1
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Jenney FE, Wang H, George SJ, Xiong J, Guo Y, Gee LB, Marizcurrena JJ, Castro-Sowinski S, Staskiewicz A, Yoda Y, Hu MY, Tamasaku K, Nagasawa N, Li L, Matsuura H, Doukov T, Cramer SP. Temperature-dependent iron motion in extremophile rubredoxins - no need for 'corresponding states'. Sci Rep 2024; 14:12197. [PMID: 38806591 PMCID: PMC11133467 DOI: 10.1038/s41598-024-62261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Extremophile organisms are known that can metabolize at temperatures down to - 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins - rubredoxins - from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of 'corresponding states' posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although 'corresponding states' would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.
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Affiliation(s)
- Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | | | | | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Leland B Gee
- LCLS, SLAC National Laboratory, Stanford, CA, 94025, USA
| | | | | | - Anna Staskiewicz
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | | | - Nobumoto Nagasawa
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Lei Li
- Synchrotron Radiation Research Center, Hyogo, 679-5165, Japan
| | | | - Tzanko Doukov
- SSRL, SLAC National Laboratory, Stanford, CA, 94025, USA
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2
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Bazayeva M, Andreini C, Rosato A. A database overview of metal-coordination distances in metalloproteins. Acta Crystallogr D Struct Biol 2024; 80:362-376. [PMID: 38682667 PMCID: PMC11066882 DOI: 10.1107/s2059798324003152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.
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Affiliation(s)
- Milana Bazayeva
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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3
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Liebschner D, Afonine PV, Poon BK, Moriarty NW, Adams PD. Improved joint X-ray and neutron refinement procedure in Phenix. Acta Crystallogr D Struct Biol 2023; 79:1079-1093. [PMID: 37942718 PMCID: PMC10833352 DOI: 10.1107/s2059798323008914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its particular strengths derive from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and thus protonation states, can be derived from crystallographic maps. However, because of technical limitations and experimental obstacles, the quality of neutron diffraction data is typically much poorer (completeness, resolution and signal to noise) than that of X-ray diffraction data for the same sample. Further, refinement is more complex as it usually requires additional parameters to describe the H (and D) atoms. The increase in the number of parameters may be mitigated by using the `riding hydrogen' refinement strategy, in which the positions of H atoms without a rotational degree of freedom are inferred from their neighboring heavy atoms. However, this does not address the issues related to poor data quality. Therefore, neutron structure determination often relies on the presence of an X-ray data set for joint X-ray and neutron (XN) refinement. In this approach, the X-ray data serve to compensate for the deficiencies of the neutron diffraction data by refining one model simultaneously against the X-ray and neutron data sets. To be applicable, it is assumed that both data sets are highly isomorphous, and preferably collected from the same crystals and at the same temperature. However, the approach has a number of limitations that are discussed in this work by comparing four separately re-refined neutron models. To address the limitations, a new method for joint XN refinement is introduced that optimizes two different models against the different data sets. This approach is tested using neutron models and data deposited in the Protein Data Bank. The efficacy of refining models with H atoms as riding or as individual atoms is also investigated.
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Affiliation(s)
- Dorothee Liebschner
- Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Billy K. Poon
- Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nigel W. Moriarty
- Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D. Adams
- Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
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4
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Ramos J, Laux V, Haertlein M, Forsyth VT, Mossou E, Larsen S, Langkilde AE. The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme. Acta Crystallogr D Struct Biol 2021; 77:1579-1590. [PMID: 34866613 PMCID: PMC8647175 DOI: 10.1107/s2059798321010950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/20/2021] [Indexed: 11/10/2022] Open
Abstract
The biological function of a protein is intimately related to its structure and dynamics, which in turn are determined by the way in which it has been folded. In vitro refolding is commonly used for the recovery of recombinant proteins that are expressed in the form of inclusion bodies and is of central interest in terms of the folding pathways that occur in vivo. Here, biophysical data are reported for in vitro-refolded hydrogenated hen egg-white lysozyme, in combination with atomic resolution X-ray diffraction analyses, which allowed detailed comparisons with native hydrogenated and refolded perdeuterated lysozyme. Distinct folding modes are observed for the hydrogenated and perdeuterated refolded variants, which are determined by conformational changes to the backbone structure of the Lys97-Gly104 flexible loop. Surprisingly, the structure of the refolded perdeuterated protein is closer to that of native lysozyme than that of the refolded hydrogenated protein. These structural differences suggest that the observed decreases in thermal stability and enzymatic activity in the refolded perdeuterated and hydrogenated proteins are consequences of the macromolecular deuteration effect and of distinct folding dynamics, respectively. These results are discussed in the context of both in vitro and in vivo folding, as well as of lysozyme amyloidogenesis.
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Affiliation(s)
- Joao Ramos
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Valerie Laux
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - V. Trevor Forsyth
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle ST5 5BG, United Kingdom
- Faculty of Medicine, Lund University, 221 00 Lund, Sweden
- LINXS Institute for Advanced Neutron and X-ray Science, Scheelvagen 19, 223 70 Lund, Sweden
| | - Estelle Mossou
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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5
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Harp JM, Coates L, Sullivan B, Egli M. Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography. Nucleic Acids Res 2021; 49:4782-4792. [PMID: 33872377 PMCID: PMC8096259 DOI: 10.1093/nar/gkab264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/28/2021] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 Å or higher, the orientations of first-shell water molecules remain unclear. We used cryo neutron crystallography to gain insight into the H-bonding patterns of water molecules around the left-handed Z-DNA duplex [d(CGCGCG)]2. The neutron density visualized at 1.5 Å resolution for the first time allows us to pinpoint the orientations of most of the water molecules directly contacting the DNA and of many second-shell waters. In particular, H-bond acceptor and donor patterns for water participating in prominent hydration motifs inside the minor groove, on the convex surface or bridging nucleobase and phosphate oxygen atoms are finally revealed. Several water molecules display entirely unexpected orientations. For example, a water molecule located at H-bonding distance from O6 keto oxygen atoms of two adjacent guanines directs both its deuterium atoms away from the keto groups. Exocyclic amino groups of guanine (N2) and cytosine (N4) unexpectedly stabilize waters H-bonded to O2 keto oxygens from adjacent cytosines and O6 keto oxygens from adjacent guanines, respectively. Our structure offers the most detailed view to date of DNA solvation in the solid-state undistorted by metal ions or polyamines.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Martin Egli
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
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6
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Wan Q, Bennett BC, Wymore T, Li Z, Wilson MA, Brooks CL, Langan P, Kovalevsky A, Dealwis CG. Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis. ACS Catal 2021; 11:5873-5884. [PMID: 34055457 PMCID: PMC8154319 DOI: 10.1021/acscatal.1c00417] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/19/2021] [Indexed: 02/04/2023]
Abstract
![]()
Acid–base
catalysis, which involves one or more proton transfer
reactions, is a chemical mechanism commonly employed by many enzymes.
