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Hossain MA, Sarin R, Donnelly DP, Miller BC, Weiss A, McAlary L, Antonyuk SV, Salisbury JP, Amin J, Conway JB, Watson SS, Winters JN, Xu Y, Alam N, Brahme RR, Shahbazian H, Sivasankar D, Padmakumar S, Sattarova A, Ponmudiyan AC, Gawde T, Verrill DE, Yang W, Kannapadi S, Plant LD, Auclair JR, Makowski L, Petsko GA, Ringe D, Agar NYR, Greenblatt DJ, Ondrechen MJ, Chen Y, Yerbury JJ, Manetsch R, Hasnain SS, Brown RH, Agar JN. Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS. PLoS Biol 2024; 22:e3002462. [PMID: 38289969 PMCID: PMC10826971 DOI: 10.1371/journal.pbio.3002462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/05/2023] [Indexed: 02/01/2024] Open
Abstract
Mutations in the gene encoding Cu-Zn superoxide dismutase 1 (SOD1) cause a subset of familial amyotrophic lateral sclerosis (fALS) cases. A shared effect of these mutations is that SOD1, which is normally a stable dimer, dissociates into toxic monomers that seed toxic aggregates. Considerable research effort has been devoted to developing compounds that stabilize the dimer of fALS SOD1 variants, but unfortunately, this has not yet resulted in a treatment. We hypothesized that cyclic thiosulfinate cross-linkers, which selectively target a rare, 2 cysteine-containing motif, can stabilize fALS-causing SOD1 variants in vivo. We created a library of chemically diverse cyclic thiosulfinates and determined structure-cross-linking-activity relationships. A pre-lead compound, "S-XL6," was selected based upon its cross-linking rate and drug-like properties. Co-crystallographic structure clearly establishes the binding of S-XL6 at Cys 111 bridging the monomers and stabilizing the SOD1 dimer. Biophysical studies reveal that the degree of stabilization afforded by S-XL6 (up to 24°C) is unprecedented for fALS, and to our knowledge, for any protein target of any kinetic stabilizer. Gene silencing and protein degrading therapeutic approaches require careful dose titration to balance the benefit of diminished fALS SOD1 expression with the toxic loss-of-enzymatic function. We show that S-XL6 does not share this liability because it rescues the activity of fALS SOD1 variants. No pharmacological agent has been proven to bind to SOD1 in vivo. Here, using a fALS mouse model, we demonstrate oral bioavailability; rapid engagement of SOD1G93A by S-XL6 that increases SOD1G93A's in vivo half-life; and that S-XL6 crosses the blood-brain barrier. S-XL6 demonstrated a degree of selectivity by avoiding off-target binding to plasma proteins. Taken together, our results indicate that cyclic thiosulfinate-mediated SOD1 stabilization should receive further attention as a potential therapeutic approach for fALS.
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Affiliation(s)
- Md Amin Hossain
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
- Department of Neurosurgery and Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richa Sarin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Biogen Inc, Cambridge, Massachusetts, United States of America
| | - Daniel P. Donnelly
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Brandon C. Miller
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Luke McAlary
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Joseph P. Salisbury
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Jakal Amin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Jeremy B. Conway
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Samantha S. Watson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Jenifer N. Winters
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yu Xu
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Novera Alam
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Rutali R. Brahme
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Haneyeh Shahbazian
- School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Durgalakshmi Sivasankar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Swathi Padmakumar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Aziza Sattarova
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Aparna C. Ponmudiyan
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Tanvi Gawde
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - David E. Verrill
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Wensheng Yang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Sunanda Kannapadi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Leigh D. Plant
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Jared R. Auclair
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Lee Makowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Gregory A. Petsko
- Ann Romney Center for Neurologic Diseases at Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Departments of Chemistry and Biochemistry, and Rosenstiel Center for Basic Medical Research, Brandeis University, Waltham, Massachusetts, United States of America
| | - Dagmar Ringe
- Departments of Chemistry and Biochemistry, and Rosenstiel Center for Basic Medical Research, Brandeis University, Waltham, Massachusetts, United States of America
| | - Nathalie Y. R. Agar
- Department of Neurosurgery and Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David J. Greenblatt
- School of Medicine, Tufts University, Boston, Massachusetts, United States of America
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yunqiu Chen
- Biogen Inc, Cambridge, Massachusetts, United States of America
| | - Justin J. Yerbury
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Roman Manetsch
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - S. Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jeffrey N. Agar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
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Flynn AJ, Antonyuk SV, Eady RR, Muench SP, Hasnain SS. A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases. Nat Commun 2023; 14:3416. [PMID: 37296134 PMCID: PMC10256718 DOI: 10.1038/s41467-023-39140-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.
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Affiliation(s)
- Alex J Flynn
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Robert R Eady
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England.
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Amporndanai K, Pinthong N, O’Neill PM, Hong WD, Amewu RK, Pidathala C, Berry NG, Leung SC, Ward SA, Biagini GA, Hasnain SS, Antonyuk SV. Targeting the Ubiquinol-Reduction (Q i) Site of the Mitochondrial Cytochrome bc1 Complex for the Development of Next Generation Quinolone Antimalarials. Biology (Basel) 2022; 11:biology11081109. [PMID: 35892964 PMCID: PMC9330653 DOI: 10.3390/biology11081109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022]
Abstract
Antimalarials targeting the ubiquinol-oxidation (Qo) site of the Plasmodium falciparum bc1 complex, such as atovaquone, have become less effective due to the rapid emergence of resistance linked to point mutations in the Qo site. Recent findings showed a series of 2-aryl quinolones mediate inhibitions of this complex by binding to the ubiquinone-reduction (Qi) site, which offers a potential advantage in circumventing drug resistance. Since it is essential to understand how 2-aryl quinolone lead compounds bind within the Qi site, here we describe the co-crystallization and structure elucidation of the bovine cytochrome bc1 complex with three different antimalarial 4(1H)-quinolone sub-types, including two 2-aryl quinolone derivatives and a 3-aryl quinolone analogue for comparison. Currently, no structural information is available for Plasmodial cytochrome bc1. Our crystallographic studies have enabled comparison of an in-silico homology docking model of P. falciparum with the mammalian's equivalent, enabling an examination of how binding compares for the 2- versus 3-aryl analogues. Based on crystallographic and computational modeling, key differences in human and P. falciparum Qi sites have been mapped that provide new insights that can be exploited for the development of next-generation antimalarials with greater selective inhibitory activity against the parasite bc1 with improved antimalarial properties.
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Affiliation(s)
- Kangsa Amporndanai
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Nattapon Pinthong
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Paul M. O’Neill
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Correspondence: (P.M.O.); (S.V.A.); Tel.: +44-(0)-1517955145 (S.V.A.); +44-(0)-1517943552 (P.M.O.)
| | - W. David Hong
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Richard K. Amewu
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Department of Chemistry, School of Physical and Mathematical Sciences, University of Ghana, Accra P.O. Box LG 586, Ghana
| | - Chandrakala Pidathala
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Composite Interceptive Med-Science Laboratories Pvt. Ltd., Bengaluru 60099, Karnataka, India
| | - Neil G. Berry
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Suet C. Leung
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Stephen A. Ward
- Centre for Drugs and Diagnostics, Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (S.A.W.); (G.A.B.)
| | - Giancarlo A. Biagini
- Centre for Drugs and Diagnostics, Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (S.A.W.); (G.A.B.)
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Correspondence: (P.M.O.); (S.V.A.); Tel.: +44-(0)-1517955145 (S.V.A.); +44-(0)-1517943552 (P.M.O.)
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4
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Gopalasingam CC, Hasnain SS. Frontiers in metalloprotein crystallography and cryogenic electron microscopy. Curr Opin Struct Biol 2022; 75:102420. [PMID: 35841747 DOI: 10.1016/j.sbi.2022.102420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/03/2022]
Abstract
Metalloproteins comprise at least a third of all proteins that utilize redox properties of transition metals on their own or as parts of cofactors. The development of third generation storage ring sources and X-ray free-electron lasers with femtosecond pulses in the first decade of the 21st century has transformed metalloprotein crystallography. In the past decade, cryogenic-electron microscopy single-particle analysis, which does not require crystallization of biological samples has been extensively utilized, particularly for membrane-bound metalloprotein systems. Here, we explore recent frontiers in metalloprotein crystallography and cryogenic electron microscopy, organized for convenience under three metalloprotein-centered biological cycles, focusing on contributions from each technique, their synergy and the ability to preserve metals' redox states when subjected to a particular probe.
