1
|
Drago VN, Devos JM, Blakeley MP, Forsyth VT, Parks JM, Kovalevsky A, Mueser TC. Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase. Cell Rep Phys Sci 2024; 5:101827. [PMID: 38645802 PMCID: PMC11027755 DOI: 10.1016/j.xcrp.2024.101827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin B6, is an essential cofactor in many biosynthetic pathways. The emergence of PLP-dependent enzymes as drug targets and biocatalysts, such as tryptophan synthase (TS), has underlined the demand to understand PLP-dependent catalysis and reaction specificity. The ability of neutron diffraction to resolve the positions of hydrogen atoms makes it an ideal technique to understand how the electrostatic environment and selective protonation of PLP regulates PLP-dependent activities. Facilitated by microgravity crystallization of TS with the Toledo Crystallization Box, we report the 2.1 Å joint X-ray/neutron (XN) structure of TS with PLP in the internal aldimine form. Positions of hydrogens were directly determined in both the α- and β-active sites, including PLP cofactor. The joint XN structure thus provides insight into the selective protonation of the internal aldimine and the electrostatic environment of TS necessary to understand the overall catalytic mechanism.
Collapse
Affiliation(s)
- Victoria N. Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Juliette M. Devos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 38000 Grenoble, France
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - V. Trevor Forsyth
- Faculty of Medicine, Lund University, and LINXS Institute for Advanced Neutron and X-ray Science, Lund, Sweden
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Lead contact
| |
Collapse
|
2
|
Sørensen HV, Montserrat-Canals M, Loose JSM, Fisher SZ, Moulin M, Blakeley MP, Cordara G, Bjerregaard-Andersen K, Krengel U. Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase. ACS Omega 2023; 8:29101-29112. [PMID: 37599915 PMCID: PMC10433351 DOI: 10.1021/acsomega.3c02168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/14/2023] [Indexed: 08/22/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are surface-active redox enzymes that catalyze the degradation of recalcitrant polysaccharides, making them important tools for energy production from renewable sources. In addition, LPMOs are important virulence factors for fungi, bacteria, and viruses. However, many knowledge gaps still exist regarding their catalytic mechanism and interaction with their insoluble, crystalline substrates. Moreover, conventional structural biology techniques, such as X-ray crystallography, usually do not reveal the protonation state of catalytically important residues. In contrast, neutron crystallography is highly suited to obtain this information, albeit with significant sample volume requirements and challenges associated with hydrogen's large incoherent scattering signal. We set out to demonstrate the feasibility of neutron-based techniques for LPMOs using N-acetylglucosamine-binding protein A (GbpA) from Vibrio cholerae as a target. GbpA is a multifunctional protein that is secreted by the bacteria to colonize and degrade chitin. We developed an efficient deuteration protocol, which yields >10 mg of pure 97% deuterated protein per liter expression media, which was scaled up further at international facilities. The deuterated protein retains its catalytic activity and structure, as demonstrated by small-angle X-ray and neutron scattering studies of full-length GbpA and X-ray crystal structures of its LPMO domain (to 1.1 Å resolution), setting the stage for neutron scattering experiments with its substrate chitin.
Collapse
Affiliation(s)
- H. V. Sørensen
- Department
of Chemistry, University of Oslo, NO-0315 Oslo, Norway
| | - Mateu Montserrat-Canals
- Department
of Chemistry, University of Oslo, NO-0315 Oslo, Norway
- Centre
for Molecular Medicine Norway, University
of Oslo, NO-0318 Oslo, Norway
| | - Jennifer S. M. Loose
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), NO-1340 Ås, Norway
| | - S. Zoë Fisher
- Science
Directorate, European Spallation Source
ERIC, P.O. Box 176, SE-221 00 Lund, Sweden
- Department
of Biology, Lund University, 35 Sölvegatan, SE-223 62 Lund, Sweden
| | - Martine Moulin
- Life Sciences
Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9 Grenoble, France
| | - Matthew P. Blakeley
- Large-Scale
Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Gabriele Cordara
- Department
of Chemistry, University of Oslo, NO-0315 Oslo, Norway
| | | | - Ute Krengel
- Department
of Chemistry, University of Oslo, NO-0315 Oslo, Norway
| |
Collapse
|
3
|
Drago VN, Campos C, Hooper M, Collins A, Gerlits O, Weiss KL, Blakeley MP, Phillips RS, Kovalevsky A. Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography. Commun Chem 2023; 6:162. [PMID: 37532884 PMCID: PMC10397204 DOI: 10.1038/s42004-023-00964-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize a vitamin B6-derived cofactor to perform a myriad of chemical transformations on amino acids and other small molecules. Some PLP-dependent enzymes, such as serine hydroxymethyltransferase (SHMT), are promising drug targets for the design of small-molecule antimicrobials and anticancer therapeutics, while others have been used to synthesize pharmaceutical building blocks. Understanding PLP-dependent catalysis and the reaction specificity is crucial to advance structure-assisted drug design and enzyme engineering. Here we report the direct determination of the protonation states in the active site of Thermus thermophilus SHMT (TthSHMT) in the internal aldimine state using room-temperature joint X-ray/neutron crystallography. Conserved active site architecture of the model enzyme TthSHMT and of human mitochondrial SHMT (hSHMT2) were compared by obtaining a room-temperature X-ray structure of hSHMT2, suggesting identical protonation states in the human enzyme. The amino acid substrate serine pathway through the TthSHMT active site cavity was tracked, revealing the peripheral and cationic binding sites that correspond to the pre-Michaelis and pseudo-Michaelis complexes, respectively. At the peripheral binding site, the substrate is bound in the zwitterionic form. By analyzing the observed protonation states, Glu53, but not His residues, is proposed as the general base catalyst, orchestrating the retro-aldol transformation of L-serine into glycine.
Collapse
Affiliation(s)
- Victoria N Drago
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Claudia Campos
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, 37303, USA
| | - Mattea Hooper
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, 37303, USA
| | - Aliyah Collins
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, 37303, USA
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, 37303, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| |
Collapse
|
4
|
Drago VN, Devos JM, Blakeley MP, Forsyth VT, Kovalevsky AY, Schall CA, Mueser TC. Microgravity crystallization of perdeuterated tryptophan synthase for neutron diffraction. NPJ Microgravity 2022; 8:13. [PMID: 35508463 PMCID: PMC9068912 DOI: 10.1038/s41526-022-00199-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 09/17/2021] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
Biologically active vitamin B6-derivative pyridoxal 5′-phosphate (PLP) is an essential cofactor in amino acid metabolic pathways. PLP-dependent enzymes catalyze a multitude of chemical reactions but, how reaction diversity of PLP-dependent enzymes is achieved is still not well understood. Such comprehension requires atomic-level structural studies of PLP-dependent enzymes. Neutron diffraction affords the ability to directly observe hydrogen positions and therefore assign protonation states to the PLP cofactor and key active site residues. The low fluxes of neutron beamlines require large crystals (≥0.5 mm3). Tryptophan synthase (TS), a Fold Type II PLP-dependent enzyme, crystallizes in unit gravity with inclusions and high mosaicity, resulting in poor diffraction. Microgravity offers the opportunity to grow large, well-ordered crystals by reducing gravity-driven convection currents that impede crystal growth. We developed the Toledo Crystallization Box (TCB), a membrane-barrier capillary-dialysis device, to grow neutron diffraction-quality crystals of perdeuterated TS in microgravity. Here, we present the design of the TCB and its implementation on Center for Advancement of Science in Space (CASIS) supported International Space Station (ISS) Missions Protein Crystal Growth (PCG)-8 and PCG-15. The TCB demonstrated the ability to improve X-ray diffraction and mosaicity on PCG-8. In comparison to ground control crystals of the same size, microgravity-grown crystals from PCG-15 produced higher quality neutron diffraction data. Neutron diffraction data to a resolution of 2.1 Å has been collected using microgravity-grown perdeuterated TS crystals from PCG-15.