The molecular basis for catalysis is often derived from structures
determined at the optimal pH for enzyme activity. However, direct
observation of protons from experimental structures is quite difficult;
thus, a complete mechanistic description for most enzymes remains
lacking. Dihydrofolate reductase (DHFR) exemplifies general acid–base
catalysis, requiring hydride transfer and protonation of its substrate,
DHF, to form the product, tetrahydrofolate (THF). Previous X-ray and
neutron crystal structures coupled with theoretical calculations have
proposed that solvent mediates the protonation step. However, visualization
of a proton transfer has been elusive. Based on a 2.1 Å resolution
neutron structure of a pseudo-Michaelis complex of E. coli DHFR determined at acidic pH, we report the
direct observation of the catalytic proton and its parent solvent
molecule. Comparison of X-ray and neutron structures elucidated at
acidic and neutral pH reveals dampened dynamics at acidic pH, even
for the regulatory Met20 loop. Guided by the structures and calculations,
we propose a mechanism where dynamics are crucial for solvent entry
and protonation of substrate. This mechanism invokes the release of
a sole proton from a hydronium (H3O+) ion, its
pathway through a narrow channel that sterically hinders the passage
of water, and the ultimate protonation of DHF at the N5 atom.
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Affiliation(s)
| | - Brad C. Bennett
- Biological and Environmental Science Department, Samford University, Birmingham, Alabama 35229, United States
| | - Troy Wymore
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Charles L. Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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7
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Ramos J, Laux V, Haertlein M, Boeri Erba E, McAuley KE, Forsyth VT, Mossou E, Larsen S, Langkilde AE. Structural insights into protein folding, stability and activity using in vivo perdeuteration of hen egg-white lysozyme. IUCRJ 2021; 8:372-386. [PMID: 33953924 PMCID: PMC8086161 DOI: 10.1107/s2052252521001299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
This structural and biophysical study exploited a method of perdeuterating hen egg-white lysozyme based on the expression of insoluble protein in Escherichia coli followed by in-column chemical refolding. This allowed detailed comparisons with perdeuterated lysozyme produced in the yeast Pichia pastoris, as well as with unlabelled lysozyme. Both perdeuterated variants exhibit reduced thermal stability and enzymatic activity in comparison with hydrogenated lysozyme. The thermal stability of refolded perdeuterated lysozyme is 4.9°C lower than that of the perdeuterated variant expressed and secreted in yeast and 6.8°C lower than that of the hydrogenated Gallus gallus protein. However, both perdeuterated variants exhibit a comparable activity. Atomic resolution X-ray crystallographic analyses show that the differences in thermal stability and enzymatic function are correlated with refolding and deuteration effects. The hydrogen/deuterium isotope effect causes a decrease in the stability and activity of the perdeuterated analogues; this is believed to occur through a combination of changes to hydrophobicity and protein dynamics. The lower level of thermal stability of the refolded perdeuterated lysozyme is caused by the unrestrained Asn103 peptide-plane flip during the unfolded state, leading to a significant increase in disorder of the Lys97-Gly104 region following subsequent refolding. An ancillary outcome of this study has been the development of an efficient and financially viable protocol that allows stable and active perdeuterated lysozyme to be more easily available for scientific applications.
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Affiliation(s)
- Joao Ramos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Valerie Laux
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Elisabetta Boeri Erba
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale, Université de Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Katherine E. McAuley
- Diamond Light Source, Didcot OX11 0DE, United Kingdom
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Estelle Mossou
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, United Kingdom
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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8
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Lin S, He C. Streamlined purification and characterization of Pyrococcus furiosus rubredoxins with different N-terminal modifications by reversed-phase HPLC. Anal Biochem 2021; 619:114128. [PMID: 33577792 DOI: 10.1016/j.ab.2021.114128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/21/2021] [Accepted: 01/31/2021] [Indexed: 01/12/2023]
Abstract
Rubredoxins (Rds), like those from Pyrococcus furious (Pf), have largely been found to be expressed in Escherichia coli (E. coli) as a mixture of different N-terminal forms, which may affect the properties of the protein. The typical procedures for the purification of Rds are cumbersome and usually with low yield. We present herein a streamlined purification strategy based on the reversed-phase high performance liquid chromatography (RP-HPLC), which offers high yield and high resolution after simply one-step purification following pre-treatment. We also show that RP-HPLC can be a valuable tool to gain information related to the thermal decomposition pathway of Pf-Rds.
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Affiliation(s)
- Shaomin Lin
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China.
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9
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Eriksson A, Caldararu O, Ryde U, Oksanen E. Automated orientation of water molecules in neutron crystallographic structures of proteins. Acta Crystallogr D Struct Biol 2020; 76:1025-1032. [PMID: 33021504 DOI: 10.1107/s2059798320011729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/26/2020] [Indexed: 11/10/2022] Open
Abstract
The structure and function of proteins are strongly affected by the surrounding solvent water, for example through hydrogen bonds and the hydrophobic effect. These interactions depend not only on the position, but also on the orientation, of the water molecules around the protein. Therefore, it is often vital to know the detailed orientations of the surrounding ordered water molecules. Such information can be obtained by neutron crystallography. However, it is tedious and time-consuming to determine the correct orientation of every water molecule in a structure (there are typically several hundred of them), which is presently performed by manual evaluation. Here, a method has been developed that reliably automates the orientation of a water molecules in a simple and relatively fast way. Firstly, a quantitative quality measure, the real-space correlation coefficient, was selected, together with a threshold that allows the identification of water molecules that are oriented. Secondly, the refinement procedure was optimized by varying the refinement method and parameters, thus finding settings that yielded the best results in terms of time and performance. It turned out to be favourable to employ only the neutron data and a fixed protein structure when reorienting the water molecules. Thirdly, a method has been developed that identifies and reorients inadequately oriented water molecules systematically and automatically. The method has been tested on three proteins, galectin-3C, rubredoxin and inorganic pyrophosphatase, and it is shown that it yields improved orientations of the water molecules for all three proteins in a shorter time than manual model building. It also led to an increased number of hydrogen bonds involving water molecules for all proteins.
