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Sekiya H, Nonaka Y, Kamitori S, Miyaji T, Tamai E. X-ray structure and mutagenesis analyses of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain. Biochem Biophys Res Commun 2024; 715:149957. [PMID: 38688057 DOI: 10.1016/j.bbrc.2024.149957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Clostridioides difficile endolysin (Ecd09610) consists of an unknown domain at its N terminus, followed by two catalytic domains, a glucosaminidase domain and endopeptidase domain. X-ray structure and mutagenesis analyses of the Ecd09610 catalytic domain with glucosaminidase activity (Ecd09610CD53) were performed. Ecd09610CD53 was found to possess an α-bundle-like structure with nine helices, which is well conserved among GH73 family enzymes. The mutagenesis analysis based on X-ray structures showed that Glu405 and Asn470 were essential for enzymatic activity. Ecd09610CD53 may adopt a neighboring-group mechanism for a catalytic reaction in which Glu405 acted as an acid/base catalyst and Asn470 helped to stabilize the oxazolinium ion intermediate. Structural comparisons with the newly identified Clostridium perfringens autolysin catalytic domain (AcpCD) in the P1 form and a zymography analysis demonstrated that AcpCD was 15-fold more active than Ecd09610CD53. The strength of the glucosaminidase activity of the GH73 family appears to be dependent on the depth of the substrate-binding groove.
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Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Yasuhiro Nonaka
- Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Shigehiro Kamitori
- Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan; Research Facility Center for Science & Technology, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Tomomi Miyaji
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan.
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2
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Brookner DE, Hekstra DR. MatchMaps: non-isomorphous difference maps for X-ray crystallography. J Appl Crystallogr 2024; 57:885-895. [PMID: 38846758 PMCID: PMC11151677 DOI: 10.1107/s1600576724003510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/19/2024] [Indexed: 06/09/2024] Open
Abstract
Conformational change mediates the biological functions of macromolecules. Crystallographic measurements can map these changes with extraordinary sensitivity as a function of mutations, ligands and time. A popular method for detecting structural differences between crystallographic data sets is the isomorphous difference map. These maps combine the phases of a chosen reference state with the observed changes in structure factor amplitudes to yield a map of changes in electron density. Such maps are much more sensitive to conformational change than structure refinement is, and are unbiased in the sense that observed differences do not depend on refinement of the perturbed state. However, even modest changes in unit-cell properties can render isomorphous difference maps useless. This is unnecessary. Described here is a generalized procedure for calculating observed difference maps that retains the high sensitivity to conformational change and avoids structure refinement of the perturbed state. This procedure is implemented in an open-source Python package, MatchMaps, that can be run in any software environment supporting PHENIX [Liebschner et al. (2019). Acta Cryst. D75, 861-877] and CCP4 [Agirre et al. (2023). Acta Cryst. D79, 449-461]. Worked examples show that MatchMaps 'rescues' observed difference electron-density maps for poorly isomorphous crystals, corrects artifacts in nominally isomorphous difference maps, and extends to detecting differences across copies within the asymmetric unit or across altogether different crystal forms.
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Affiliation(s)
- Dennis E. Brookner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Doeke R. Hekstra
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
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3
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Grigas AT, Fisher A, Shattuck MD, O'Hern CS. Connecting polymer collapse and the onset of jamming. Phys Rev E 2024; 109:034406. [PMID: 38632799 DOI: 10.1103/physreve.109.034406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 02/13/2024] [Indexed: 04/19/2024]
Abstract
Previous studies have shown that the interiors of proteins are densely packed, reaching packing fractions that are as large as those found for static packings of individual amino-acid-shaped particles. How can the interiors of proteins take on such high packing fractions given that amino acids are connected by peptide bonds and many amino acids are hydrophobic with attractive interactions? We investigate this question by comparing the structural and mechanical properties of collapsed attractive disk-shaped bead-spring polymers to those of three reference systems: static packings of repulsive disks, of attractive disks, and of repulsive disk-shaped bead-spring polymers. We show that the attractive systems quenched to temperatures below the glass transition T≪T_{g} and static packings of both repulsive disks and bead-spring polymers possess similar interior packing fractions. Previous studies have shown that static packings of repulsive disks are isostatic at jamming onset, i.e., the number of interparticle contacts N_{c} matches the number of degrees of freedom, which strongly influences their mechanical properties. We find that repulsive polymer packings are hypostatic at jamming onset (i.e., with fewer contacts than degrees of freedom) but are effectively isostatic when including stabilizing quartic modes, which give rise to quartic scaling of the potential energy with displacements along these modes. While attractive disk and polymer packings are often considered hyperstatic with excess contacts over the isostatic number, we identify a definition for interparticle contacts for which they can also be considered as effectively isostatic. As a result, we show that the mechanical properties (e.g., scaling of the potential energy with excess contact number and low-frequency contribution to the density of vibrational modes) of weakly attractive disk and polymer packings are similar to those of isostatic repulsive disk and polymer packings. Our results demonstrate that static packings generated via attractive collapse or compression of repulsive particles possess similar structural and mechanical properties.