Collapse
Affiliation(s)
- Victoria N Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, 43606, USA
| | - Juliette M Devos
- Life Sciences Group, Institut Laue-Langevin, 38000, Grenoble, France.,Partnership for Structural Biology (PSB), 38000, Grenoble, France
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue-Langevin, 38000, Grenoble, France
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, 38000, Grenoble, France.,Partnership for Structural Biology (PSB), 38000, Grenoble, France.,Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK.,Faculty of Medicine, Lund University, and LINXS Institute for Advanced Neutron and X-ray Science, Lund, Sweden
| | - Andrey Y Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Constance A Schall
- Department of Chemical Engineering, University of Toledo, Toledo, OH, 43606, USA
| | - Timothy C Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, 43606, USA.
| |
Collapse
|
5
|
Drago VN, Dajnowicz S, Parks JM, Blakeley MP, Keen DA, Coquelle N, Weiss KL, Gerlits O, Kovalevsky A, Mueser TC. An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction. Chem Sci 2022; 13:10057-10065. [PMID: 36128223 PMCID: PMC9430417 DOI: 10.1039/d2sc02285k] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/20/2022] [Indexed: 11/21/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP)-dependent enzymes have been extensively studied for their ability to fine-tune PLP cofactor electronics to promote a wide array of chemistries. Neutron crystallography offers a straightforward approach to studying the electronic states of PLP and the electrostatics of enzyme active sites, responsible for the reaction specificities, by enabling direct visualization of hydrogen atom positions. Here we report a room-temperature joint X-ray/neutron structure of aspartate aminotransferase (AAT) with pyridoxamine 5′-phosphate (PMP), the cofactor product of the first half reaction catalyzed by the enzyme. Between PMP NSB and catalytic Lys258 Nζ amino groups an equally shared deuterium is observed in an apparent low-barrier hydrogen bond (LBHB). Density functional theory calculations were performed to provide further evidence of this LBHB interaction. The structural arrangement and the juxtaposition of PMP and Lys258, facilitated by the LBHB, suggests active site preorganization for the incoming ketoacid substrate that initiates the second half-reaction. The neutron structure of pyridoxal 5′-phosphate-dependent enzyme aspartate aminotransferase with pyridoxamine 5′-phosphate (PMP) reveals a low-barrier hydrogen bond between the amino groups of PMP and catalytic Lys258, preorganizing the active site for catalysis![]()
Collapse
Affiliation(s)
- Victoria N. Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven Dajnowicz
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - David A. Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Nicolas Coquelle
- Large Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN 37303, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| |
Collapse
|
6
|
Gerlits O, Blakeley MP, Keen DA, Radić Z, Kovalevsky A. Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure. Curr Res Struct Biol 2021; 3:206-215. [PMID: 34541552 PMCID: PMC8435639 DOI: 10.1016/j.crstbi.2021.08.003] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/29/2021] [Indexed: 11/19/2022] Open
Abstract
Acetylcholinesterase (AChE) catalyzes hydrolysis of acetylcholine thereby terminating cholinergic nerve impulses for efficient neurotransmission. Human AChE (hAChE) is a target of nerve agent and pesticide organophosphorus compounds that covalently attach to the catalytic Ser203 residue. Reactivation of inhibited hAChE can be achieved with nucleophilic antidotes, such as oximes. Understanding structural and electrostatic (i.e. protonation states) determinants of the catalytic and reactivation processes is crucial to improve design of oxime reactivators. Here we report X-ray structures of hAChE conjugated with a reversible covalent inhibitor 4K-TMA (4K-TMA:hAChE) at 2.8 Å resolution and of 4K-TMA:hAChE conjugate with oxime reactivator methoxime, MMB4 (4K-TMA:hAChE:MMB4) at 2.6 Å resolution, both at physiologically relevant room temperature, as well as cryo-crystallographic structure of 4K-TMA:hAChE at 2.4 Å resolution. 4K-TMA acts as a substrate analogue reacting with the hydroxyl of Ser203 and generating a reversible tetrahedral hemiketal intermediate that closely resembles the first tetrahedral intermediate state during hAChE-catalyzed acetylcholine hydrolysis. Structural comparisons of room temperature with cryo-crystallographic structures of 4K-TMA:hAChE and published mAChE complexes with 4K-TMA, as well as the effect of MMB4 binding to the peripheral anionic site (PAS) of the 4K-TMA:hAChE complex, revealed only discrete, minor differences. The active center geometry of AChE, already highly evolved for the efficient catalysis, was thus indicative of only minor conformational adjustments to accommodate the tetrahedral intermediate in the hydrolysis of the neurotransmitter acetylcholine (ACh). To map protonation states in the hAChE active site gorge we collected 3.5 Å neutron diffraction data paving the way for obtaining higher resolution datasets that will be needed to determine locations of individual hydrogen atoms.
Collapse
Affiliation(s)
- Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, 37303, USA
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue–Langevin, 38000, Grenoble, France
| | - David A. Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Zoran Radić
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093-0751, USA
- Corresponding author.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Corresponding author.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Uusitalo M, Klenow MB, Laulumaa S, Blakeley MP, Simonsen AC, Ruskamo S, Kursula P. Human myelin protein P2: from crystallography to time-lapse membrane imaging and neuropathy-associated variants. FEBS J 2021; 288:6716-6735. [PMID: 34138518 DOI: 10.1111/febs.16079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 04/20/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 12/11/2022]
Abstract
Peripheral myelin protein 2 (P2) is a fatty acid-binding protein expressed in vertebrate peripheral nervous system myelin, as well as in human astrocytes. Suggested functions of P2 include membrane stacking and lipid transport. Mutations in the PMP2 gene, encoding P2, are associated with Charcot-Marie-Tooth disease (CMT). Recent studies have revealed three novel PMP2 mutations in CMT patients. To shed light on the structure and function of these P2 variants, we used X-ray and neutron crystallography, small-angle X-ray scattering, circular dichroism spectroscopy, computer simulations and lipid binding assays. The crystal and solution structures of the I50del, M114T and V115A variants of P2 showed minor differences to the wild-type protein, whereas their thermal stability was reduced. Vesicle aggregation assays revealed no change in membrane stacking characteristics, while the variants showed altered fatty acid binding. Time-lapse imaging of lipid bilayers indicated formation of double-membrane structures induced by P2, which could be related to its function in stacking of two myelin membrane surfaces in vivo. In order to better understand the links between structure, dynamics and function, the crystal structure of perdeuterated P2 was refined from room temperature data using neutrons and X-rays, and the results were compared to simulations and cryocooled crystal structures. Our data indicate similar properties for all known human P2 CMT variants; while crystal structures are nearly identical, thermal stability and function of CMT variants are impaired. Our data provide new insights into the structure-function relationships and dynamics of P2 in health and disease.