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Affiliation(s)
- Chai C Gopalasingam
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK; Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan. https://twitter.com/@Chai_Gopal
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK.
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Amporndanai K, Meng X, Shang W, Jin Z, Rogers M, Zhao Y, Rao Z, Liu ZJ, Yang H, Zhang L, O'Neill PM, Samar Hasnain S. Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives. Nat Commun 2021; 12:3061. [PMID: 34031399 PMCID: PMC8144557 DOI: 10.1038/s41467-021-23313-7] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/23/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 pandemic has triggered global efforts to develop therapeutics. The main protease of SARS-CoV-2 (Mpro), critical for viral replication, is a key target for therapeutic development. An organoselenium drug called ebselen has been demonstrated to have potent Mpro inhibition and antiviral activity. We have examined the binding modes of ebselen and its derivative in Mpro via high resolution co-crystallography and investigated their chemical reactivity via mass spectrometry. Stronger Mpro inhibition than ebselen and potent ability to rescue infected cells were observed for a number of derivatives. A free selenium atom bound with cysteine of catalytic dyad has been revealed in crystallographic structures of Mpro with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct and formation of a phenolic by-product, confirmed by mass spectrometry. The target engagement with selenation mechanism of inhibition suggests wider therapeutic applications of these compounds against SARS-CoV-2 and other zoonotic beta-corona viruses. Ebselen is an organoselenium drug that inhibits the SARS-CoV-2 main protease (Mpro). Here, the authors co-crystallised Mpro with ebselen and an ebselen derivative and observed an enzyme bound organoselenium covalent adduct in the crystal structures, which was also confirmed by mass spectrometry analysis.
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Affiliation(s)
- Kangsa Amporndanai
- Molecular Biophysics Group, Department of Biochemistry and System Biology, Institute of System, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Xiaoli Meng
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK
| | - Weijuan Shang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Zhenmig Jin
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Michael Rogers
- Department of Chemistry, Faculty of Science and Engineering, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Yao Zhao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zhi-Jie Liu
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.
| | - Paul M O'Neill
- Department of Chemistry, Faculty of Science and Engineering, University of Liverpool, Liverpool, L69 7ZD, UK.
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and System Biology, Institute of System, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK.
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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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hough MA, Conradie J, Strange RW, Antonyuk SV, Eady RR, Ghosh A, Hasnain SS. Nature of the copper-nitrosyl intermediates of copper nitrite reductases during catalysis. Chem Sci 2020; 11:12485-12492. [PMID: 34094452 PMCID: PMC8163067 DOI: 10.1039/d0sc04797j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The design and synthesis of copper complexes that can reduce nitrite to NO has attracted considerable interest. They have been guided by the structural information on the catalytic Cu centre of the widespread enzymes Cu nitrite reductases but the chemically novel side-on binding of NO observed in all crystallographic studies of these enzymes has been questioned in terms of its functional relevance. We show conversion of NO2− to NO in the crystal maintained at 170 K and present ‘molecular movies’ defining events during enzyme turnover including the formation of side-on Cu-NO intermediate. DFT modelling suggests that both true {CuNO}11 and formal {CuNO}10 states may occur as side-on forms in an enzymatic active site with the stability of the {CuNO}10 side-on form governed by the protonation state of the histidine ligands. Formation of a copper-nitrosyl intermediate thus needs to be accommodated in future design templates for functional synthetic Cu-NiR complexes. Observation of side-on copper-nitrosyl intermediate and its confirmation by DFT during catalysis of copper nitrite reductases.![]()
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Affiliation(s)
- Michael A Hough
- School of Life Sciences, University of Essex Wivenhoe Park Colchester CO4 3SQW UK
| | - Jeanet Conradie
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of the Free State PO Box 339 Bloemfontein South Africa.,Department of Chemistry, UiT, The Arctic University of Tromsø 9037 Tromsø Norway
| | - Richard W Strange
- School of Life Sciences, University of Essex Wivenhoe Park Colchester CO4 3SQW UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool Liverpool L69 7ZB UK
| | - Robert R Eady
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool Liverpool L69 7ZB UK
| | - Abhik Ghosh
- Department of Chemistry, UiT, The Arctic University of Tromsø 9037 Tromsø Norway
| | - S Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool Liverpool L69 7ZB UK
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Amporndanai K, Rogers M, Watanabe S, Yamanaka K, O'Neill PM, Hasnain SS. Novel Selenium-based compounds with therapeutic potential for SOD1-linked amyotrophic lateral sclerosis. EBioMedicine 2020; 59:102980. [PMID: 32862101 PMCID: PMC7456458 DOI: 10.1016/j.ebiom.2020.102980] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease as well as Lou Gehrig's disease, is a progressive neurological disorder selectively affecting motor neurons with no currently known cure. Around 20% of the familial ALS cases arise from dominant mutations in the sod1 gene encoding superoxide dismutase1 (SOD1) enzyme. Aggregation of mutant SOD1 in familial cases and of wild-type SOD1 in at least some sporadic ALS cases is one of the known causes of the disease. Riluzole, approved in 1995 and edaravone in 2017 remain the only drugs with limited therapeutic benefits. Methods We have utilised the ebselen template to develop novel compounds that redeem stability of mutant SOD1 dimer and prevent aggregation. Binding modes of compounds have been visualised by crystallography. In vitro neuroprotection and toxicity of lead compounds have been performed in mouse neuronal cells and disease onset delay of ebselen has been demonstrated in transgenic ALS mice model. Finding We have developed a number of ebselen-based compounds with improvements in A4V SOD1 stabilisation and in vitro therapeutic effects with significantly better potency than edaravone. Structure-activity relationship of hits has been guided by high resolution structures of ligand-bound A4V SOD1. We also show clear disease onset delay of ebselen in transgenic ALS mice model holding encouraging promise for potential therapeutic compounds. Interpretation Our finding established the new generation of organo-selenium compounds with better in vitro neuroprotective activity than edaravone. The potential of this class of compounds may offer an alternative therapeutic agent for ALS treatment. The ability of these compounds to target cysteine 111 in SOD may have wider therapeutic applications targeting cysteines of enzymes involved in pathogenic and viral diseases including main protease of SARS-Cov-2 (COVID-19). Funding Project funding was supported by the 10.13039/100000971ALS Association grant (WA1128) and Fostering Joint International Research (19KK0214) from the 10.13039/100009950Ministry of Education, Culture, Sports, Science and Technology (10.13039/501100001700MEXT), Japan.
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Affiliation(s)
- Kangsa Amporndanai
- Molecular Biophysics Group, Department of Biochemistry and System Biology, Institute of System, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Michael Rogers
- Department of Chemistry, Faculty of Science and Engineering, University of Liverpool, Liverpool, L69 7ZD, United Kingdom
| | - Seiji Watanabe
- Department of Neuroscience & Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Aichi, 466-8550, Japan
| | - Koji Yamanaka
- Department of Neuroscience & Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Aichi, 466-8550, Japan
| | - Paul M O'Neill
- Department of Chemistry, Faculty of Science and Engineering, University of Liverpool, Liverpool, L69 7ZD, United Kingdom
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and System Biology, Institute of System, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
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10
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Wright GSA, Watanabe TF, Amporndanai K, Plotkin SS, Cashman NR, Antonyuk SV, Hasnain SS. Purification and Structural Characterization of Aggregation-Prone Human TDP-43 Involved in Neurodegenerative Diseases. iScience 2020; 23:101159. [PMID: 32480125 PMCID: PMC7262455 DOI: 10.1016/j.isci.2020.101159] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/29/2020] [Accepted: 05/08/2020] [Indexed: 02/05/2023] Open
Abstract
Mislocalization, cleavage, and aggregation of the human protein TDP-43 is found in many neurodegenerative diseases. As is the case with many other proteins that are completely or partially structurally disordered, production of full-length recombinant TDP-43 in the quantities necessary for structural characterization has proved difficult. We show that the full-length TDP-43 protein and two truncated N-terminal constructs 1-270 and 1-263 can be heterologously expressed in E. coli. Full-length TDP-43 could be prevented from aggregation during purification using a detergent. Crystals grown from an N-terminal construct (1-270) revealed only the N-terminal domain (residues 1-80) with molecules arranged as parallel spirals with neighboring molecules arranged in head-to-tail fashion. To obtain detergent-free, full-length TDP-43 we mutated all six tryptophan residues to alanine. This provided sufficient soluble protein to collect small-angle X-ray scattering data. Refining relative positions of individual domains and intrinsically disordered regions against this data yielded a model of full-length TDP-43.