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Affiliation(s)
- Alex T Grigas
- Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Aliza Fisher
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520, USA
| | - Mark D Shattuck
- Benjamin Levich Institute and Physics Department, The City College of New York, New York, New York 10031, USA
| | - Corey S O'Hern
- Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
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4
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP. Commun Biol 2024; 7:59. [PMID: 38216663 PMCID: PMC10786866 DOI: 10.1038/s42003-023-05609-0] [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: 05/09/2023] [Accepted: 11/20/2023] [Indexed: 01/14/2024] Open
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature versus. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY, 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY, 10016, USA.
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5
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Colloc'h N, Dhaussy AC, Girard E. Exploring the structural dynamics of proteins by pressure perturbation using macromolecular crystallography. Methods Enzymol 2023; 688:349-381. [PMID: 37748831 DOI: 10.1016/bs.mie.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
High pressure is a convenient thermodynamic parameter to probe the dynamics of proteins as it is intimately related to volume which is essential for protein function. To be biologically active, a protein fluctuates between different substates. Pressure perturbation can promote some hidden substates by modifying the population between them. High pressure macromolecular crystallography (HPMX) is a perfect tool to capture and to characterize such substates at a molecular level providing new insights on protein dynamics. The present chapter describes the use of the diamond anvil cell to perform HPMX experiments. It also provides tips on sample preparation and optimal data collection as well as on efficient analysis of the resulting high-pressure structures.
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Affiliation(s)
- Nathalie Colloc'h
- Imagerie et stratégies thérapeutiques pour les cancers et tissus cérébraux (ISTCT), CNRS Université de Caen Normandie, Centre Cyceron, Caen, France
| | | | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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6
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.538097. [PMID: 37205580 PMCID: PMC10187168 DOI: 10.1101/2023.05.02.538097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature vs. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes novel interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Together, our work argues that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY 10016
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY 10016
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7
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Pressure, motion, and conformational entropy in molecular recognition by proteins. BIOPHYSICAL REPORTS 2022; 3:100098. [PMID: 36647534 PMCID: PMC9840116 DOI: 10.1016/j.bpr.2022.100098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
The thermodynamics of molecular recognition by proteins is a central determinant of complex biochemistry. For over a half-century, detailed cryogenic structures have provided deep insight into the energetic contributions to ligand binding by proteins. More recently, a dynamical proxy based on NMR-relaxation methods has revealed an unexpected richness in the contributions of conformational entropy to the thermodynamics of ligand binding. Here, we report the pressure dependence of fast internal motion within the ribonuclease barnase and its complex with the protein barstar. In what we believe is a first example, we find that protein dynamics are conserved along the pressure-binding thermodynamic cycle. The femtomolar affinity of the barnase-barstar complex exists despite a penalty by -TΔSconf of +11.7 kJ/mol at ambient pressure. At high pressure, however, the overall change in side-chain dynamics is zero, and binding occurs with no conformational entropy penalty, suggesting an important role of conformational dynamics in the adaptation of protein function to extreme environments. Distinctive clustering of the pressure sensitivity is observed in response to both pressure and binding, indicating the presence of conformational heterogeneity involving less efficiently packed alternative conformation(s). The structural segregation of dynamics observed in barnase is striking and shows how changes in both the magnitude and the sign of regional contributions of conformational entropy to the thermodynamics of protein function are possible.
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8
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Wang J, Liu J, Gisriel CJ, Wu S, Maschietto F, Flesher DA, Lolis E, Lisi GP, Brudvig GW, Xiong Y, Batista VS. How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM. J Struct Biol 2022; 214:107902. [PMID: 36202310 DOI: 10.1016/j.jsb.2022.107902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/23/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20-30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA.
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | | | - Shenping Wu
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, USA
| | | | - David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | - Elias Lolis
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, USA
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA; Department of Chemistry, Yale University, New Haven, CT 06511-8499, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, USA
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9
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Lv L, Ye L, Lin X, Li L, Chen J, Yue W, Wu X. Functional and Allergenic Properties Assessment of Conalbumin (Ovotransferrin) after Oxidation. Foods 2022; 11:foods11152308. [PMID: 35954072 PMCID: PMC9367811 DOI: 10.3390/foods11152308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Conalbumin (CA) is an iron-binding egg protein that has various bioactivities and causes major allergenicity in humans. This study investigated how oxidation affects the multiple functional properties of CA. The lipid peroxidation method was used to prepare treated CA [2,2′-azobis (2-amidinopropane) dihydrochloride (AAPH)-CA and acrolein-CA] complexes. CA induced structural changes through oxidation. These changes enhanced the digestibility, rate of endocytosis in dendritic cells, and emulsifying and foaming properties of CA. ELISA and immunoblot analysis showed that the complexes reduced the IgE-binding ability of CA through lipid oxidation. KU812 cell assays showed that modification by AAPH and acrolein caused the release of IL-4 and histamine to decline. In conclusion, oxidation treatment modified the functional and structural properties of CA, reducing allergenicity during processing and preservation.