Collapse
Affiliation(s)
- Maiju Uusitalo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Martin Berg Klenow
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.,European Spallation Source, Lund, Sweden
| | | | - Adam Cohen Simonsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.,Department of Biomedicine, University of Bergen, Norway
| |
Collapse
|
9
|
Gajdos L, Blakeley MP, Kumar A, Wimmerová M, Haertlein M, Forsyth VT, Imberty A, Devos JM. Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions. Structure 2021; 29:1003-1013.e4. [PMID: 33765407 DOI: 10.1016/j.str.2021.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/01/2021] [Accepted: 03/03/2021] [Indexed: 11/30/2022]
Abstract
Carbohydrate-binding proteins from pathogenic bacteria and fungi have been shown to be implicated in various pathological processes, where they interact with glycans present on the surface of the host cells. These interactions are part of the initial processes of infection of the host and are very important to study at the atomic level. Here, we report the room temperature neutron structures of PLL lectin from Photorhabdus laumondii in its apo form and in complex with deuterated L-fucose, which is, to our knowledge, the first neutron structure of a carbohydrate-binding protein in complex with a fully deuterated carbohydrate ligand. A detailed structural analysis of the lectin-carbohydrate interactions provides information on the hydrogen bond network, the role of water molecules, and the extent of the CH-π stacking interactions between fucose and the aromatic amino acids in the binding site.
Collapse
Affiliation(s)
- Lukas Gajdos
- Life Sciences Group, Institut Laue-Langevin, 38000 Grenoble, France; Partnership for Structural Biology (PSB), 38000 Grenoble, France; Université Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 38000 Grenoble, France
| | - Atul Kumar
- CEITEC, Masaryk University, 625 00 Brno, Czech Republic; NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Michaela Wimmerová
- CEITEC, Masaryk University, 625 00 Brno, Czech Republic; NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Michael Haertlein
- Life Sciences Group, Institut Laue-Langevin, 38000 Grenoble, France; Partnership for Structural Biology (PSB), 38000 Grenoble, France
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, 38000 Grenoble, France; Partnership for Structural Biology (PSB), 38000 Grenoble, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, UK
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.
| | - Juliette M Devos
- Life Sciences Group, Institut Laue-Langevin, 38000 Grenoble, France; Partnership for Structural Biology (PSB), 38000 Grenoble, France.
| |
Collapse
|
10
|
McGregor L, Földes T, Bui S, Moulin M, Coquelle N, Blakeley MP, Rosta E, Steiner RA. Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis. IUCrJ 2021; 8:46-59. [PMID: 33520242 PMCID: PMC7792999 DOI: 10.1107/s2052252520013615] [Citation(s) in RCA: 4] [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] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/12/2020] [Indexed: 06/12/2023]
Abstract
Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O2 to de-hydro-isourate (DHU) via a peroxo intermediate. DHU then undergoes hydration to 5-hy-droxy-isourate (5HIU). At different stages of the reaction both catalytic O2 and water occupy the 'peroxo hole' above the organic substrate. Here, high-resolution neutron/X-ray crystallographic analysis at room temperature has been integrated with molecular dynamics simulations to investigate the hydration step of the reaction. The joint neutron/X-ray structure of perdeuterated Aspergillus flavus UOX in complex with its 8-azaxanthine (8AZA) inhibitor shows that the catalytic water molecule (W1) is present in the peroxo hole as neutral H2O, oriented at 45° with respect to the ligand. It is stabilized by Thr57 and Asn254 on different UOX protomers as well as by an O-H⋯π interaction with 8AZA. The active site Lys10-Thr57 dyad features a charged Lys10-NH3 + side chain engaged in a strong hydrogen bond with Thr57OG1, while the Thr57OG1-HG1 bond is rotationally dynamic and oriented toward the π system of the ligand, on average. Our analysis offers support for a mechanism in which W1 performs a nucleophilic attack on DHUC5 with Thr57HG1 central to a Lys10-assisted proton-relay system. Room-temperature crystallography and simulations also reveal conformational heterogeneity for Asn254 that modulates W1 stability in the peroxo hole. This is proposed to be an active mechanism to facilitate W1/O2 exchange during catalysis.
Collapse
Affiliation(s)
- Lindsay McGregor
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Tamás Földes
- Department of Chemistry, King’s College London, London SE1 1DB, United Kingdom
- Department of Physics and Astronomy, University College, London WC1E 6BT, United Kingdom
| | - Soi Bui
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| | - Martine Moulin
- Life Sciences Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Nicolas Coquelle
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Edina Rosta
- Department of Chemistry, King’s College London, London SE1 1DB, United Kingdom
- Department of Physics and Astronomy, University College, London WC1E 6BT, United Kingdom
| | - Roberto A. Steiner
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| |
Collapse
|
11
|
Gajdos L, Forsyth VT, Blakeley MP, Haertlein M, Imberty A, Samain E, Devos JM. Production of perdeuterated fucose from glyco-engineered bacteria. Glycobiology 2020; 31:151-158. [PMID: 32601663 PMCID: PMC7874385 DOI: 10.1093/glycob/cwaa059] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 12/31/2022] Open
Abstract
l-Fucose and l-fucose-containing polysaccharides, glycoproteins or glycolipids play an important role in a variety of biological processes. l-Fucose-containing glycoconjugates have been implicated in many diseases including cancer and rheumatoid arthritis. Interest in fucose and its derivatives is growing in cancer research, glyco-immunology, and the study of host–pathogen interactions. l-Fucose can be extracted from bacterial and algal polysaccharides or produced (bio)synthetically. While deuterated glucose and galactose are available, and are of high interest for metabolic studies and biophysical studies, deuterated fucose is not easily available. Here, we describe the production of perdeuterated l-fucose, using glyco-engineered Escherichia coli in a bioreactor with the use of a deuterium oxide-based growth medium and a deuterated carbon source. The final yield was 0.2 g L−1 of deuterated sugar, which was fully characterized by mass spectrometry and nuclear magnetic resonance spectroscopy. We anticipate that the perdeuterated fucose produced in this way will have numerous applications in structural biology where techniques such as NMR, solution neutron scattering and neutron crystallography are widely used. In the case of neutron macromolecular crystallography, the availability of perdeuterated fucose can be exploited in identifying the details of its interaction with protein receptors and notably the hydrogen bonding network around the carbohydrate binding site.
Collapse
Affiliation(s)
- Lukas Gajdos
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.,Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, Grenoble 38000, France.,Université Grenoble Alpes, CNRS, CERMAV, Grenoble 38000, France
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.,Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, Grenoble 38000, France.,Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, UK
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.,Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, Grenoble 38000, France
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble 38000, France
| | - Eric Samain
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble 38000, France
| | - Juliette M Devos
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France.,Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, Grenoble 38000, France
| |
Collapse
|
12
|
Kumar M, Mandal K, Blakeley MP, Wymore T, Kent SBH, Louis JM, Das A, Kovalevsky A. Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design. ACS Omega 2020; 5:11605-11617. [PMID: 32478251 PMCID: PMC7254801 DOI: 10.1021/acsomega.0c00835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
HIV-1 protease is indispensable for virus propagation and an important therapeutic target for antiviral inhibitors to treat AIDS. As such inhibitors are transition-state mimics, a detailed understanding of the enzyme mechanism is crucial for the development of better anti-HIV drugs. Here, we used room-temperature joint X-ray/neutron crystallography to directly visualize hydrogen atoms and map hydrogen bonding interactions in a protease complex with peptidomimetic inhibitor KVS-1 containing a reactive nonhydrolyzable ketomethylene isostere, which, upon reacting with the catalytic water molecule, is converted into a tetrahedral intermediate state, KVS-1TI. We unambiguously determined that the resulting tetrahedral intermediate is an oxyanion, rather than the gem-diol, and both catalytic aspartic acid residues are protonated. The oxyanion tetrahedral intermediate appears to be unstable, even though the negative charge on the oxyanion is delocalized through a strong n → π* hyperconjugative interaction into the nearby peptidic carbonyl group of the inhibitor. To better understand the influence of the ketomethylene isostere as a protease inhibitor, we have also examined the protease structure and binding affinity with keto-darunavir (keto-DRV), which similar to KVS-1 includes the ketomethylene isostere. We show that keto-DRV is a significantly less potent protease inhibitor than DRV. These findings shed light on the reaction mechanism of peptide hydrolysis catalyzed by HIV-1 protease and provide valuable insights into further improvements in the design of protease inhibitors.