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Affiliation(s)
- Gareth S A Wright
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, Liverpool L69 7ZB, UK
| | - Tatiana F Watanabe
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, Liverpool L69 7ZB, UK
| | - Kangsa Amporndanai
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, Liverpool L69 7ZB, UK
| | - Steven S Plotkin
- Department of Physics & Astronomy, The University of British Columbia, Vancouver, BC, Canada
| | - Neil R Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, Liverpool L69 7ZB, UK
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, Liverpool L69 7ZB, UK.
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11
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Panmanee J, Antonyuk SV, Hasnain SS. Structural basis of the dominant inheritance of hypermethioninemia associated with the Arg264His mutation in the MAT1A gene. Acta Crystallogr D Struct Biol 2020; 76:594-607. [PMID: 32496220 PMCID: PMC7271947 DOI: 10.1107/s2059798320006002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/01/2020] [Indexed: 02/06/2023] Open
Abstract
Methionine adenosyltransferase (MAT) deficiency, characterized by isolated persistent hypermethioninemia (IPH), is caused by mutations in the MAT1A gene encoding MATαl, one of the major hepatic enzymes. Most of the associated hypermethioninemic conditions are inherited as autosomal recessive traits; however, dominant inheritance of hypermethioninemia is caused by an Arg264His (R264H) mutation. This mutation has been confirmed in a screening programme of newborns as the most common mutation in babies with IPH. Arg264 makes an inter-subunit salt bridge located at the dimer interface where the active site assembles. Here, it is demonstrated that the R264H mutation results in greatly reduced MAT activity, while retaining its ability to dimerize, indicating that the lower activity arises from alteration at the active site. The first crystallographic structure of the apo form of the wild-type MATαl enzyme is provided, which shows a tetrameric assembly in which two compact dimers combine to form a catalytic tetramer. In contrast, the crystal structure of the MATαl R264H mutant reveals a weaker dimeric assembly, suggesting that the mutation lowers the affinity for dimer-dimer interaction. The formation of a hetero-oligomer with the regulatory MATβV1 subunit or incubation with a quinolone-based compound (SCR0911) results in the near-full recovery of the enzymatic activity of the pathogenic mutation R264H, opening a clear avenue for a therapeutic solution based on chemical interventions that help to correct the defect of the enzyme in its ability to metabolize methionine.
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Affiliation(s)
- Jiraporn Panmanee
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
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12
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Sasaki D, Watanabe TF, Eady RR, Garratt RC, Antonyuk SV, Hasnain SS. Structures of substrate- and product-bound forms of a multi-domain copper nitrite reductase shed light on the role of domain tethering in protein complexes. IUCrJ 2020; 7:557-565. [PMID: 32431838 PMCID: PMC7201279 DOI: 10.1107/s2052252520005230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
Copper-containing nitrite reductases (CuNiRs) are found in all three kingdoms of life and play a major role in the denitrification branch of the global nitro-gen cycle where nitrate is used in place of di-oxy-gen as an electron acceptor in respiratory energy metabolism. Several C- and N-terminal redox domain tethered CuNiRs have been identified and structurally characterized during the last decade. Our understanding of the role of tethered domains in these new classes of three-domain CuNiRs, where an extra cytochrome or cupredoxin domain is tethered to the catalytic two-domain CuNiRs, has remained limited. This is further compounded by a complete lack of substrate-bound structures for these tethered CuNiRs. There is still no substrate-bound structure for any of the as-isolated wild-type tethered enzymes. Here, structures of nitrite and product-bound states from a nitrite-soaked crystal of the N-terminal cupredoxin-tethered enzyme from the Hyphomicrobium denitrificans strain 1NES1 (Hd 1NES1NiR) are provided. These, together with the as-isolated structure of the same species, provide clear evidence for the role of the N-terminal peptide bearing the conserved His27 in water-mediated anchoring of the substrate at the catalytic T2Cu site. Our data indicate a more complex role of tethering than the intuitive advantage for a partner-protein electron-transfer complex by narrowing the conformational search in such a combined system.
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Affiliation(s)
- Daisuke Sasaki
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Tatiana F. Watanabe
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- The São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Richard C. Garratt
- The São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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13
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Sasaki D, Watanabe TF, Eady RR, Garratt RC, Antonyuk SV, Hasnain SS. Reverse protein engineering of a novel 4-domain copper nitrite reductase reveals functional regulation by protein-protein interaction. FEBS J 2020; 288:262-280. [PMID: 32255260 DOI: 10.1111/febs.15324] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/16/2020] [Accepted: 04/01/2020] [Indexed: 01/03/2023]
Abstract
Cu-containing nitrite reductases that convert NO2 - to NO are critical enzymes in nitrogen-based energy metabolism. Among organisms in the order Rhizobiales, we have identified two copies of nirK, one encoding a new class of 4-domain CuNiR that has both cytochrome and cupredoxin domains fused at the N terminus and the other, a classical 2-domain CuNiR (Br2D NiR). We report the first enzymatic studies of a novel 4-domain CuNiR from Bradyrhizobium sp. ORS 375 (BrNiR), its genetically engineered 3- and 2-domain variants, and Br2D NiR revealing up to ~ 500-fold difference in catalytic efficiency in comparison with classical 2-domain CuNiRs. Contrary to the expectation that tethering would enhance electron delivery by restricting the conformational search by having a self-contained donor-acceptor system, we demonstrate that 4-domain BrNiR utilizes N-terminal tethering for downregulating enzymatic activity instead. Both Br2D NiR and an engineered 2-domain variant of BrNiR (Δ(Cytc-Cup) BrNiR) have 3 to 5% NiR activity compared to the well-characterized 2-domain CuNiRs from Alcaligenes xylosoxidans (AxNiR) and Achromobacter cycloclastes (AcNiR). Structural comparison of Δ(Cytc-Cup) BrNiR and Br2D NiR with classical 2-domain AxNiR and AcNiR reveals structural differences of the proton transfer pathway that could be responsible for the lowering of activity. Our study provides insights into unique structural and functional characteristics of naturally occurring 4-domain CuNiR and its engineered 3- and 2-domain variants. The reverse protein engineering approach utilized here has shed light onto the broader question of the evolution of transient encounter complexes and tethered electron transfer complexes. ENZYME: Copper-containing nitrite reductase (CuNiR) (EC 1.7.2.1). DATABASE: The atomic coordinate and structure factor of Δ(Cytc-Cup) BrNiR and Br2D NiR have been deposited in the Protein Data Bank (http://www.rcsb.org/) under the accession code 6THE and 6THF, respectively.