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10
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Fernández Del Río B, Rey A. Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures. J Phys Chem B 2021; 125:6179-6191. [PMID: 34100621 PMCID: PMC8478274 DOI: 10.1021/acs.jpcb.1c03313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-based models are coarse-grained representations of the interactions responsible for the protein folding process. In their simplest form, they use only the native contact map of a given protein to predict the main features of its folding process by computer simulation. Given their limitations, these models are frequently complemented with sequence-dependent contributions or additional information. Specifically, to analyze the effect of pressure on the folding/unfolding transition, special forms of these interaction potentials are employed, which may a priori determine the outcome of the simulations. In this work, we have tried to keep the original simplicity of structure-based models. Therefore, we have used folded structures that have been experimentally determined at different pressures to define native contact maps and thus interactions dependent on pressure. Despite the apparently tiny structural differences induced by pressure, our simulation results provide different thermodynamic and kinetic behaviors, which roughly correspond to experimental observations (when there is a possible comparison) of two proteins used as benchmarks, hen egg-white lysozyme and dihydrofolate reductase. Therefore, this work shows the feasibility of using experimental native structures at different pressures to analyze the global effects of this physical property on the protein folding process.
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Affiliation(s)
- Beatriz Fernández Del Río
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Antonio Rey
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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Grünbein ML, Gorel A, Foucar L, Carbajo S, Colocho W, Gilevich S, Hartmann E, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Lewandowski J, Lutman A, Nass K, Nass Kovacs G, Roome CM, Sheppard J, Shoeman RL, Stricker M, van Driel T, Vetter S, Doak RB, Boutet S, Aquila A, Decker FJ, Barends TRM, Stan CA, Schlichting I. Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet. Nat Commun 2021; 12:1672. [PMID: 33723266 PMCID: PMC7960726 DOI: 10.1038/s41467-021-21819-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
X-ray free-electron lasers (XFELs) enable obtaining novel insights in structural biology. The recently available MHz repetition rate XFELs allow full data sets to be collected in shorter time and can also decrease sample consumption. However, the microsecond spacing of MHz XFEL pulses raises new challenges, including possible sample damage induced by shock waves that are launched by preceding pulses in the sample-carrying jet. We explored this matter with an X-ray-pump/X-ray-probe experiment employing haemoglobin microcrystals transported via a liquid jet into the XFEL beam. Diffraction data were collected using a shock-wave-free single-pulse scheme as well as the dual-pulse pump-probe scheme. The latter, relative to the former, reveals significant degradation of crystal hit rate, diffraction resolution and data quality. Crystal structures extracted from the two data sets also differ. Since our pump-probe attributes were chosen to emulate EuXFEL operation at its 4.5 MHz maximum pulse rate, this prompts concern about such data collection.
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Affiliation(s)
- Marie Luise Grünbein
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Alexander Gorel
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Lutz Foucar
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Sergio Carbajo
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - William Colocho
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Sasha Gilevich
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Elisabeth Hartmann
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Mario Hilpert
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Mark Hunter
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Marco Kloos
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany ,grid.434729.f0000 0004 0590 2900Present Address: European XFEL GmbH, Schenefeld, Germany
| | - Jason E. Koglin
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA ,grid.148313.c0000 0004 0428 3079Present Address: Los Alamos National Laboratory, Los Alamos, NM USA
| | - Thomas J. Lane
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA ,grid.466493.a0000 0004 0390 1787Present Address: Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Jim Lewandowski
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Alberto Lutman
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Karol Nass
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany ,grid.5991.40000 0001 1090 7501Present Address: Paul Scherrer Institut, Villigen, Switzerland
| | - Gabriela Nass Kovacs
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Christopher M. Roome
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - John Sheppard
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Robert L. Shoeman
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Miriam Stricker
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany ,grid.4991.50000 0004 1936 8948Present Address: Department of Statistics, University of Oxford, Oxford, UK
| | - Tim van Driel
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Sharon Vetter
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - R. Bruce Doak
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Sébastien Boutet
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Andrew Aquila
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Franz Josef Decker
- grid.445003.60000 0001 0725 7771SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Thomas R. M. Barends
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
| | - Claudiu Andrei Stan
- grid.430387.b0000 0004 1936 8796Department of Physics, Rutgers University Newark, Newark, NJ USA
| | - Ilme Schlichting
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany
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12
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Tanaka I, Nishinomiya R, Goto R, Shimazaki S, Chatake T. Recent structural insights into the mechanism of lysozyme hydrolysis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:288-292. [PMID: 33645532 PMCID: PMC7919404 DOI: 10.1107/s2059798321000346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
The complex of lysozyme with an N-acetylglucosamine tetramer shows a relatively strong hydrogen-bond network around a catalytic residue via high-resolution X-ray structural analysis. This indicates a potentially different hydrolysis mechanism to that through a glycosyl intermediate, and this is expected to be proved using neutron experiments. Lysozyme hydrolyzes the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycans located in the bacterial cell wall. The mechanism of the hydrolysis reaction of lysozyme was first studied more than 50 years ago; however, it has not yet been fully elucidated and various mechanisms are still being investigated. One reaction system that has commonly been proposed is that the lysozyme intermediate undergoes covalent ligand binding during hydrolysis. However, these findings resulted from experiments performed under laboratory conditions using fluorine-based ligands, which facilitate the formation of covalent bonds between the ligands and the catalytic side chain of lysozyme. More recently, high-resolution X-ray structural analysis was used to study the complex of lysozyme with an N-acetylglucosamine tetramer. As a result, the carboxyl group of Asp52 was found to form a relatively strong hydrogen-bond network and had difficulty binding covalently to C1 of the carbohydrate ring. To confirm this hydrogen-bond network, neutron test measurements were successfully performed to a resolution of better than 1.9 Å.