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Affiliation(s)
- Axl Eriksson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source (ESS) ERIC, PO Box 176, SE-221 00 Lund, Sweden
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10
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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] [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.
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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
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11
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Palese LL. Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters. Biochim Biophys Acta Gen Subj 2020; 1864:129480. [DOI: 10.1016/j.bbagen.2019.129480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/27/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022]
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12
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Abstract
This chapter aims to give an overview of the process of interactive model building in macromolecular neutron crystallography for the researcher transitioning from X-ray crystallography alone. The two most popular programs for refinement and model building, phenix.refine and Coot, respectively, are used as examples, and familiarity with the programs is assumed. Some work-arounds currently required for proper communication between the programs are described. We also discuss the appearance of nuclear density maps and how this differs from that of electron density maps. Advice is given to facilitate deposition of jointly refined neutron/X-ray structures in the Protein Data Bank.
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13
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Shibazaki C, Shimizu R, Kagotani Y, Ostermann A, Schrader TE, Adachi M. Direct Observation of the Protonation States in the Mutant Green Fluorescent Protein. J Phys Chem Lett 2020; 11:492-496. [PMID: 31880458 DOI: 10.1021/acs.jpclett.9b03252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Neutron crystallography has been used to elucidate the protonation states for the enhanced green fluorescent protein, which has revolutionized imaging technologies. The structure has a deprotonated hydroxyl group in the fluorescent chromophore. Also, the protonation states of His148 and Thr203, as well as the orientation of a critical water molecule in direct contact with the chromophore, could be determined. The results demonstrate that the deprotonated hydroxyl group in the chromophore and the nitrogen atom ND1 in His148 are charged negatively and positively, respectively, forming an ion pair. The position of the two deuterium atoms in the critical water molecule appears to be displaced slightly toward the acceptor oxygen atoms according to their omit maps. This displacement implies the formation of an intriguing electrostatic potential realized inside of the protein. Our findings provide new insights into future protein design strategies along with developments in quantum chemical calculations.
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Affiliation(s)
- Chie Shibazaki
- Institute for Quantum Life Science , National Institutes for Quantum and Radiological Science and Technology (QST) , 2-4 Shirakata , Tokai , Ibaraki 319-1106 , Japan
| | - Rumi Shimizu
- Institute for Quantum Life Science , National Institutes for Quantum and Radiological Science and Technology (QST) , 2-4 Shirakata , Tokai , Ibaraki 319-1106 , Japan
| | - Yuji Kagotani
- Institute for Quantum Life Science , National Institutes for Quantum and Radiological Science and Technology (QST) , 2-4 Shirakata , Tokai , Ibaraki 319-1106 , Japan
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ) , Technische Universität München , Lichtenbergstrasse 1 , 85748 Garching , Germany
| | - Tobias E Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) , Forschungszentrum Jülich GmbH , Lichtenbergstrasse 1 , 85748 Garching , Germany
| | - Motoyasu Adachi
- Institute for Quantum Life Science , National Institutes for Quantum and Radiological Science and Technology (QST) , 2-4 Shirakata , Tokai , Ibaraki 319-1106 , Japan
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14
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Hanazono Y, Takeda K, Miki K. Characterization of perdeuterated high-potential iron-sulfur protein with high-resolution X-ray crystallography. Proteins 2019; 88:251-259. [PMID: 31365157 DOI: 10.1002/prot.25793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 11/12/2022]
Abstract
Perdeuteration in neutron crystallography is an effective method for determining the positions of hydrogen atoms in proteins. However, there is shortage of evidence that the high-resolution details of perdeuterated proteins are consistent with those of the nondeuterated proteins. In this study, we determined the X-ray structure of perdeuterated high-potential iron-sulfur protein (HiPIP) at a high resolution of 0.85 å resolution. The comparison of the nondeuterated and perdeuterated structures of HiPIP revealed slight differences between the two structures. The spectroscopic and spectroelectrochemical studies also showed that perdeuterated HiPIP has approximately the same characteristics as nondeuterated HiPIP. These results further emphasize the suitability of using perdeuterated proteins in the high-resolution neutron crystallography.
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Affiliation(s)
- Yuya Hanazono
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
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15
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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16
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Forsyth VT, Moody P. Neutron scattering for the study of biological systems - major opportunities within a rapidly changing landscape. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1126-1128. [PMID: 30605129 DOI: 10.1107/s2059798318017886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- V Trevor Forsyth
- Partnership for Structural Biology, Institut Laue-Langevin, 6 rue Jules Horowitz, 38042 Grenoble CEDEX 9 France
| | - Peter Moody
- Henry Wellcome Laboratories for Structural Biology, Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
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17
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Harp JM, Coates L, Sullivan B, Egli M. Cryo-neutron crystallographic data collection and preliminary refinement of left-handed Z-DNA d(CGCGCG). Acta Crystallogr F Struct Biol Commun 2018; 74:603-609. [PMID: 30279310 PMCID: PMC6168769 DOI: 10.1107/s2053230x1801066x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/24/2018] [Indexed: 11/10/2022] Open
Abstract
Crystals of left-handed Z-DNA [d(CGCGCG)]2 diffract X-rays to beyond 1 Å resolution, feature a small unit cell (∼18 × 31 × 44 Å) and are well hydrated, with around 90 water molecules surrounding the duplex in the asymmetric unit. The duplex shows regular hydration patterns in the narrow minor groove, on the convex surface and around sugar-phosphate backbones. Therefore, Z-DNA offers an ideal case to test the benefits of low-temperature neutron diffraction data collection to potentially determine the donor-acceptor patterns of first- and second-shell water molecules. Nucleic acid fragments pose challenges for neutron crystallography because water molecules are located on the surface rather than inside sequestered spaces such as protein active sites or channels. Water molecules can be expected to display dynamic behavior, particularly in cases where water is not part of an inner shell and directly coordinated to DNA atoms. Thus, nuclear density maps based on room-temperature diffraction data with a resolution of 1.6 Å did not allow an unequivocal determination of the orientations of water molecules. Here, cryo-neutron diffraction data collection for a Z-DNA crystal on the Macromolecular Neutron Diffractometer at the Spallation Neutron Source at Oak Ridge National Laboratory and the outcome of an initial refinement of the structure are reported. A total of 12 diffraction images were recorded with an exposure time of 3.5 h per image, whereby the crystal was static for each diffraction image with a 10° ϕ rotation between images. Initial refinements using these neutron data indicated the positions and orientations of 30 water molecules within the first hydration shell of the DNA molecule. This experiment constitutes a state-of-the-art approach and is the first attempt to our knowledge to determine the low-temperature neutron structure of a DNA crystal.