Collapse
Affiliation(s)
- Mukesh Kumar
- Protein Crystallography
Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Kalyaneswar Mandal
- Departments of Chemistry, and Biochemistry and Molecular Biology,
Institute for Biophysical Dynamics, University
of Chicago, Chicago, Illinois 60637, United States
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue−Langevin, 38000 Grenoble, France
| | - Troy Wymore
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen B. H. Kent
- Departments of Chemistry, and Biochemistry and Molecular Biology,
Institute for Biophysical Dynamics, University
of Chicago, Chicago, Illinois 60637, United States
| | - John M. Louis
- Laboratory of Chemical Physics, National
Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - Amit Das
- Protein Crystallography
Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Andrey Kovalevsky
- Neutron Scattering
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| |
Collapse
|
13
|
Kwon H, Basran J, Devos JM, Suardíaz R, van der Kamp MW, Mulholland AJ, Schrader TE, Ostermann A, Blakeley MP, Moody PCE, Raven EL. Visualizing the protons in a metalloenzyme electron proton transfer pathway. Proc Natl Acad Sci U S A 2020; 117:6484-6490. [PMID: 32152099 PMCID: PMC7104402 DOI: 10.1073/pnas.1918936117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In redox metalloenzymes, the process of electron transfer often involves the concerted movement of a proton. These processes are referred to as proton-coupled electron transfer, and they underpin a wide variety of biological processes, including respiration, energy conversion, photosynthesis, and metalloenzyme catalysis. The mechanisms of proton delivery are incompletely understood, in part due to an absence of information on exact proton locations and hydrogen bonding structures in a bona fide metalloenzyme proton pathway. Here, we present a 2.1-Å neutron crystal structure of the complex formed between a redox metalloenzyme (ascorbate peroxidase) and its reducing substrate (ascorbate). In the neutron structure of the complex, the protonation states of the electron/proton donor (ascorbate) and all of the residues involved in the electron/proton transfer pathway are directly observed. This information sheds light on possible proton movements during heme-catalyzed oxygen activation, as well as on ascorbate oxidation.
Collapse
Affiliation(s)
- Hanna Kwon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Jaswir Basran
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Juliette M Devos
- Life Sciences Group, Institut Laue-Langevin, 38000 Grenoble, France
| | - Reynier Suardíaz
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Marc W van der Kamp
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | | | - Tobias E Schrader
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, 85748 Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, D-85748 Garching, Germany
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue-Langevin, 38000 Grenoble, France
| | - Peter C E Moody
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom;
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Emma L Raven
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| |
Collapse
|
14
|
Abstract
By combining the normal practice for X-ray crystallography of collecting diffraction data at 100K with neutron crystallography the structures of cryo-trapped enzyme intermediates have been determined, revealing the positions of the previously hidden hydrogens that are essential to a better understanding of the involved mechanism.
Collapse
Affiliation(s)
- Hanna Kwon
- School of Chemistry, University of Bristol, Bristol, United Kingdom.
| | - Tobias E Schrader
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Garching, Germany
| | | | - Emma L Raven
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Peter C E Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
| |
Collapse
|
15
|
Kovalevsky A, Gerlits O, Beltran K, Weiss KL, Keen DA, Blakeley MP, Louis JM, Weber IT. Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease. Methods Enzymol 2020; 634:257-279. [PMID: 32093836 DOI: 10.1016/bs.mie.2019.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
HIV-1 protease is an essential therapeutic target for the design and development of antiviral inhibitors to treat AIDS. We used room temperature neutron crystallography to accurately determine hydrogen atom positions in several protease complexes with clinical drugs, amprenavir and darunavir. Hydrogen bonding interactions were carefully mapped to provide an unprecedented picture of drug binding to the protease target. We demonstrate that hydrogen atom positions within the enzyme catalytic site can be altered by introducing drug resistant mutations and by protonating surface residues that trigger proton transfer reactions between the catalytic Asp residues and the hydroxyl group of darunavir. When protein perdeuteration is not feasible, we validate the use of initial H/D exchange with unfolded protein and partial deuteration in pure D2O with hydrogenous glycerol to maximize deuterium incorporation into the protein, with no detrimental effects on the growth of quality crystals suitable for neutron diffraction experiments.
Collapse
Affiliation(s)
- Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, United States
| | - Kaira Beltran
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, United States
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, United Kingdom
| | | | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, United States
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA, United States; Department of Chemistry, Georgia State University, Atlanta, GA, United States
| |
Collapse
|
16
|
Halsted TP, Yamashita K, Gopalasingam CC, Shenoy RT, Hirata K, Ago H, Ueno G, Blakeley MP, Eady RR, Antonyuk SV, Yamamoto M, Hasnain SS. Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography. IUCrJ 2019; 6:761-772. [PMID: 31316819 PMCID: PMC6608623 DOI: 10.1107/s2052252519008285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/12/2019] [Indexed: 05/31/2023]
Abstract
Copper-containing nitrite reductases (CuNiRs) that convert NO2 - to NO via a CuCAT-His-Cys-CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD-, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2 - a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed.
Collapse
Affiliation(s)
- Thomas P. Halsted
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Chai C. Gopalasingam
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Rajesh T. Shenoy
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Hideo Ago
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Go Ueno
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Masaki Yamamoto
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| |
Collapse
|
17
|
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.
Collapse
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
| | | |
Collapse
|
18
|
Gerlits O, Weiss KL, Blakeley MP, Veglia G, Taylor SS, Kovalevsky A. Zooming in on protons: Neutron structure of protein kinase A trapped in a product complex. Sci Adv 2019; 5:eaav0482. [PMID: 30906862 PMCID: PMC6426457 DOI: 10.1126/sciadv.aav0482] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/31/2019] [Indexed: 05/06/2023]
Abstract
The question vis-à-vis the chemistry of phosphoryl group transfer catalyzed by protein kinases remains a major challenge. The neutron diffraction structure of the catalytic subunit of cAMP-dependent protein kinase (PKA-C) provides a more complete chemical portrait of key proton interactions at the active site. By using a high-affinity protein kinase substrate (PKS) peptide, we captured the reaction products, dephosphorylated nucleotide [adenosine diphosphate (ADP)] and phosphorylated PKS (pPKS), bound at the active site. In the complex, the phosphoryl group of the peptide is protonated, whereas the carboxyl group of the catalytic Asp166 is not. Our structure, including conserved waters, shows how the peptide links the distal parts of the cleft together, creating a network that engages the entire molecule. By comparing slow-exchanging backbone amides to those determined by the NMR analysis of PKA-C with ADP and inhibitor peptide (PKI), we identified exchangeable amides that likely distinguish catalytic and inhibited states.
