1
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Chen Z, Zanotti G. Emerging Topics in Protein Crystallography. Int J Mol Sci 2024; 25:5311. [PMID: 38791349 PMCID: PMC11121128 DOI: 10.3390/ijms25105311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Protein crystallography is the discipline concerned with the determination of the three-dimensional structure of biological macromolecules in a crystalline state [...].
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Affiliation(s)
- Zhongzhou Chen
- State Key Laboratory of Animal Biotech Breeding and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 48B, 35131 Padova, Italy
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2
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Liutkus M, Sasselli IR, Rojas AL, Cortajarena AL. Diverse crystalline protein scaffolds through metal-dependent polymorphism. Protein Sci 2024; 33:e4971. [PMID: 38591647 PMCID: PMC11002994 DOI: 10.1002/pro.4971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 04/10/2024]
Abstract
As protein crystals are increasingly finding diverse applications as scaffolds, controlled crystal polymorphism presents a facile strategy to form crystalline assemblies with controllable porosity with minimal to no protein engineering. Polymorphs of consensus tetratricopeptide repeat proteins with varying porosity were obtained through co-crystallization with metal salts, exploiting the innate metal ion geometric requirements. A single structurally exposed negative amino acid cluster was responsible for metal coordination, despite the abundance of negatively charged residues. Density functional theory calculations showed that while most of the crystals were the most thermodynamically stable assemblies, some were kinetically trapped states. Thus, crystalline porosity diversity is achieved and controlled with metal coordination, opening a new scope in the application of proteins as biocompatible protein-metal-organic frameworks (POFs). In addition, metal-dependent polymorphic crystals allow direct comparison of metal coordination preferences.
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Affiliation(s)
- Mantas Liutkus
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
| | - Ivan R. Sasselli
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
- Present address:
Centro de Física de Materiales (CFM)CSIC‐UPV/EHUSan SebastiánSpain
| | - Adriana L. Rojas
- Centre for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology AllianceBilbaoSpain
| | - Aitziber L. Cortajarena
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE)Basque Research and Technology AllianceSan SebastianSpain
- IkerbasqueBasque Foundation for ScienceBilbaoSpain
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3
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Paloyan A, Sargsyan A, Karapetyan MD, Hambardzumyan A, Kocharov S, Panosyan H, Dyukova K, Kinosyan M, Krueger A, Piergentili C, Stanley WA, Djoko KY, Baslé A, Marles‐Wright J, Antranikian G. Structural and biochemical characterisation of the N-carbamoyl-β-alanine amidohydrolase from Rhizobium radiobacter MDC 8606. FEBS J 2023; 290:5566-5580. [PMID: 37634202 PMCID: PMC10952681 DOI: 10.1111/febs.16943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
N-carbamoyl-β-alanine amidohydrolase (CβAA) constitutes one of the most important groups of industrially relevant enzymes used in the production of optically pure amino acids and derivatives. In this study, a CβAA-encoding gene from Rhizobium radiobacter strain MDC 8606 was cloned and overexpressed in Escherichia coli. The purified recombinant enzyme (RrCβAA) showed a specific activity of 14 U·mg-1 using N-carbamoyl-β-alanine as a substrate with an optimum activity at 55 °C and pH 8.0. In this work, we report also the first prokaryotic CβAA structure at a resolution of 2.0 Å. A discontinuous catalytic domain and a dimerisation domain attached through a flexible hinge region at the domain interface have been revealed. We identify key ligand binding residues, including a conserved glutamic acid (Glu131), histidine (H385) and arginine (Arg291). Our results allowed us to explain the preference of the enzyme for linear carbamoyl substrates, as large and branched carbamoyl substrates cannot fit in the active site of the enzyme. This work envisages the use of RrCβAA from R. radiobacter MDC 8606 for the industrial production of L-α-, L-β- and L-γ-amino acids. The structural analysis provides new insights on enzyme-substrate interaction, which shed light on engineering of CβAAs for high catalytic activity and broad substrate specificity.
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Affiliation(s)
- Ani Paloyan
- Scientific and Production Center “Armbiotechnology” of NAS RAYerevanArmenia
| | - Armen Sargsyan
- Scientific and Production Center “Armbiotechnology” of NAS RAYerevanArmenia
| | | | | | - Sergei Kocharov
- The Scientific Technological Centre of Organic and Pharmaceutical Chemistry SNPO of NAS RAYerevanArmenia
| | - Henry Panosyan
- The Scientific Technological Centre of Organic and Pharmaceutical Chemistry SNPO of NAS RAYerevanArmenia
| | - Karine Dyukova
- Scientific and Production Center “Armbiotechnology” of NAS RAYerevanArmenia
| | - Marina Kinosyan
- Scientific and Production Center “Armbiotechnology” of NAS RAYerevanArmenia
| | - Anna Krueger
- Authority for the Environment, Climate, Energy and Agriculture in HamburgHamburgGermany
| | - Cecilia Piergentili
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Will A. Stanley
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
| | | | - Arnaud Baslé
- Newcastle University Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Jon Marles‐Wright
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
- Newcastle University Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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4
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Tan B, Liu C, Li K, Jadhav P, Lambrinidis G, Zhu L, Olson L, Tan H, Wen Y, Kolocouris A, Liu W, Wang J. Structure-Based Lead Optimization of Enterovirus D68 2A Protease Inhibitors. J Med Chem 2023; 66:14544-14563. [PMID: 37857371 DOI: 10.1021/acs.jmedchem.3c00995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Enterovirus D68 (EV-D68) virus is a nonpolio enterovirus that typically causes respiratory illness and, in severe cases, can lead to paralysis and death in children. There is currently no vaccine or antiviral for EV-D68. We previously discovered the viral 2A protease (2Apro) as a viable antiviral drug target and identified telaprevir as a 2Apro inhibitor. 2Apro is a viral cysteine protease that cleaves the viral VP1-2A polyprotein junction. In this study, we report the X-ray crystal structures of EV-D68 2Apro, wild-type, and the C107A mutant and the structure-based lead optimization of telaprevir. Guided by the X-ray crystal structure, we predicted the binding pose of telaprevir in 2Apro using molecular dynamics simulations. We then utilized this model to inform structure-based optimization of the telaprevir's reactive warhead and P1-P4 substitutions. These efforts led to the discovery of 2Apro inhibitors with improved antiviral activity than telaprevir. These compounds represent promising lead compounds for further development as EV-D68 antivirals.
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Affiliation(s)
- Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Chang Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - George Lambrinidis
- Laboratory of Medicinal Chemistry, Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Lan Zhu
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Linda Olson
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Yu Wen
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Wei Liu
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
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5
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Brehm W, Triviño J, Krahn JM, Usón I, Diederichs K. XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO. J Appl Crystallogr 2023; 56:1585-1594. [PMID: 37791359 PMCID: PMC10543682 DOI: 10.1107/s1600576723007057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/08/2023] [Indexed: 10/05/2023] Open
Abstract
XDSGUI is a lightweight graphical user interface (GUI) for the XDS, SHELX and ARCIMBOLDO program packages that serves both novice and experienced users in obtaining optimal processing and phasing results for X-ray, neutron and electron diffraction data. The design of the program enables data processing and phasing without command line usage, and supports advanced command flows in a simple user-modifiable and user-extensible way. The GUI supplies graphical information based on the tabular log output of the programs, which is more intuitive, comprehensible and efficient than text output can be.
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Affiliation(s)
- Wolfgang Brehm
- Department of Physics, University of Hamburg, Hamburg 22761, Germany
| | - Josep Triviño
- Instituto de Biologia Molecular de Barcelona (IBMB), Baldiri Reixach 15, Barcelona 08028, Spain
| | - Juno M. Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Isabel Usón
- Instituto de Biologia Molecular de Barcelona (IBMB), Baldiri Reixach 15, Barcelona 08028, Spain
- ICREA: Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Universitätsstrasse, Konstanz 78457, Germany
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6
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Simpkin AJ, Caballero I, McNicholas S, Stevenson K, Jiménez E, Sánchez Rodríguez F, Fando M, Uski V, Ballard C, Chojnowski G, Lebedev A, Krissinel E, Usón I, Rigden DJ, Keegan RM. Predicted models and CCP4. Acta Crystallogr D Struct Biol 2023; 79:806-819. [PMID: 37594303 PMCID: PMC10478639 DOI: 10.1107/s2059798323006289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Abstract
In late 2020, the results of CASP14, the 14th event in a series of competitions to assess the latest developments in computational protein structure-prediction methodology, revealed the giant leap forward that had been made by Google's Deepmind in tackling the prediction problem. The level of accuracy in their predictions was the first instance of a competitor achieving a global distance test score of better than 90 across all categories of difficulty. This achievement represents both a challenge and an opportunity for the field of experimental structural biology. For structure determination by macromolecular X-ray crystallography, access to highly accurate structure predictions is of great benefit, particularly when it comes to solving the phase problem. Here, details of new utilities and enhanced applications in the CCP4 suite, designed to allow users to exploit predicted models in determining macromolecular structures from X-ray diffraction data, are presented. The focus is mainly on applications that can be used to solve the phase problem through molecular replacement.