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Affiliation(s)
- Ichiro Tanaka
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Ryota Nishinomiya
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Ryosuke Goto
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Shun Shimazaki
- College of Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Toshiyuki Chatake
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
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13
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Inoue M, Hayashi T, Hikiri S, Ikeguchi M, Kinoshita M. Hydration properties of a protein at low and high pressures: Physics of pressure denaturation. J Chem Phys 2020; 152:065103. [PMID: 32061219 DOI: 10.1063/1.5140499] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Using experimentally determined structures of ubiquitin at 1 and 3000 bar, we generate sufficiently large ensembles of model structures in the native and pressure-induced (denatured) states by means of molecular dynamics simulations with explicit water. We calculate the values of a free-energy function (FEF), which comprises the hydration free energy (HFE) and the intramolecular (conformational) energy and entropy, for the two states at 1 and 3000 bar. The HFE and the conformational entropy, respectively, are calculated using our statistical-mechanical method, which has recently been shown to be accurate, and the Boltzmann-quasi-harmonic method. The HFE is decomposed into a variety of physically insightful components. We show that the FEF of the native state is lower than that of the denatured state at 1 bar, whereas the opposite is true at 3000 bar, thus being successful in reproducing the pressure denaturation. We argue that the following two quantities of hydration play essential roles in the denaturation: the WASA-dependent term in the water-entropy loss upon cavity creation for accommodating the protein (WASA is the water-accessible surface area of the cavity) and the protein-water Lennard-Jones interaction energy. At a high pressure, the mitigation of the serious water crowding in the system is the most important, and the WASA needs to be sufficiently enlarged with the increase in the excluded-volume being kept as small as possible. The denatured structure thus induced is characterized by the water penetration into the protein interior. The pressure denaturation is accompanied by a significantly large gain of water entropy.
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Affiliation(s)
- Masao Inoue
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Simon Hikiri
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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14
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Helliwell JR. What is the structural chemistry of the living organism at its temperature and pressure? Acta Crystallogr D Struct Biol 2020; 76:87-93. [PMID: 32038039 PMCID: PMC7008516 DOI: 10.1107/s2059798320000546] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/15/2020] [Indexed: 12/02/2022] Open
Abstract
The three probes of the structure of matter (X-rays, neutrons and electrons) in biology have complementary properties and strengths. The balance between these three probes within their strengths and weaknesses is perceived to change, even dramatically so at times. For the study of combined states of order and disorder, NMR crystallography is also applicable. Of course, to understand biological systems the required perspectives are surely physiologically relevant temperatures and relevant chemical conditions, as well as a minimal perturbation owing to the needs of the probe itself. These remain very tough challenges because, for example, cryoEM by its very nature will never be performed at room temperature, crystallization often requires nonphysiological chemical conditions, and X-rays and electrons cause beam damage. However, integrated structural biology techniques and functional assays provide a package towards physiological relevance of any given study. Reporting of protein crystal structures, and their associated database entries, could usefully indicate how close to the biological situation they are, as discussed in detail in this feature article.
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Affiliation(s)
- John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, England
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15
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Salinas-Garcia MC, Plaza-Garrido M, Alba-Elena D, Camara-Artigas A. Major conformational changes in the structure of lysozyme obtained from a crystal with a very low solvent content. Acta Crystallogr F Struct Biol Commun 2019; 75:687-696. [PMID: 31702582 PMCID: PMC6839823 DOI: 10.1107/s2053230x19013189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022] Open
Abstract
A new crystal form of lysozyme with a very low solvent content (26.35%) has been obtained in the orthorhombic space group P212121 (with unit-cell parameters a = 30.04, b = 51.68, c = 61.53 Å). The lysozyme structure obtained from these crystals does not show the typical overall fold. Instead, major conformational changes take place in some elements of the secondary structure and in the hydrophobic core of the protein. At the end of the central α-helix (α2), Glu35 is usually buried in the catalytic site and shows an abnormally high pKa value, which is key to the activity of the enzyme. The high pKa value of this glutamate residue is favoured by the hydrophobic environment, particularly by its neighbour Trp108, which is important for structural stability and saccharide binding. In this new structure, Trp108 shows a 90° rotation of its side chain, which results in the rearrangement of the hydrophobic core. Conformational changes also result in the exposure of Glu35 to the solvent, which impairs the catalytic site by increasing the distance between Glu35 and Asp52 and lowering the pKa value of the glutamate. Altogether, this new lysozyme structure reveals major conformational changes in the hydrophobic core and catalytic site that might play a role in the folding and bactericidal function of the protein.