Collapse
Affiliation(s)
- Oksana Gerlits
- Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, Grenoble Cedex 9, 38042, France
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Susan S. Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
19
|
Yee AW, Aldeghi M, Blakeley MP, Ostermann A, Mas PJ, Moulin M, de Sanctis D, Bowler MW, Mueller-Dieckmann C, Mitchell EP, Haertlein M, de Groot BL, Boeri Erba E, Forsyth VT. A molecular mechanism for transthyretin amyloidogenesis. Nat Commun 2019; 10:925. [PMID: 30804345 PMCID: PMC6390107 DOI: 10.1038/s41467-019-08609-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [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: 08/03/2018] [Accepted: 01/14/2019] [Indexed: 01/12/2023] Open
Abstract
Human transthyretin (TTR) is implicated in several fatal forms of amyloidosis. Many mutations of TTR have been identified; most of these are pathogenic, but some offer protective effects. The molecular basis underlying the vastly different fibrillation behaviours of these TTR mutants is poorly understood. Here, on the basis of neutron crystallography, native mass spectrometry and modelling studies, we propose a mechanism whereby TTR can form amyloid fibrils via a parallel equilibrium of partially unfolded species that proceeds in favour of the amyloidogenic forms of TTR. It is suggested that unfolding events within the TTR monomer originate at the C-D loop of the protein, and that destabilising mutations in this region enhance the rate of TTR fibrillation. Furthermore, it is proposed that the binding of small molecule drugs to TTR stabilises non-amyloidogenic states of TTR in a manner similar to that occurring for the protective mutants of the protein.
Collapse
Affiliation(s)
- Ai Woon Yee
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Matteo Aldeghi
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Matthew P Blakeley
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, 85748, Garching, Germany
| | - Philippe J Mas
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France
| | - Martine Moulin
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Daniele de Sanctis
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Matthew W Bowler
- EMBL, Grenoble Outstation, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | | | - Edward P Mitchell
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Michael Haertlein
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Bert L de Groot
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | | | - V Trevor Forsyth
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK.
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France.
| |
Collapse
|
20
|
Koruza K, Mahon BP, Blakeley MP, Ostermann A, Schrader TE, McKenna R, Knecht W, Fisher SZ. Using neutron crystallography to elucidate the basis of selective inhibition of carbonic anhydrase by saccharin and a derivative. J Struct Biol 2019; 205:147-154. [DOI: 10.1016/j.jsb.2018.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/30/2018] [Accepted: 12/21/2018] [Indexed: 11/25/2022]
|
21
|
Vandavasi VG, Blakeley MP, Keen DA, Hu LR, Huang Z, Kovalevsky A. Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA. Structure 2018; 26:1645-1650.e3. [PMID: 30244969 PMCID: PMC6281803 DOI: 10.1016/j.str.2018.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/02/2018] [Accepted: 08/01/2018] [Indexed: 11/18/2022]
Abstract
Nucleic acids can fold into well-defined 3D structures that help determine their function. Knowing precise nucleic acid structures can also be used for the design of nucleic acid-based therapeutics. However, locations of hydrogen atoms, which are key players of nucleic acid function, are normally not determined with X-ray crystallography. Accurate determination of hydrogen atom positions can provide indispensable information on protonation states, hydrogen bonding, and water architecture in nucleic acids. Here, we used neutron crystallography in combination with X-ray diffraction to obtain joint X-ray/neutron structures at both room and cryo temperatures of a self-complementary A-DNA oligonucleotide d[GTGG(CSe)CAC]2 containing 2'-SeCH3 modification on Cyt5 (CSe) at pH 5.6. We directly observed protonation of a backbone phosphate oxygen of Ade7 at room temperature. The proton is replaced with hydrated Mg2+ upon cooling the crystal to 100 K, indicating that metal binding is favored at low temperature, whereas proton binding is dominant at room temperature.
Collapse
Affiliation(s)
- Venu Gopal Vandavasi
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37922, USA
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, Grenoble 38000, France
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | | | - Zhen Huang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37922, USA.
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Gerlits O, Campbell JC, Blakeley MP, Kim C, Kovalevsky A. Neutron Crystallography Detects Differences in Protein Dynamics: Structure of the PKG II Cyclic Nucleotide Binding Domain in Complex with an Activator. Biochemistry 2018. [PMID: 29517905 DOI: 10.1021/acs.biochem.8b00010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As one of the main receptors of a second messenger, cGMP, cGMP-dependent protein kinase (PKG) isoforms I and II regulate distinct physiological processes. The design of isoform-specific activators is thus of great biomedical importance and requires detailed structural information about PKG isoforms bound with activators, including accurate positions of hydrogen atoms and a description of the hydrogen bonding and water architecture. Here, we determined a 2.2 Å room-temperature joint X-ray/neutron (XN) structure of the human PKG II carboxyl cyclic nucleotide binding (CNB-B) domain bound with a potent PKG II activator, 8-pCPT-cGMP. The XN structure directly visualizes intermolecular interactions and reveals changes in hydrogen bonding patterns upon comparison to the X-ray structure determined at cryo-temperatures. Comparative analysis of the backbone hydrogen/deuterium exchange patterns in PKG II:8-pCPT-cGMP and previously reported PKG Iβ:cGMP XN structures suggests that the ability of these agonists to activate PKG is related to how effectively they quench dynamics of the cyclic nucleotide binding pocket and the surrounding regions.
Collapse
Affiliation(s)
- Oksana Gerlits
- Bredesen Center , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - James C Campbell
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Matthew P Blakeley
- Large-Scale Structures Group , Institut Laue Langevin , 38042 Grenoble Cedex 9, France
| | - Choel Kim
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , Houston , Texas 77030 , United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Neutron Sciences Directorate , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| |
Collapse
|
24
|
Kovalevsky A, Aggarwal M, Velazquez H, Cuneo MJ, Blakeley MP, Weiss KL, Smith JC, Fisher SZ, McKenna R. "To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation. Structure 2018; 26:383-390.e3. [PMID: 29429876 DOI: 10.1016/j.str.2018.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 10/23/2017] [Revised: 12/15/2017] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
Abstract
Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes. We present room temperature neutron structures of hCA II in complex with three clinical drugs that provide in-depth analysis of drug binding, including protonation states of the inhibitors, hydration water structure, and direct visualization of hydrogen-bonding networks in the enzyme's active site. All sulfonamide inhibitors studied bind to the Zn metal center in the deprotonated, anionic, form. Other chemical groups of the drugs can remain neutral or be protonated when bound to hCA II. MD simulations have shown that flexible functional groups of the inhibitors may alter their conformations at room temperature and occupy different sub-sites. This study offers insights into the design of specific drugs to target cancer-related hCA isoform IX.
Collapse
Affiliation(s)
- Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Mayank Aggarwal
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hector Velazquez
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Matthew J Cuneo
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Kevin L Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - S Zoë Fisher
- Scientific Activities Division, Science Directorate, European Spallation Source ERIC, 22100 Lund, Sweden; Department of Biology, Lund University, 35 Sölvegatan, 22362 Lund, Sweden
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
| |
Collapse
|
25
|
Yee AW, Blakeley MP, Moulin M, Haertlein M, Mitchell E, Forsyth VT. Back-exchange of deuterium in neutron crystallography: characterization by IR spectroscopy. J Appl Crystallogr 2017; 50:660-664. [PMID: 28381984 PMCID: PMC5377354 DOI: 10.1107/s1600576717003624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 12/06/2016] [Accepted: 03/07/2017] [Indexed: 01/02/2023] Open
Abstract
The application of IR spectroscopy to the characterization and quality control of samples used in neutron crystallography is described. While neutron crystallography is a growing field, the limited availability of neutron beamtime means that there may be a delay between crystallogenesis and data collection. Since essentially all neutron crystallographic work is carried out using D2O-based solvent buffers, a particular concern for these experiments is the possibility of H2O back-exchange across reservoir or capillary sealants. This may limit the quality of neutron scattering length density maps and of the associated analysis. Given the expense of central facility beamtime and the effort that goes into the production of suitably sized (usually perdeuterated) crystals, a systematic method of exploiting IR spectroscopy for the analysis of back-exchange phenomena in the reservoirs used for crystal growth is valuable. Examples are given in which the characterization of D2O/H2O back-exchange in transthyretin crystals is described.
