1
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Ferdous S, Dasgupta T, Annamalai T, Tan K, Tse-Dinh YC. The interaction between transport-segment DNA and topoisomerase IA-crystal structure of MtbTOP1 in complex with both G- and T-segments. Nucleic Acids Res 2022; 51:349-364. [PMID: 36583363 PMCID: PMC9841409 DOI: 10.1093/nar/gkac1205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/16/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022] Open
Abstract
Each catalytic cycle of type IA topoisomerases has been proposed to comprise multistep reactions. The capture of the transport-segment DNA (T-segment) into the central cavity of the N-terminal toroidal structure is an important action, which is preceded by transient gate-segment (G-segment) cleavage and succeeded by G-segment religation for the relaxation of negatively supercoiled DNA and decatenation of DNA. The T-segment passage in and out of the central cavity requires significant domain-domain rearrangements, including the movement of D3 relative to D1 and D4 for the opening and closing of the gate towards the central cavity. Here we report a direct observation of the interaction of a duplex DNA in the central cavity of a type IA topoisomerase and its associated domain-domain conformational changes in a crystal structure of a Mycobacterium tuberculosis topoisomerase I complex that also has a bound G-segment. The duplex DNA within the central cavity illustrates the non-sequence-specific interplay between the T-segment DNA and the enzyme. The rich structural information revealed from the novel topoisomerase-DNA complex, in combination with targeted mutagenesis studies, provides new insights into the mechanism of the topoisomerase IA catalytic cycle.
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Affiliation(s)
| | | | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA,Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA
| | - Kemin Tan
- Correspondence may also be addressed to Kemin Tan. Tel: +1 630 252 3948;
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2
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Brzezinski D, Kowiel M, Cooper DR, Cymborowski M, Grabowski M, Wlodawer A, Dauter Z, Shabalin IG, Gilski M, Rupp B, Jaskolski M, Minor W. Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models. Protein Sci 2021; 30:115-124. [PMID: 32981130 PMCID: PMC7537053 DOI: 10.1002/pro.3959] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic has triggered numerous scientific activities aimed at understanding the SARS-CoV-2 virus and ultimately developing treatments. Structural biologists have already determined hundreds of experimental X-ray, cryo-EM, and NMR structures of proteins and nucleic acids related to this coronavirus, and this number is still growing. To help biomedical researchers, who may not necessarily be experts in structural biology, navigate through the flood of structural models, we have created an online resource, covid19.bioreproducibility.org, that aggregates expert-verified information about SARS-CoV-2-related macromolecular models. In this article, we describe this web resource along with the suite of tools and methodologies used for assessing the structures presented therein.
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Affiliation(s)
- Dariusz Brzezinski
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
- Center for Biocrystallographic Research, Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
- Institute of Computing SciencePoznan University of TechnologyPoznanPoland
| | - Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
| | - David R. Cooper
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Marek Grabowski
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer InstituteFrederickMarylandUSA
| | - Zbigniew Dauter
- Macromolecular Crystallography Laboratory, National Cancer InstituteFrederickMarylandUSA
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Miroslaw Gilski
- Center for Biocrystallographic Research, Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
- Department of Crystallography, Faculty of ChemistryAdam Mickiewicz UniversityPoznanPoland
| | - Bernhard Rupp
- k.‐k. HofkristallamtSan DiegoCaliforniaUSA
- Institute of Genetic EpidemiologyMedical University InnsbruckSchöpfstr. 41InnsbruckTyrol6020Austria
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
- Department of Crystallography, Faculty of ChemistryAdam Mickiewicz UniversityPoznanPoland
| | - Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
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3
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Czub MP, Handing KB, Venkataramany BS, Cooper DR, Shabalin IG, Minor W. Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma. J Med Chem 2020; 63:6847-6862. [PMID: 32469516 DOI: 10.1021/acs.jmedchem.0c00225] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Every day, hundreds of millions of people worldwide take nonsteroidal anti-inflammatory drugs (NSAIDs), often in conjunction with multiple other medications. In the bloodstream, NSAIDs are mostly bound to serum albumin (SA). We report the crystal structures of equine serum albumin complexed with four NSAIDs (ibuprofen, ketoprofen, etodolac, and nabumetone) and the active metabolite of nabumetone (6-methoxy-2-naphthylacetic acid, 6-MNA). These compounds bind to seven drug-binding sites on SA. These sites are generally well-conserved between equine and human SAs, but ibuprofen binds to both SAs in two drug-binding sites, only one of which is common. We also compare the binding of ketoprofen by equine SA to binding of it by bovine and leporine SAs. Our comparative analysis of known SA complexes with FDA-approved drugs clearly shows that multiple medications compete for the same binding sites, indicating possibilities for undesirable physiological effects caused by drug-drug displacement or competition with common metabolites. We discuss the consequences of NSAID binding to SA in a broader scientific and medical context, particularly regarding achieving desired therapeutic effects based on an individual's drug regimen.
