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Catapano L, Long F, Yamashita K, Nicholls RA, Steiner RA, Murshudov GN. Neutron crystallographic refinement with REFMAC5 from the CCP4 suite. Acta Crystallogr D Struct Biol 2023; 79:1056-1070. [PMID: 37921806 PMCID: PMC7615533 DOI: 10.1107/s2059798323008793] [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: 08/06/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023] Open
Abstract
Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein-protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium-low resolution.
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Affiliation(s)
- Lucrezia Catapano
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Fei Long
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Keitaro Yamashita
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Roberto A. Steiner
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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2
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Nakamura T, Yamagata Y. Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Proc Natl Acad Sci U S A 2022; 119:e2203118119. [PMID: 35594391 PMCID: PMC9173781 DOI: 10.1073/pnas.2203118119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/09/2022] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli MutT prevents mutations by hydrolyzing mutagenic 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP) in the presence of Mg2+ or Mn2+ ions. MutT is one of the most studied enzymes in the nucleoside diphosphate-linked moiety X (Nudix) hydrolase superfamily, which is widely distributed in living organisms. However, the catalytic mechanisms of most Nudix hydrolases, including two- or three-metal-ion mechanisms, are still unclear because these mechanisms are proposed using the structures mimicking the reaction states, such as substrate analog complexes. Here, we visualized the hydrolytic reaction process of MutT by time-resolved X-ray crystallography using a biological substrate, 8-oxo-dGTP, and an active metal ion, Mn2+. The reaction was initiated by soaking MutT crystals in a MnCl2 solution and stopped by freezing the crystals at various time points. In total, five types of intermediate structures were refined by investigating the time course of the electron densities in the active site as well as the anomalous signal intensities of Mn2+ ions. The structures and electron densities show that three Mn2+ ions bind to the Nudix motif of MutT and align the substrate 8-oxo-dGTP for catalysis. Accompanied by the coordination of the three Mn2+ ions, a water molecule, bound to a catalytic base, forms a binuclear Mn2+ center for nucleophilic substitution at the β-phosphorus of 8-oxo-dGTP. The reaction condition using Mg2+ also captured a structure in complex with three Mg2+ ions. This study provides the structural details essential for understanding the three-metal-ion mechanism of Nudix hydrolases and proposes that some of the Nudix hydrolases share this mechanism.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Shokei University and Shokei University Junior College, Kumamoto, 862-8678, Japan
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3
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Chemo-Enzymatic Baeyer-Villiger Oxidation Facilitated with Lipases Immobilized in the Supported Ionic Liquid Phase. MATERIALS 2021; 14:ma14133443. [PMID: 34206178 PMCID: PMC8269471 DOI: 10.3390/ma14133443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/27/2022]
Abstract
A novel method for chemo-enzymatic Baeyer–Villiger oxidation of cyclic ketones in the presence of supported ionic liquid-like phase biocatalyst was designed. In this work, multi-walled carbon nanotubes were applied as a support for ionic liquids which were anchored to nanotubes covalently by amide or imine bonds. Next, lipases B from Candida antarctica, Candida rugosa, or Aspergillus oryzae were immobilized on the prepared materials. The biocatalysts were characterized using various techniques, like thermogravimetry, IR spectroscopy, XPS, elemental analysis, and SEM-EDS microscopy. In the proposed approach, a biocatalyst consisting of a lipase as an active phase allowed the generation of peracid in situ from the corresponding precursor and a green oxidant–hydrogen peroxide. The activity and stability of the obtained biocatalysts in the model oxidation of 2-adamantanone were demonstrated. High conversion of substrate (92%) was achieved under favorable conditions (toluene: n-octanoic acid ratio 1:1 = v:v, 35% aq. H2O2 2 eq., 0.080 g of biocatalyst per 1 mmol of ketone at 20 °C, reaction time 4 h) with four reaction cycles without a drop in its activity. Our ‘properties-by-design’ approach is distinguished by its short reaction time at low temperature and higher thermal stability in comparison with other biocatalysts presented in the literature reports.
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4
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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: 1] [Impact Index Per Article: 0.3] [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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Rose SL, Antonyuk SV, Sasaki D, Yamashita K, Hirata K, Ueno G, Ago H, Eady RR, Tosha T, Yamamoto M, Hasnain SS. An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures. SCIENCE ADVANCES 2021; 7:eabd8523. [PMID: 33523860 PMCID: PMC7775769 DOI: 10.1126/sciadv.abd8523] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/27/2020] [Indexed: 05/31/2023]
Abstract
Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br 2DNiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br 2DNiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated.
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Affiliation(s)
- Samuel L Rose
- Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Daisuke Sasaki
- Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kunio Hirata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Robert R Eady
- Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
| | - S Samar Hasnain
- Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK.