Collapse
Affiliation(s)
- Ai Woon Yee
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
| | - Martine Moulin
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
| | - Michael Haertlein
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
| | - Edward Mitchell
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
- European Synchrotron Research Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
| |
Collapse
|
26
|
Gerlits O, Keen DA, Blakeley MP, Louis JM, Weber IT, Kovalevsky A. Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K. J Med Chem 2017; 60:2018-2025. [PMID: 28195728 DOI: 10.1021/acs.jmedchem.6b01767] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly alter the drug-enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.
Collapse
Affiliation(s)
- Oksana Gerlits
- UT/ORNL Joint Institute of Biological Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory , Harwell Campus, Didcot, OX11 0QX, U.K
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue Langevin , 71 avenue des Martyrs, 38000 Grenoble, France
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , DHHS, Bethesda, Maryland 20892-0520, United States
| | - Irene T Weber
- Departments of Chemistry and Biology, Georgia State University , Atlanta, Georgia 30302, United States
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Podjarny A, Howard EI, Guillot B, Blakeley MP, Haertlein M, Moulin M, Mitschler A, Cousido-Siah A, Fadel F, Valsecchi W, Tomizaki T, Petrova T, Claudot J. High resolution neutron and X-ray diffraction RT studies of an H-FABP – Oleic acid complex: study of the internal water cluster and the ligand binding by a transferred multipolar electron density distribution. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316099332] [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
|
29
|
Gerlits O, Wymore T, Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, Kovalevsky A. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site. Angew Chem Int Ed Engl 2016; 55:4924-7. [PMID: 26958828 DOI: 10.1002/anie.201509989] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [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: 10/26/2015] [Revised: 01/27/2016] [Indexed: 11/11/2022]
Abstract
Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.
Collapse
Affiliation(s)
- Oksana Gerlits
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Troy Wymore
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Amit Das
- Solid State Physics Division, BARC, Trombay, Mumbai, 400085, India
| | - Chen-Hsiang Shen
- Departments of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kevin L Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue Langevin, 71 avenue des Martyrs - CS 20156, 38042, Grenoble Cedex 9, France
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, 20892-0520, USA
| | - Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Irene T Weber
- Departments of Chemistry and Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| |
Collapse
|
30
|
Gerlits O, Wymore T, Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, Kovalevsky A. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Oksana Gerlits
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Troy Wymore
- UT/ORNL Center for Molecular Biophysics; Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Amit Das
- Solid State Physics Division; BARC; Trombay Mumbai 400085 India
| | - Chen-Hsiang Shen
- Departments of Chemistry and Biology; Georgia State University; Atlanta GA 30302 USA
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics; Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics; Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Kevin L. Weiss
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - David A. Keen
- ISIS Facility; Rutherford Appleton Laboratory; Harwell Oxford Didcot OX11 0QX UK
| | - Matthew P. Blakeley
- Large-Scale Structures Group; Institut Laue Langevin; 71 avenue des Martyrs - CS 20156 38042 Grenoble Cedex 9 France
| | - John M. Louis
- Laboratory of Chemical Physics; National Institute of Diabetes and Digestive and Kidney Diseases; National Institutes of Health, DHHS; Bethesda MD 20892-0520 USA
| | - Paul Langan
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Irene T. Weber
- Departments of Chemistry and Biology; Georgia State University; Atlanta GA 30302 USA
| | - Andrey Kovalevsky
- Biology and Soft Matter Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| |
Collapse
|
31
|
Laulumaa S, Blakeley MP, Raasakka A, Moulin M, Härtlein M, Kursula P. Production, crystallization and neutron diffraction of fully deuterated human myelin peripheral membrane protein P2. Acta Crystallogr F Struct Biol Commun 2015; 71:1391-5. [PMID: 26527266 PMCID: PMC4631588 DOI: 10.1107/s2053230x15017902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 09/01/2015] [Accepted: 09/24/2015] [Indexed: 11/11/2022] Open
Abstract
The molecular details of the formation of the myelin sheath, a multilayered membrane in the nervous system, are to a large extent unknown. P2 is a peripheral membrane protein from peripheral nervous system myelin, which is believed to play a role in this process. X-ray crystallographic studies and complementary experiments have provided information on the structure-function relationships in P2. In this study, a fully deuterated sample of human P2 was produced. Crystals that were large enough for neutron diffraction were grown by a ten-month procedure of feeding, and neutron diffraction data were collected to a resolution of 2.4 Å from a crystal of 0.09 mm(3) in volume. The neutron crystal structure will allow the positions of H atoms in P2 and its fatty-acid ligand to be visualized, as well as shedding light on the fine details of the hydrogen-bonding networks within the P2 ligand-binding cavity.
Collapse
Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- European Spallation Source, Lund, Sweden
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Arne Raasakka
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Martine Moulin
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Härtlein
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| |
Collapse
|
32
|
Blakeley MP, Mossou E. Neutron macromolecular crystallography at the Institut Laue-Langevin. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315097879] [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
|
33
|
Blakeley MP, Hasnain SS, Antonyuk SV. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential. IUCrJ 2015; 2:464-74. [PMID: 26175905 PMCID: PMC4491318 DOI: 10.1107/s2052252515011239] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/09/2015] [Indexed: 05/20/2023]
Abstract
The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.
Collapse
Affiliation(s)
- Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Samar S. Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, UK
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, UK
| |
Collapse
|
34
|
Haupt M, Blakeley MP, Fisher SJ, Mason SA, Cooper JB, Mitchell EP, Forsyth VT. Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein. IUCrJ 2014; 1:429-38. [PMID: 25485123 PMCID: PMC4224461 DOI: 10.1107/s2052252514021113] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/22/2014] [Indexed: 05/12/2023]
Abstract
Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer-monomer interface is more extensive than that at the dimer-dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.
Collapse
Affiliation(s)
- Melina Haupt
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Matthew P. Blakeley
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Stuart J. Fisher
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, Salzburg, 5020, Austria
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Sax A. Mason
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Jon B. Cooper
- Division of Medicine (Royal Free Campus), University College London, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Edward P. Mitchell
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Business Development Office, European Synchrotron Radiation Facility, Grenoble, 38042, France
| | - V. Trevor Forsyth
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| |
Collapse
|
35
|
Huang GY, Gerlits OO, Blakeley MP, Sankaran B, Kovalevsky AY, Kim C. Neutron diffraction reveals hydrogen bonds critical for cGMP-selective activation: insights for cGMP-dependent protein kinase agonist design. Biochemistry 2014; 53:6725-7. [PMID: 25271401 PMCID: PMC4222537 DOI: 10.1021/bi501012v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
High selectivity of cyclic-nucleotide
binding (CNB) domains for
cAMP and cGMP are required for segregating signaling pathways; however,
the mechanism of selectivity remains unclear. To investigate the mechanism
of high selectivity in cGMP-dependent protein kinase (PKG), we determined
a room-temperature joint X-ray/neutron (XN) structure of PKG Iβ
CNB-B, a domain 200-fold selective for cGMP over cAMP, bound to cGMP
(2.2 Å), and a low-temperature X-ray structure of CNB-B with
cAMP (1.3 Å). The XN structure directly describes the hydrogen
bonding interactions that modulate high selectivity for cGMP, while
the structure with cAMP reveals that all these contacts are disrupted,
explaining its low affinity for cAMP.