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Affiliation(s)
- Adam J. Simpkin
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Iracema Caballero
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona, Spain
| | - Stuart McNicholas
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Kyle Stevenson
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona, Spain
| | - Filomeno Sánchez Rodríguez
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Maria Fando
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Ville Uski
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Charles Ballard
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrey Lebedev
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Eugene Krissinel
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Ronan M. Keegan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
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7
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Abellon-Ruiz J, Jana K, Silale A, Frey AM, Baslé A, Trost M, Kleinekathöfer U, van den Berg B. BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B 12 uptake in gut Bacteroides. Nat Commun 2023; 14:4714. [PMID: 37543597 PMCID: PMC10404256 DOI: 10.1038/s41467-023-40427-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
Vitamin B12 (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition for this keystone micronutrient is severe. Contrasting with Enterobacteria, members of the dominant genus Bacteroides often encode several BtuB vitamin B12 outer membrane transporters together with a conserved array of surface-exposed B12-binding lipoproteins. Here we show that the BtuB transporters from Bacteroides thetaiotaomicron form stable, pedal bin-like complexes with surface-exposed BtuG lipoprotein lids, which bind B12 with high affinities. Closing of the BtuG lid following B12 capture causes destabilisation of the bound B12 by a conserved BtuB extracellular loop, causing translocation of the vitamin to BtuB and subsequent transport. We propose that TonB-dependent, lipoprotein-assisted small molecule uptake is a general feature of Bacteroides spp. that is important for the success of this genus in colonising the human gut.
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Affiliation(s)
- Javier Abellon-Ruiz
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Kalyanashis Jana
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany
| | - Augustinas Silale
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Andrew M Frey
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Arnaud Baslé
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Matthias Trost
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Bert van den Berg
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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8
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White JBR, Silale A, Feasey M, Heunis T, Zhu Y, Zheng H, Gajbhiye A, Firbank S, Baslé A, Trost M, Bolam DN, van den Berg B, Ranson NA. Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes. Nature 2023:10.1038/s41586-023-06146-w. [PMID: 37286596 DOI: 10.1038/s41586-023-06146-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023]
Abstract
Bacteroidetes are abundant members of the human microbiota, utilizing a myriad of diet- and host-derived glycans in the distal gut1. Glycan uptake across the bacterial outer membrane of these bacteria is mediated by SusCD protein complexes, comprising a membrane-embedded barrel and a lipoprotein lid, which is thought to open and close to facilitate substrate binding and transport. However, surface-exposed glycan-binding proteins and glycoside hydrolases also play critical roles in the capture, processing and transport of large glycan chains. The interactions between these components in the outer membrane are poorly understood, despite being crucial for nutrient acquisition by our colonic microbiota. Here we show that for both the levan and dextran utilization systems of Bacteroides thetaiotaomicron, the additional outer membrane components assemble on the core SusCD transporter, forming stable glycan-utilizing machines that we term utilisomes. Single-particle cryogenic electron microscopy structures in the absence and presence of substrate reveal concerted conformational changes that demonstrate the mechanism of substrate capture, and rationalize the role of each component in the utilisome.
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Affiliation(s)
- Joshua B R White
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Augustinas Silale
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew Feasey
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Tiaan Heunis
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Yiling Zhu
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Hong Zheng
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Akshada Gajbhiye
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Susan Firbank
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Arnaud Baslé
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Matthias Trost
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - David N Bolam
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Bert van den Berg
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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9
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Lee J, Dalton RA, Baslé A, Vita N, Dennison C. Important Structural Features of Thiolate-Rich Four-Helix Bundles for Cu(I) Uptake and Removal. Inorg Chem 2023; 62:6617-6628. [PMID: 37057906 PMCID: PMC10155185 DOI: 10.1021/acs.inorgchem.2c04490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Indexed: 04/15/2023]
Abstract
A family of bacterial copper storage proteins (the Csps) possess thiolate-lined four-helix bundles whose cores can be filled with Cu(I) ions. The majority of Csps are cytosolic (Csp3s), and in vitro studies carried out to date indicate that the Csp3s from Methylosinus trichosporium OB3b (MtCsp3), Bacillus subtilis (BsCsp3), and Streptomyces lividans (SlCsp3) are alike. Bioinformatics have highlighted homologues with potentially different Cu(I)-binding properties from these characterized "classical" Csp3s. Determination herein of the crystal structure of the protein (RkCsp3) from the methanotroph Methylocystis sp. strain Rockwell with Cu(I) bound identifies this as the first studied example of a new subgroup of Csp3s. The most significant structural difference from classical Csp3s is the presence of only two Cu(I) sites at the mouth of the bundle via which Cu(I) ions enter and leave. This is due to the absence of three Cys residues and a His-containing motif, which allow classical Csp3s to bind five to six Cu(I) ions in this region. Regardless, RkCsp3 exhibits rapid Cu(I) binding and the fastest measured Cu(I) removal rate for a Csp3 when using high-affinity ligands as surrogate partners. New experiments on classical Csp3s demonstrate that their His-containing motif is not essential for fast Cu(I) uptake and removal. Other structural features that could be important for these functionally relevant in vitro properties are discussed.
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Affiliation(s)
- Jaeick Lee
- Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Rosemary A. Dalton
- Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Nicolas Vita
- Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, U.K.
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10
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Sendra KM, Barwinska-Sendra A, Mackenzie ES, Baslé A, Kehl-Fie TE, Waldron KJ. An ancient metalloenzyme evolves through metal preference modulation. Nat Ecol Evol 2023; 7:732-744. [PMID: 37037909 PMCID: PMC10172142 DOI: 10.1038/s41559-023-02012-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/15/2023] [Indexed: 04/12/2023]
Abstract
Evolution creates functional diversity of proteins, the essential building blocks of all biological systems. However, studies of natural proteins sampled across the tree of life and evaluated in a single experimental system are lacking. Almost half of enzymes require metals, and metalloproteins tend to optimally utilize the physicochemical properties of a specific metal co-factor. Life must adapt to changes in metal bioavailability, including those during the transition from anoxic to oxic Earth or pathogens' exposure to nutritional immunity. These changes can challenge the ability of metalloenzymes to maintain activity, presumptively driving their evolution. Here we studied metal-preference evolution within the natural diversity of the iron/manganese superoxide dismutase (SodFM) family of reactive oxygen species scavengers. We identified and experimentally verified residues with conserved roles in determining metal preference that, when combined with an understanding of the protein's evolutionary history, improved prediction of metal utilization across the five SodFM subfamilies defined herein. By combining phylogenetics, biochemistry and structural biology, we demonstrate that SodFM metal utilization can be evolutionarily fine tuned by sliding along a scale between perfect manganese and iron specificities. Over the history of life, SodFM metal preference has been modulated multiple independent times within different evolutionary and ecological contexts, and can be changed within short evolutionary timeframes.
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Affiliation(s)
- K M Sendra
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - A Barwinska-Sendra
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - E S Mackenzie
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - A Baslé
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - T E Kehl-Fie
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - K J Waldron
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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11
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Day MA, Christofferson AJ, Anderson JLR, Vass SO, Evans A, Searle PF, White SA, Hyde EI. Structure and Dynamics of Three Escherichia coli NfsB Nitro-Reductase Mutants Selected for Enhanced Activity with the Cancer Prodrug CB1954. Int J Mol Sci 2023; 24:ijms24065987. [PMID: 36983061 PMCID: PMC10051150 DOI: 10.3390/ijms24065987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/30/2023] Open
Abstract
Escherichia coli NfsB has been studied extensively for its potential for cancer gene therapy by reducing the prodrug CB1954 to a cytotoxic derivative. We have previously made several mutants with enhanced activity for the prodrug and characterised their activity in vitro and in vivo. Here, we determine the X-ray structure of our most active triple and double mutants to date, T41Q/N71S/F124T and T41L/N71S. The two mutant proteins have lower redox potentials than wild-type NfsB, and the mutations have lowered activity with NADH so that, in contrast to the wild-type enzyme, the reduction of the enzyme by NADH, rather than the reaction with CB1954, has a slower maximum rate. The structure of the triple mutant shows the interaction between Q41 and T124, explaining the synergy between these two mutations. Based on these structures, we selected mutants with even higher activity. The most active one contains T41Q/N71S/F124T/M127V, in which the additional M127V mutation enlarges a small channel to the active site. Molecular dynamics simulations show that the mutations or reduction of the FMN cofactors of the protein has little effect on its dynamics and that the largest backbone fluctuations occur at residues that flank the active site, contributing towards its broad substrate range.