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6
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Lubkowski J, Vanegas J, Chan WK, Lorenzi PL, Weinstein JN, Sukharev S, Fushman D, Rempe S, Anishkin A, Wlodawer A. Mechanism of Catalysis by l-Asparaginase. Biochemistry 2020; 59:1927-1945. [PMID: 32364696 DOI: 10.1021/acs.biochem.0c00116] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two bacterial type II l-asparaginases, from Escherichia coli and Dickeya chrysanthemi, have played a critical role for more than 40 years as therapeutic agents against juvenile leukemias and lymphomas. Despite a long history of successful pharmacological applications and the apparent simplicity of the catalytic reaction, controversies still exist regarding major steps of the mechanism. In this report, we provide a detailed description of the reaction catalyzed by E. coli type II l-asparaginase (EcAII). Our model was developed on the basis of new structural and biochemical experiments combined with previously published data. The proposed mechanism is supported by quantum chemistry calculations based on density functional theory. We provide strong evidence that EcAII catalyzes the reaction according to the double-displacement (ping-pong) mechanism, with formation of a covalent intermediate. Several steps of catalysis by EcAII are unique when compared to reactions catalyzed by other known hydrolytic enzymes. Here, the reaction is initiated by a weak nucleophile, threonine, without direct assistance of a general base, although a distant general base is identified. Furthermore, tetrahedral intermediates formed during the catalytic process are stabilized by a never previously described motif. Although the scheme of the catalytic mechanism was developed only on the basis of data obtained from EcAII and its variants, this novel mechanism of enzymatic hydrolysis could potentially apply to most (and possibly all) l-asparaginases.
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Affiliation(s)
- Jacek Lubkowski
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Juan Vanegas
- Department of Physics, The University of Vermont, Burlington, Vermont 05408, United States
| | - Wai-Kin Chan
- Department of Bioinformatics and Computational Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, United States
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, United States
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, United States
| | - Sergei Sukharev
- Department of Biology, University of Maryland, College Park, Maryland 20742, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Susan Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, Maryland 20742, United States
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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7
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Szelwicka A, Kolanowska A, Latos P, Jurczyk S, Boncel S, Chrobok A. Carbon nanotube/PTFE as a hybrid platform for lipase B from Candida antarctica in transformation of α-angelica lactone into alkyl levulinates. Catal Sci Technol 2020. [DOI: 10.1039/d0cy00545b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly active biocatalyst based on a hybrid platform was designed for the conversion of α-angelica lactone to alkyl levulinates.
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Affiliation(s)
- Anna Szelwicka
- Department of Organic Chemical Technology and Petrochemistry
- Silesian University of Technology
- 44-100 Gliwice
- Poland
| | - Anna Kolanowska
- Department of Organic Chemistry
- Bioorganic Chemistry and Biotechnology
- Silesian University of Technology
- 44-100 Gliwice
- Poland
| | - Piotr Latos
- Department of Organic Chemical Technology and Petrochemistry
- Silesian University of Technology
- 44-100 Gliwice
- Poland
| | - Sebastian Jurczyk
- Łukasiewicz Research Network - Institute for Engineering of Polymer Materials and Dyes
- 87-100 Toruń
- Poland
| | - Slawomir Boncel
- Department of Organic Chemistry
- Bioorganic Chemistry and Biotechnology
- Silesian University of Technology
- 44-100 Gliwice
- Poland
| | - Anna Chrobok
- Department of Organic Chemical Technology and Petrochemistry
- Silesian University of Technology
- 44-100 Gliwice
- Poland
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8
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Malaspina LA, Wieduwilt EK, Bergmann J, Kleemiss F, Meyer B, Ruiz-López MF, Pal R, Hupf E, Beckmann J, Piltz RO, Edwards AJ, Grabowsky S, Genoni A. Fast and Accurate Quantum Crystallography: From Small to Large, from Light to Heavy. J Phys Chem Lett 2019; 10:6973-6982. [PMID: 31633355 DOI: 10.1021/acs.jpclett.9b02646] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The coupling of the crystallographic refinement technique Hirshfeld atom refinement (HAR) with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) gives rise to the new quantum-crystallographic method HAR-ELMO. This method is significantly faster than HAR but as accurate and precise, especially concerning the free refinement of hydrogen atoms from X-ray diffraction data, so that the first fully quantum-crystallographic refinement of a protein is presented here. However, the promise of HAR-ELMO exceeds large molecules and protein crystallography. In fact, it also renders possible electron-density investigations of heavy elements in small molecules and facilitates the detection and isolation of systematic errors from physical effects.
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Affiliation(s)
- Lorraine A Malaspina
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Erna K Wieduwilt
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Justin Bergmann
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Florian Kleemiss
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Departement für Chemie und Biochemie , Universität Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Benjamin Meyer
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Manuel F Ruiz-López
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Rumpa Pal
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Ross O Piltz
- Australian Nuclear Science and Technology Organisation , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , NSW 2234 , Australia
| | - Alison J Edwards
- Australian Nuclear Science and Technology Organisation , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , NSW 2234 , Australia
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Departement für Chemie und Biochemie , Universität Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Alessandro Genoni
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
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9
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Takaba K, Tai Y, Eki H, Dao HA, Hanazono Y, Hasegawa K, Miki K, Takeda K. Subatomic resolution X-ray structures of green fluorescent protein. IUCRJ 2019; 6:387-400. [PMID: 31098020 PMCID: PMC6503917 DOI: 10.1107/s205225251900246x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/17/2019] [Indexed: 05/06/2023]
Abstract
Green fluorescent protein (GFP) is a light-emitting protein that does not require a prosthetic group for its fluorescent activity. As such, GFP has become indispensable as a molecular tool in molecular biology. Nonetheless, there has been no subatomic elucidation of the GFP structure owing to the structural polymorphism around the chromophore. Here, subatomic resolution X-ray structures of GFP without the structural polymorphism are reported. The positions of H atoms, hydrogen-bonding network patterns and accurate geometric parameters were determined for the two protonated forms. Compared with previously determined crystal structures and theoretically optimized structures, the anionic chromophores of the structures represent the authentic resonance state of GFP. In addition, charge-density analysis based on atoms-in-molecules theory and noncovalent interaction analysis highlight weak but substantial interactions between the chromophore and the protein environment. Considered with the derived chemical indicators, the lone pair-π interactions between the chromophore and Thr62 should play a sufficient role in maintaining the electronic state of the chromophore. These results not only reveal the fine structural features that are critical to understanding the properties of GFP, but also highlight the limitations of current quantum-chemical calculations.