Collapse
Affiliation(s)
- Gilbert Y Huang
- Verna and Mars McClean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , One Baylor Plaza, Houston, Texas 77004, United States
| | | | | | | | | | | |
Collapse
|
36
|
Casadei CM, Gumiero A, Metcalfe CL, Murphy EJ, Basran J, Concilio MG, Teixeira SCM, Schrader TE, Fielding AJ, Ostermann A, Blakeley MP, Raven EL, Moody PCE. Heme enzymes. Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase. Science 2014; 345:193-7. [PMID: 25013070 DOI: 10.1126/science.1254398] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Heme enzymes activate oxygen through formation of transient iron-oxo (ferryl) intermediates of the heme iron. A long-standing question has been the nature of the iron-oxygen bond and, in particular, the protonation state. We present neutron structures of the ferric derivative of cytochrome c peroxidase and its ferryl intermediate; these allow direct visualization of protonation states. We demonstrate that the ferryl heme is an Fe(IV)=O species and is not protonated. Comparison of the structures shows that the distal histidine becomes protonated on formation of the ferryl intermediate, which has implications for the understanding of O-O bond cleavage in heme enzymes. The structures highlight the advantages of neutron cryo-crystallography in probing reaction mechanisms and visualizing protonation states in enzyme intermediates.
Collapse
Affiliation(s)
- Cecilia M Casadei
- Department of Biochemistry and Henry Wellcome Laboratories for Structural Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK. Institut Laue-Langevin, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Andrea Gumiero
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Clive L Metcalfe
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Emma J Murphy
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Jaswir Basran
- Department of Biochemistry and Henry Wellcome Laboratories for Structural Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | | | - Susana C M Teixeira
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000, Grenoble, France. EPSAM, Keele University, Keele, Staffordshire ST5 5BG, UK
| | - Tobias E Schrader
- Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Alistair J Fielding
- The Photon Science Institute, The University of Manchester, Manchester M13 9PL, UK
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstraße 1, D-85748 Garching, Germany
| | | | - Emma L Raven
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, UK.
| | - Peter C E Moody
- Department of Biochemistry and Henry Wellcome Laboratories for Structural Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK.
| |
Collapse
|
37
|
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.
Collapse
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:
| |
Collapse
|
38
|
Weber IT, Waltman MJ, Mustyakimov M, Blakeley MP, Keen DA, Ghosh AK, Langan P, Kovalevsky AY. Joint X-ray/neutron crystallographic study of HIV-1 protease with clinical inhibitor amprenavir: insights for drug design. J Med Chem 2013; 56:5631-5. [PMID: 23772563 DOI: 10.1021/jm400684f] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
HIV-1 protease is an important target for the development of antiviral inhibitors to treat AIDS. A room-temperature joint X-ray/neutron structure of the protease in complex with clinical drug amprenavir has been determined at 2.0 Å resolution. The structure provides direct determination of hydrogen atom positions in the enzyme active site. Analysis of the enzyme-drug interactions suggests that some hydrogen bonds may be weaker than deduced from the non-hydrogen interatomic distances. This information may be valuable for the design of improved protease inhibitors.
Collapse
Affiliation(s)
- Irene T Weber
- Departments of Chemistry and Biology, Georgia State University , Atlanta, Georgia, United States
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Cuypers MG, Mason SA, Blakeley MP, Mitchell EP, Haertlein M, Forsyth VT. Near-atomic resolution neutron crystallography on perdeuterated Pyrococcus furiosus rubredoxin: implication of hydronium ions and protonation state equilibria in redox changes. Angew Chem Int Ed Engl 2012; 52:1022-5. [PMID: 23225503 DOI: 10.1002/anie.201207071] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Indexed: 11/09/2022]
Affiliation(s)
- M G Cuypers
- EPSAM/ISTM, Keele University, Staffordshire, ST5 5BG, UK
| | | | | | | | | | | |
Collapse
|
40
|
Hughes RC, Coates L, Blakeley MP, Tomanicek SJ, Langan P, Kovalevsky AY, García-Ruiz JM, Ng JD. Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012. [PMID: 23192028 DOI: 10.1107/s1744309112032447] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Inorganic pyrophosphatase (IPPase) from the archaeon Thermococcus thioreducens was cloned, overexpressed in Escherichia coli, purified and crystallized in restricted geometry, resulting in large crystal volumes exceeding 5 mm3. IPPase is thermally stable and is able to resist denaturation at temperatures above 348 K. Owing to the high temperature tolerance of the enzyme, the protein was amenable to room-temperature manipulation at the level of protein preparation, crystallization and X-ray and neutron diffraction analyses. A complete synchrotron X-ray diffraction data set to 1.85 Å resolution was collected at room temperature from a single crystal of IPPase (monoclinic space group C2, unit-cell parameters a=106.11, b=95.46, c=113.68 Å, α=γ=90.0, β=98.12°). As large-volume crystals of IPPase can be obtained, preliminary neutron diffraction tests were undertaken. Consequently, Laue diffraction images were obtained, with reflections observed to 2.1 Å resolution with I/σ(I) greater than 2.5. The preliminary crystallographic results reported here set in place future structure-function and mechanism studies of IPPase.
Collapse
Affiliation(s)
- Ronny C Hughes
- Department of Biological Sciences and Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Kovalevsky A, Hanson BL, Mason SA, Forsyth VT, Fisher Z, Mustyakimov M, Blakeley MP, Keen DA, Langan P. Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography. Acta Crystallogr D Biol Crystallogr 2012; 68:1201-6. [PMID: 22948921 PMCID: PMC3489103 DOI: 10.1107/s0907444912024808] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/30/2012] [Indexed: 11/10/2022]
Abstract
D-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 Å resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni(2+) cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg(2+) ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni(2+) ions occupying the catalytic metal site (M2) were found at two locations, while Mg(2+) in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH.
Collapse
Affiliation(s)
- Andrey Kovalevsky
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Abstract
Techniques and equipment have been developed that enable large protein crystals (1–6 mm3) flash-cooled in liquid nitrogen at 77 K to be transferred and mounted on a liquid helium Displex cryorefrigerator and cooled to temperatures down to 15 K for accurate neutron diffraction analysis. In preliminary experiments, it was possible to collect high-quality high-resolution neutron diffraction data to 1.55 Å resolution from several large crystals of triclinic hen egg white lysozyme cooled to 15 K. This enabled the subsequent cryogenic analysis of two further proteins, rubredoxin and concanavalin A, at 1.7 and 2.5 Å, respectively, demonstrating the generality of the approach. The ability to flash-cool such large crystals for cryogenic neutron analysis should significantly broaden the range of scientific questions examined by neutron protein crystallography, allowing the analysis of structures and transitions as a function of temperature and enabling freeze-trapped capture of kinetic intermediates in protein systems.
Collapse
|
43
|
Fisher SJ, Blakeley MP, Cianci M, McSweeney S, Helliwell JR. Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness. Acta Crystallogr D Biol Crystallogr 2012; 68:800-9. [PMID: 22751665 DOI: 10.1107/s0907444912012589] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/22/2012] [Indexed: 11/11/2022]
Abstract
A bond-distance analysis has been undertaken to determine the protonation states of ionizable amino acids in trypsin, subtilisin and lysozyme. The diffraction resolutions were 1.2 Å for trypsin (97% complete, 12% H-atom visibility at 2.5σ), 1.26 Å for subtilisin (100% complete, 11% H-atom visibility at 2.5σ) and 0.65 Å for lysozyme (PDB entry 2vb1; 98% complete, 30% H-atom visibility at 3σ). These studies provide a wide diffraction resolution range for assessment. The bond-length e.s.d.s obtained are as small as 0.008 Å and thus provide an exceptional opportunity for bond-length analyses. The results indicate that useful information can be obtained from diffraction data at around 1.2-1.3 Å resolution and that minor increases in resolution can have significant effects on reducing the associated bond-length standard deviations. The protonation states in histidine residues were also considered; however, owing to the smaller differences between the protonated and deprotonated forms it is much more difficult to infer the protonation states of these residues. Not even the 0.65 Å resolution lysozyme structure provided the necessary accuracy to determine the protonation states of histidine.