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Affiliation(s)
- Martin A Day
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | | | - Simon O Vass
- Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Adam Evans
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Peter F Searle
- Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Scott A White
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Eva I Hyde
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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12
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Huo C, Ming T, Wu Y, Huan H, Qiu X, Lu C, Li Y, Zhang Z, Han J, Su X. Structural and Biochemical Characterization of Silver/Copper Binding by Dendrorhynchus zhejiangensis Ferritin. Polymers (Basel) 2023; 15:polym15051297. [PMID: 36904538 PMCID: PMC10007213 DOI: 10.3390/polym15051297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Ferritin with a highly symmetrical cage-like structure is not only key in the reversible storage of iron in efficient ferroxidase activity; it also provides unique coordination environments for the conjugation of heavy metal ions other than those associated with iron. However, research regarding the effect of these bound heavy metal ions on ferritin is scarce. In the present study, we prepared a marine invertebrate ferritin from Dendrorhynchus zhejiangensis (DzFer) and found that it could withstand extreme pH fluctuation. We then demonstrated its capacity to interact with Ag+ or Cu2+ ions using various biochemical and spectroscopic methods and X-ray crystallography. Structural and biochemical analyses revealed that both Ag+ and Cu2+ were able to bind to the DzFer cage via metal-coordination bonds and that their binding sites were mainly located inside the three-fold channel of DzFer. Furthermore, Ag+ was shown to have a higher selectivity for sulfur-containing amino acid residues and appeared to bind preferentially at the ferroxidase site of DzFer as compared with Cu2+. Thus, it is far more likely to inhibit the ferroxidase activity of DzFer. The results provide new insights into the effect of heavy metal ions on the iron-binding capacity of a marine invertebrate ferritin.
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Affiliation(s)
- Chunheng Huo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
| | - Tinghong Ming
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- Correspondence: (T.M.); (X.S.); Tel./Fax: +86-574-87608368 (X.S.)
| | - Yan Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Hengshang Huan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Xiaoting Qiu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
| | - Ye Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
| | - Zhen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
| | - Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- Correspondence: (T.M.); (X.S.); Tel./Fax: +86-574-87608368 (X.S.)
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13
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Chánique AM, Polidori N, Sovic L, Kracher D, Assil-Companioni L, Galuska P, Parra LP, Gruber K, Kourist R. A Cold-Active Flavin-Dependent Monooxygenase from Janthinobacterium svalbardensis Unlocks Applications of Baeyer–Villiger Monooxygenases at Low Temperature. ACS Catal 2023; 13:3549-3562. [PMID: 36970468 PMCID: PMC10028610 DOI: 10.1021/acscatal.2c05160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/31/2023] [Indexed: 03/02/2023]
Abstract
Cold-active enzymes maintain a large part of their optimal activity at low temperatures. Therefore, they can be used to avoid side reactions and preserve heat-sensitive compounds. Baeyer-Villiger monooxygenases (BVMO) utilize molecular oxygen as a co-substrate to catalyze reactions widely employed for steroid, agrochemical, antibiotic, and pheromone production. Oxygen has been described as the rate-limiting factor for some BVMO applications, thereby hindering their efficient utilization. Considering that oxygen solubility in water increases by 40% when the temperature is decreased from 30 to 10 °C, we set out to identify and characterize a cold-active BVMO. Using genome mining in the Antarctic organism Janthinobacterium svalbardensis, a cold-active type II flavin-dependent monooxygenase (FMO) was discovered. The enzyme shows promiscuity toward NADH and NADPH and high activity between 5 and 25 °C. The enzyme catalyzes the monooxygenation and sulfoxidation of a wide range of ketones and thioesters. The high enantioselectivity in the oxidation of norcamphor (eeS = 56%, eeP > 99%, E > 200) demonstrates that the generally higher flexibility observed in the active sites of cold-active enzymes, which compensates for the lower motion at cold temperatures, does not necessarily reduce the selectivity of these enzymes. To gain a better understanding of the unique mechanistic features of type II FMOs, we determined the structure of the dimeric enzyme at 2.5 Å resolution. While the unusual N-terminal domain has been related to the catalytic properties of type II FMOs, the structure shows a SnoaL-like N-terminal domain that is not interacting directly with the active site. The active site of the enzyme is accessible only through a tunnel, with Tyr-458, Asp-217, and His-216 as catalytic residues, a combination not observed before in FMOs and BVMOs.
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Affiliation(s)
- Andrea M. Chánique
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7810000, Chile
| | - Nakia Polidori
- NAWI Graz, BioTechMed Graz, Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, Graz 8010, Austria
| | - Lucija Sovic
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Daniel Kracher
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Leen Assil-Companioni
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- ACIB GmbH, Petersgasse 14/1, Graz 8010, Austria
| | - Philipp Galuska
- NAWI Graz, BioTechMed Graz, Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, Graz 8010, Austria
| | - Loreto P. Parra
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7810000, Chile
| | - Karl Gruber
- NAWI Graz, BioTechMed Graz, Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, Graz 8010, Austria
| | - Robert Kourist
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- ACIB GmbH, Petersgasse 14/1, Graz 8010, Austria
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14
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Gilep A, Varaksa T, Bukhdruker S, Kavaleuski A, Ryzhykau Y, Smolskaya S, Sushko T, Tsumoto K, Grabovec I, Kapranov I, Okhrimenko I, Marin E, Shevtsov M, Mishin A, Kovalev K, Kuklin A, Gordeliy V, Kaluzhskiy L, Gnedenko O, Yablokov E, Ivanov A, Borshchevskiy V, Strushkevich N. Structural insights into 3Fe-4S ferredoxins diversity in M. tuberculosis highlighted by a first redox complex with P450. Front Mol Biosci 2023; 9:1100032. [PMID: 36699703 PMCID: PMC9868604 DOI: 10.3389/fmolb.2022.1100032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
Ferredoxins are small iron-sulfur proteins and key players in essential metabolic pathways. Among all types, 3Fe-4S ferredoxins are less studied mostly due to anaerobic requirements. Their complexes with cytochrome P450 redox partners have not been structurally characterized. In the present work, we solved the structures of both 3Fe-4S ferredoxins from M. tuberculosis-Fdx alone and the fusion FdxE-CYP143. Our SPR analysis demonstrated a high-affinity binding of FdxE to CYP143. According to SAXS data, the same complex is present in solution. The structure reveals extended multipoint interactions and the shape/charge complementarity of redox partners. Furthermore, FdxE binding induced conformational changes in CYP143 as evident from the solved CYP143 structure alone. The comparison of FdxE-CYP143 and modeled Fdx-CYP51 complexes further revealed the specificity of ferredoxins. Our results illuminate the diversity of electron transfer complexes for the production of different secondary metabolites.
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Affiliation(s)
- Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus,Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Tatsiana Varaksa
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anton Kavaleuski
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Yury Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia,Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Sviatlana Smolskaya
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Tatsiana Sushko
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Irina Grabovec
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mikhail Shevtsov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- European Molecular Biology Laboratory, Hamburg Unit C/O DESY, Hamburg, Germany
| | - Alexander Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia,Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Valentin Gordeliy
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Leonid Kaluzhskiy
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Oksana Gnedenko
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Evgeniy Yablokov
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Alexis Ivanov
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia,Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia,*Correspondence: Valentin Borshchevskiy, ; Natallia Strushkevich,
| | - Natallia Strushkevich
- Skolkovo Institute of Science and Technology, Moscow, Russia,*Correspondence: Valentin Borshchevskiy, ; Natallia Strushkevich,
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15
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The Crystal Structure of Mouse Ces2c, a Potential Ortholog of Human CES2, Shows Structural Similarities in Substrate Regulation and Product Release to Human CES1. Int J Mol Sci 2022; 23:ijms232113101. [DOI: 10.3390/ijms232113101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
Members of the carboxylesterase 2 (Ces2/CES2) family have been studied intensively with respect to their hydrolytic function on (pro)drugs, whereas their physiological role in lipid and energy metabolism has been realized only within the last few years. Humans have one CES2 gene which is highly expressed in liver, intestine, and kidney. Interestingly, eight homologous Ces2 (Ces2a to Ces2h) genes exist in mice and the individual roles of the corresponding proteins are incompletely understood. Mouse Ces2c (mCes2c) is suggested as potential ortholog of human CES2. Therefore, we aimed at its structural and biophysical characterization. Here, we present the first crystal structure of mCes2c to 2.12 Å resolution. The overall structure of mCes2c resembles that of the human CES1 (hCES1). The core domain adopts an α/β hydrolase-fold with S230, E347, and H459 forming a catalytic triad. Access to the active site is restricted by the cap, the flexible lid, and the regulatory domain. The conserved gate (M417) and switch (F418) residues might have a function in product release similar as suggested for hCES1. Biophysical characterization confirms that mCes2c is a monomer in solution. Thus, this study broadens our understanding of the mammalian carboxylesterase family and assists in delineating the similarities and differences of the different family members.
