finally, we identified three changes, (MANF)I10-->K(CDNF), (MANF)E79-->M(CDNF) and (MANF)K88-->L(CDNF), that may account for the biological differences between the proteins.
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Affiliation(s)
- Vimal Parkash
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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46
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Abstract
Actin dynamics provide the driving force for many cellular processes including motility and endocytosis. Among the central cytoskeletal regulators are actin-depolymerizing factor (ADF)/cofilin, which depolymerizes actin filaments, and twinfilin, which sequesters actin monomers and caps filament barbed ends. Both interact with actin through an ADF homology (ADF-H) domain, which is also found in several other actin-binding proteins. However, in the absence of an atomic structure for the ADF-H domain in complex with actin, the mechanism by which these proteins interact with actin has remained unknown. Here, we present the crystal structure of twinfilin's C-terminal ADF-H domain in complex with an actin monomer. This domain binds between actin subdomains 1 and 3 through an interface that is conserved among ADF-H domain proteins. Based on this structure, we suggest a mechanism by which ADF/cofilin and twinfilin inhibit nucleotide exchange of actin monomers and present a model for how ADF/cofilin induces filament depolymerization by weakening intrafilament interactions.
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Affiliation(s)
- Ville O Paavilainen
- Program in Cellular Biotechnology, Institute of Biotechnology, University of Helsinki, Helsinki FIN-00014, Finland
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47
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Büker P, Emberson LD, Ashmore MR, Cambridge HM, Jacobs CMJ, Massman WJ, Müller J, Nikolov N, Novak K, Oksanen E, Schaub M, de la Torre D. Comparison of different stomatal conductance algorithms for ozone flux modelling. Environ Pollut 2007; 146:726-35. [PMID: 16766104 DOI: 10.1016/j.envpol.2006.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Accepted: 04/04/2006] [Indexed: 05/10/2023]
Abstract
A multiplicative and a semi-mechanistic, BWB-type [Ball, J.T., Woodrow, I.E., Berry, J.A., 1987. A model predicting stomatal conductance and its contribution to the control of photosynthesis under different environmental conditions. In: Biggens, J. (Ed.), Progress in Photosynthesis Research, vol. IV. Martinus Nijhoff, Dordrecht, pp. 221-224.] algorithm for calculating stomatal conductance (g(s)) at the leaf level have been parameterised for two crop and two tree species to test their use in regional scale ozone deposition modelling. The algorithms were tested against measured, site-specific data for durum wheat, grapevine, beech and birch of different European provenances. A direct comparison of both algorithms showed a similar performance in predicting hourly means and daily time-courses of g(s), whereas the multiplicative algorithm outperformed the BWB-type algorithm in modelling seasonal time-courses due to the inclusion of a phenology function. The re-parameterisation of the algorithms for local conditions in order to validate ozone deposition modelling on a European scale reveals the higher input requirements of the BWB-type algorithm as compared to the multiplicative algorithm because of the need of the former to model net photosynthesis (A(n)).
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Affiliation(s)
- P Büker
- Stockholm Environment Institute, University of York, York, North Yorkshire YO 10 5DD, UK.
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48
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Karlsson PE, Braun S, Broadmeadow M, Elvira S, Emberson L, Gimeno BS, Le Thiec D, Novak K, Oksanen E, Schaub M, Uddling J, Wilkinson M. Risk assessments for forest trees: the performance of the ozone flux versus the AOT concepts. Environ Pollut 2007; 146:608-16. [PMID: 16938368 DOI: 10.1016/j.envpol.2006.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 06/12/2006] [Accepted: 06/15/2006] [Indexed: 05/10/2023]
Abstract
Published ozone exposure-response relationships from experimental studies with young trees performed at different sites across Europe were re-analysed in order to test the performance of ozone exposure indices based on AOTX (Accumulated exposure Over a Threshold of X nmol mol(-1)) and AF(st)Y (Accumulated Stomatal Flux above a threshold of Y nmol m(-2) s(-1)). AF(st)1.6 was superior, as compared to AOT40, for explaining biomass reductions, when ozone sensitive species with differing leaf morphology were included in the analysis, while this was not the case for less sensitive species. A re-analysis of data with young black cherry trees, subject to different irrigation regimes, indicated that leaf visible injuries were more strongly related to the estimated stomatal ozone uptake, as compared to the ozone concentration in the air. Experimental data with different clones of silver birch indicated that leaf thickness was also an important factor influencing the development of ozone induced leaf visible injury.
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Affiliation(s)
- P E Karlsson
- Swedish Environmental Research Institute (IVL), PO Box 5302, S-400 14, Göteborg, Sweden.
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49
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Oksanen E, Ahonen AK, Tuominen H, Tuominen V, Lahti R, Goldman A, Heikinheimo P. A complete structural description of the catalytic cycle of yeast pyrophosphatase. Biochemistry 2007; 46:1228-39. [PMID: 17260952 DOI: 10.1021/bi0619977] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have determined the structures of the wild type and seven active site variants of yeast inorganic pyrophosphatase (PPase) in the presence of Mg2+ and phosphate, providing the first complete structural description of its catalytic cycle. PPases catalyze the hydrolysis of pyrophosphate and require four divalent metal cations for catalysis; magnesium provides the highest activity. The crystal form chosen contains two monomers in the asymmetric unit, corresponding to distinct catalytic intermediates. In the "closed" wild-type active site, one of the two product phosphates has already dissociated, while the D115E variant "open" conformation is of the hitherto unobserved two-phosphate and two-"bridging" water active site. The mutations affect metal binding and the hydrogen bonding network in the active site, allowing us to explain the effects of mutations. For instance, in Y93F, F93 binds in a cryptic hydrophobic pocket in the absence of substrate, preserving hydrogen bonding in the active site and leading to relatively small changes in solution properties. This is not true in the presence of substrate, when F93 is forced back into the active site. Such subtle changes underline how low the energy barriers are between thermodynamically favorable conformations of the enzyme. The structures also allow us to associate metal binding constants to specific sites. Finally, the wild type and the D152E variant contain a phosphate ion adjacent to the active site, showing for the first time how product is released through a channel of flexible cationic side chains.
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Affiliation(s)
- Esko Oksanen
- Structural Biology and Biophysics, Institute of Biotechnology, P.O. Box 65, University of Helsinki, FIN-00014 Helsinki, Finland
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50
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Karnosky DF, Werner H, Holopainen T, Percy K, Oksanen T, Oksanen E, Heerdt C, Fabian P, Nagy J, Heilman W, Cox R, Nelson N, Matyssek R. Free-air exposure systems to scale up ozone research to mature trees. Plant Biol (Stuttg) 2007; 9:181-90. [PMID: 17357013 DOI: 10.1055/s-2006-955915] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Because seedlings and mature trees do not necessarily respond similarly to O(3) stress, it is critically important that exposure systems be developed that allow exposure of seedlings through to mature trees. Here we describe three different O(3) Free-Air Exposure Systems that have been used successfully for exposure at all growth stages. These systems of spatially uniform O(3) release have been shown to provide reliable O(3) exposure with minimal, if any, impact on the microclimate. This methodology offers a welcome alternative to chamber studies which had severe space constraints precluding stand or community-level studies and substantial chamber effects on the microclimate and, hence physiological tree performance.
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Affiliation(s)
- D F Karnosky
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
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