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Affiliation(s)
- Daisuke Sasaki
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - Tatiana F Watanabe
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK.,The São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Robert R Eady
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - Richard C Garratt
- The São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - S Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
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14
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McPhillie M, Zhou Y, El Bissati K, Dubey J, Lorenzi H, Capper M, Lukens AK, Hickman M, Muench S, Verma SK, Weber CR, Wheeler K, Gordon J, Sanders J, Moulton H, Wang K, Kim TK, He Y, Santos T, Woods S, Lee P, Donkin D, Kim E, Fraczek L, Lykins J, Esaa F, Alibana-Clouser F, Dovgin S, Weiss L, Brasseur G, Wirth D, Kent M, Hood L, Meunieur B, Roberts CW, Hasnain SS, Antonyuk SV, Fishwick C, McLeod R. Author Correction: New paradigms for understanding and step changes in treating active and chronic, persistent apicomplexan infections. Sci Rep 2020; 10:5512. [PMID: 32251362 PMCID: PMC7089975 DOI: 10.1038/s41598-020-62323-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | | | | | | | | | - Amanda K Lukens
- Harvard School of Public Health, Boston, Massachusetts, USA.,The Broad Institute, Boston, Massachusetts, USA
| | - Mark Hickman
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | | | | | | | | | - Kai Wang
- Institute for Systems Biology, Seattle, Washington, USA
| | - Taek-Kyun Kim
- Institute for Systems Biology, Seattle, Washington, USA
| | - Yuqing He
- Institute for Systems Biology, Seattle, Washington, USA
| | - Tatiana Santos
- Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Patty Lee
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - David Donkin
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Eric Kim
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | | | | | - Louis Weiss
- Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Dyann Wirth
- Harvard School of Public Health, Boston, Massachusetts, USA.,The Broad Institute, Boston, Massachusetts, USA
| | | | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, USA
| | - Brigitte Meunieur
- Institute for Integrative Biology of the Cell (12BC), Gif-sur-Yvette, France
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15
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Chantadul V, Wright GSA, Amporndanai K, Shahid M, Antonyuk SV, Washbourn G, Rogers M, Roberts N, Pye M, O'Neill PM, Hasnain SS. Ebselen as template for stabilization of A4V mutant dimer for motor neuron disease therapy. Commun Biol 2020; 3:97. [PMID: 32139772 PMCID: PMC7058017 DOI: 10.1038/s42003-020-0826-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/13/2020] [Indexed: 11/09/2022] Open
Abstract
Mutations to the gene encoding superoxide dismutase-1 (SOD1) were the first genetic elements discovered that cause motor neuron disease (MND). These mutations result in compromised SOD1 dimer stability, with one of the severest and most common mutations Ala4Val (A4V) displaying a propensity to monomerise and aggregate leading to neuronal death. We show that the clinically used ebselen and related analogues promote thermal stability of A4V SOD1 when binding to Cys111 only. We have developed a A4V SOD1 differential scanning fluorescence-based assay on a C6S mutation background that is effective in assessing suitability of compounds. Crystallographic data show that the selenium atom of these compounds binds covalently to A4V SOD1 at Cys111 at the dimer interface, resulting in stabilisation. This together with chemical amenability for hit expansion of ebselen and its on-target SOD1 pharmacological chaperone activity holds remarkable promise for structure-based therapeutics for MND using ebselen as a template.
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Affiliation(s)
- Varunya Chantadul
- Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Faculty of Dentistry, Department of Anatomy, Mahidol University, Bangkok, 10400, Thailand
| | - Gareth S A Wright
- Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Kangsa Amporndanai
- Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Munazza Shahid
- Department of Chemistry and Chemical Engineering, Lahore University of Management Sciences, Punjab, 54792, Pakistan
| | - Svetlana V Antonyuk
- Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Gina Washbourn
- Faculty of Science and Engineering, Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Michael Rogers
- Faculty of Science and Engineering, Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Natalie Roberts
- Faculty of Science and Engineering, Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Matthew Pye
- Faculty of Science and Engineering, Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Paul M O'Neill
- Faculty of Science and Engineering, Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - S Samar Hasnain
- Faculty of Health and Life Sciences, Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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16
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Sala FA, Wright G, Antonyuk S, Garratt RC, Hasnain SS. The SOD1-hCCS mechanism involved in copper homeostasis. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319094853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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17
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Gopalasingam CC, Johnson RM, Chiduza GN, Tosha T, Yamamoto M, Shiro Y, Antonyuk SV, Muench SP, Hasnain SS. Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy. Sci Adv 2019; 5:eaax1803. [PMID: 31489376 PMCID: PMC6713497 DOI: 10.1126/sciadv.aax1803] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
Quinol-dependent nitric oxide reductases (qNORs) are membrane-integrated, iron-containing enzymes of the denitrification pathway, which catalyze the reduction of nitric oxide (NO) to the major ozone destroying gas nitrous oxide (N2O). Cryo-electron microscopy structures of active qNOR from Alcaligenes xylosoxidans and an activity-enhancing mutant have been determined to be at local resolutions of 3.7 and 3.2 Å, respectively. They unexpectedly reveal a dimeric conformation (also confirmed for qNOR from Neisseria meningitidis) and define the active-site configuration, with a clear water channel from the cytoplasm. Structure-based mutagenesis has identified key residues involved in proton transport and substrate delivery to the active site of qNORs. The proton supply direction differs from cytochrome c-dependent NOR (cNOR), where water molecules from the cytoplasm serve as a proton source similar to those from cytochrome c oxidase.
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Affiliation(s)
- Chai C. Gopalasingam
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Rachel M. Johnson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - George N. Chiduza
- Molecular Biophysics Group, Institute of 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
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
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18
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Hedison T, Shenoy RT, Iorgu AI, Heyes DJ, Fisher K, Wright GSA, Hay S, Eady RR, Antonyuk SV, Hasnain SS, Scrutton NS. Unexpected Roles of a Tether Harboring a Tyrosine Gatekeeper Residue in Modular Nitrite Reductase Catalysis. ACS Catal 2019; 9:6087-6099. [PMID: 32051772 PMCID: PMC7007197 DOI: 10.1021/acscatal.9b01266] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/19/2019] [Indexed: 01/26/2023]
Abstract
It is generally assumed that tethering enhances rates of electron harvesting and delivery to active sites in multidomain enzymes by proximity and sampling mechanisms. Here, we explore this idea in a tethered 3-domain, trimeric copper-containing nitrite reductase. By reverse engineering, we find that tethering does not enhance the rate of electron delivery from its pendant cytochrome c to the catalytic copper-containing core. Using a linker that harbors a gatekeeper tyrosine in a nitrite access channel, the tethered haem domain enables catalysis by other mechanisms. Tethering communicates the redox state of the haem to the distant T2Cu center that helps initiate substrate binding for catalysis. It also tunes copper reduction potentials, suppresses reductive enzyme inactivation, enhances enzyme affinity for substrate, and promotes intercopper electron transfer. Tethering has multiple unanticipated beneficial roles, the combination of which fine-tunes function beyond simplistic mechanisms expected from proximity and restrictive sampling models.
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Affiliation(s)
- Tobias
M. Hedison
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rajesh T. Shenoy
- Molecular
Biophysics Group, Institute of Integrative Biology, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Andreea I. Iorgu
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Derren J. Heyes
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Karl Fisher
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Gareth S. A. Wright
- Molecular
Biophysics Group, Institute of Integrative Biology, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Robert R. Eady
- Molecular
Biophysics Group, Institute of Integrative Biology, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Svetlana V. Antonyuk
- Molecular
Biophysics Group, Institute of Integrative Biology, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - S. Samar Hasnain
- Molecular
Biophysics Group, Institute of Integrative Biology, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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19
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Halsted TP, Yamashita K, Gopalasingam CC, Shenoy RT, Hirata K, Ago H, Ueno G, Blakeley MP, Eady RR, Antonyuk SV, Yamamoto M, Hasnain SS. Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography. IUCrJ 2019; 6:761-772. [PMID: 31316819 PMCID: PMC6608623 DOI: 10.1107/s2052252519008285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/12/2019] [Indexed: 05/31/2023]
Abstract
Copper-containing nitrite reductases (CuNiRs) that convert NO2 - to NO via a CuCAT-His-Cys-CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD-, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2 - a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed.
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Affiliation(s)
- Thomas P. Halsted
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Chai C. Gopalasingam
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Rajesh T. Shenoy
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Hideo Ago
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Go Ueno
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Masaki Yamamoto
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
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20
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Chiduza GN, Johnson RM, Wright GSA, Antonyuk SV, Muench SP, Hasnain SS. LAT1 (SLC7A5) and CD98hc (SLC3A2) complex dynamics revealed by single-particle cryo-EM. Acta Crystallogr D Struct Biol 2019; 75:660-669. [PMID: 31282475 PMCID: PMC7285653 DOI: 10.1107/s2059798319009094] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022] Open
Abstract
Solute carriers are a large class of transporters that play key roles in normal and disease physiology. Among the solute carriers, heteromeric amino-acid transporters (HATs) are unique in their quaternary structure. LAT1-CD98hc, a HAT, transports essential amino acids and drugs across the blood-brain barrier and into cancer cells. It is therefore an important target both biologically and therapeutically. During the course of this work, cryo-EM structures of LAT1-CD98hc in the inward-facing conformation and in either the substrate-bound or apo states were reported to 3.3-3.5 Å resolution [Yan et al. (2019), Nature (London), 568, 127-130]. Here, these structures are analyzed together with our lower resolution cryo-EM structure, and multibody 3D auto-refinement against single-particle cryo-EM data was used to characterize the dynamics of the interaction of CD98hc and LAT1. It is shown that the CD98hc ectodomain and the LAT1 extracellular surface share no substantial interface. This allows the CD98hc ectodomain to have a high degree of movement within the extracellular space. The functional implications of these aspects are discussed together with the structure determination.