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16
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White SA, Christofferson AJ, Grainger AI, Day MA, Jarrom D, Graziano AE, Searle PF, Hyde EI. The 3D-structure, kinetics and dynamics of the E. coli nitroreductase NfsA with NADP + provide glimpses of its catalytic mechanism. FEBS Lett 2022; 596:2425-2440. [PMID: 35648111 PMCID: PMC9912195 DOI: 10.1002/1873-3468.14413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022]
Abstract
Nitroreductases activate nitroaromatic antibiotics and cancer prodrugs to cytotoxic hydroxylamines and reduce quinones to quinols. Using steady-state and stopped-flow kinetics, we show that the Escherichia coli nitroreductase NfsA is 20-50 fold more active with NADPH than with NADH and that product release may be rate-limiting. The crystal structure of NfsA with NADP+ shows that a mobile loop forms a phosphate-binding pocket. The nicotinamide ring and nicotinamide ribose are mobile, as confirmed in molecular dynamics (MD) simulations. We present a model of NADPH bound to NfsA. Only one NADP+ is seen bound to the NfsA dimers, and MD simulations show that binding of a second NADP(H) cofactor is unfavourable, suggesting that NfsA and other members of this protein superfamily may have a half-of-sites mechanism.
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Affiliation(s)
| | | | - Alastair I. Grainger
- School of BiosciencesUniversity of BirminghamUK,Present address:
School of Life and Health SciencesAston UniversityBirminghamB4 7ETUK
| | - Martin A. Day
- School of BiosciencesUniversity of BirminghamUK,Institute for Cancer and Genomic SciencesUniversity of BirminghamUK,Present address:
DurhamUK
| | - David Jarrom
- School of BiosciencesUniversity of BirminghamUK,Present address:
Health Technology WalesCardiffCF10 4PLUK
| | - Antonio E. Graziano
- School of BiosciencesUniversity of BirminghamUK,Present address:
Carlsberg Marstons Brewing CompanyNorthamptonNN1 1PZUK
| | - Peter F. Searle
- Institute for Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Eva I. Hyde
- School of BiosciencesUniversity of BirminghamUK
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17
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Bond PS, Cowtan KD. ModelCraft: an advanced automated model-building pipeline using Buccaneer. Acta Crystallogr D Struct Biol 2022; 78:1090-1098. [PMID: 36048149 PMCID: PMC9435595 DOI: 10.1107/s2059798322007732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/01/2022] [Indexed: 01/16/2023] Open
Abstract
Interactive model building can be a difficult and time-consuming step in the structure-solution process. Automated model-building programs such as Buccaneer often make it quicker and easier by completing most of the model in advance. However, they may fail to do so with low-resolution data or a poor initial model or map. The Buccaneer pipeline is a relatively simple program that iterates Buccaneer with REFMAC to refine the model and update the map. A new pipeline called ModelCraft has been developed that expands on this to include shift-field refinement, machine-learned pruning of incorrect residues, classical density modification, addition of water and dummy atoms, building of nucleic acids and final rebuilding of side chains. Testing was performed on 1180 structures solved by experimental phasing, 1338 structures solved by molecular replacement using homologues and 2030 structures solved by molecular replacement using predicted AlphaFold models. Compared with the previous Buccaneer pipeline, ModelCraft increased the mean completeness of the protein models in the experimental phasing cases from 91% to 95%, the molecular-replacement cases from 50% to 78% and the AlphaFold cases from 82% to 91%.
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18
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Krissinel E, Lebedev AA, Uski V, Ballard CB, Keegan RM, Kovalevskiy O, Nicholls RA, Pannu NS, Skubák P, Berrisford J, Fando M, Lohkamp B, Wojdyr M, Simpkin AJ, Thomas JMH, Oliver C, Vonrhein C, Chojnowski G, Basle A, Purkiss A, Isupov MN, McNicholas S, Lowe E, Triviño J, Cowtan K, Agirre J, Rigden DJ, Uson I, Lamzin V, Tews I, Bricogne G, Leslie AGW, Brown DG. CCP4 Cloud for structure determination and project management in macromolecular crystallography. Acta Crystallogr D Struct Biol 2022; 78:1079-1089. [PMID: 36048148 PMCID: PMC9435598 DOI: 10.1107/s2059798322007987] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at the cost of increasing data volumes. This is due to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.
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19
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Tetreau G, Sawaya MR, De Zitter E, Andreeva EA, Banneville AS, Schibrowsky NA, Coquelle N, Brewster AS, Grünbein ML, Kovacs GN, Hunter MS, Kloos M, Sierra RG, Schiro G, Qiao P, Stricker M, Bideshi D, Young ID, Zala N, Engilberge S, Gorel A, Signor L, Teulon JM, Hilpert M, Foucar L, Bielecki J, Bean R, de Wijn R, Sato T, Kirkwood H, Letrun R, Batyuk A, Snigireva I, Fenel D, Schubert R, Canfield EJ, Alba MM, Laporte F, Després L, Bacia M, Roux A, Chapelle C, Riobé F, Maury O, Ling WL, Boutet S, Mancuso A, Gutsche I, Girard E, Barends TRM, Pellequer JL, Park HW, Laganowsky AD, Rodriguez J, Burghammer M, Shoeman RL, Doak RB, Weik M, Sauter NK, Federici B, Cascio D, Schlichting I, Colletier JP. De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals. Nat Commun 2022; 13:4376. [PMID: 35902572 PMCID: PMC9334358 DOI: 10.1038/s41467-022-31746-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/30/2022] [Indexed: 11/08/2022] Open
Abstract
Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.
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Affiliation(s)
- Guillaume Tetreau
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
| | - Elke De Zitter
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Elena A Andreeva
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Anne-Sophie Banneville
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Natalie A Schibrowsky
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Nicolas Coquelle
- Large-Scale Structures Group, Institut Laue-Langevin, F-38000, Grenoble, France
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Marie Luise Grünbein
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Marco Kloos
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Giorgio Schiro
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Pei Qiao
- Department of Chemistry, Texas A&M University, College Station, TX, 77845, USA
| | - Myriam Stricker
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Dennis Bideshi
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Biological Sciences, California Baptist University, Riverside, CA, 92504, USA
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ninon Zala
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Sylvain Engilberge
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Alexander Gorel
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Jean-Marie Teulon
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Mario Hilpert
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tokushi Sato
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Irina Snigireva
- European Synchrotron Radiation Facility (ESRF), BP 220, 38043, Grenoble, France
| | - Daphna Fenel
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Ethan J Canfield
- Mass Spectrometry Core Facility, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mario M Alba
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | | | | | - Maria Bacia
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Amandine Roux
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342, Lyon, France
| | | | - François Riobé
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342, Lyon, France
| | - Olivier Maury
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342, Lyon, France
| | - Wai Li Ling
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Adrian Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Irina Gutsche
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Eric Girard
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Thomas R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Jean-Luc Pellequer
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Hyun-Woo Park
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Biological Sciences, California Baptist University, Riverside, CA, 92504, USA
| | - Arthur D Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, 77845, USA
| | - Jose Rodriguez
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Manfred Burghammer
- European Synchrotron Radiation Facility (ESRF), BP 220, 38043, Grenoble, France
| | - Robert L Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - R Bruce Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Martin Weik
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian Federici
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Jacques-Philippe Colletier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France.
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20
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Ferrario E, Miggiano R, Rizzi M, Ferraris DM. The integration of AlphaFold-predicted and crystal structures of human trans-3-hydroxy-l-proline dehydratase reveals a regulatory catalytic mechanism. Comput Struct Biotechnol J 2022; 20:3874-3883. [PMID: 35891782 PMCID: PMC9309405 DOI: 10.1016/j.csbj.2022.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Computational methods for protein structure prediction have made significant strides forward, as evidenced by the last development of the neural network AlphaFold, which outperformed the CASP14 competitors by consistently predicting the structure of target proteins. Here we show an integrated structural investigation that combines the AlphaFold and crystal structures of human trans-3-Hydroxy-l-proline dehydratase, an enzyme involved in hydroxyproline catabolism and whose structure had never been reported before, identifying a structural element, absent in the AlphaFold model but present in the crystal structure, that was subsequently proved to be functionally relevant. Although the AlphaFold model lacked information on protein oligomerization, the native dimer was reconstructed using template-based and ab initio computational approaches. Moreover, molecular phasing of the diffraction data using the AlphaFold model resulted in dimer reconstruction and straightforward structure solution. Our work adds to the integration of AlphaFold with experimental structural and functional data for protein analysis, crystallographic phasing and structure solution.