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Affiliation(s)
- Kiyofumi Takaba
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yang Tai
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Haruhiko Eki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hoang-Anh Dao
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuya Hanazono
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuya Hasegawa
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- Correspondence e-mail:
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10
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Si W, Zhang Y, Wu G, Kan Y, Zhang Y, Sha J, Chen Y. Discrimination of Protein Amino Acid or Its Protonated State at Single-Residue Resolution by Graphene Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900036. [PMID: 30848871 DOI: 10.1002/smll.201900036] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/24/2019] [Indexed: 05/03/2023]
Abstract
The function of a protein is determined by the composition of amino acids and is essential to proteomics. However, protein sequencing remains challenging due to the protein's irregular charge state and its high-order structure. Here, a proof of principle study on the capability of protein sequencing by graphene nanopores integrated with atomic force microscopy is performed using molecular dynamics simulations. It is found that nanopores can discriminate a protein sequence and even its protonation state at single-residue resolution. Both the pulling forces and current blockades induced by the permeation of protein residues are found to be highly correlated with the type of amino acids, which makes the residues identifiable. It is also found that aside from the dimension, both the conformation and charge state of the residue can significantly influence the force and current signal during its permeation through the nanopore. In particular, due to the electro-osmotic flow effect, the blockade current for the double-protonated histidine is slightly smaller than that for single-protonated histidine, which makes it possible for discrimination of different protonation states of amino acids. The results reported here present a novel protein sequencing scheme using graphene nanopores combined with nanomanipulation technology.
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Affiliation(s)
- Wei Si
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yin Zhang
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yajing Kan
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yan Zhang
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Jingjie Sha
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yunfei Chen
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
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11
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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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Matsuo T, Kono T, Shobu I, Ishida M, Gonda K, Hirota S. Global Structural Flexibility of Metalloproteins Regulates Reactivity of Transition Metal Ion in the Protein Core: An Experimental Study Using Thiol-subtilisin as a Model Protein. Chemistry 2018; 24:2767-2775. [DOI: 10.1002/chem.201705920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Takashi Matsuo
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Takamasa Kono
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Isamu Shobu
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Masaya Ishida
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Katsuya Gonda
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Shun Hirota
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
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13
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Tang H, Cui F, Li H, Huang Q, Li Y. Understanding the inhibitory mechanism of tea polyphenols against tyrosinase using fluorescence spectroscopy, cyclic voltammetry, oximetry, and molecular simulations. RSC Adv 2018; 8:8310-8318. [PMID: 35542029 PMCID: PMC9078569 DOI: 10.1039/c7ra12749a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/15/2018] [Indexed: 11/21/2022] Open
Abstract
Inhibiting the activity of tyrosinase is a very effective and safe way to prevent enzymatic browning in food and to resist pests in agriculture. Tea polyphenols (TPs), regarded as safe and non-toxic food additives, have been reported due to their potential inhibitory capability against tyrosinase, but their ambiguous inhibitory mechanisms have severely limited their application. In the present work, fluorescence spectroscopy, cyclic voltammetry (CV), oximetry and molecular simulation approaches were employed to shed light on the underlying inhibitory mechanisms of TPs with different structures including (+)-catechin, (−)-epicatechin gallate (ECG) and (−)-epigallocatechin gallate (EGCG) against tyrosinase. Fluorescence spectra show that the three TPs are capable of binding tyrosinase with a molar proportion of 1 : 1. The analysis of CV curves and oxygen utilization suggests that these three TPs can be oxidized by tyrosinase, revealing that these three TPs are suicide inhibitors of tyrosinase. Furthermore, ECG and catechin make tyrosinase irreversibly inactivated due to their catechol group (ring B) being catalyzed by tyrosinase through a cresolase-like pathway, while EGCG inhibits the activity of tyrosinase by competing with or delaying the oxidation of substrate. Molecular simulations further confirm that ring B of ECG and catechin makes a significant contribution to tyrosinase inhibitory activities, and has a direct interaction with the coupled binuclear copper ions in the optimal orientation required by the cresolase-like pathway. Revealing the inactivation mechanism of TPs on inhibiting the activity of tyrosinase.![]()
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Affiliation(s)
- Haifeng Tang
- Key Laboratory of Synthetic Rubber
- Changchun Institute of Applied Chemistry (CIAC)
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Fengchao Cui
- Key Laboratory of Synthetic Rubber
- Changchun Institute of Applied Chemistry (CIAC)
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry (CIAC)
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Qingrong Huang
- Department of Food Science
- Rutgers University
- New Brunswick
- USA
| | - Yunqi Li
- Key Laboratory of Synthetic Rubber
- Changchun Institute of Applied Chemistry (CIAC)
- Chinese Academy of Sciences
- Changchun
- P. R. China
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14
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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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15
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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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16