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Affiliation(s)
- George N. Chiduza
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Rachel M. Johnson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Gareth S. A. Wright
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Stephen P. Muench
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
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21
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Hasnain SS, Catlow CRA. Synchrotron science in the UK: NINA, the SRS and Diamond. Philos Trans A Math Phys Eng Sci 2019; 377:20190147. [PMID: 31030660 PMCID: PMC6501895 DOI: 10.1098/rsta.2019.0147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The development of synchrotron science over the last 50 years is reviewed from the perspective of the authors' own scientific programmes. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.
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Affiliation(s)
- S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
- e-mail:
| | - C. Richard A. Catlow
- Department of Chemistry, University College London, 20 Gordon Street, London WC1 HOAJ, UK
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
- e-mail:
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22
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Panmanee J, Bradley-Clarke J, Mato JM, O'Neill PM, Antonyuk SV, Hasnain SS. Control and regulation of S-Adenosylmethionine biosynthesis by the regulatory β subunit and quinolone-based compounds. FEBS J 2019; 286:2135-2154. [PMID: 30776190 PMCID: PMC6850014 DOI: 10.1111/febs.14790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/17/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
Methylation is an underpinning process of life and provides control for biological processes such as DNA synthesis, cell growth, and apoptosis. Methionine adenosyltransferases (MAT) produce the cellular methyl donor, S‐Adenosylmethionine (SAMe). Dysregulation of SAMe level is a relevant event in many diseases, including cancers such as hepatocellular carcinoma and colon cancer. In addition, mutation of Arg264 in MATα1 causes isolated persistent hypermethioninemia, which is characterized by low activity of the enzyme in liver and high level of plasma methionine. In mammals, MATα1/α2 and MATβV1/V2 are the catalytic and the major form of regulatory subunits, respectively. A gating loop comprising residues 113–131 is located beside the active site of catalytic subunits (MATα1/α2) and provides controlled access to the active site. Here, we provide evidence of how the gating loop facilitates the catalysis and define some of the key elements that control the catalytic efficiency. Mutation of several residues of MATα2 including Gln113, Ser114, and Arg264 lead to partial or total loss of enzymatic activity, demonstrating their critical role in catalysis. The enzymatic activity of the mutated enzymes is restored to varying degrees upon complex formation with MATβV1 or MATβV2, endorsing its role as an allosteric regulator of MATα2 in response to the levels of methionine or SAMe. Finally, the protein–protein interacting surface formed in MATα2:MATβ complexes is explored to demonstrate that several quinolone‐based compounds modulate the activity of MATα2 and its mutants, providing a rational for chemical design/intervention responsive to the level of SAMe in the cellular environment. Enzymes Methionine adenosyltransferase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/5/1/6.html). Database Structural data are available in the RCSB PDB database under the PDB ID http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FBN (Q113A), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FBP (S114A: P22121), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FBO (S114A: I222), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FCB (P115G), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FCD (R264A), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FAJ (wtMATα2: apo), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6G6R (wtMATα2: holo)
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Affiliation(s)
- Jiraporn Panmanee
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - Jack Bradley-Clarke
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - Jose M Mato
- Metabolomics Unit, CIC bioGUNE, CIBERehd, Parque Tecnologico de Bizkaia, Derio, Spain
| | - Paul M O'Neill
- Department of Chemistry, School of Physical Sciences, University of Liverpool, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - S Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
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23
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Muench SP, Antonyuk SV, Hasnain SS. The expanding toolkit for structural biology: synchrotrons, X-ray lasers and cryoEM. IUCrJ 2019; 6:167-177. [PMID: 30867914 PMCID: PMC6400194 DOI: 10.1107/s2052252519002422] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/15/2019] [Indexed: 05/10/2023]
Abstract
Structural biology continues to benefit from an expanding toolkit, which is helping to gain unprecedented insight into the assembly and organization of multi-protein machineries, enzyme mechanisms and ligand/inhibitor binding. The combination of results from X-ray free-electron lasers (XFELs), modern synchrotron crystallographic beamlines and cryo-electron microscopy (cryoEM) is proving to be particularly powerful. The highly brilliant undulator beamlines at modern synchrotron facilities have empowered the crystallographic revolution of high-throughput structure determination at high resolution. The brilliance of the X-rays at these crystallographic beamlines has enabled this to be achieved using microcrystals, but at the expense of an increased absorbed X-ray dose and a consequent vulnerability to radiation-induced changes. The advent of serial femtosecond crystallography (SFX) with X-ray free-electron lasers provides a new opportunity in which damage-free structures can be obtained from much smaller crystals (2 µm) and more complex macromolecules, including membrane proteins and multi-protein complexes. For redox enzymes, SFX provides a unique opportunity by providing damage-free structures at both cryogenic and ambient temperatures. The promise of being able to visualize macromolecular structures and complexes at high resolution without the need for crystals using X-rays has remained a dream, but recent technological advancements in cryoEM have made this come true and hardly a month goes by when the structure of a new/novel macromolecular assembly is not revealed. The uniqueness of cryoEM in providing structural information for multi-protein complexes, particularly membrane proteins, has been demonstrated by examples such as respirasomes. The synergistic use of cryoEM and crystallography in lead-compound optimization is highlighted by the example of the visualization of antimalarial compounds in cytochrome bc 1. In this short review, using some recent examples including our own work, we share the excitement of these powerful structural biology methods.
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Affiliation(s)
- Stephen P. Muench
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
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24
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Sala FA, Wright GSA, Antonyuk SV, Garratt RC, Hasnain SS. Molecular recognition and maturation of SOD1 by its evolutionarily destabilised cognate chaperone hCCS. PLoS Biol 2019; 17:e3000141. [PMID: 30735496 PMCID: PMC6383938 DOI: 10.1371/journal.pbio.3000141] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/21/2019] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
Superoxide dismutase-1 (SOD1) maturation comprises a string of posttranslational modifications which transform the nascent peptide into a stable and active enzyme. The successive folding, metal ion binding, and disulphide acquisition steps in this pathway can be catalysed through a direct interaction with the copper chaperone for SOD1 (CCS). This process confers enzymatic activity and reduces access to noncanonical, aggregation-prone states. Here, we present the functional mechanisms of human copper chaperone for SOD1 (hCCS)-catalysed SOD1 activation based on crystal structures of reaction precursors, intermediates, and products. Molecular recognition of immature SOD1 by hCCS is driven by several interface interactions, which provide an extended surface upon which SOD1 folds. Induced-fit complexation is reliant on the structural plasticity of the immature SOD1 disulphide sub-loop, a characteristic which contributes to misfolding and aggregation in neurodegenerative disease. Complexation specifically stabilises the SOD1 disulphide sub-loop, priming it and the active site for copper transfer, while delaying disulphide formation and complex dissociation. Critically, a single destabilising amino acid substitution within the hCCS interface reduces hCCS homodimer affinity, creating a pool of hCCS available to interact with immature SOD1. hCCS substrate specificity, segregation between solvent and biological membranes, and interaction transience are direct results of this substitution. In this way, hCCS-catalysed SOD1 maturation is finessed to minimise copper wastage and reduce production of potentially toxic SOD1 species.