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Affiliation(s)
- Eugenio Ferrario
- University of Piemonte Orientale, Department of Pharmaceutical Sciences, Largo Donegani 2, 28100 Novara, Italy
| | - Riccardo Miggiano
- University of Piemonte Orientale, Department of Pharmaceutical Sciences, Largo Donegani 2, 28100 Novara, Italy
- IXTAL srl, Via Bovio 6, 28100 Novara, Italy
| | - Menico Rizzi
- University of Piemonte Orientale, Department of Pharmaceutical Sciences, Largo Donegani 2, 28100 Novara, Italy
| | - Davide M. Ferraris
- University of Piemonte Orientale, Department of Pharmaceutical Sciences, Largo Donegani 2, 28100 Novara, Italy
- IXTAL srl, Via Bovio 6, 28100 Novara, Italy
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21
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Bhatia I, Yadav S, Biswal BK. Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously. Acta Crystallogr F Struct Biol Commun 2022; 78:252-264. [DOI: 10.1107/s2053230x22005738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/26/2022] [Indexed: 11/11/2022] Open
Abstract
The unintended crystallization of proteins which generally originate from the expression host instead of the target recombinant proteins is periodically reported. Despite the massive technological advances in the field, assigning a structural model to the corresponding diffraction data is not a trivial task. Here, the structure of acyl-carrier protein synthase (AcpS) from Mycobacterium smegmatis (msAcpS), which crystallized inadvertently in an experimental setup to grow crystals of a Mycobacterium tuberculosis protein using M. smegmatis as an expression system, is reported. After numerous unsuccessful attempts to solve the structure of the target protein by the molecular-replacement method no convincing solutions were obtained, indicating that the diffraction data may correspond to a crystal of an artifactual protein, which was finally identified by the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) server. The msAcpS structure was solved at 2.27 Å resolution and structural analysis showed an overall conserved fold. msAcpS formed a trimeric structure similar to those of other reported structures of AcpS from various organisms; however, the residues involved in trimer formation are not strictly conserved. An unrelated metal ion (Ni2+), which was possibly incorporated during protein purification, was observed in the proximity of His49 and His116. Structural and sequence differences were observed in the loop connecting the α3 and α4 helices that is responsible for the open and closed conformations of the enzyme. Moreover, the structural analysis of msAcpS augments the current understanding of this enzyme, which plays a crucial role in the functional activation of acyl-carrier proteins in the fatty-acid biosynthesis pathway.
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22
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Characterization of inositol lipid metabolism in gut-associated Bacteroidetes. Nat Microbiol 2022; 7:986-1000. [PMID: 35725777 PMCID: PMC9246714 DOI: 10.1038/s41564-022-01152-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/17/2022] [Indexed: 12/13/2022]
Abstract
Inositol lipids are ubiquitous in eukaryotes and have finely tuned roles in cellular signalling and membrane homoeostasis. In Bacteria, however, inositol lipid production is relatively rare. Recently, the prominent human gut bacterium Bacteroides thetaiotaomicron (BT) was reported to produce inositol lipids and sphingolipids, but the pathways remain ambiguous and their prevalence unclear. Here, using genomic and biochemical approaches, we investigated the gene cluster for inositol lipid synthesis in BT using a previously undescribed strain with inducible control of sphingolipid synthesis. We characterized the biosynthetic pathway from myo-inositol-phosphate (MIP) synthesis to phosphoinositol dihydroceramide, determined the crystal structure of the recombinant BT MIP synthase enzyme and identified the phosphatase responsible for the conversion of bacterially-derived phosphatidylinositol phosphate (PIP-DAG) to phosphatidylinositol (PI-DAG). In vitro, loss of inositol lipid production altered BT capsule expression and antimicrobial peptide resistance. In vivo, loss of inositol lipids decreased bacterial fitness in a gnotobiotic mouse model. We identified a second putative, previously undescribed pathway for bacterial PI-DAG synthesis without a PIP-DAG intermediate, common in Prevotella. Our results indicate that inositol sphingolipid production is widespread in host-associated Bacteroidetes and has implications for symbiosis. The pathways responsible for inositol lipid production in human gut Bacteroides are characterized and these lipids are important for capsule expression and antimicrobial peptide resistance in vitro and colonization in vivo.
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23
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Minor W, Cymborowski M, Borek D, Cooper DR, Chruszcz M, Otwinowski Z. Optimal structure determination from sub-optimal diffraction data. Protein Sci 2022; 31:259-268. [PMID: 34783106 PMCID: PMC8740829 DOI: 10.1002/pro.4235] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/06/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023]
Abstract
Herein we present the newest version of the HKL-3000 system that integrates data collection, data reduction, phasing, model building, refinement, and validation. The system significantly accelerates the process of structure determination and has proven its high value for the determination of very high-quality structures. The heuristic for choosing the best approach for every step of structure determination for various quality samples and diffraction data has been optimized. The latest modifications increase the likelihood of a successful structure determination with challenging data. The HKL-3000 is a successor of HKL and HKL-2000 programs. The use of the HKL family of programs has been reported for over 73,000 PDB deposits, that is, almost 50% of macromolecular structures determined with X-ray diffraction.
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Affiliation(s)
- Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Dominika Borek
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexas,Department of BiochemistryThe University of Texas Southwestern Medical CenterDallasTexas
| | - David R. Cooper
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Maksymilian Chruszcz
- Department of Chemistry and BiochemistryUniversity of South CarolinaColumbiaSouth Carolina
| | - Zbyszek Otwinowski
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexas,Department of BiochemistryThe University of Texas Southwestern Medical CenterDallasTexas
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24
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Chojnowski G, Simpkin AJ, Leonardo DA, Seifert-Davila W, Vivas-Ruiz DE, Keegan RM, Rigden DJ. findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM. IUCRJ 2022; 9:86-97. [PMID: 35059213 PMCID: PMC8733886 DOI: 10.1107/s2052252521011088] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/22/2021] [Indexed: 05/15/2023]
Abstract
Although experimental protein-structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or appear as a contaminant. Regardless of the source of the problem, the unknown protein always requires characterization. Here, an automated pipeline is presented for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. The method's application to characterize the crystal structure of an unknown protein purified from a snake venom is presented. It is also shown that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
- Correspondence e-mail:
| | - Adam J. Simpkin
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Diego A. Leonardo
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | | | - Dan E. Vivas-Ruiz
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Avenida Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima, Peru
| | - Ronan M. Keegan
- Rutherford Appleton Laboratory, Research Complex at Harwell, UKRI-STFC, Didcot OX11 0FA, United Kingdom
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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25
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Nicholls RA, Joosten RP, Long F, Wojdyr M, Lebedev A, Krissinel E, Catapano L, Fischer M, Emsley P, Murshudov GN. Modelling covalent linkages in CCP4. Acta Crystallogr D Struct Biol 2021; 77:712-726. [PMID: 34076587 PMCID: PMC8171069 DOI: 10.1107/s2059798321001753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/12/2021] [Indexed: 11/10/2022] Open
Abstract
In this contribution, the current protocols for modelling covalent linkages within the CCP4 suite are considered. The mechanism used for modelling covalent linkages is reviewed: the use of dictionaries for describing changes to stereochemistry as a result of the covalent linkage and the application of link-annotation records to structural models to ensure the correct treatment of individual instances of covalent linkages. Previously, linkage descriptions were lacking in quality compared with those of contemporary component dictionaries. Consequently, AceDRG has been adapted for the generation of link dictionaries of the same quality as for individual components. The approach adopted by AceDRG for the generation of link dictionaries is outlined, which includes associated modifications to the linked components. A number of tools to facilitate the practical modelling of covalent linkages available within the CCP4 suite are described, including a new restraint-dictionary accumulator, the Make Covalent Link tool and AceDRG interface in Coot, the 3D graphical editor JLigand and the mechanisms for dealing with covalent linkages in the CCP4i2 and CCP4 Cloud environments. These integrated solutions streamline and ease the covalent-linkage modelling workflow, seamlessly transferring relevant information between programs. Current recommended practice is elucidated by means of instructive practical examples. By summarizing the different approaches to modelling linkages that are available within the CCP4 suite, limitations and potential pitfalls that may be encountered are highlighted in order to raise awareness, with the intention of improving the quality of future modelled covalent linkages in macromolecular complexes.
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Affiliation(s)
- Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robbie P. Joosten
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Fei Long
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Marcin Wojdyr
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge CB3 0AX, United Kingdom
| | - Andrey Lebedev
- CCP4, STFC Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Eugene Krissinel
- CCP4, STFC Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Lucrezia Catapano
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
| | - Marcus Fischer
- Chemical Biology and Therapeutics and Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Paul Emsley
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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26
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Advancements in macromolecular crystallography: from past to present. Emerg Top Life Sci 2021; 5:127-149. [PMID: 33969867 DOI: 10.1042/etls20200316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.