Collapse
Affiliation(s)
- S J Fisher
- School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, England.
| | | | | | | | | |
Collapse
|
44
|
Munshi P, Chung SL, Blakeley MP, Weiss KL, Myles DAA, Meilleur F. Rapid visualization of hydrogen positions in protein neutron crystallographic structures. Acta Crystallogr D Biol Crystallogr 2011; 68:35-41. [PMID: 22194331 DOI: 10.1107/s0907444911048402] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 11/15/2011] [Indexed: 11/10/2022]
Abstract
Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.
Collapse
Affiliation(s)
- Parthapratim Munshi
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | | | | | | | | |
Collapse
|
45
|
Haupt M, Blakeley MP, Teixeira SCM, Mason SA, Mitchell EP, Cooper JB, Forsyth VT. Preliminary neutron crystallographic study of human transthyretin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1428-31. [PMID: 22102249 PMCID: PMC3212468 DOI: 10.1107/s1744309111036244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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: 06/28/2011] [Accepted: 09/05/2011] [Indexed: 11/10/2022]
Abstract
Preliminary studies of perdeuterated crystals of human transthyretin (TTR) have been carried out using the LADI-III and D19 diffractometers at the Institut Laue-Langevin in Grenoble. The results demonstrate the feasibility of a full crystallographic analysis to a resolution of 2.0 Å using Laue diffraction and also illustrate the potential of using monochromatic instruments such as D19 for higher resolution studies where larger crystals having smaller unit cells are available. This study will yield important information on hydrogen bonding, amino-acid protonation states and hydration in the protein. Such information will be of general interest for an understanding of the factors that stabilize/destabilize TTR and for the design of ligands that may be used to counter TTR amyloid fibrillogenesis.
Collapse
Affiliation(s)
- Melina Haupt
- EPSAM, Keele University, Keele, Staffordshire ST5 5BG, England
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Partnership for Structural Biology (PSB), Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | | | - Susana C. M. Teixeira
- EPSAM, Keele University, Keele, Staffordshire ST5 5BG, England
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Sax A. Mason
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Edward P. Mitchell
- EPSAM, Keele University, Keele, Staffordshire ST5 5BG, England
- European Synchrotron Radiation Facility (ESRF), 6 Rue Jules Horowitz, 38043 Grenoble, France
| | - Jonathan B. Cooper
- Division of Medicine, University College London, Rowland Hill Street, London NW3 2PF, England
| | - V. Trevor Forsyth
- EPSAM, Keele University, Keele, Staffordshire ST5 5BG, England
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Partnership for Structural Biology (PSB), Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| |
Collapse
|
46
|
Howard EI, Blakeley MP, Haertlein M, Petit-Haertlein I, Mitschler A, Fisher SJ, Cousido-Siah A, Salvay AG, Popov A, Muller-Dieckmann C, Petrova T, Podjarny A. Neutron structure of type-III antifreeze protein allows the reconstruction of AFP-ice interface. J Mol Recognit 2011; 24:724-32. [PMID: 21472814 DOI: 10.1002/jmr.1130] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Antifreeze proteins (AFPs) inhibit ice growth at sub-zero temperatures. The prototypical type-III AFPs have been extensively studied, notably by X-ray crystallography, solid-state and solution NMR, and mutagenesis, leading to the identification of a compound ice-binding surface (IBS) composed of two adjacent ice-binding sections, each which binds to particular lattice planes of ice crystals, poisoning their growth. This surface, including many hydrophobic and some hydrophilic residues, has been extensively used to model the interaction of AFP with ice. Experimentally observed water molecules facing the IBS have been used in an attempt to validate these models. However, these trials have been hindered by the limited capability of X-ray crystallography to reliably identify all water molecules of the hydration layer. Due to the strong diffraction signal from both the oxygen and deuterium atoms, neutron diffraction provides a more effective way to determine the water molecule positions (as D(2) O). Here we report the successful structure determination at 293 K of fully perdeuterated type-III AFP by joint X-ray and neutron diffraction providing a very detailed description of the protein and its solvent structure. X-ray data were collected to a resolution of 1.05 Å, and neutron Laue data to a resolution of 1.85 Å with a "radically small" crystal volume of 0.13 mm(3). The identification of a tetrahedral water cluster in nuclear scattering density maps has allowed the reconstruction of the IBS-bound ice crystal primary prismatic face. Analysis of the interactions between the IBS and the bound ice crystal primary prismatic face indicates the role of the hydrophobic residues, which are found to bind inside the holes of the ice surface, thus explaining the specificity of AFPs for ice versus water.
Collapse
Affiliation(s)
- Eduardo I Howard
- IFLYSIB, UNLP-CONICET, Calle 59, 789, B1900BTE, La Plata, Argentina.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Kovalevsky AY, Hanson BL, Mason SA, Yoshida T, Fisher SZ, Mustyakimov M, Forsyth VT, Blakeley MP, Keen DA, Langan P. Identification of the elusive hydronium ion exchanging roles with a proton in an enzyme at lower pH values. Angew Chem Int Ed Engl 2011; 50:7520-3. [PMID: 21604345 DOI: 10.1002/anie.201101753] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Andrey Y Kovalevsky
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Tomanicek SJ, Wang KK, Weiss KL, Blakeley MP, Cooper J, Chen Y, Coates L. The active site protonation states of perdeuterated Toho-1 β-lactamase determined by neutron diffraction support a role for Glu166 as the general base in acylation. FEBS Lett 2010; 585:364-8. [PMID: 21168411 DOI: 10.1016/j.febslet.2010.12.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 12/11/2010] [Accepted: 12/13/2010] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen J Tomanicek
- Oak Ridge National Laboratory, Neutron Scattering Science Division, Oak Ridge, TN 37831, USA
| | | | | | | | | | | | | |
Collapse
|
49
|
Blakeley MP, Teixeira SCM, Petit-Haertlein I, Hazemann I, Mitschler A, Haertlein M, Howard E, Podjarny AD. Neutron macromolecular crystallography with LADI-III. Acta Crystallogr D Biol Crystallogr 2010; 66:1198-205. [DOI: 10.1107/s0907444910019797] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 05/26/2010] [Indexed: 11/10/2022]
|
50
|
Teixeira SCM, Blakeley MP, Leal RMF, Gillespie SM, Mitchell EP, Forsyth VT. Sweet neutron crystallography. Acta Crystallogr D Biol Crystallogr 2010; 66:1139-43. [PMID: 21041928 DOI: 10.1107/s0907444910019785] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 05/26/2010] [Indexed: 11/11/2022]
Abstract
Extremely sweet proteins isolated from tropical fruit extracts are promising healthy alternatives to sugar and synthetic sweeteners. Sweetness and taste in general are, however, still poorly understood. The engineering of stable sweet proteins with tailored properties is made difficult by the lack of supporting high-resolution structural data. Experimental information on charge distribution, protonation states and solvent structure are vital for an understanding of the mechanism through which sweet proteins interact with taste receptors. Neutron studies of the crystal structures of sweet proteins allow a detailed study of these biophysical properties, as illustrated by a neutron study on the native protein thaumatin in which deuterium labelling was used to improve data quality.
Collapse
Affiliation(s)
- S C M Teixeira
- EPSAM, Keele University, Keele, Staffordshire ST5 5BG, England.
| | | | | | | | | | | |
Collapse
|