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Affiliation(s)
- M. Carmen Salinas-Garcia
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - Marina Plaza-Garrido
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - Daniel Alba-Elena
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
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16
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Kordonskaya YV, Timofeev VI, Dyakova YA, Marchenkova MA, Pisarevsky YV, Podshivalov DD, Kovalchuk MV. Study of the Behavior of Lysozyme Oligomers in Solutions by the Molecular Dynamics Method. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518060196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Characterization of low-lying excited states of proteins by high-pressure NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:350-358. [PMID: 30366154 DOI: 10.1016/j.bbapap.2018.10.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/17/2018] [Accepted: 10/22/2018] [Indexed: 12/26/2022]
Abstract
Hydrostatic pressure alters the free energy of proteins by a few kJ mol-1, with the amount depending on their partial molar volumes. Because the folded ground state of a protein contains cavities, it is always a state of large partial molar volume. Therefore pressure always destabilises the ground state and increases the population of partially and completely unfolded states. This is a mild and reversible conformational change, which allows the study of excited states under thermodynamic equilibrium conditions. Many of the excited states studied in this way are functionally relevant; they also seem to be very similar to kinetic folding intermediates, thus suggesting that evolution has made use of the 'natural' dynamic energy landscape of the protein fold and sculpted it to optimise function. This includes features such as ligand binding, structural change during the catalytic cycle, and dynamic allostery.
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18
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Nagae T, Yamada H, Watanabe N. High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP . Acta Crystallogr D Struct Biol 2018; 74:895-905. [PMID: 30198899 PMCID: PMC6130465 DOI: 10.1107/s2059798318009397] [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: 02/26/2018] [Accepted: 06/29/2018] [Indexed: 11/10/2022] Open
Abstract
A high-pressure crystallographic study was conducted on Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ in crystal forms containing both the open and closed conformations of the M20 loop under high-pressure conditions of up to 800 MPa. At pressures between 270 and 500 MPa the crystal form containing the open conformation exhibited a phase transition from P21 to C2. Several structural changes in ecDHFR were observed at high pressure that were also accompanied by structural changes in the NADP+ cofactor and the hydration structure. In the crystal form with the closed conformation the M20 loop moved as the pressure changed, with accompanying conformational changes around the active site, including NADP+ and folate. These movements were consistent with the suggested hypothesis that movement of the M20 loop was necessary for ecDHFR to catalyze the reaction. In the crystal form with the open conformation the nicotinamide ring of the NADP+ cofactor undergoes a large flip as an intermediate step in the reaction, despite being in a crystalline state. Furthermore, observation of the water molecules between Arg57 and folate elucidated an early step in the substrate-binding pathway. These results demonstrate the possibility of using high-pressure protein crystallography as a method to capture high-energy substates or transient structures related to the protein reaction cycle.
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Affiliation(s)
- Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Hiroyuki Yamada
- Venture Business Laboratory, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Nobuhisa Watanabe
- Synchrotron Radiation Research Center, Nagoya University, Chikusa, Nagoya 464-8603, Japan
- Venture Business Laboratory, Nagoya University, Chikusa, Nagoya 464-8603, Japan
- Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
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19
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Juers DH, Farley CA, Saxby CP, Cotter RA, Cahn JKB, Holton-Burke RC, Harrison K, Wu Z. The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order. Acta Crystallogr D Struct Biol 2018; 74:922-938. [PMID: 30198901 PMCID: PMC6130464 DOI: 10.1107/s2059798318008793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/15/2018] [Indexed: 11/11/2022] Open
Abstract
Cryocooling of macromolecular crystals is commonly employed to limit radiation damage during X-ray diffraction data collection. However, cooling itself affects macromolecular conformation and often damages crystals via poorly understood processes. Here, the effects of cryosolution thermal contraction on macromolecular conformation and crystal order in crystals ranging from 32 to 67% solvent content are systematically investigated. It is found that the solution thermal contraction affects macromolecule configurations and volumes, unit-cell volumes, crystal packing and crystal order. The effects occur through not only thermal contraction, but also pressure caused by the mismatched contraction of cryosolvent and pores. Higher solvent-content crystals are more affected. In some cases the solvent contraction can be adjusted to reduce mosaicity and increase the strength of diffraction. Ice formation in some crystals is found to cause damage via a reduction in unit-cell volume, which is interpreted through solvent transport out of unit cells during cooling. The results point to more deductive approaches to cryoprotection optimization by adjusting the cryosolution composition to reduce thermal contraction-induced stresses in the crystal with cooling.