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27
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Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc. PLoS One 2021; 16:e0251459. [PMID: 33989344 PMCID: PMC8121366 DOI: 10.1371/journal.pone.0251459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/23/2021] [Indexed: 12/22/2022] Open
Abstract
Synaptic plasticity is vital for brain function and memory formation. One of the key proteins in long-term synaptic plasticity and memory is the activity-regulated cytoskeleton-associated protein (Arc). Mammalian Arc forms virus-like capsid structures in a process requiring the N-terminal domain and contains two C-terminal lobes that are structural homologues to retroviral capsids. Drosophila has two isoforms of Arc, dArc1 and dArc2, with low sequence similarity to mammalian Arc, but lacking a large N-terminal domain. Both dArc isoforms are related to the Ty3/gypsy retrotransposon capsid, consisting of N- and C-terminal lobes. Structures of dArc1, as well as capsids formed by both dArc isoforms, have been recently determined. We carried out structural characterization of the four individual dArc lobe domains. As opposed to the corresponding mammalian Arc lobe domains, which are monomeric, the dArc lobes were all oligomeric in solution, indicating a strong propensity for homophilic interactions. A truncated N-lobe from dArc2 formed a domain-swapped dimer in the crystal structure, resulting in a novel dimer interaction that could be relevant for capsid assembly or other dArc functions. This domain-swapped structure resembles the dimeric protein C of flavivirus capsids, as well as the structure of histones dimers, domain-swapped transcription factors, and membrane-interacting BAK domains. The strong oligomerization properties of the isolated dArc lobe domains explain the ability of dArc to form capsids in the absence of any large N-terminal domain, in contrast to the mammalian protein.
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28
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Specificity of AMPylation of the human chaperone BiP is mediated by TPR motifs of FICD. Nat Commun 2021; 12:2426. [PMID: 33893288 PMCID: PMC8065156 DOI: 10.1038/s41467-021-22596-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
To adapt to fluctuating protein folding loads in the endoplasmic reticulum (ER), the Hsp70 chaperone BiP is reversibly modified with adenosine monophosphate (AMP) by the ER-resident Fic-enzyme FICD/HYPE. The structural basis for BiP binding and AMPylation by FICD has remained elusive due to the transient nature of the enzyme-substrate-complex. Here, we use thiol-reactive derivatives of the cosubstrate adenosine triphosphate (ATP) to covalently stabilize the transient FICD:BiP complex and determine its crystal structure. The complex reveals that the TPR-motifs of FICD bind specifically to the conserved hydrophobic linker of BiP and thus mediate specificity for the domain-docked conformation of BiP. Furthermore, we show that both AMPylation and deAMPylation of BiP are not directly regulated by the presence of unfolded proteins. Together, combining chemical biology, crystallography and biochemistry, our study provides structural insights into a key regulatory mechanism that safeguards ER homeostasis.
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29
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Chung IYW, Li L, Tyurin O, Gagarinova A, Wibawa R, Li P, Hartland EL, Cygler M. Structural and functional study of Legionella pneumophila effector RavA. Protein Sci 2021; 30:940-955. [PMID: 33660322 DOI: 10.1002/pro.4057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 01/20/2023]
Abstract
Legionella pneumophila is an intracellular pathogen that causes Legionnaire's disease in humans. This bacterium can be found in freshwater environments as a free-living organism, but it is also an intracellular parasite of protozoa. Human infection occurs when inhaled aerosolized pathogen comes into contact with the alveolar mucosa and replicates in alveolar macrophages. Legionella enters the host cell by phagocytosis and redirects the Legionella-containing phagosomes from the phagocytic maturation pathway. These nascent phagosomes fuse with ER-derived secretory vesicles and membranes forming the Legionella-containing vacuole. Legionella subverts many host cellular processes by secreting over 300 effector proteins into the host cell via the Dot/Icm type IV secretion system. The cellular function for many Dot/Icm effectors is still unknown. Here, we present a structural and functional study of L. pneumophila effector RavA (Lpg0008). Structural analysis revealed that the RavA consists of four ~85 residue long α-helical domains with similar folds, which show only a low level of structural similarity to other protein domains. The ~90 residues long C-terminal segment is predicted to be natively unfolded. We show that during L. pneumophila infection of human cells, RavA localizes to the Golgi apparatus and to the plasma membrane. The same localization is observed when RavA is expressed in human cells. The localization signal resides within the C-terminal sequence C409 WTSFCGLF417 . Yeast-two-hybrid screen using RavA as bait identified RAB11A as a potential binding partner. RavA is present in L. pneumophila strains but only distant homologs are found in other Legionella species, where the number of repeats varies.
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Affiliation(s)
- Ivy Y W Chung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lei Li
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Oleg Tyurin
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Symvivo Corporation, Burnaby, British Columbia, Canada
| | - Alla Gagarinova
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Raissa Wibawa
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, and Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Pengfei Li
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, and Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Elizabeth L Hartland
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, and Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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30
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Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Arch Biochem Biophys 2021; 699:108750. [PMID: 33421379 DOI: 10.1016/j.abb.2020.108750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 01/14/2023]
Abstract
Bovine β-lactoglobulin, an abundant protein in whey, is a promising nanocarrier for peroral administration of drug-like hydrophobic molecules, a process that involves transit through the different acidic conditions of the human digestive tract. Among the several pH-induced conformational rearrangements that this lipocalin undergoes, the Tanford transition is particularly relevant. This transition, which occurs with a midpoint around neutral pH, involves a conformational change of the E-F loop that regulates accessibility to the primary binding site. The effect of this transition on the ligand binding properties of this protein has scarcely been explored. In this study, we carried out an energetic and structural characterization of β-lactoglobulin molecular recognition at pH values above and below the zone in which the Tanford transition occurs. The combined analysis of crystallographic, calorimetric, and molecular dynamics data sheds new light on the interplay between self-association, ligand binding, and the Tanford pre- and post-transition conformational states, revealing novel aspects underlying the molecular recognition mechanism of this enigmatic lipocalin.
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31
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McCoy AJ, Stockwell DH, Sammito MD, Oeffner RD, Hatti KS, Croll TI, Read RJ. Phasertng: directed acyclic graphs for crystallographic phasing. Acta Crystallogr D Struct Biol 2021; 77:1-10. [PMID: 33404520 PMCID: PMC7787104 DOI: 10.1107/s2059798320014746] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 11/06/2020] [Indexed: 12/01/2022] Open
Abstract
Crystallographic phasing strategies increasingly require the exploration and ranking of many hypotheses about the number, types and positions of atoms, molecules and/or molecular fragments in the unit cell, each with only a small chance of being correct. Accelerating this move has been improvements in phasing methods, which are now able to extract phase information from the placement of very small fragments of structure, from weak experimental phasing signal or from combinations of molecular replacement and experimental phasing information. Describing phasing in terms of a directed acyclic graph allows graph-management software to track and manage the path to structure solution. The crystallographic software supporting the graph data structure must be strictly modular so that nodes in the graph are efficiently generated by the encapsulated functionality. To this end, the development of new software, Phasertng, which uses directed acyclic graphs natively for input/output, has been initiated. In Phasertng, the codebase of Phaser has been rebuilt, with an emphasis on modularity, on scripting, on speed and on continuing algorithm development. As a first application of phasertng, its advantages are demonstrated in the context of phasertng.xtricorder, a tool to analyse and triage merged data in preparation for molecular replacement or experimental phasing. The description of the phasing strategy with directed acyclic graphs is a generalization that extends beyond the functionality of Phasertng, as it can incorporate results from bioinformatics and other crystallographic tools, and will facilitate multifaceted search strategies, dynamic ranking of alternative search pathways and the exploitation of machine learning to further improve phasing strategies.
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Affiliation(s)
- Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Duncan H. Stockwell
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Massimo D. Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Robert D. Oeffner
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Kaushik S. Hatti
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Tristan I. Croll
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
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32
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Yilmazer B, Isupov MN, De Rose SA, Bulut H, Benninghoff JC, Binay B, Littlechild JA. Structural insights into the NAD+-dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD+ ternary complex of the Chaetomium thermophilum enzyme. J Struct Biol 2020; 212:107657. [DOI: 10.1016/j.jsb.2020.107657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/23/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
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33
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Yang J, Guan X, Zhang D, Zhao P, Guo S, Kuang Z. Crystal structure of the SPRY domain-containing protein 7 reveals unique structural features. Biochem Biophys Res Commun 2020; 531:350-356. [PMID: 32800543 DOI: 10.1016/j.bbrc.2020.07.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
Abstract
The SPRY/B30.2 domain is one of the most abundant protein domains found in eukaryotes. Vast majority of the SPRY domain-containing proteins are multi-domain proteins. The SPRY domain-containing protein 7 (SPRY7, also named C13orf1, and named chronic lymphocytic leukemia deletion region gene 6 protein, CCLD6, encoded by the spryd7 gene) is the smallest SPRY domain protein in human that does not contain other accessory domains. Here we have determined the crystal structure of human SPRY7 at a resolution of 1.62 Å and found that SPRY7 has some unique structural features that are not present in other previously reported SRPY domain structures. Overall, SPRY7 may represent an evolutionary early version of the SPRY domain, and subsequent loop insertions and expansions, residue substitutions, as well as domain combinations have rendered the SPRY domain versatile binding specificities and broad biological functions. These results serve as a useful basis for a profound characterization of the molecular interactions of SPRY7.