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Affiliation(s)
- Fernanda A. Sala
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Gareth S. A. Wright
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Richard C. Garratt
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
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25
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David Hong W, Leung SC, Amporndanai K, Davies J, Priestley RS, Nixon GL, Berry NG, Samar Hasnain S, Antonyuk S, Ward SA, Biagini GA, O’Neill PM. Potent Antimalarial 2-Pyrazolyl Quinolone bc 1 (Q i) Inhibitors with Improved Drug-like Properties. ACS Med Chem Lett 2018; 9:1205-1210. [PMID: 30613327 DOI: 10.1021/acsmedchemlett.8b00371] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/19/2018] [Indexed: 01/29/2023] Open
Abstract
A series of 2-pyrazolyl quinolones has been designed and synthesized in 5-7 steps to optimize for both in vitro antimalarial potency and various in vitro drug metabolism and pharmacokinetics (DMPK) features. The most potent compounds display no cross-resistance with multidrug resistant parasite strains (W2) compared to drug sensitive strains (3D7), with IC50 (concentration of drug required to achieve half maximal growth suppression) values in the range of 15-33 nM. Furthermore, members of the series retain moderate activity against the atovaquone-resistant parasite isolate (TM90C2B). The described 2-pyrazoyl series displays improved DMPK properties, including improved aqueous solubility compared to previously reported quinolone series and acceptable safety margin through in vitro cytotoxicity assessment. The 2-pyrazolyl quinolones are believed to bind to the ubiquinone-reducing Qi site of the parasite bc 1 complex, which is supported by crystallographic studies of bovine cytochrome bc 1 complex.
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Affiliation(s)
- W. David Hong
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, U.K
| | - Suet C. Leung
- Research Centre for Drugs & Diagnostics, Parasitology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, U.K
| | - Kangsa Amporndanai
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K
| | - Jill Davies
- Research Centre for Drugs & Diagnostics, Parasitology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, U.K
| | - Richard S. Priestley
- Research Centre for Drugs & Diagnostics, Parasitology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, U.K
| | - Gemma L. Nixon
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, U.K
| | - Neil G. Berry
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, U.K
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K
| | - Svetlana Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K
| | - Stephen A. Ward
- Research Centre for Drugs & Diagnostics, Parasitology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, U.K
| | - Giancarlo A. Biagini
- Research Centre for Drugs & Diagnostics, Parasitology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, U.K
| | - Paul M. O’Neill
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, U.K
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26
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Dong J, Sasaki D, Eady RR, Antonyuk SV, Hasnain SS. Identification of a tyrosine switch in copper-haem nitrite reductases. IUCrJ 2018; 5:510-518. [PMID: 30002851 PMCID: PMC6038957 DOI: 10.1107/s2052252518008242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
There are few cases where tyrosine has been shown to be involved in catalysis or the control of catalysis despite its ability to carry out chemistry at much higher potentials (1 V versus NHE). Here, it is shown that a tyrosine that blocks the hydrophobic substrate-entry channel in copper-haem nitrite reductases can be activated like a switch by the treatment of crystals of Ralstonia pickettii nitrite reductase (RpNiR) with nitric oxide (NO) (-0.8 ± 0.2 V). Treatment with NO results in an opening of the channel originating from the rotation of Tyr323 away from AspCAT97. Remarkably, the structure of a catalytic copper-deficient enzyme also shows Tyr323 in the closed position despite the absence of type 2 copper (T2Cu), clearly demonstrating that the status of Tyr323 is not controlled by T2Cu or its redox chemistry. It is also shown that the activation by NO is not through binding to haem. It is proposed that activation of the Tyr323 switch is controlled by NO through proton abstraction from tyrosine and the formation of HNO. The insight gained here for the use of tyrosine as a switch in catalysis has wider implications for catalysis in biology.
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Affiliation(s)
- Jianshu Dong
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
| | - Daisuke Sasaki
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
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27
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Horrell S, Kekilli D, Sen K, Owen RL, Dworkowski FSN, Antonyuk SV, Keal TW, Yong CW, Eady RR, Hasnain SS, Strange RW, Hough MA. Enzyme catalysis captured using multiple structures from one crystal at varying temperatures. IUCrJ 2018; 5:283-292. [PMID: 29755744 PMCID: PMC5929374 DOI: 10.1107/s205225251800386x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 03/05/2018] [Indexed: 05/24/2023]
Abstract
High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a 'top-hat' geometry, which was rapidly transformed to a 'side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.
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Affiliation(s)
- Sam Horrell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Demet Kekilli
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Kakali Sen
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | | | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Thomas W. Keal
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, England
| | - Chin W. Yong
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, England
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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28
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Wright GSA, Saeki A, Hikima T, Nishizono Y, Hisano T, Kamaya M, Nukina K, Nishitani H, Nakamura H, Yamamoto M, Antonyuk SV, Hasnain SS, Shiro Y, Sawai H. Architecture of the complete oxygen-sensing FixL-FixJ two-component signal transduction system. Sci Signal 2018; 11:11/525/eaaq0825. [PMID: 29636388 DOI: 10.1126/scisignal.aaq0825] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The symbiotic nitrogen-fixing bacterium Bradyrhizobium japonicum is critical to the agro-industrial production of soybean because it enables the production of high yields of soybeans with little use of nitrogenous fertilizers. The FixL and FixJ two-component system (TCS) of this bacterium ensures that nitrogen fixation is only stimulated under conditions of low oxygen. When it is not bound to oxygen, the histidine kinase FixL undergoes autophosphorylation and transfers phosphate from adenosine triphosphate (ATP) to the response regulator FixJ, which, in turn, stimulates the expression of genes required for nitrogen fixation. We purified full-length B. japonicum FixL and FixJ proteins and defined their structures individually and in complex using small-angle x-ray scattering, crystallographic, and in silico modeling techniques. Comparison of active and inactive forms of FixL suggests that intramolecular signal transduction is driven by local changes in the sensor domain and in the coiled-coil region connecting the sensor and histidine kinase domains. We also found that FixJ exhibits conformational plasticity not only in the monomeric state but also in tetrameric complexes with FixL during phosphotransfer. This structural characterization of a complete TCS contributes both a mechanistic and evolutionary understanding to TCS signal relay, specifically in the context of the control of nitrogen fixation in root nodules.
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Affiliation(s)
- Gareth S A Wright
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Akane Saeki
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Takaaki Hikima
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Yoko Nishizono
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Tamao Hisano
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Misaki Kamaya
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Kohei Nukina
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Hideo Nishitani
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Hiro Nakamura
- 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
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - S Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan. .,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan. .,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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Amporndanai K, Johnson RM, O’Neill PM, Fishwick CWG, Jamson AH, Rawson S, Muench SP, Hasnain SS, Antonyuk SV. X-ray and cryo-EM structures of inhibitor-bound cytochrome bc1 complexes for structure-based drug discovery. IUCrJ 2018; 5:200-210. [PMID: 29765610 PMCID: PMC5947725 DOI: 10.1107/s2052252518001616] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/26/2018] [Indexed: 05/10/2023]
Abstract
Cytochrome bc1, a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome bc1 from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome bc1 that may be available from parasites, all efforts have been focused on homologous cytochrome bc1 complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome bc1 is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes.
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Affiliation(s)
- Kangsa Amporndanai
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Rachel M. Johnson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
- School of Chemistry, University of Leeds, Leeds LS2 9JT, England
| | - Paul M. O’Neill
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, England
| | - Colin W. G. Fishwick
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
- School of Chemistry, University of Leeds, Leeds LS2 9JT, England
| | - Alexander H. Jamson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
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30
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Halsted TP, Yamashita K, Hirata K, Ago H, Ueno G, Tosha T, Eady RR, Antonyuk SV, Yamamoto M, Hasnain SS. An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase. IUCrJ 2018; 5:22-31. [PMID: 29354268 PMCID: PMC5755574 DOI: 10.1107/s2052252517016128] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 11/07/2017] [Indexed: 05/24/2023]
Abstract
Synchrotron-based X-ray structural studies of ligand-bound enzymes are powerful tools to further our understanding of reaction mechanisms. For redox enzymes, it is necessary to study both the oxidized and reduced active sites to fully elucidate the reaction, an objective that is complicated by potential X-ray photoreduction. In the presence of the substrate, this can be exploited to construct a structural movie of the events associated with catalysis. Using the newly developed approach of serial femtosecond rotation crystallography (SF-ROX), an X-ray damage-free structure of the as-isolated copper nitrite reductase (CuNiR) was visualized. The sub-10 fs X-ray pulse length from the SACLA X-ray free-electron laser allowed diffraction data to be collected to 1.6 Å resolution in a 'time-frozen' state. The extremely short duration of the X-ray pulses ensures the capture of data prior to the onset of radiation-induced changes, including radiolysis. Unexpectedly, an O2 ligand was identified bound to the T2Cu in a brand-new binding mode for a diatomic ligand in CuNiRs. The observation of O2 in a time-frozen structure of the as-isolated oxidized enzyme provides long-awaited clear-cut evidence for the mode of O2 binding in CuNiRs. This provides an insight into how CuNiR from Alcaligenes xylosoxidans can function as an oxidase, reducing O2 to H2O2, or as a superoxide dismutase (SOD) since it was shown to have ∼56% of the dismutase activity of the bovine SOD enzyme some two decades ago.