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Affiliation(s)
- Douglas H. Juers
- Department of Physics, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
- Program in BBMB, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Christopher A. Farley
- Department of Physics, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | | | - Rosemary A. Cotter
- Program in BBMB, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Jackson K. B. Cahn
- Program in BBMB, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | | | - Kaitlin Harrison
- Program in BBMB, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
| | - Zhenguo Wu
- Department of Physics, Whitman College, 345 Boyer Avenue, Walla Walla, WA 99362, USA
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20
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Tanaka I, Komatsuzaki N, Yue WX, Chatake T, Kusaka K, Niimura N, Miura D, Iwata T, Miyachi Y, Nukazuka G, Matsuda H. Cryoprotectant-free high-pressure cooling and dynamic nuclear polarization for more sensitive detection of hydrogen in neutron protein crystallography. Acta Crystallogr D Struct Biol 2018; 74:787-791. [PMID: 30082514 PMCID: PMC6079630 DOI: 10.1107/s2059798318005028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/27/2018] [Indexed: 11/21/2022] Open
Abstract
To improve the sensitivity of hydrogen detection using neutrons, a proton-polarization technique together with a high-pressure cooling method is necessary. The highest pressure (200 MPa) used in the experiment described here enabled relatively large protein crystals to be cooled without any cryoprotectants while retaining the protein structure, and it was confirmed that high-pressure-cooled crystals diffracted to nearly the same resolution as flash-cooled small crystals soaked with cryoprotectants. Dynamic nuclear polarization was used as a proton-polarization technique for protein crystals, and ∼300 mg polycrystalline protein doped with TEMPOL gave a maximum proton polarization of 22.3% at a temperature of 0.5 K in a 2.5 T magnetic field.
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Affiliation(s)
- Ichiro Tanaka
- College of Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106, Japan
| | - Naoya Komatsuzaki
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Wen-Xue Yue
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Toshiyuki Chatake
- Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106, Japan
| | - Daisuke Miura
- Faculty of Science, Yamagata University, Yamagata, Yamagata 990-8560, Japan
| | - Takahiro Iwata
- Faculty of Science, Yamagata University, Yamagata, Yamagata 990-8560, Japan
| | - Yoshiyuki Miyachi
- Faculty of Science, Yamagata University, Yamagata, Yamagata 990-8560, Japan
| | - Genki Nukazuka
- Faculty of Science, Yamagata University, Yamagata, Yamagata 990-8560, Japan
| | - Hiroki Matsuda
- Faculty of Science, Yamagata University, Yamagata, Yamagata 990-8560, Japan
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21
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Okamoto T, Ohmichi E, Saito Y, Sakurai T, Ohta H. Pressure Effect on Zero-Field Splitting Parameter of Hemin: Model Case of Hemoproteins under Pressure. J Phys Chem B 2018; 122:6880-6887. [PMID: 29902002 DOI: 10.1021/acs.jpcb.8b03128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We experimentally studied the pressure dependence of the zero-field splitting (ZFS) parameter of hemin (iron(III) protoporphyrin IX chloride), which is a model complex of hemoproteins, via high-frequency and high-field electron paramagnetic resonance (HFEPR) under pressure. Owing to the large ZFS, the pressure effect on the electronic structure of iron-porphyrin complexes has not yet been explored using EPR. Therefore, we systematically studied this effect using our newly developed sub-terahertz EPR spectroscopy system in the frequency range of 80-515 GHz, under magnetic fields up to 10 T and pressure up to 2 GPa. We observed a systematic shift of the resonance fields of hemin upon pressure application, from which the axial component of the ZFS parameter was found to increase from D = 6.9 to 7.9 cm-1 at 2 GPa. In contrast to the previous methods used to study proteins under pressure, which mainly focused on conformational changes, our HFEPR technique can obtain more microscopic insights into the electronic structures of metal ions under pressure. In this sense, our technique provides novel opportunities to study the pressure effects on biofunctional active centers of versatile metalloproteins.