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Waz S, Nakamura T, Hirata K, Koga-Ogawa Y, Chirifu M, Arimori T, Tamada T, Ikemizu S, Nakabeppu Y, Yamagata Y. Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity. J Biol Chem 2016; 292:2785-2794. [PMID: 28035004 PMCID: PMC5314174 DOI: 10.1074/jbc.m116.749713] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/23/2016] [Indexed: 01/29/2023] Open
Abstract
The human MutT homolog 1 (hMTH1, human NUDT1) hydrolyzes oxidatively damaged nucleoside triphosphates and is the main enzyme responsible for nucleotide sanitization. hMTH1 recently has received attention as an anticancer target because hMTH1 blockade leads to accumulation of oxidized nucleotides in the cell, resulting in mutations and death of cancer cells. Unlike Escherichia coli MutT, which shows high substrate specificity for 8-oxoguanine nucleotides, hMTH1 has broad substrate specificity for oxidized nucleotides, including 8-oxo-dGTP and 2-oxo-dATP. However, the reason for this broad substrate specificity remains unclear. Here, we determined crystal structures of hMTH1 in complex with 8-oxo-dGTP or 2-oxo-dATP at neutral pH. These structures based on high quality data showed that the base moieties of two substrates are located on the similar but not the same position in the substrate binding pocket and adopt a different hydrogen-bonding pattern, and both triphosphate moieties bind to the hMTH1 Nudix motif (i.e. the hydrolase motif) similarly and align for the hydrolysis reaction. We also performed kinetic assays on the substrate-binding Asp-120 mutants (D120N and D120A), and determined their crystal structures in complex with the substrates. Analyses of bond lengths with high-resolution X-ray data and the relationship between the structure and enzymatic activity revealed that hMTH1 recognizes the different oxidized nucleotides via an exchange of the protonation state at two neighboring aspartate residues (Asp-119 and Asp-120) in its substrate binding pocket. To our knowledge, this mechanism of broad substrate recognition by enzymes has not been reported previously and may have relevance for anticancer drug development strategies targeting hMTH1.
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Affiliation(s)
- Shaimaa Waz
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Teruya Nakamura
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973.,the Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto 862-0973
| | - Keisuke Hirata
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Yukari Koga-Ogawa
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Mami Chirifu
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Takao Arimori
- the Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, and
| | - Taro Tamada
- the Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, and
| | - Shinji Ikemizu
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Yusaku Nakabeppu
- the Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuriko Yamagata
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973,
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17
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Zhang L, Li Y, Yuan Y, Jiang Y, Guo Y, Li M, Pu X. Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media. Sci Rep 2016; 6:36838. [PMID: 27874101 PMCID: PMC5118797 DOI: 10.1038/srep36838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/17/2016] [Indexed: 02/04/2023] Open
Abstract
In the work, we mainly used molecular dynamics (MD) simulation and protein structure network (PSN) to study subtilisin Carlsberg (SC) immobilized onto carbon nanotube (CNT) in water, acetonitrile and heptane solvents, in order to explore activation mechanism of enzymes in non-aqueous media. The result indicates that the affinity of SC with CNT follows the decreasing order of water > acetonitrile > heptane. The overall structure of SC and the catalytic triad display strong robustness to the change of environments, responsible for the activity retaining. However, the distances between two β-strands of substrate-binding pocket are significantly expanded by the immobilization in the increasing order of water < acetonitrile < heptane, contributing to the highest substrate-binding energy in heptane media. PSN analysis further reveals that the immobilization enhances structural communication paths to the substrate-binding pocket, leading to its larger change than the free-enzymes. Interestingly, the increase in the number of the pathways upon immobilization is not dependent on the absorbed extent but the desorbed one, indicating significant role of shifting process of experimental operations in influencing the functional region. In addition, some conserved and important hot-residues in the paths are identified, providing molecular information for functional modification.
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Affiliation(s)
- Liyun Zhang
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yuzhi Li
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu 610041, People's Republic of China
| | - Yuanyuan Jiang
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Menglong Li
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
| | - Xuemei Pu
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
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Structure of the unliganded form of the proprotein convertase furin suggests activation by a substrate-induced mechanism. Proc Natl Acad Sci U S A 2016; 113:11196-11201. [PMID: 27647913 DOI: 10.1073/pnas.1613630113] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Proprotein convertases (PCs) are highly specific proteases required for the proteolytic modification of many secreted proteins. An unbalanced activity of these enzymes is connected to pathologies like cancer, atherosclerosis, hypercholesterolaemia, and infectious diseases. Novel protein crystallographic structures of the prototypical PC family member furin in different functional states were determined to 1.8-2.0 Å. These, together with biochemical data and modeling by molecular dynamics calculations, suggest essential elements underlying its unusually high substrate specificity. Furin shows a complex activation mechanism and exists in at least four defined states: (i) the "off state," incompatible with substrate binding as seen in the unliganded enzyme; (ii) the active "on state" seen in inhibitor-bound furin; and the respective (iii) calcium-free and (iv) calcium-bound forms. The transition from the off to the on state is triggered by ligand binding at subsites S1 to S4 and appears to underlie the preferential recognition of the four-residue sequence motif of furin. The molecular dynamics simulations of the four structural states reflect the experimental observations in general and provide approximations of the respective stabilities. Ligation by calcium at the PC-specific binding site II influences the active-site geometry and determines the rotamer state of the oxyanion hole-forming Asn295, and thus adds a second level of the activity modulation of furin. The described crystal forms and the observations of different defined functional states may foster the development of new tools and strategies for pharmacological intervention targeting furin.