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Affiliation(s)
- Thomas P. Halsted
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Hideo Ago
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Go Ueno
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Takehiko Tosha
- Biometal Science Laboratory, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Masaki Yamamoto
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
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31
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Hough MA, Kekilli D, Horrell S, Sen K, Yong C, Keal TWK, Antonyuk SV, Eady RR, Hasnain SS, Strange RW. MSOX crystallography and simulations to capture redox enzyme catalysis. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317089227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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32
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Hasnain SS. Seventy years of publications. IUCrJ 2017; 4:512-513. [PMID: 28932403 PMCID: PMC5600020 DOI: 10.1107/s205225251701168x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The IUCr, which was established 70 years ago, will be celebrating 70 years of peer-reviewed publications in 2018. Three of its journals, including IUCrJ, are ranked in the top 10% of all journals, with the remainder striving to be in the top quartile in the next five years.
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Affiliation(s)
- S. Samar Hasnain
- Max Perutz Professor of Molecular Biophysics at the University of Liverpool and Editor-in-Chief of IUCr, Barkla X-ray Laboratory of Biophysics, Institute of Integrative Biology, Life Sciences Building, Liverpool, L69 7ZB, UK
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33
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Hasnain SS. Seventy years of publications. J Synchrotron Radiat 2017; 24:904-905. [PMID: 28862610 DOI: 10.1107/s1600577517012292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- S Samar Hasnain
- Max Perutz Professor of Molecular Biophysics at the University of Liverpool and Editor-in-Chief of IUCr, Barkla X-ray Laboratory of Biophysics, Institute of Integrative Biology, Life Sciences Building, Liverpool L69 7ZB, UK
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34
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Hasnain SS. Seventy years of publications. Acta Crystallogr C 2017; 73:652-653. [DOI: 10.1107/s205322961701172x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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35
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McPhillie M, Zhou Y, El Bissati K, Dubey J, Lorenzi H, Capper M, Lukens AK, Hickman M, Muench S, Verma SK, Weber CR, Wheeler K, Gordon J, Sanders J, Moulton H, Wang K, Kim TK, He Y, Santos T, Woods S, Lee P, Donkin D, Kim E, Fraczek L, Lykins J, Esaa F, Alibana-Clouser F, Dovgin S, Weiss L, Brasseur G, Wirth D, Kent M, Hood L, Meunieur B, Roberts CW, Hasnain SS, Antonyuk SV, Fishwick C, McLeod R. New paradigms for understanding and step changes in treating active and chronic, persistent apicomplexan infections. Sci Rep 2016; 6:29179. [PMID: 27412848 PMCID: PMC4944145 DOI: 10.1038/srep29179] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/31/2016] [Indexed: 12/24/2022] Open
Abstract
Toxoplasma gondii, the most common parasitic infection of human brain and eye, persists across lifetimes, can progressively damage sight, and is currently incurable. New, curative medicines are needed urgently. Herein, we develop novel models to facilitate drug development: EGS strain T. gondii forms cysts in vitro that induce oocysts in cats, the gold standard criterion for cysts. These cysts highly express cytochrome b. Using these models, we envisioned, and then created, novel 4-(1H)-quinolone scaffolds that target the cytochrome bc1 complex Qi site, of which, a substituted 5,6,7,8-tetrahydroquinolin-4-one inhibits active infection (IC50, 30 nM) and cysts (IC50, 4 μM) in vitro, and in vivo (25 mg/kg), and drug resistant Plasmodium falciparum (IC50, <30 nM), with clinically relevant synergy. Mutant yeast and co-crystallographic studies demonstrate binding to the bc1 complex Qi site. Our results have direct impact on improving outcomes for those with toxoplasmosis, malaria, and ~2 billion persons chronically infected with encysted bradyzoites.
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Affiliation(s)
| | | | | | | | | | | | - Amanda K Lukens
- Harvard School of Public Health, Boston, Massachusetts, USA
- The Broad Institute, Boston, Massachusetts, USA
| | - Mark Hickman
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | | | | | | | | | - Kai Wang
- Institute for Systems Biology, Seattle, Washington, USA
| | - Taek-Kyun Kim
- Institute for Systems Biology, Seattle, Washington, USA
| | - Yuqing He
- Institute for Systems Biology, Seattle, Washington, USA
| | - Tatiana Santos
- Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Patty Lee
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - David Donkin
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Eric Kim
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | | | | | - Louis Weiss
- Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Dyann Wirth
- Harvard School of Public Health, Boston, Massachusetts, USA
- The Broad Institute, Boston, Massachusetts, USA
| | | | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, USA
| | - Brigitte Meunieur
- Institute for Integrative Biology of the Cell (12BC), Gif-sur-Yvette, France
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Horrell S, Antonyuk SV, Eady RR, Hasnain SS, Hough MA, Strange RW. Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal. IUCrJ 2016; 3:271-81. [PMID: 27437114 PMCID: PMC4937782 DOI: 10.1107/s205225251600823x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/20/2016] [Indexed: 05/24/2023]
Abstract
Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07-1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a 'catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.
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Affiliation(s)
- Sam Horrell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Life Sciences Building, Liverpool L69 7ZB, England
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Life Sciences Building, Liverpool L69 7ZB, England
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Life Sciences Building, Liverpool L69 7ZB, England
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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37
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Abstract
A proportion of Amyotrophic lateral sclerosis (ALS) cases result from impaired mutant superoxide dismutase-1 (SOD1) maturation. The copper chaperone for SOD1 (hCCS) forms a transient complex with SOD1 and catalyses the final stages of its maturation. We find that a neurodegenerative disease-associated hCCS mutation abrogates the interaction with SOD1 by inhibiting hCCS zinc binding. Analogously, SOD1 zinc loss has a detrimental effect on the formation, structure and disassociation of the hCCS-SOD1 heterodimer. This suggests that hCCS functionality is impaired by ALS mutations that reduce SOD1 zinc affinity. Furthermore, stabilization of wild-type SOD1 by chemical modification including cisplatination, inhibits complex formation. We hypothesize that drug molecules designed to stabilize ALS SOD1 mutants that also target the wild-type form will lead to characteristics common in SOD1 knock-outs. Our work demonstrates the applicability of chromatographic SAXS when studying biomolecules predisposed to aggregation or dissociation; attributes frequently reported for complexes involved in neurodegenerative disease.
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Affiliation(s)
- Gareth S. A. Wright
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
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Abstract
The global nitrogen cycle is the process in which different forms of environmental N are interconverted by microorganisms either for assimilation into biomass or in respiratory energy-generating pathways. This short review highlights developments over the last 5 years in our understanding of functionality of nitrogenase, Cu-nitrite reductase, NO reductase and N2O reductase, complex metalloenzymes that catalyze electron/proton-coupled substrate reduction reactions.
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Affiliation(s)
- Robert R Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - S Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK.
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Eady RR, Antonyuk SV, Hasnain SS. Fresh insight to functioning of selected enzymes of the nitrogen cycle. Curr Opin Chem Biol 2016; 31:103-12. [DOI: 10.1016/j.cbpa.2016.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/18/2016] [Indexed: 11/26/2022]
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40
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Hasnain SS. Crystallography in the 21st century. Acta Crystallogr A Found Adv 2015; 71:559-61. [DOI: 10.1107/s2053273315019464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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41
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Hasnain SS. Crystallography in the 21st century. IUCrJ 2015; 2:602-4. [PMID: 26594364 PMCID: PMC4645101 DOI: 10.1107/s2052252515017509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The field of crystallography, which has had a major impact on the sciences in the last 100 years, is continuing to expand scientific horizons as technical and conceptual boundaries are overcome. Structure-function-dynamics will become an integrated theme for many studies as will obtaining structures without the 'benevolent tyranny' of crystals.