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22
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Jeszenői N, Schilli G, Bálint M, Horváth I, Hetényi C. Analysis of the influence of simulation parameters on biomolecule-linked water networks. J Mol Graph Model 2018; 82:117-128. [DOI: 10.1016/j.jmgm.2018.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/27/2018] [Accepted: 04/21/2018] [Indexed: 12/11/2022]
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23
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Quirnheim Pais D, Rathmann B, Koepke J, Tomova C, Wurzinger P, Thielmann Y. A standardized technique for high-pressure cooling of protein crystals. Acta Crystallogr D Struct Biol 2017; 73:997-1006. [PMID: 29199979 PMCID: PMC6116161 DOI: 10.1107/s2059798317016357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/14/2017] [Indexed: 12/02/2022] Open
Abstract
Cryogenic temperatures slow down secondary radiation damage during data collection from macromolecular crystals. In 1973, cooling at high pressure was identified as a method for cryopreserving crystals in their mother liquor [Thomanek et al. (1973). Acta Cryst. A29, 263-265]. Results from different groups studying different crystal systems indicated that the approach had merit, although difficulties in making the process work have limited its widespread use. Therefore, a simplified and reliable technique has been developed termed high-pressure cooling (HPC). An essential requirement for HPC is to protect crystals in capillaries. These capillaries form part of new sample holders with SPINE standard dimensions. Crystals are harvested with the capillary, cooled at high pressure (220 MPa) and stored in a cryovial. This system also allows the usage of the standard automation at the synchrotron. Crystals of hen egg-white lysozyme and concanavalin A have been successfully cryopreserved and yielded data sets to resolutions of 1.45 and 1.35 Å, respectively. Extensive work has been performed to define the useful working range of HPC in capillaries with 250 µm inner diameter. Three different 96-well crystallization screens that are most frequently used in our crystallization facility were chosen to study the formation of amorphous ice in this cooling setup. More than 89% of the screening solutions were directly suitable for HPC. This achievement represents a drastic improvement for crystals that suffered from cryoprotection or were not previously eligible for cryoprotection.
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Affiliation(s)
- David Quirnheim Pais
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Barbara Rathmann
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Juergen Koepke
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Cveta Tomova
- Leica Microsystems Vienna, Hernalser Hauptstrasse 219, 1170 Vienna, Austria
| | - Paul Wurzinger
- Leica Microsystems Vienna, Hernalser Hauptstrasse 219, 1170 Vienna, Austria
| | - Yvonne Thielmann
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
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24
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Molitor C, Bijelic A, Rompel A. The potential of hexatungstotellurate(VI) to induce a significant entropic gain during protein crystallization. IUCRJ 2017; 4:734-740. [PMID: 29123675 PMCID: PMC5668858 DOI: 10.1107/s2052252517012349] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/25/2017] [Indexed: 06/01/2023]
Abstract
The limiting factor in protein crystallography is still the production of high-quality crystals. In this regard, the authors have recently introduced hexatungstotellurate(VI) (TEW) as a new crystallization additive, which proved to be successful within the liquid-liquid phase separation (LLPS) zone. Presented here are comparative crystal structure analyses revealing that protein-TEW binding not only induces and stabilizes crystal contacts, but also exhibits a significant impact on the solvent-driven crystallization entropy, which is the driving force for the crystallization process. Upon the formation of TEW-mediated protein-protein contacts, the release of water molecules from the hydration shells of both molecules, i.e. TEW and the protein, causes a reduced solvent-accessible surface area, leading to a significant gain in solvent entropy. Based on the crystal structures of aurone synthase (in the presence and absence of TEW), insights have also been provided into the formation of a metastable LLPS, which is caused by the formation of protein clusters, representing an ideal starting point in protein crystallization. The results strongly encourage the classification of TEW as a valuable crystallization additive.
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Affiliation(s)
- Christian Molitor
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstrasse 14, Wien 1090, Austria
| | - Aleksandar Bijelic
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstrasse 14, Wien 1090, Austria
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstrasse 14, Wien 1090, Austria
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25
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Boikova AS, Dyakova YA, Ilina KB, Konarev PV, Kryukova AE, Kuklin AI, Marchenkova MA, Nabatov BV, Blagov AE, Pisarevsky YV, Kovalchuk MV. Octamer formation in lysozyme solutions at the initial crystallization stage detected by small-angle neutron scattering. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:591-599. [PMID: 28695859 DOI: 10.1107/s2059798317007422] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/19/2017] [Indexed: 11/10/2022]
Abstract
Solutions of lysozyme in heavy water were studied by small-angle neutron scattering (SANS) at concentrations of 40, 20 and 10 mg ml-1 with and without the addition of precipitant, and at temperatures of 10, 20 and 30°C. In addition to the expected protein monomers, dimeric and octameric species were identified in solutions at the maximum concentration and close to the optimal conditions for crystallization. An optimal temperature for octamer formation was identified and both deviation from this temperature and a reduction in protein concentration led to a significant decrease in the volume fractions of octamers detected. In the absence of precipitant, only monomers and a minor fraction of dimers are present in solution.