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Affiliation(s)
- Joel M. Harp
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Martin Egli
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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18
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Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD. Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. Acta Crystallogr D Struct Biol 2018; 74:800-813. [PMID: 30082516 PMCID: PMC6079631 DOI: 10.1107/s2059798318004588] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/19/2018] [Indexed: 11/10/2022] Open
Abstract
The Protein Data Bank (PDB) contains a growing number of models that have been determined using neutron diffraction or a hybrid method that combines X-ray and neutron diffraction. The advantage of neutron diffraction experiments is that the positions of all atoms can be determined, including H atoms, which are hardly detectable by X-ray diffraction. This allows the determination of protonation states and the assignment of H atoms to water molecules. Because neutrons are scattered differently by hydrogen and its isotope deuterium, neutron diffraction in combination with H/D exchange can provide information on accessibility, dynamics and chemical lability. In this study, the deposited data, models and model-to-data fit for all PDB entries that used neutron diffraction as the source of experimental data have been analysed. In many cases, the reported Rwork and Rfree values were not reproducible. In such cases, the model and data files were analysed to identify the reasons for this mismatch. The issues responsible for the discrepancies are summarized and explained. The analysis unveiled limitations to the annotation, deposition and validation of models and data, and a lack of community-wide accepted standards for the description of neutron models and data, as well as deficiencies in current model refinement tools. Most of the issues identified concern the handling of H atoms. Since the primary use of neutron macromolecular crystallography is to locate and directly visualize H atoms, it is important to address these issues, so that the deposited neutron models allow the retrieval of the maximum amount of information with the smallest effort of manual intervention. A path forward to improving the annotation, validation and deposition of neutron models and hybrid X-ray and neutron models is suggested.
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Affiliation(s)
- Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People’s Republic of China
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul Langan
- Neutron Science Directorate, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
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19
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Neutron macromolecular crystallography. Emerg Top Life Sci 2018; 2:39-55. [DOI: 10.1042/etls20170083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023]
Abstract
Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.
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20
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Moulin M, Strohmeier GA, Hirz M, Thompson KC, Rennie AR, Campbell RA, Pichler H, Maric S, Forsyth VT, Haertlein M. Perdeuteration of cholesterol for neutron scattering applications using recombinant Pichia pastoris. Chem Phys Lipids 2018; 212:80-87. [PMID: 29357283 DOI: 10.1016/j.chemphyslip.2018.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/20/2017] [Accepted: 01/15/2018] [Indexed: 02/08/2023]
Abstract
Deuteration of biomolecules has a major impact on both quality and scope of neutron scattering experiments. Cholesterol is a major component of mammalian cells, where it plays a critical role in membrane permeability, rigidity and dynamics, and contributes to specific membrane structures such as lipid rafts. Cholesterol is the main cargo in low and high-density lipoprotein complexes (i.e. LDL, HDL) and is directly implicated in several pathogenic conditions such as coronary artery disease which leads to 17 million deaths annually. Neutron scattering studies on membranes or lipid-protein complexes exploiting contrast variation have been limited by the lack of availability of fully deuterated biomolecules and especially perdeuterated cholesterol. The availability of perdeuterated cholesterol provides a unique way of probing the structural and dynamical properties of the lipoprotein complexes that underly many of these disease conditions. Here we describe a procedure for in vivo production of perdeuterated recombinant cholesterol in lipid-engineered Pichia pastoris using flask and fed-batch fermenter cultures in deuterated minimal medium. Perdeuteration of the purified cholesterol was verified by mass spectrometry and its use in a neutron scattering study was demonstrated by neutron reflectometry measurements using the FIGARO instrument at the ILL.
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Affiliation(s)
- Martine Moulin
- Institut Laue-Langevin, 71, Avenue des Martyrs, Grenoble 38042, France; Faculty of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Gernot A Strohmeier
- acib, Austrian Centre of Industrial Biotechnology GmbH, 8010 Graz, Austria; Institute of Organic Chemistry, NAWI Graz, Graz University of Technology, 8010 Graz, Austria
| | - Melanie Hirz
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, 8010 Graz, Austria
| | - Katherine C Thompson
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
| | - Adrian R Rennie
- Centre for Neutron Scattering, Uppsala University, 751 20 Uppsala, Sweden
| | | | - Harald Pichler
- acib, Austrian Centre of Industrial Biotechnology GmbH, 8010 Graz, Austria; Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, 8010 Graz, Austria
| | - Selma Maric
- Biofilms - Research Centre for Biointerfaces and Biomedical Science Department, Faculty of Health and Society, Malmö University, Malmö 20506, Sweden
| | - V Trevor Forsyth
- Institut Laue-Langevin, 71, Avenue des Martyrs, Grenoble 38042, France; Faculty of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
| | - Michael Haertlein
- Institut Laue-Langevin, 71, Avenue des Martyrs, Grenoble 38042, France.