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Affiliation(s)
- Jinjin Yang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Xueyan Guan
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Danting Zhang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Panqi Zhao
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Shujun Guo
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Zhihe Kuang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China.
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Bond PS, Wilson KS, Cowtan KD. Predicting protein model correctness in Coot using machine learning. Acta Crystallogr D Struct Biol 2020; 76:713-723. [PMID: 32744253 PMCID: PMC7397494 DOI: 10.1107/s2059798320009080] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/02/2020] [Indexed: 11/11/2022] Open
Abstract
Manually identifying and correcting errors in protein models can be a slow process, but improvements in validation tools and automated model-building software can contribute to reducing this burden. This article presents a new correctness score that is produced by combining multiple sources of information using a neural network. The residues in 639 automatically built models were marked as correct or incorrect by comparing them with the coordinates deposited in the PDB. A number of features were also calculated for each residue using Coot, including map-to-model correlation, density values, B factors, clashes, Ramachandran scores, rotamer scores and resolution. Two neural networks were created using these features as inputs: one to predict the correctness of main-chain atoms and the other for side chains. The 639 structures were split into 511 that were used to train the neural networks and 128 that were used to test performance. The predicted correctness scores could correctly categorize 92.3% of the main-chain atoms and 87.6% of the side chains. A Coot ML Correctness script was written to display the scores in a graphical user interface as well as for the automatic pruning of chains, residues and side chains with low scores. The automatic pruning function was added to the CCP4i2 Buccaneer automated model-building pipeline, leading to significant improvements, especially for high-resolution structures.
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Affiliation(s)
- Paul S. Bond
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Keith S. Wilson
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Kevin D. Cowtan
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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35
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Chojnowski G, Choudhury K, Heuser P, Sobolev E, Pereira J, Oezugurel U, Lamzin VS. The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution. Acta Crystallogr D Struct Biol 2020; 76:248-260. [PMID: 32133989 PMCID: PMC7057216 DOI: 10.1107/s2059798320000455] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/14/2020] [Indexed: 12/18/2022] Open
Abstract
The performance of automated protein model building usually decreases with resolution, mainly owing to the lower information content of the experimental data. This calls for a more elaborate use of the available structural information about macromolecules. Here, a new method is presented that uses structural homologues to improve the quality of protein models automatically constructed using ARP/wARP. The method uses local structural similarity between deposited models and the model being built, and results in longer main-chain fragments that in turn can be more reliably docked to the protein sequence. The application of the homology-based model extension method to the example of a CFA synthase at 2.7 Å resolution resulted in a more complete model with almost all of the residues correctly built and docked to the sequence. The method was also evaluated on 1493 molecular-replacement solutions at a resolution of 4.0 Å and better that were submitted to the ARP/wARP web service for model building. A significant improvement in the completeness and sequence coverage of the built models has been observed.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Koushik Choudhury
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Philipp Heuser
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Egor Sobolev
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Joana Pereira
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Umut Oezugurel
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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36
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Simpkin AJ, Simkovic F, Thomas JMH, Savko M, Lebedev A, Uski V, Ballard CC, Wojdyr M, Shepard W, Rigden DJ, Keegan RM. Using Phaser and ensembles to improve the performance of SIMBAD. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1-8. [PMID: 31909738 PMCID: PMC6939438 DOI: 10.1107/s2059798319015031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/06/2019] [Indexed: 01/07/2023]
Abstract
The conventional approach to search-model identification in molecular replacement (MR) is to screen a database of known structures using the target sequence. However, this strategy is not always effective, for example when the relationship between sequence and structural similarity fails or when the crystal contents are not those expected. An alternative approach is to identify suitable search models directly from the experimental data. SIMBAD is a sequence-independent MR pipeline that uses either a crystal lattice search or MR functions to directly locate suitable search models from databases. The previous version of SIMBAD used the fast AMoRe rotation-function search. Here, a new version of SIMBAD which makes use of Phaser and its likelihood scoring to improve the sensitivity of the pipeline is presented. It is shown that the additional compute time potentially required by the more sophisticated scoring is counterbalanced by the greater sensitivity, allowing more cases to trigger early-termination criteria, rather than running to completion. Using Phaser solved 17 out of 25 test cases in comparison to the ten solved with AMoRe, and it is shown that use of ensemble search models produces additional performance benefits.
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Affiliation(s)
- Adam J Simpkin
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Jens M H Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Martin Savko
- Synchrotron SOLEIL, L'Orme des Merisiers, BP 48, 91192 Saint Aubin, Gif-sur-Yvette, France
| | - Andrey Lebedev
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Ville Uski
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Charles C Ballard
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | | | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, BP 48, 91192 Saint Aubin, Gif-sur-Yvette, France
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan M Keegan
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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37
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Lange J, Baakman C, Pistorius A, Krieger E, Hooft R, Joosten RP, Vriend G. Facilities that make the PDB data collection more powerful. Protein Sci 2019; 29:330-344. [PMID: 31724231 PMCID: PMC6933850 DOI: 10.1002/pro.3788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/11/2019] [Indexed: 01/13/2023]
Abstract
We describe a series of databases and tools that directly or indirectly support biomedical research on macromolecules, with focus on their applicability in protein structure bioinformatics research. DSSP, that determines secondary structures of proteins, has been updated to work well with extremely large structures in multiple formats. The PDBREPORT database that lists anomalies in protein structures has been remade to remove many small problems. These reports are now available as PDF-formatted files with a computer-readable summary. The VASE software has been added to analyze and visualize HSSP multiple sequence alignments for protein structures. The Lists collection of databases has been extended with a series of databases, most noticeably with a database that gives each protein structure a grade for usefulness in protein structure bioinformatics projects. The PDB-REDO collection of reanalyzed and re-refined protein structures that were solved by X-ray crystallography has been improved by dealing better with sugar residues and with hydrogen bonds, and adding many missing surface loops. All academic software underlying these protein structure bioinformatics applications and databases are now publicly accessible, either directly from the authors or from the GitHub software repository.
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Affiliation(s)
- Joanna Lange
- Bio-Prodict, Nijmegen, The Netherlands.,Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc, Nijmegen, The Netherlands
| | - Coos Baakman
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc, Nijmegen, The Netherlands
| | - Arthur Pistorius
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc, Nijmegen, The Netherlands
| | - Elmar Krieger
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc, Nijmegen, The Netherlands
| | - Rob Hooft
- Department of Computer Science, Dutch Techcentre for Life Sciences (DTL), Amsterdam, The Netherlands.,Department of Computer Science, Vrije Universiteit Amsterdam (VU), Amsterdam, The Netherlands
| | - Robbie P Joosten
- Biochemistry department, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboudumc, Nijmegen, The Netherlands.,Baco Institute of Protein Science (BIPS), Mindoro, Philippines
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38
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Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut. Nat Microbiol 2019; 4:2393-2404. [PMID: 31636419 PMCID: PMC6881182 DOI: 10.1038/s41564-019-0590-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/12/2019] [Indexed: 12/26/2022]
Abstract
Sialic acid (Neu5Ac) is commonly found in terminal location of colonic mucins glycans where it is a much-coveted nutrient for gut bacteria including Ruminococcus gnavus. R. gnavus is part of the healthy gut microbiota in humans but shows a disproportionate representation in diseases. There is therefore a need in understanding the molecular mechanisms underpinning its adaptation to the gut. Previous in vitro work demonstrated that R. gnavus mucin glycan-foraging strategy is strain-dependent and associated with the expression of an intramolecular trans-sialidase releasing 2,7-anhydro-Neu5Ac instead of Neu5Ac from mucins. Here, we have unravelled the metabolism pathway of 2,7-anhydro-Neu5Ac in R. gnavus which is underpinned by the exquisite specificity of the sialic transporter for 2,7-anhydro-Neu5Ac, and by the action of an oxidoreductase converting 2,7-anhydro-Neu5Ac into Neu5Ac which then becomes substrate of a Neu5Ac-specific aldolase. Having generated a R. gnavus nan cluster deletion mutant that lost the ability to grow on sialylated substrates, we showed that in gnotobiotic mice colonised with R. gnavus wild-type and mutant strains, the fitness of the nan mutant was significantly impaired with a reduced ability to colonise the mucus layer. Overall, our study revealed a unique sialic acid pathway in bacteria, with significant implications for the spatial adaptation of mucin-foraging gut symbionts in health and disease.