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Affiliation(s)
- Anastasiia S Boikova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Yulia A Dyakova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Kseniia B Ilina
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Petr V Konarev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Alyona E Kryukova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Alexandr I Kuklin
- The Joint Institute for Nuclear Research, Joliot-Curie str. 6, Dubna 141980, Russian Federation
| | - Margarita A Marchenkova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Boris V Nabatov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Alexandr E Blagov
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Yurii V Pisarevsky
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
| | - Mikhail V Kovalchuk
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics', Russian Academy of Sciences, Leninskii pr. 59, Moscow 119333, Russian Federation
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Tamai E, Sekiya H, Goda E, Makihata N, Maki J, Yoshida H, Kamitori S. Structural and biochemical characterization of the Clostridium perfringens autolysin catalytic domain. FEBS Lett 2016; 591:231-239. [PMID: 27926788 DOI: 10.1002/1873-3468.12515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/17/2016] [Accepted: 11/26/2016] [Indexed: 11/08/2022]
Abstract
Bacterial autolysins can partially hydrolyze cell wall peptidoglycans into small sections to regulate cell separation/division and the growth phase. Clostridium perfringens autolysin (Acp) has an N-terminal cell wall-binding domain and a C-terminal catalytic domain with glucosaminidase activity that belongs to the glycoside hydrolase 73 family. Here, we determined the X-ray structure of the Acp catalytic domain (AcpCD) at 1.76 Å resolution. AcpCD has a unique crescent-shaped structure, forming a deep groove for substrate-binding at the center of the protein. The modeling study of the enzyme/substrate complex demonstrated that the length of the substrate-binding groove is closely related to the glucosaminidase activity. Mutagenesis analysis showed that AcpCD likely adopts a neighboring-group mechanism for the catalytic reaction.
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Affiliation(s)
- Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan.,Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Eri Goda
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Nahomi Makihata
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Jun Maki
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
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Tidey JP, Wong HLS, McMaster J, Schröder M, Blake AJ. High-pressure studies of three polymorphs of a palladium(II) oxathioether macrocyclic complex. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:357-371. [PMID: 27240767 DOI: 10.1107/s2052520616007435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/04/2016] [Indexed: 06/05/2023]
Abstract
The three reported phases of the mononuclear macrocyclic Pd(II) complex [PdCl2([9]aneS2O)] [(1); [9]aneS2O = 1-oxa-4,7-dithiacyclononane] were each studied up to pressures exceeding 9 GPa using high-pressure single-crystal X-ray diffraction. The α- and γ-phases both exhibit smooth compression of the unit-cell parameters with third-order Birch-Murnaghan bulk moduli of 14.4 (8) and 7.6 (6) GPa, respectively. Between 6.81 and 6.87 GPa β-[PdCl2([9]aneS2O)] was found to undergo a reversible transition to a phase denoted as β' and characterized by a tripling of the unit-cell volume. Across the phase transition, rearrangement of the conformation of the bound macrocycle at two of the resulting three unique sites gives rise to an extensively disordered structure.
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Affiliation(s)
- Jeremiah P Tidey
- School of Chemistry, The University of Nottingham, University Park, Nottingham NG7 2RD, England
| | - Henry L S Wong
- School of Chemistry, The University of Nottingham, University Park, Nottingham NG7 2RD, England
| | - Jonathan McMaster
- School of Chemistry, The University of Nottingham, University Park, Nottingham NG7 2RD, England
| | - Martin Schröder
- School of Chemistry, The University of Nottingham, University Park, Nottingham NG7 2RD, England
| | - Alexander J Blake
- School of Chemistry, The University of Nottingham, University Park, Nottingham NG7 2RD, England
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Hayashi M, Nishiyama M, Kazayama Y, Toyota T, Harada Y, Takiguchi K. Reversible Morphological Control of Tubulin-Encapsulating Giant Liposomes by Hydrostatic Pressure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3794-3802. [PMID: 27023063 DOI: 10.1021/acs.langmuir.6b00799] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Liposomes encapsulating cytoskeletons have drawn much recent attention to develop an artificial cell-like chemical-machinery; however, as far as we know, there has been no report showing isothermally reversible morphological changes of liposomes containing cytoskeletons because the sets of various regulatory factors, that is, their interacting proteins, are required to control the state of every reaction system of cytoskeletons. Here we focused on hydrostatic pressure to control the polymerization state of microtubules (MTs) within cell-sized giant liposomes (diameters ∼10 μm). MT is the cytoskeleton formed by the polymerization of tubulin, and cytoskeletal systems consisting of MTs are very dynamic and play many important roles in living cells, such as the morphogenesis of nerve cells and formation of the spindle apparatus during mitosis. Using real-time imaging with a high-pressure microscope, we examined the effects of hydrostatic pressure on the morphology of tubulin-encapsulating giant liposomes. At ambient pressure (0.1 MPa), many liposomes formed protrusions due to tubulin polymerization within them. When high pressure (60 MPa) was applied, the protrusions shrank within several tens of seconds. This process was repeatedly inducible (around three times), and after the pressure was released, the protrusions regenerated within several minutes. These deformation rates of the liposomes are close to the velocities of migrating or shape-changing living cells rather than the shortening and elongation rates of the single MTs, which have been previously measured. These results demonstrate that the elongation and shortening of protrusions of giant liposomes is repeatedly controllable by regulating the polymerization state of MTs within them by applying and releasing hydrostatic pressure.
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Affiliation(s)
- Masahito Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University , Nagoya 464-8602, Japan
| | | | | | | | | | - Kingo Takiguchi
- Division of Biological Science, Graduate School of Science, Nagoya University , Nagoya 464-8602, Japan
- Structural Biology Research Center, Nagoya University , Nagoya 464-8601, Japan
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