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21
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Maiti BK, Almeida RM, Moura I, Moura JJ. Rubredoxins derivatives: Simple sulphur-rich coordination metal sites and its relevance for biology and chemistry. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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Hiromoto T, Meilleur F, Shimizu R, Shibazaki C, Adachi M, Tamada T, Kuroki R. Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type. Protein Sci 2017; 26:1953-1963. [PMID: 28707339 PMCID: PMC5606550 DOI: 10.1002/pro.3230] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 11/23/2022]
Abstract
T4 phage lysozyme is an inverting glycoside hydrolase that degrades the murein of bacterial cell walls by cleaving the β‐1,4‐glycosidic bond. The substitution of the catalytic Thr26 residue to a histidine converts the wild type from an inverting to a retaining enzyme, which implies that the original general acid Glu11 can also act as an acid/base catalyst in the hydrolysis. Here, we have determined the neutron structure of the perdeuterated T26H mutant to clarify the protonation states of Glu11 and the substituted His26, which are key in the retaining reaction. The 2.09‐Å resolution structure shows that the imidazole group of His26 is in its singly protonated form in the active site, suggesting that the deprotonated Nɛ2 atom of His26 can attack the anomeric carbon of bound substrate as a nucleophile. The carboxyl group of Glu11 is partially protonated and interacts with the unusual neutral state of the guanidine moiety of Arg145, as well as two heavy water molecules. Considering that one of the water‐binding sites has the potential to be occupied by a hydronium ion, the bulk solvent could be the source for the protonation of Glu11. The respective protonation states of Glu11 and His26 are consistent with the bond lengths determined by an unrestrained refinement of the high‐resolution X‐ray structure of T26H at 1.04‐Å resolution. The detail structural information, including the coordinates of the deuterium atoms in the active site, provides insight into the distinctively different catalytic activities of the mutant and wild type enzymes. PDB Code(s): 5XPE; 5XPF
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Affiliation(s)
- Takeshi Hiromoto
- Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki, 319-1195, Japan
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831.,Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - Rumi Shimizu
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, 319-1106, Japan
| | - Chie Shibazaki
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, 319-1106, Japan
| | - Motoyasu Adachi
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, 319-1106, Japan
| | - Taro Tamada
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, 319-1106, Japan
| | - Ryota Kuroki
- Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki, 319-1195, Japan
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23
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Ikeda T, Saito K, Hasegawa R, Ishikita H. The Existence of an Isolated Hydronium Ion in the Interior of Proteins. Angew Chem Int Ed Engl 2017; 56:9151-9154. [PMID: 28613440 PMCID: PMC5575531 DOI: 10.1002/anie.201705512] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Indexed: 12/20/2022]
Abstract
Neutron diffraction analysis studies reported an isolated hydronium ion (H3O+) in the interior of d‐xylose isomerase (XI) and phycocyanobilin‐ferredoxin oxidoreductase (PcyA). H3O+ forms hydrogen bonds (H‐bonds) with two histidine side‐chains and a backbone carbonyl group in PcyA, whereas H3O+ forms H‐bonds with three acidic residues in XI. Using a quantum mechanical/molecular mechanical (QM/MM) approach, we analyzed stabilization of H3O+ by the protein environment. QM/MM calculations indicated that H3O+ was unstable in the PcyA crystal structure, releasing a proton to an H‐bond partner His88, producing H2O and protonated His88. On the other hand, H3O+ was stable in the XI crystal structure. H‐bond partners of isolated H3O+ would be practically limited to acidic residues such as aspartic and glutamic acids in the protein environment.
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Affiliation(s)
- Takuya Ikeda
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Ryo Hasegawa
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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Ikeda T, Saito K, Hasegawa R, Ishikita H. The Existence of an Isolated Hydronium Ion in the Interior of Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takuya Ikeda
- Department of Applied Chemistry The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
| | - Keisuke Saito
- Department of Applied Chemistry The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
- Research Center for Advanced Science and Technology The University of Tokyo 4-6-1 Komaba, Meguro-ku Tokyo 153-8904 Japan
| | - Ryo Hasegawa
- Department of Applied Chemistry The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
- Research Center for Advanced Science and Technology The University of Tokyo 4-6-1 Komaba, Meguro-ku Tokyo 153-8904 Japan
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25
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Oksanen E, Chen JCH, Fisher SZ. Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules. Molecules 2017; 22:molecules22040596. [PMID: 28387738 PMCID: PMC6154725 DOI: 10.3390/molecules22040596] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/21/2022] Open
Abstract
The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.
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Affiliation(s)
- Esko Oksanen
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biochemistry and Structural Biology, Lund University, Sölvegatan 39, 22362 Lund, Sweden.
| | - Julian C-H Chen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Suzanne Zoë Fisher
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.
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26
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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] [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.
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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
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Bax B, Chung CW, Edge C. Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry. Acta Crystallogr D Struct Biol 2017; 73:131-140. [PMID: 28177309 PMCID: PMC5297916 DOI: 10.1107/s2059798316020283] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/21/2016] [Indexed: 11/13/2023] Open
Abstract
There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms. This ambiguity is far from rare, since about 25% of drugs have more than one tautomeric form. This paper focuses on the most common, `prototropic', tautomers, which are isomers that readily interconvert by the exchange of an H atom accompanied by the switch of a single and an adjacent double bond. Hydrogen-exchange rates and different protonation states of compounds (e.g. buffers) are also briefly discussed. The difference in heavy (non-H) atom positions between two tautomers can be small, and careful refinement of all possible tautomers may single out the likely bound ligand tautomer. Experimental methods to determine H-atom positions, such as neutron crystallography, are often technically challenging. Therefore, chemical knowledge and computational approaches are frequently used in conjugation with experimental data to deduce the bound tautomer state. Proton movement is a key feature of many enzymatic reactions, so understanding the orchestration of hydrogen/proton motion is of critical importance to biological chemistry. For example, structural studies have suggested that, just as a chemist may use heat, some enzymes use directional movement to protonate specific O atoms on phosphates to catalyse phosphotransferase reactions. To inhibit `wriggly' enzymes that use movement to effect catalysis, it may be advantageous to have inhibitors that can maintain favourable contacts by adopting different tautomers as the enzyme `wriggles'.
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Affiliation(s)
- Ben Bax
- Structural Biology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Chun-wa Chung
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Colin Edge
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
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Chen JCH, Unkefer CJ. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography. IUCRJ 2017; 4:72-86. [PMID: 28250943 PMCID: PMC5331467 DOI: 10.1107/s205225251601664x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002-2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo-graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.
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Affiliation(s)
- Julian C.-H. Chen
- Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Clifford J. Unkefer
- Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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29
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Cuypers MG, Mason SA, Mossou E, Haertlein M, Forsyth VT, Mitchell EP. Macromolecular structure phasing by neutron anomalous diffraction. Sci Rep 2016; 6:31487. [PMID: 27511806 PMCID: PMC4980602 DOI: 10.1038/srep31487] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/20/2016] [Indexed: 01/07/2023] Open
Abstract
In this report we show for the first time that neutron anomalous dispersion can be used in a practical manner to determine experimental phases of a protein crystal structure, providing a new tool for structural biologists. The approach is demonstrated through the use of a state-of-the-art monochromatic neutron diffractometer at the Institut Laue-Langevin (ILL) in combination with crystals of perdeuterated protein that minimise the level of hydrogen incoherent scattering and enhance the visibility of the anomalous signal. The protein used was rubredoxin in which cadmium replaced the iron at the iron-sulphur site. While this study was carried out using a steady-state neutron beam source, the results will be of major interest for capabilities at existing and emerging spallation neutron sources where time-of-flight instruments provide inherent energy discrimination. In particular this capability may be expected to offer unique opportunities to a rapidly developing structural biology community where there is increasing interest in the identification of protonation states, protein/water interactions and protein-ligand interactions - all of which are of central importance to a wide range of fundamental and applied areas in the biosciences.