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19
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Stauch B, Fisher SJ, Cianci M. Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation. J Lipid Res 2015; 56:2348-58. [PMID: 26447231 PMCID: PMC4655990 DOI: 10.1194/jlr.m063388] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 11/20/2022] Open
Abstract
Lipases (EC 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates, such as triacylglycerols, phospholipids, and other insoluble substrates, acting in aqueous as well as in low-water media, thus being of considerable physiological significance with high interest also for their industrial applications. The hydrolysis reaction follows a two-step mechanism, or “interfacial activation,” with adsorption of the enzyme to a heterogeneous interface and subsequent enhancement of the lipolytic activity. Among lipases, Candida antarctica lipase B (CALB) has never shown any significant interfacial activation, and a closed conformation of CALB has never been reported, leading to the conclusion that its behavior was due to the absence of a lid regulating the access to the active site. The lid open and closed conformations and their protonation states are observed in the crystal structure of CALB at 0.91 Å resolution. Having the open and closed states at atomic resolution allows relating protonation to the conformation, indicating the role of Asp145 and Lys290 in the conformation alteration. The findings explain the lack of interfacial activation of CALB and offer new elements to elucidate this mechanism, with the consequent implications for the catalytic properties and classification of lipases.
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Affiliation(s)
- Benjamin Stauch
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Robinson College, University of Cambridge, Cambridge CB3 9AN, United Kingdom
| | - Stuart J Fisher
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Michele Cianci
- European Molecular Biology Laboratory (EMBL), Deutsches Elektronen-Synchrotron (DESY), Hamburg 22607, Germany
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Anishkin A, Vanegas JM, Rogers DM, Lorenzi PL, Chan WK, Purwaha P, Weinstein JN, Sukharev S, Rempe SB. Catalytic Role of the Substrate Defines Specificity of Therapeutic l-Asparaginase. J Mol Biol 2015; 427:2867-85. [DOI: 10.1016/j.jmb.2015.06.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/20/2015] [Accepted: 06/26/2015] [Indexed: 12/23/2022]
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21
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Malinska M, Dauter M, Kowiel M, Jaskolski M, Dauter Z. Protonation and geometry of histidine rings. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1444-54. [PMID: 26143916 PMCID: PMC4498602 DOI: 10.1107/s1399004715007816] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/20/2015] [Indexed: 11/10/2022]
Abstract
The presence of H atoms connected to either or both of the two N atoms of the imidazole moiety in a histidine residue affects the geometry of the five-membered ring. Analysis of the imidazole moieties found in histidine residues of atomic resolution protein crystal structures in the Protein Data Bank (PDB), and in small-molecule structures retrieved from the Cambridge Structural Database (CSD), identified characteristic patterns of bond lengths and angles related to the protonation state of the imidazole moiety. Using discriminant analysis, two functions could be defined, corresponding to linear combinations of the four most sensitive stereochemical parameters, two bond lengths (ND1-CE1 and CE1-NE2) and two endocyclic angles (-ND1- and -NE2-), that uniquely identify the protonation states of all imidazole moieties in the CSD and can be used to predict which N atom(s) of the histidine side chains in protein structures are protonated. Updated geometrical restraint target values are proposed for differently protonated histidine side chains for use in macromolecular refinement.
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Affiliation(s)
- Maura Malinska
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miroslawa Dauter
- Leidos Biomedical Research Inc., Basic Science Program, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Marcin Kowiel
- Department of Organic Chemistry, Poznan University of Medical Sciences, Poznan, Poland
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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22
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Cui F, Yang K, Li Y. Investigate the binding of catechins to trypsin using docking and molecular dynamics simulation. PLoS One 2015; 10:e0125848. [PMID: 25938485 PMCID: PMC4418572 DOI: 10.1371/journal.pone.0125848] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/25/2015] [Indexed: 01/31/2023] Open
Abstract
To explore the inhibitory mechanism of catechins for digestive enzymes, we investigated the binding mode of catechins to a typical digestive enzyme-trypsin and analyzed the structure-activity relationship of catechins, using an integration of molecular docking, molecular dynamics simulation and binding free energy calculation. We found that catechins with different structures bound to a conservative pocket S1 of trypsin, which is comprised of residues 189–195, 214–220 and 225–228. In the trypsin-catechin complexes, Asp189 by forming strong hydrogen bonding, and Gln192, Trp215 and Gly216 through hydrophobic interactions, all significantly contribute to the binding of catechins. The number and the position of hydroxyl and aromatic groups, the structure of stereoisomers, and the orientation of catechins in the binding pocket S1 of trypsin all affect the binding affinity. The binding affinity is in the order of Epigallocatechin gallate (EGCG) > Epicatechin gallate (ECG) > Epicatechin (EC) > Epigallocatechin (EGC), and 2R-3R EGCG shows the strongest binding affinity out of other stereoisomers. Meanwhile, the synergic conformational changes of residues and catechins were also analyzed. These findings will be helpful in understanding the knowledge of interactions between catechins and trypsin and referable for the design of novel polyphenol based functional food and nutriceutical formulas.
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Affiliation(s)
- Fengchao Cui
- Key Laboratory of Synthetic Rubber & Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun, P. R. China
| | - Kecheng Yang
- Key Laboratory of Synthetic Rubber & Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun, P. R. China
| | - Yunqi Li
- Key Laboratory of Synthetic Rubber & Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun, P. R. China
- * E-mail:
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Kumar KSD, Gurusaran M, Satheesh SN, Radha P, Pavithra S, Thulaa Tharshan KPS, Helliwell JR, Sekar K. Online_DPI: a web server to calculate the diffraction precision index for a protein structure. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715006287] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An online computing server,Online_DPI(where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three-dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e.atomic displacement parameters). In addition, the computing engine is interfaced with an up-to-date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.