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Affiliation(s)
- S. Samar Hasnain
- Max Perutz Professor of Molecular Biophysics at the University of Liverpool and Editor-in-Chief of IUCr Journals, Barkla X-ray Laboratory of Biophysics, Institute of Integrative Biology, Life Sciences Building, Liverpool L69 7ZB, UK
- Correspondence e-mail: ,
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42
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Hasnain SS. Crystallography in the 21st century. J Synchrotron Radiat 2015; 22:1331-1333. [PMID: 26524295 DOI: 10.1107/s1600577515019578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- S Samar Hasnain
- Max Perutz Professor of Molecular Biophysics at the University of Liverpool and Editor-in-Chief of IUCr Journals, Barkla X-ray Laboratory of Biophysics, Institute of Integrative Biology, Life Sciences Building, Liverpool L69 7ZB, UK
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43
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Hasnain SS. Crystallography in the 21st century: pure and applied. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715019524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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44
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Hasnain SS. IUCrJ celebrates its first year of publication. IUCrJ 2015; 2:1-2. [PMID: 25610619 PMCID: PMC4285872 DOI: 10.1107/s205225251402750x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
IUCrJ is a fully open-access journal that publishes high-quality structural science papers. It has had a successful first year of publication.
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Affiliation(s)
- S. Samar Hasnain
- Max Perutz Professor of Molecular Biophysics, University of Liverpool, Crown Street, Liverpool, Merseyside L69 7ZB, United Kingdom, and Editor-in-chief of IUCr Journals
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45
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Leferink NGH, Antonyuk SV, Houwman JA, Scrutton NS, Eady RR, Hasnain SS. Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase. Nat Commun 2014; 5:4395. [PMID: 25022223 PMCID: PMC4104443 DOI: 10.1038/ncomms5395] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/13/2014] [Indexed: 11/29/2022] Open
Abstract
Enzyme mechanisms are often probed by structure-informed point mutations and measurement of their effects on enzymatic properties to test mechanistic hypotheses. In many cases, the challenge is to report on complex, often inter-linked elements of catalysis. Evidence for long-range effects on enzyme mechanism resulting from mutations remains sparse, limiting the design/redesign of synthetic catalysts in a predictable way. Here we show that improving the accessibility of the active site pocket of copper nitrite reductase by mutation of a surface-exposed phenylalanine residue (Phe306), located 12 Å away from the catalytic site type-2 Cu (T2Cu), profoundly affects intra-molecular electron transfer, substrate-binding and catalytic activity. Structures and kinetic studies provide an explanation for the lower affinity for the substrate and the alteration of the rate-limiting step in the reaction. Our results demonstrate that distant residues remote from the active site can have marked effects on enzyme catalysis, by driving mechanistic change through relatively minor structural perturbations. Residues within the catalytic site of enzymes are important for activity, but whether more distant residues are also sensitive to mutation is unclear. Here, Leferink et al. show that mutation of residues in copper nitrate reductase that are 12Å away from the active site perturb enzyme function.
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Affiliation(s)
- Nicole G H Leferink
- 1] Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK [2]
| | - Svetlana V Antonyuk
- 1] Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK [2]
| | - Joseline A Houwman
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Robert R Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - S Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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46
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Hasnain SS. Acta E transforms from Structure Reports Online to Crystallographic Communications. Acta Crystallogr Sect E Struct Rep Online 2014; 70:1-2. [PMID: 25161494 PMCID: PMC4120596 DOI: 10.1107/s1600536814011775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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47
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Murray B, Antonyuk SV, Marina A, Van Liempd SM, Lu SC, Mato JM, Hasnain SS, Rojas AL. Structure and function study of the complex that synthesizes S-adenosylmethionine. IUCrJ 2014; 1:240-9. [PMID: 25075345 PMCID: PMC4107924 DOI: 10.1107/s2052252514012585] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/30/2014] [Indexed: 05/08/2023]
Abstract
S-Adenosylmethionine (SAMe) is the principal methyl donor of the cell and is synthesized via an ATP-driven process by methionine adenosyltransferase (MAT) enzymes. It is tightly linked with cell proliferation in liver and colon cancer. In humans, there are three genes, mat1A, mat2A and mat2B, which encode MAT enzymes. mat2A and mat2B transcribe MATα2 and MATβ enzyme subunits, respectively, with catalytic and regulatory roles. The MATα2β complex is expressed in nearly all tissues and is thought to be essential in providing the necessary SAMe flux for methylation of DNA and various proteins including histones. In human hepatocellular carcinoma mat2A and mat2B genes are upregulated, highlighting the importance of the MATα2β complex in liver disease. The individual subunits have been structurally characterized but the nature of the complex has remained elusive despite its existence having been postulated for more than 20 years and the observation that MATβ is often co-localized with MATα2. Though SAMe can be produced by MAT(α2)4 alone, this paper shows that the V max of the MATα2β complex is three- to fourfold higher depending on the variants of MATβ that participate in complex formation. Using X-ray crystallography and solution X-ray scattering, the first structures are provided of this 258 kDa functional complex both in crystals and solution with an unexpected stoichiometry of 4α2 and 2βV2 subunits. It is demonstrated that the N-terminal regulates the activity of the complex and it is shown that complex formation takes place surprisingly via the C-terminal of MATβV2 that buries itself in a tunnel created at the interface of the MAT(α2)2. The structural data suggest a unique mechanism of regulation and provide a gateway for structure-based drug design in anticancer therapies.
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Affiliation(s)
- Ben Murray
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, L69 7ZX, England
- Structural Biology Unit CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, L69 7ZX, England
| | - Alberto Marina
- Structural Biology Unit CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Sebastiaan M. Van Liempd
- Metabolomics Unit, CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Shelly C. Lu
- Division of Gastroenterology and Liver Diseases, USC Research Center for Liver Diseases, USC–UCLA Research Center for ALPD and Cirrhosis, Keck School of Medicine, Los Angeles, California, CA 90033, USA
| | - Jose M. Mato
- Metabolomics Unit, CIC bioGUNE, CIBERehd, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, L69 7ZX, England
| | - Adriana L. Rojas
- Structural Biology Unit CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain
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48
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Kekilli D, Dworkowski FSN, Pompidor G, Fuchs MR, Andrew CR, Antonyuk S, Strange RW, Eady RR, Hasnain SS, Hough MA. Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy. ACTA ACUST UNITED AC 2014; 70:1289-96. [PMID: 24816098 DOI: 10.1107/s1399004714004039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 02/20/2014] [Indexed: 11/10/2022]
Abstract
It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.
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Affiliation(s)
- Demet Kekilli
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | | | - Guillaume Pompidor
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Martin R Fuchs
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Colin R Andrew
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, OR 97850-2899, USA
| | - Svetlana Antonyuk
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Richard W Strange
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Robert R Eady
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - S Samar Hasnain
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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49
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Kershaw NM, Wright GSA, Sharma R, Antonyuk SV, Strange RW, Berry NG, O'Neill PM, Hasnain SS. X-ray crystallography and computational docking for the detection and development of protein-ligand interactions. Curr Med Chem 2014; 20:569-75. [PMID: 23278398 DOI: 10.2174/0929867311320040008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 12/13/2012] [Accepted: 12/14/2012] [Indexed: 11/22/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder characterised by the selective dysfunction and death of the upper and lower motor neurons. Median survival rates are between 3 and 5 years after diagnosis. Mutations in the gene encoding Cu/Zn superoxide dismutase (SOD1) have been linked to a subset of familial forms of ALS (fALS). Herein, we describe a fragment- based drug discovery (FBDD) approach for the investigation of small molecule binding sites in SOD1. X-ray crystallography has been used as the primary screening method and has been shown to directly detect protein-ligand interactions which cannot be unambiguously identified using other biophysical methods. The structural requirements for effective binding at Trp32 are detailed for a series of quinazoline-containing compounds. The investigation of an additional site that binds a range of catecholamines and the use of computational modelling to assist fragment evolution is discussed. This study also highlights the importance of ligand solubility for successful Xray crystallographic campaigns in lead compound design.
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Affiliation(s)
- N M Kershaw
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK.
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50
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Abstract
IUCrJ is a fully open-access journal that aims to publish high-quality structural science papers. It has been launched for the International Year of Crystallography (IYCr2014).
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Affiliation(s)
- S. Samar Hasnain
- Max Perutz Professor of Molecular Biophysics, University of Liverpool, Crown Street, Liverpool, Merseyside L69 7ZB, United Kingdom, and Editor-in-chief of IUCr Journals
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