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Affiliation(s)
- Maxime G. Cuypers
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, United Kingdom
- ILL, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Sax A. Mason
- ILL, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Estelle Mossou
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, United Kingdom
- ILL, 71 avenue des Martyrs, 38000 Grenoble, France
| | | | - V. Trevor Forsyth
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, United Kingdom
- ILL, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Edward P. Mitchell
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, United Kingdom
- ESRF, 71 avenue des Martyrs, 38000 Grenoble, France
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30
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The use of neutron scattering to determine the functional structure of glycoside hydrolase. Curr Opin Struct Biol 2016; 40:54-61. [PMID: 27494120 DOI: 10.1016/j.sbi.2016.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/19/2016] [Accepted: 07/21/2016] [Indexed: 11/21/2022]
Abstract
Neutron diffraction provides different information from X-ray diffraction, because neutrons are scattered by atomic nuclei, whereas X-rays are scattered by electrons. One of the key advantages of neutron crystallography is the ability to visualize hydrogen and deuterium atoms, making it possible to observe the protonation state of amino acid residues, hydrogen bonds, networks of water molecules and proton relay pathways in enzymes. But, because of technical difficulties, less than 100 enzyme structures have been evaluated by neutron crystallography to date. In this review, we discuss the advantages and disadvantages of neutron crystallography as a tool to investigate the functional structure of glycoside hydrolases, with some examples.
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31
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Yee AW, Moulin M, Breteau N, Haertlein M, Mitchell EP, Cooper JB, Boeri Erba E, Forsyth VT. Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ai Woon Yee
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
| | - Martine Moulin
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
| | - Nina Breteau
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
| | - Michael Haertlein
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
| | - Edward P. Mitchell
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
- ESRF 71 avenue des Martyrs 38042 Grenoble France
| | - Jonathan B. Cooper
- Laboratory of Protein Crystallography, Drug Discovery GroupWolfson Institute for Biomedical Research, UCL London WC1E 6BT UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, IBS 38044 Grenoble France
- CNRS, IBS 38044 Grenoble France
- CEA, IBS 38044 Grenoble France
| | - V. Trevor Forsyth
- Life Sciences group, ILL 71 avenue des Martyrs 38042 Grenoble France
- Faculty of Natural SciencesKeele University Staffordshire ST5 5BG UK
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32
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Yee AW, Moulin M, Breteau N, Haertlein M, Mitchell EP, Cooper JB, Boeri Erba E, Forsyth VT. Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses. Angew Chem Int Ed Engl 2016; 55:9292-6. [PMID: 27311939 PMCID: PMC5094506 DOI: 10.1002/anie.201602747] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 01/13/2023]
Abstract
It is well established that the formation of transthyretin (TTR) amyloid fibrils is linked to the destabilization and dissociation of its tetrameric structure into insoluble aggregates. Isotope labeling is used for the study of TTR by NMR, neutron diffraction, and mass spectrometry (MS). Here MS, thioflavin T fluorescence, and crystallographic data demonstrate that while the X-ray structures of unlabeled and deuterium-labeled TTR are essentially identical, subunit exchange kinetics and amyloid formation are accelerated for the deuterated protein. However, a slower subunit exchange is noted in deuterated solvent, reflecting the poorer solubility of non-polar protein side chains in such an environment. These observations are important for the interpretation of kinetic studies involving deuteration. The destabilizing effects of TTR deuteration are rather similar in character to those observed for aggressive mutations of TTR such as L55P (associated with familial amyloid polyneuropathy).
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Affiliation(s)
- Ai Woon Yee
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Martine Moulin
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Nina Breteau
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Michael Haertlein
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Edward P Mitchell
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- ESRF, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Jonathan B Cooper
- Laboratory of Protein Crystallography, Drug Discovery Group, Wolfson Institute for Biomedical Research, UCL, London, WC1E 6BT, UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, IBS, 38044, Grenoble, France.
- CNRS, IBS, 38044, Grenoble, France.
- CEA, IBS, 38044, Grenoble, France.
| | - V Trevor Forsyth
- Life Sciences group, ILL, 71 avenue des Martyrs, 38042, Grenoble, France.
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK.
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33
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O'Dell WB, Bodenheimer AM, Meilleur F. Neutron protein crystallography: A complementary tool for locating hydrogens in proteins. Arch Biochem Biophys 2016; 602:48-60. [DOI: 10.1016/j.abb.2015.11.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
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34
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Wacklin HP, Bremec BB, Moulin M, Rojko N, Haertlein M, Forsyth T, Anderluh G, Norton RS. Neutron reflection study of the interaction of the eukaryotic pore-forming actinoporin equinatoxin II with lipid membranes reveals intermediate states in pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:640-52. [DOI: 10.1016/j.bbamem.2015.12.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 11/02/2015] [Accepted: 12/15/2015] [Indexed: 01/07/2023]
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35
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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] [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.
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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.
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36
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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] [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
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37
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Haertlein M, Moulin M, Devos JM, Laux V, Dunne O, Trevor Forsyth V. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. Methods Enzymol 2016; 566:113-57. [DOI: 10.1016/bs.mie.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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38
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Ohlin M, von Schantz L, Schrader TE, Ostermann A, Logan DT, Fisher SZ. Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase. Acta Crystallogr F Struct Biol Commun 2015; 71:1072-7. [PMID: 26249702 PMCID: PMC4528944 DOI: 10.1107/s2053230x15011383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/11/2015] [Indexed: 11/10/2022] Open
Abstract
Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that bind specific types of carbohydrates. Ultra high-resolution X-ray crystallographic studies of CBMs have helped to decipher the basis for specificity in carbohydrate-protein interactions. However, additional studies are needed to better understand which structural determinants confer which carbohydrate-binding properties. To address these issues, neutron crystallographic studies were initiated on one experimentally engineered CBM derived from a xylanase, X-2 L110F, a protein that is able to bind several different plant carbohydrates such as xylan, β-glucan and xyloglucan. This protein evolved from a CBM present in xylanase Xyn10A of Rhodothermus marinus. The protein was complexed with a branched xyloglucan heptasaccharide. Large single crystals of hydrogenous protein (∼1.6 mm(3)) were grown at room temperature and subjected to H/D exchange. Both neutron and X-ray diffraction data sets were collected to 1.6 Å resolution. Joint neutron and X-ray refinement using phenix.refine showed significant density for residues involved in carbohydrate binding and revealed the details of a hydrogen-bonded water network around the binding site. This is the first report of a neutron structure of a CBM and will add to the understanding of protein-carbohydrate binding interactions.