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D’Ascenzo L, Auffinger P. A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2015; 71:164-75. [PMID: 25827369 PMCID: PMC4383392 DOI: 10.1107/s205252061500270x] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 02/08/2015] [Indexed: 05/13/2023]
Abstract
Carboxyl and carboxylate groups form important supramolecular motifs (synthons). Besides carboxyl cyclic dimers, carboxyl and carboxylate groups can associate through a single hydrogen bond. Carboxylic groups can further form polymeric-like catemer chains within crystals. To date, no exhaustive classification of these motifs has been established. In this work, 17 association types were identified (13 carboxyl-carboxyl and 4 carboxyl-carboxylate motifs) by taking into account the syn and anti carboxyl conformers, as well as the syn and anti lone pairs of the O atoms. From these data, a simple rule was derived stating that only eight distinct catemer motifs involving repetitive combinations of syn and anti carboxyl groups can be formed. Examples extracted from the Cambridge Structural Database (CSD) for all identified dimers and catemers are presented, as well as statistical data related to their occurrence and conformational preferences. The inter-carboxyl(ate) and carboxyl(ate)-water hydrogen-bond properties are described, stressing the occurrence of very short (strong) hydrogen bonds. The precise characterization and classification of these supramolecular motifs should be of interest in crystal engineering, pharmaceutical and also biomolecular sciences, where similar motifs occur in the form of pairs of Asp/Glu amino acids or motifs involving ligands bearing carboxyl(ate) groups. Hence, we present data emphasizing how the analysis of hydrogen-containing small molecules of high resolution can help understand structural aspects of larger and more complex biomolecular systems of lower resolution.
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Affiliation(s)
- Luigi D’Ascenzo
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
| | - Pascal Auffinger
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
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25
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Su XD, Zhang H, Terwilliger TC, Liljas A, Xiao J, Dong Y. Protein Crystallography from the Perspective of Technology Developments. CRYSTALLOGR REV 2014; 21:122-153. [PMID: 25983389 DOI: 10.1080/0889311x.2014.973868] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Early on, crystallography was a domain of mineralogy and mathematics and dealt mostly with symmetry properties and imaginary crystal lattices. This changed when Wilhelm Conrad Röntgen discovered X-rays in 1895, and in 1912 Max von Laue and his associates discovered X-ray irradiated salt crystals would produce diffraction patterns that could reveal the internal atomic periodicity of the crystals. In the same year the father-and-son team, Henry and Lawrence Bragg successfully solved the first crystal structure of sodium chloride and the era of modern crystallography began. Protein crystallography (PX) started some 20 years later with the pioneering work of British crystallographers. In the past 50-60 years, the achievements of modern crystallography and particularly those in protein crystallography have been due to breakthroughs in theoretical and technical advancements such as phasing and direct methods; to more powerful X-ray sources such as synchrotron radiation (SR); to more sensitive and efficient X-ray detectors; to ever faster computers and to improvements in software. The exponential development of protein crystallography has been accelerated by the invention and applications of recombinant DNA technology that can yield nearly any protein of interest in large amounts and with relative ease. Novel methods, informatics platforms, and technologies for automation and high-throughput have allowed the development of large-scale, high efficiency macromolecular crystallography efforts in the field of structural genomics (SG). Very recently, the X-ray free-electron laser (XFEL) sources and its applications in protein crystallography have shown great potential for revolutionizing the whole field again in the near future.
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Affiliation(s)
- Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Heng Zhang
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Thomas C Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545, USA
| | - Anders Liljas
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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26
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Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography. Proc Natl Acad Sci U S A 2014; 111:18225-30. [PMID: 25453083 DOI: 10.1073/pnas.1415856111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF). An important step in the mechanism involves proton donation to the N5 atom of DHF. The inability to determine the protonation states of active site residues and substrate has led to a lack of consensus regarding the catalytic mechanism involved. To resolve this ambiguity, we conducted neutron and ultrahigh-resolution X-ray crystallographic studies of the pseudo-Michaelis ternary complex of Escherichia coli DHFR with folate and NADP(+). The neutron data were collected to 2.0-Å resolution using a 3.6-mm(3) crystal with the quasi-Laue technique. The structure reveals that the N3 atom of folate is protonated, whereas Asp27 is negatively charged. Previous mechanisms have proposed a keto-to-enol tautomerization of the substrate to facilitate protonation of the N5 atom. The structure supports the existence of the keto tautomer owing to protonation of the N3 atom, suggesting that tautomerization is unnecessary for catalysis. In the 1.05-Å resolution X-ray structure of the ternary complex, conformational disorder of the Met20 side chain is coupled to electron density for a partially occupied water within hydrogen-bonding distance of the N5 atom of folate; this suggests direct protonation of substrate by solvent. We propose a catalytic mechanism for DHFR that involves stabilization of the keto tautomer of the substrate, elevation of the pKa value of the N5 atom of DHF by Asp27, and protonation of N5 by water that gains access to the active site through fluctuation of the Met20 side chain even though the Met20 loop is closed.