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39
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Sporny M, Guez-Haddad J, Lebendiker M, Ulisse V, Volf A, Mim C, Isupov MN, Opatowsky Y. Structural Evidence for an Octameric Ring Arrangement of SARM1. J Mol Biol 2019; 431:3591-3605. [PMID: 31278906 DOI: 10.1016/j.jmb.2019.06.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/16/2019] [Accepted: 06/25/2019] [Indexed: 12/11/2022]
Abstract
SARM1 induces axonal degeneration in response to various insults and is therefore considered an attractive drug target for the treatment of neuro-degenerative diseases as well as for brain and spinal cord injuries. SARM1 activity depends on the integrity of the protein's SAM domains, as well as on the enzymatic conversion of NAD+ to ADPR (ADP Ribose) products by the SARM1's TIR domain. Therefore, inhibition of either SAM or TIR functions may constitute an effective therapeutic strategy. However, there is currently no SARM1-directed therapeutic approach available because of an insufficient structural and mechanistic understanding of this protein. In this study, we found that SARM1 assembles into an octameric ring. This arrangement was not described before in other SAM proteins, but is reminiscent of the apoptosome and inflammasome-well-known apoptotic ring-like oligomers. We show that both SARM1 and the isolated tandem SAM1-2 domains form octamers in solution, and electron microscopy analysis reveals an octameric ring of SARM1. We determined the crystal structure of SAM1-2 and found that it also forms a closed octameric ring in the crystal lattice. The SAM1-2 ring interactions are mediated by complementing "lock and key" hydrophobic grooves and inserts and electrostatic charges between the neighboring protomers. We have mutated several interacting SAM1-2 interfaces and measured how these mutations affect SARM1 apoptotic activity in cultured cells, and in this way identified critical oligomerization sites that facilitate cell death. These results highlight the importance of oligomerization for SARM1 function and reveal critical epitopes for future targeted drug development.
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Affiliation(s)
- Michael Sporny
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Mario Lebendiker
- Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Israel
| | - Valeria Ulisse
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Allison Volf
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Carsten Mim
- Department of Biomedical Engineering and Health Solutions, Royal Technical Institute (KTH), Stockholm, Sweden; Department of Nutrition and Biosciences, Karolinska Institute, Huddinge, Sweden
| | | | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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40
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Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Crystallogr D Struct Biol 2019; 75:451-454. [PMID: 30988261 PMCID: PMC6465986 DOI: 10.1107/s2059798319004522] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/03/2019] [Indexed: 11/10/2022] Open
Abstract
This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).
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Affiliation(s)
- Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kumaran Baskaran
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gerard Bricogne
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - David G. Brown
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Minyu Chen
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Claus Flensburg
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jeffrey C. Hoch
- BioMagResBank (BMRB), UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Yasuyo Ikegawa
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yumiko Kengaku
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Eugene Krissinel
- CCP4, Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
| | - Genji Kurisu
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yuhe Liang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - John L. Markley
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Martin Noble
- Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Irina Persikova
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eldon L. Ulrich
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Clemens Vonrhein
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - John Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Marcin Wojdyr
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
- CCP4, Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
| | - Masashi Yokochi
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Cuppari A, Körschgen H, Fahrenkamp D, Schmitz C, Guevara T, Karmilin K, Kuske M, Olf M, Dietzel E, Yiallouros I, de Sanctis D, Goulas T, Weiskirchen R, Jahnen-Dechent W, Floehr J, Stoecker W, Jovine L, Gomis-Rüth FX. Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition. IUCRJ 2019; 6:317-330. [PMID: 30867929 PMCID: PMC6400186 DOI: 10.1107/s2052252519001568] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
Mammalian fetuin-A and fetuin-B are abundant serum proteins with pleiotropic functions. Fetuin-B is a highly selective and potent inhibitor of metallo-peptidases (MPs) of the astacin family, which includes ovastacin in mammals. By inhibiting ovastacin, fetuin-B is essential for female fertility. The crystal structure of fetuin-B was determined unbound and in complex with archetypal astacin, and it was found that the inhibitor has tandem cystatin-type modules (CY1 and CY2). They are connected by an exposed linker with a rigid, disulfide-linked 'CPDCP-trunk', and are followed by a C-terminal region (CTR) with little regular secondary structure. The CPDCP-trunk and a hairpin of CY2 form a bipartite wedge, which slots into the active-site cleft of the MP. These elements occupy the nonprimed and primed sides of the cleft, respectively, but spare the specificity pocket so that the inhibitor is not cleaved. The aspartate in the trunk blocks the catalytic zinc of astacin, while the CY2 hairpin binds through a QWVXGP motif. The CY1 module assists in structural integrity and the CTR is not involved in inhibition, as verified by in vitro studies using a cohort of mutants and variants. Overall, the inhibition conforms to a novel 'raised-elephant-trunk' mechanism for MPs, which is reminiscent of single-domain cystatins that target cysteine peptidases. Over 200 sequences from vertebrates have been annotated as fetuin-B, underpinning its ubiquity and physiological relevance; accordingly, sequences with conserved CPDCP- and QWVXGP-derived motifs have been found from mammals to cartilaginous fishes. Thus, the raised-elephant-trunk mechanism is likely to be generally valid for the inhibition of astacins by orthologs of fetuin-B.
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Affiliation(s)
- Anna Cuppari
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Hagen Körschgen
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Dirk Fahrenkamp
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - Carlo Schmitz
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Konstantin Karmilin
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Michael Kuske
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Mario Olf
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Eileen Dietzel
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - Irene Yiallouros
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Daniele de Sanctis
- ESRF – The European Synchrotron, 71 Rue Jules Horowitz, F-38000 Grenoble, France
| | - Theodoros Goulas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, RWTH Aachen University Hospital, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Willi Jahnen-Dechent
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Julia Floehr
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Walter Stoecker
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Luca Jovine
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
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Simpkin AJ, Simkovic F, Thomas JMH, Savko M, Lebedev A, Uski V, Ballard C, Wojdyr M, Wu R, Sanishvili R, Xu Y, Lisa MN, Buschiazzo A, Shepard W, Rigden DJ, Keegan RM. SIMBAD: a sequence-independent molecular-replacement pipeline. Acta Crystallogr D Struct Biol 2018; 74:595-605. [PMID: 29968670 PMCID: PMC6038384 DOI: 10.1107/s2059798318005752] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/12/2018] [Indexed: 12/13/2022] Open
Abstract
The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here, SIMBAD, a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD, this approach has solved novel cases that have otherwise proved difficult to solve.
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Affiliation(s)
- Adam J. Simpkin
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Martin Savko
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Andrey Lebedev
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Ville Uski
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Charles Ballard
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Marcin Wojdyr
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- Global Phasing Ltd, Cambridge CB3 0AX, England
| | - Rui Wu
- Feil Family Brain and Mind Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ruslan Sanishvili
- GM/CA@APS, The X-Ray Science Division, The Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Yibin Xu
- Division of Structural Biology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Royal Parade, Parkville, VIC 3050, Australia
| | - María-Natalia Lisa
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - William Shepard
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan M. Keegan
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
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Keegan RM, McNicholas SJ, Thomas JMH, Simpkin AJ, Simkovic F, Uski V, Ballard CC, Winn MD, Wilson KS, Rigden DJ. Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment. Acta Crystallogr D Struct Biol 2018; 74:167-182. [PMID: 29533225 PMCID: PMC5947758 DOI: 10.1107/s2059798318003455] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/27/2018] [Indexed: 01/21/2023] Open
Abstract
Increasing sophistication in molecular-replacement (MR) software and the rapid expansion of the PDB in recent years have allowed the technique to become the dominant method for determining the phases of a target structure in macromolecular X-ray crystallography. In addition, improvements in bioinformatic techniques for finding suitable homologous structures for use as MR search models, combined with developments in refinement and model-building techniques, have pushed the applicability of MR to lower sequence identities and made weak MR solutions more amenable to refinement and improvement. MrBUMP is a CCP4 pipeline which automates all stages of the MR procedure. Its scope covers everything from the sourcing and preparation of suitable search models right through to rebuilding of the positioned search model. Recent improvements to the pipeline include the adoption of more sensitive bioinformatic tools for sourcing search models, enhanced model-preparation techniques including better ensembling of homologues, and the use of phase improvement and model building on the resulting solution. The pipeline has also been deployed as an online service through CCP4 online, which allows its users to exploit large bioinformatic databases and coarse-grained parallelism to speed up the determination of a possible solution. Finally, the molecular-graphics application CCP4mg has been combined with MrBUMP to provide an interactive visual aid to the user during the process of selecting and manipulating search models for use in MR. Here, these developments in MrBUMP are described with a case study to explore how some of the enhancements to the pipeline and to CCP4mg can help to solve a difficult case.
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Affiliation(s)
- Ronan M. Keegan
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Stuart J. McNicholas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Adam J. Simpkin
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ville Uski
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Charles C. Ballard
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Martyn D. Winn
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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