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Affiliation(s)
- Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village, Building 406, 223 81 Lund, Sweden
| | - Laura von Schantz
- Department of Immunotechnology, Lund University, Medicon Village, Building 406, 223 81 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
| | - Derek T. Logan
- Department of Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden
| | - S. Zoë Fisher
- Scientific Activities Division, European Spallation Source, Tunavägen 24, 221 00 Lund, Sweden
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39
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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] [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.
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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
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40
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Edlich-Muth C, Artero JB, Callow P, Przewloka MR, Watson AA, Zhang W, Glover DM, Debski J, Dadlez M, Round AR, Forsyth VT, Laue ED. The pentameric nucleoplasmin fold is present in Drosophila FKBP39 and a large number of chromatin-related proteins. J Mol Biol 2015; 427:1949-63. [PMID: 25813344 PMCID: PMC4414354 DOI: 10.1016/j.jmb.2015.03.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 03/17/2015] [Accepted: 03/17/2015] [Indexed: 11/28/2022]
Abstract
Nucleoplasmin is a histone chaperone that consists of a pentameric N-terminal domain and an unstructured C-terminal tail. The pentameric core domain, a doughnut-like structure with a central pore, is only found in the nucleoplasmin family. Here, we report the first structure of a nucleoplasmin-like domain (NPL) from the unrelated Drosophila protein, FKBP39, and we present evidence that this protein associates with chromatin. Furthermore, we show that two other chromatin proteins, Arabidopsis thaliana histone deacetylase type 2 (HD2) and Saccharomyces cerevisiae Fpr4, share the NPL fold and form pentamers, or a dimer of pentamers in the case of HD2. Thus, we propose a new family of proteins that share the pentameric nucleoplasmin-like NPL domain and are found in protists, fungi, plants and animals.
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Affiliation(s)
- Christian Edlich-Muth
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - Jean-Baptiste Artero
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, Grenoble, Cedex 9, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - Phil Callow
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, Grenoble, Cedex 9, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - Marcin R Przewloka
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH Cambridge, United Kingdom
| | - Aleksandra A Watson
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - Wei Zhang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - David M Glover
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH Cambridge, United Kingdom
| | - Janusz Debski
- Mass Spectrometry Laboratory, Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego Street, 02-106 Warsaw, Poland
| | - Michal Dadlez
- Mass Spectrometry Laboratory, Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego Street, 02-106 Warsaw, Poland
| | - Adam R Round
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-European Molecular Biology Laboratory-CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, Grenoble, Cedex 9, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom.
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41
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Unno M, Ishikawa-Suto K, Kusaka K, Tamada T, Hagiwara Y, Sugishima M, Wada K, Yamada T, Tomoyori K, Hosoya T, Tanaka I, Niimura N, Kuroki R, Inaka K, Ishihara M, Fukuyama K. Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography. J Am Chem Soc 2015; 137:5452-60. [PMID: 25872660 DOI: 10.1021/jacs.5b00645] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXα (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH(+), a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial" water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 Nδ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H3O(+). These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis.
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Affiliation(s)
- Masaki Unno
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan.,‡Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Kumiko Ishikawa-Suto
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan.,‡Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan.,§Quantum Beam Science Center, Japan Atomic Energy Agency, Naka 319-1195, Japan
| | - Katsuhiro Kusaka
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan
| | - Taro Tamada
- §Quantum Beam Science Center, Japan Atomic Energy Agency, Naka 319-1195, Japan
| | - Yoshinori Hagiwara
- ∥Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan.,⊥Department of Biochemistry and Applied Chemistry, National Institute of Technology, Kurume College, Kurume 830-8555, Japan
| | - Masakazu Sugishima
- #Department of Medical Biochemistry, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Kei Wada
- ∇Organization for Promotion of Tenure Track, University of Miyazaki, Kiyotake 889-1692, Japan
| | - Taro Yamada
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan
| | - Katsuaki Tomoyori
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan.,§Quantum Beam Science Center, Japan Atomic Energy Agency, Naka 319-1195, Japan
| | - Takaaki Hosoya
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan.,‡Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Ichiro Tanaka
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan.,‡Graduate School of Science and Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Nobuo Niimura
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan
| | - Ryota Kuroki
- §Quantum Beam Science Center, Japan Atomic Energy Agency, Naka 319-1195, Japan
| | - Koji Inaka
- ○MARUWA Foods and Biosciences Inc., Yamatokoriyama 639-1123, Japan
| | - Makiko Ishihara
- †Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka 319-1106, Japan
| | - Keiichi Fukuyama
- ∥Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan.,◆Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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42
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Helliwell JR, Mitchell EP. Synchrotron radiation macromolecular crystallography: science and spin-offs. IUCRJ 2015; 2:283-91. [PMID: 25866664 PMCID: PMC4392420 DOI: 10.1107/s205225251402795x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 12/22/2014] [Indexed: 05/11/2023]
Abstract
A current overview of synchrotron radiation (SR) in macromolecular crystallography (MX) instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development.
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Affiliation(s)
- John R. Helliwell
- School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, England
| | - Edward P. Mitchell
- ESRF, 71 avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, England
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43
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Hussain MA, Mahadevi AS, Sastry GN. Estimating the binding ability of onium ions with CO2 and π systems: a computational investigation. Phys Chem Chem Phys 2015; 17:1763-75. [DOI: 10.1039/c4cp03434a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The impact of increasing methyl substitution on onium ions in their complexes with CO2 and aromatic systems has been analyzed using DFT calculations.
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Affiliation(s)
- M. Althaf Hussain
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
| | - A. Subha Mahadevi
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
| | - G. Narahari Sastry
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
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44
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Maric S, Thygesen MB, Schiller J, Marek M, Moulin M, Haertlein M, Forsyth VT, Bogdanov M, Dowhan W, Arleth L, Pomorski TG. Biosynthetic preparation of selectively deuterated phosphatidylcholine in genetically modified Escherichia coli. Appl Microbiol Biotechnol 2015; 99:241-54. [PMID: 25301578 PMCID: PMC4289089 DOI: 10.1007/s00253-014-6082-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/28/2014] [Accepted: 09/09/2014] [Indexed: 01/07/2023]
Abstract
Phosphatidylcholine (PC) is a major component of eukaryotic cell membranes and one of the most commonly used phospholipids for reconstitution of membrane proteins into carrier systems such as lipid vesicles, micelles and nanodiscs. Selectively deuterated versions of this lipid have many applications, especially in structural studies using techniques such as NMR, neutron reflectivity and small-angle neutron scattering. Here we present a comprehensive study of selective deuteration of phosphatidylcholine through biosynthesis in a genetically modified strain of Escherichia coli. By carefully tuning the deuteration level in E. coli growth media and varying the deuteration of supplemented carbon sources, we show that it is possible to achieve a controlled deuteration for three distinct parts of the PC lipid molecule, namely the (a) lipid head group, (b) glycerol backbone and (c) fatty acyl tail. This biosynthetic approach paves the way for the synthesis of specifically deuterated, physiologically relevant phospholipid species which remain difficult to obtain through standard chemical synthesis.