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27
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Wan Q, Kovalevsky AY, Wilson MA, Bennett BC, Langan P, Dealwis C. Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+. Acta Crystallogr F Struct Biol Commun 2014; 70:814-8. [PMID: 24915100 PMCID: PMC4051544 DOI: 10.1107/s2053230x1400942x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 04/26/2014] [Indexed: 11/10/2022] Open
Abstract
A crystal of Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ of 4×1.3×0.7 mm (3.6 mm3) in size was obtained by sequential application of microseeding and macroseeding. A neutron diffraction data set was collected to 2.0 Å resolution using the IMAGINE diffractometer at the High Flux Isotope Reactor within Oak Ridge National Laboratory. A 1.6 Å resolution X-ray data set was also collected from a smaller crystal at room temperature. The neutron and X-ray data were used together for joint refinement of the ecDHFR-folate-NADP+ ternary-complex structure in order to examine the protonation state, protein dynamics and solvent structure of the complex, furthering understanding of the catalytic mechanism.
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Affiliation(s)
- Qun Wan
- Department of Biochemistry, College of Medicine, Yangzhou University, 11 HuaiHai Road, Yangzhou 225001, People’s Republic of China
| | - Andrey Y. Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Mark A. Wilson
- Department of Biochemistry/Redox Biology Center, University of Nebraska, 1901 Vine Street, Lincoln, NE 68588, USA
| | - Brad C. Bennett
- Department of Molecular Physiology and Biological Physics, University of Virginia, PO Box 800793, Charlottesville, VA 22908, USA
| | - Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Chris Dealwis
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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28
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Dauter Z, Wlodawer A, Minor W, Jaskolski M, Rupp B. Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. IUCRJ 2014; 1:179-93. [PMID: 25075337 PMCID: PMC4086436 DOI: 10.1107/s2052252514005442] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/10/2014] [Indexed: 05/20/2023]
Abstract
Whereas the vast majority of the more than 85 000 crystal structures of macromolecules currently deposited in the Protein Data Bank are of high quality, some suffer from a variety of imperfections. Although this fact has been pointed out in the past, it is still worth periodic updates so that the metadata obtained by global analysis of the available crystal structures, as well as the utilization of the individual structures for tasks such as drug design, should be based on only the most reliable data. Here, selected abnormal deposited structures have been analysed based on the Bayesian reasoning that the correctness of a model must be judged against both the primary evidence as well as prior knowledge. These structures, as well as information gained from the corresponding publications (if available), have emphasized some of the most prevalent types of common problems. The errors are often perfect illustrations of the nature of human cognition, which is frequently influenced by preconceptions that may lead to fanciful results in the absence of proper validation. Common errors can be traced to negligence and a lack of rigorous verification of the models against electron density, creation of non-parsimonious models, generation of improbable numbers, application of incorrect symmetry, illogical presentation of the results, or violation of the rules of chemistry and physics. Paying more attention to such problems, not only in the final validation stages but during the structure-determination process as well, is necessary not only in order to maintain the highest possible quality of the structural repositories and databases but most of all to provide a solid basis for subsequent studies, including large-scale data-mining projects. For many scientists PDB deposition is a rather infrequent event, so the need for proper training and supervision is emphasized, as well as the need for constant alertness of reason and critical judgment as absolutely necessary safeguarding measures against such problems. Ways of identifying more problematic structures are suggested so that their users may be properly alerted to their possible shortcomings.
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Affiliation(s)
- Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, NCI, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics, USA
- New York Structural Genomics Consortium, USA
- Center for Structural Genomics of Infectious Diseases, USA
- Enzyme Function Initiative, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Bernhard Rupp
- k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Innsbruck Medical University, Schöpfstrasse 41, A-6020 Innsbruck, Austria
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29
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Blankenship E, Vukoti K, Miyagi M, Lodowski DT. Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:833-40. [PMID: 24598752 PMCID: PMC3949523 DOI: 10.1107/s1399004713033658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/12/2013] [Indexed: 05/20/2024]
Abstract
With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity.
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Affiliation(s)
- Elise Blankenship
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Krishna Vukoti
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Opthalmology and Visual Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - David T. Lodowski
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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30
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Fukuda Y, Tse KM, Lintuluoto M, Fukunishi Y, Mizohata E, Matsumura H, Takami H, Nojiri M, Inoue T. Structural insights into the function of a thermostable copper-containing nitrite reductase. ACTA ACUST UNITED AC 2013; 155:123-35. [DOI: 10.1093/jb/mvt107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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31
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Houben ENG, Korotkov KV, Bitter W. Take five - Type VII secretion systems of Mycobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1707-16. [PMID: 24263244 DOI: 10.1016/j.bbamcr.2013.11.003] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/07/2013] [Accepted: 11/09/2013] [Indexed: 11/18/2022]
Abstract
Mycobacteria use type VII secretion (T7S) systems to secrete proteins across their complex cell envelope. Pathogenic mycobacteria, such as the notorious pathogen Mycobacterium tuberculosis, have up to five of these secretion systems, named ESX-1 to ESX-5. At least three of these secretion systems are essential for mycobacterial virulence and/or viability. Elucidating T7S is therefore essential to understand the success of M. tuberculosis and other pathogenic mycobacteria as pathogens, and could be instrumental to identify novel targets for drug- and vaccine-development. Recently, significant progress has been achieved in the identification of T7S substrates and a general secretion motif. In addition, a start has been made with unraveling the mechanism of secretion and the structural analysis of the different subunits. This review summarizes these recent findings, which are incorporated in a working model of this complex machinery. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Edith N G Houben
- VU University, Amsterdam, The Netherlands; VU University Medical Center, Amsterdam, The Netherlands.