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Affiliation(s)
- Selma Maric
- Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
- Center for Membrane Pumps in Cells and Disease, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Mikkel B. Thygesen
- CARB Centre, Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jürgen Schiller
- Institut für Medizinische Physik und Biophysik, Medizinische Fakultät, Universität Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Magdalena Marek
- Center for Membrane Pumps in Cells and Disease, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Martine Moulin
- Life Sciences Group, Institut Laue Langevin, 6 rue Jules Horowitz, CEDEX 9, BP156, 38042 Grenoble, France
- Faculty of Natural Sciences & Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
| | - Michael Haertlein
- Life Sciences Group, Institut Laue Langevin, 6 rue Jules Horowitz, CEDEX 9, BP156, 38042 Grenoble, France
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue Langevin, 6 rue Jules Horowitz, CEDEX 9, BP156, 38042 Grenoble, France
- Faculty of Natural Sciences & Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Lise Arleth
- Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Thomas Günther Pomorski
- Center for Membrane Pumps in Cells and Disease, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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45
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Fisher SJ, Blakeley MP, Howard EI, Petit-Haertlein I, Haertlein M, Mitschler A, Cousido-Siah A, Salvay AG, Popov A, Muller-Dieckmann C, Petrova T, Podjarny A. Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography. ACTA ACUST UNITED AC 2014; 70:3266-72. [DOI: 10.1107/s1399004714021610] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/30/2014] [Indexed: 11/10/2022]
Abstract
The 1.8 Å resolution neutron structure of deuterated type III antifreeze protein in which the methyl groups of leucine and valine residues are selectively protonated is presented. Comparison between this and the 1.85 Å resolution neutron structure of perdeuterated type III antifreeze protein indicates that perdeuteration improves the visibility of solvent molecules located in close vicinity to hydrophobic residues, as cancellation effects between H atoms of the methyl groups and nearby heavy-water molecules (D2O) are avoided.
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46
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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] [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.
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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
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47
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Affiliation(s)
- John T Groves
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
| | - Nicholas C Boaz
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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48
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Sippel KH, Bacik J, Quiocho FA, Fisher SZ. Preliminary time-of-flight neutron diffraction studies of Escherichia coli ABC transport receptor phosphate-binding protein at the Protein Crystallography Station. Acta Crystallogr F Struct Biol Commun 2014; 70:819-22. [PMID: 24915101 PMCID: PMC4051545 DOI: 10.1107/s2053230x14009704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 04/29/2014] [Indexed: 11/10/2022] Open
Abstract
Inorganic phosphate is an essential molecule for all known life. Organisms have developed many mechanisms to ensure an adequate supply, even in low-phosphate conditions. In prokaryotes phosphate transport is instigated by the phosphate-binding protein (PBP), the initial receptor for the ATP-binding cassette (ABC) phosphate transporter. In the crystal structure of the PBP-phosphate complex, the phosphate is completely desolvated and sequestered in a deep cleft and is bound by 13 hydrogen bonds: 12 to protein NH and OH donor groups and one to a carboxylate acceptor group. The carboxylate plays a key recognition role by accepting a phosphate hydrogen. PBP phosphate affinity is relatively consistent across a broad pH range, indicating the capacity to bind monobasic (H2PO4-) and dibasic (HPO4(2-)) phosphate; however, the mechanism by which it might accommodate the second hydrogen of monobasic phosphate is unclear. To answer this question, neutron diffraction studies were initiated. Large single crystals with a volume of 8 mm3 were grown and subjected to hydrogen/deuterium exchange. A 2.5 Å resolution data set was collected on the Protein Crystallography Station at the Los Alamos Neutron Science Center. Initial refinement of the neutron data shows significant nuclear density, and refinement is ongoing. This is the first report of a neutron study from this superfamily.
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Affiliation(s)
- K. H. Sippel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - J. Bacik
- Bioscience Division B-11, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - F. A. Quiocho
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - S. Z. Fisher
- Scientific Activities Division, European Spallation Source, 221 00 Lund, Sweden
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49
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Gruene T, Hahn HW, Luebben AV, Meilleur F, Sheldrick GM. Refinement of macromolecular structures against neutron data with SHELXL2013.. J Appl Crystallogr 2014; 47:462-466. [PMID: 24587788 PMCID: PMC3937812 DOI: 10.1107/s1600576713027659] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/09/2013] [Indexed: 11/16/2022] Open
Abstract
Some of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to use SHELXL for refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst. (1991), A47, 392-400] restraints to H atoms and discusses several of the features of SHELXL that make the program particularly useful for the investigation of H atoms with neutron diffraction. SHELXL2013 is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures.
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Affiliation(s)
- Tim Gruene
- Department of Structural Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Hinrich W. Hahn
- Department of Structural Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Anna V. Luebben
- Department of Structural Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Flora Meilleur
- North Carolina State University, Raleigh, NC 27695, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37831-6142, USA
| | - George M. Sheldrick
- Department of Structural Chemistry, Georg-August-University Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
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50
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Golden EA, Vrielink A. Looking for Hydrogen Atoms: Neutron Crystallography Provides Novel Insights Into Protein Structure and Function. Aust J Chem 2014. [DOI: 10.1071/ch14337] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Neutron crystallography allows direct localization of hydrogen positions in biological macromolecules. Within enzymes, hydrogen atoms play a pivotal role in catalysis. Recent advances in instrumentation and sample preparation have helped to overcome the difficulties of performing neutron diffraction experiments on protein crystals. The application of neutron macromolecular crystallography to a growing number of proteins has yielded novel structural insights. The ability to accurately position water molecules, hydronium ions, and hydrogen atoms within protein structures has helped in the study of low-barrier hydrogen bonds and hydrogen-bonding networks. The determination of protonation states of protein side chains, substrates, and inhibitors in the context of the macromolecule has provided important insights into enzyme chemistry and ligand binding affinities, which can assist in the design of potent therapeutic agents. In this review, we give an overview of the method and highlight advances in knowledge attained through the application of neutron protein crystallography.
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