| | | | - Wilbert Bitter
- VU University, Amsterdam, The Netherlands; VU University Medical Center, Amsterdam, The Netherlands
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32
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Wagner JM, Evans TJ, Chen J, Zhu H, Houben ENG, Bitter W, Korotkov KV. Understanding specificity of the mycosin proteases in ESX/type VII secretion by structural and functional analysis. J Struct Biol 2013; 184:115-28. [PMID: 24113528 DOI: 10.1016/j.jsb.2013.09.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 11/28/2022]
Abstract
Mycobacteria use specialized ESX secretion systems to transport proteins across their cell membranes in order to manipulate their environment. In pathogenic Mycobacterium tuberculosis there are five paralogous ESX secretion systems, named ESX-1 through ESX-5. Each system includes a subtilisin-like protease (mycosin or MycP) as a core component essential for secretion. Here we report crystal structures of MycP1 and MycP3, the mycosins expressed by the ESX-1 and ESX-3 systems, respectively. In both mycosins the putative propeptide wraps around the catalytic domain and does not occlude the active site. The extensive contacts between the putative propeptide and catalytic domain, which include a disulfide bond, suggest that the N-terminal extension is an integral part of the active mycosin. The catalytic residues of MycP1 and MycP3 are located in a deep active site groove in contrast with an exposed active site in majority of subtilisins. We show that MycP1 specifically cleaves ESX-1 secretion-associated protein B (EspB) in vitro at residues Ala358 and Ala386. We also systematically characterize the specificity of MycP1 using peptide libraries, and show that it has evolved a narrow specificity relative to other subtilisins. Finally, comparison of the MycP1 and MycP3 structures suggest that both enzymes have stringent and different specificity profiles that result from the structurally distinct active site pockets, which could explain the system specific functioning of these proteases.
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Affiliation(s)
- Jonathan M Wagner
- Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA
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33
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Liebschner D, Dauter M, Brzuszkiewicz A, Dauter Z. On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1447-62. [PMID: 23897468 PMCID: PMC3727327 DOI: 10.1107/s0907444913009050] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 04/03/2013] [Indexed: 11/10/2022]
Abstract
Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C(α) and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments.
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Affiliation(s)
- Dorothee Liebschner
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miroslawa Dauter
- SAIC-Frederick Inc., Basic Research Program, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Anna Brzuszkiewicz
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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Liu B, Zhang J, Fang Z, Gu L, Liao X, Du G, Chen J. Enhanced thermostability of keratinase by computational design and empirical mutation. J Ind Microbiol Biotechnol 2013; 40:697-704. [PMID: 23619970 DOI: 10.1007/s10295-013-1268-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/01/2013] [Indexed: 11/25/2022]
Abstract
Keratinases are proteolytic enzymes capable of degrading insoluble keratins. The importance of these enzymes is being increasingly recognized in fields as diverse as animal feed production, textile processing, detergent formulation, leather manufacture, and medicine. To enhance the thermostability of Bacillus licheniformis BBE11-1 keratinase, the PoPMuSiC algorithm was applied to predict the folding free energy change (ΔΔG) of amino acid substitutions. Use of the algorithm in combination with molecular modification of homologous subtilisin allowed the introduction of four amino acid substitutions (N122Y, N217S, A193P, N160C) into the enzyme by site-directed mutagenesis, and the mutant genes were expressed in Bacillus subtilis WB600. The quadruple mutant displayed synergistic or additive effects with an 8.6-fold increase in the t 1/2 value at 60 °C. The N122Y substitution also led to an approximately 5.6-fold increase in catalytic efficiency compared to that of the wild-type keratinase. These results provide further insight into the thermostability of keratinase and suggest further potential industrial applications.
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Affiliation(s)
- Baihong Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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35
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Tomanicek SJ, Standaert RF, Weiss KL, Ostermann A, Schrader TE, Ng JD, Coates L. Neutron and X-ray crystal structures of a perdeuterated enzyme inhibitor complex reveal the catalytic proton network of the Toho-1 β-lactamase for the acylation reaction. J Biol Chem 2012; 288:4715-22. [PMID: 23255594 DOI: 10.1074/jbc.m112.436238] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanism by which class A β-lactamases hydrolyze β-lactam antibiotics has been the subject of intensive investigation using many different experimental techniques. Here, we report on the novel use of both neutron and high resolution x-ray diffraction to help elucidate the identity of the catalytic base in the acylation part of the catalytic cycle, wherein the β-lactam ring is opened and an acyl-enzyme intermediate forms. To generate protein crystals optimized for neutron diffraction, we produced a perdeuterated form of the Toho-1 β-lactamase R274N/R276N mutant. Protein perdeuteration, which involves replacing all of the hydrogen atoms in a protein with deuterium, gives a much stronger signal in neutron diffraction and enables the positions of individual deuterium atoms to be located. We also synthesized a perdeuterated acylation transition state analog, benzothiophene-2-boronic acid, which was also isotopically enriched with (11)B, as (10)B is a known neutron absorber. Using the neutron diffraction data from the perdeuterated enzyme-inhibitor complex, we were able to determine the positions of deuterium atoms in the active site directly rather than by inference. The neutron diffraction results, along with supporting bond-length analysis from high resolution x-ray diffraction, strongly suggest that Glu-166 acts as the general base during the acylation reaction.
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