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Affiliation(s)
- Mateusz P Czub
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Barat S Venkataramany
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
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4
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Chiu W, Holton J, Langan P, Sauter NK, Schlichting I, Terwilliger T, Martin JL, Read RJ, Wakatsuki S. Responses to `Atomic resolution': a badly abused term in structural biology. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:381-383. [PMID: 28375150 DOI: 10.1107/s205979831700417x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wah Chiu
- The Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas, USA
| | - James Holton
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Paul Langan
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Nicholas K Sauter
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Tom Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Jennifer L Martin
- The Eskitis Drug Discovery Institute, N27, Griffith University, Nathan, Australia
| | - Randy J Read
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, United Kingdom
| | - Soichi Wakatsuki
- Photon Science, SLAC and Structural Biology, School of Medicine, Stanford University, Menlo Park, USA
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5
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Abstract
Diffraction data acquisition is the final experimental stage of the crystal structure analysis. All subsequent steps involve mainly computer calculations. Optimally measured and accurate data make the structure solution and refinement easier and lead to more faithful interpretation of the final models. Here, the important factors in data collection from macromolecular crystals are discussed and strategies appropriate for various applications, such as molecular replacement, anomalous phasing, and atomic-resolution refinement are presented. Criteria useful for judging the diffraction data quality are also discussed.
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Affiliation(s)
- Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL, 60439, USA.
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6
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Abstract
Diffraction data acquisition is the final experimental stage of the crystal structure analysis. All subsequent steps involve mainly computer calculations. Optimally measured and accurate data make the structure solution and refinement easier and lead to more faithful interpretation of the final models. Here, the important factors in data collection from macromolecular crystals are discussed and strategies appropriate for various applications, such as molecular replacement, anomalous phasing, and atomic-resolution refinement are presented. Criteria useful for judging the diffraction data quality are also discussed.
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7
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Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W. A public database of macromolecular diffraction experiments. Acta Crystallogr D Struct Biol 2016; 72:1181-1193. [PMID: 27841751 PMCID: PMC5108346 DOI: 10.1107/s2059798316014716] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/17/2016] [Indexed: 12/28/2022] Open
Abstract
The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.
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Affiliation(s)
- Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Karol M. Langner
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Przemyslaw J. Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - Piotr Sroka
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Matthew D. Zimmerman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Marc-André Elsliger
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 90237, USA
| | - Stephen K. Burley
- RCSB Protein Data Bank; Center for Integrative Proteomics Research; Institute for Quantitative Biomedicine; Rutgers Cancer Institute of New Jersey; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- San Diego Supercomputer Center and Skaggs School of Pharmacological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
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8
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Huang L, Lilley DMJ. A quasi-cyclic RNA nano-scale molecular object constructed using kink turns. NANOSCALE 2016; 8:15189-95. [PMID: 27506301 PMCID: PMC5058347 DOI: 10.1039/c6nr05186c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/01/2016] [Indexed: 05/25/2023]
Abstract
k-Turns are widespread RNA architectural elements that mediate tertiary interactions. We describe a double-kink-turn motif comprising two inverted k-turns that forms a tight horse-shoe structure that can assemble into a variety of shapes by coaxial association of helical ends. Using X-ray crystallography we show that these assemble with two (dumbell), three (triangle) and four units (square), with or without bound protein, within the crystal lattice. In addition, exchange of a single basepair can almost double the pore radius or shape of a molecular assembly. On the basis of this analysis we synthesized a 114 nt self-complementary RNA containing six k-turns. The crystal structure of this species shows that it forms a quasi-cyclic triangular object. These are randomly disposed about the three-fold axis in the crystal lattice, generating a circular RNA of quasi D3 symmetry with a shape reminiscent of that of a cyclohexane molecule in its chair conformation. This work demonstrates that the k-turn is a powerful building block in the construction of nano-scale molecular objects, and illustrates why k-turns are widely used in natural RNA molecules to organize long-range architecture and mediate tertiary contacts.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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9
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Bunker RD. Tackling the crystallographic structure determination of the COP9 signalosome. Acta Crystallogr D Struct Biol 2016; 72:326-35. [PMID: 26960120 PMCID: PMC4784664 DOI: 10.1107/s2059798316001169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 01/19/2016] [Indexed: 11/23/2022] Open
Abstract
The COP9 signalosome (CSN) is an essential multi-protein complex in eukaryotes. CSN is a master regulator of intracellular protein degradation, controlling the vast family of cullin-RING ubiquitin (E3) ligases (CRLs). Important in many cellular processes, CSN has prominent roles in DNA repair, cell-cycle control and differentiation. The recent crystal structure of human CSN provides insight into its exquisite regulation and functionality [Lingaraju et al. (2014), Nature (London), 512, 161-165]. Structure determination was complicated by low-resolution diffraction from crystals affected by twinning and rotational pseudo-symmetry. Crystal instability and non-isomorphism strongly influenced by flash-cooling, radiation damage and difficulty in obtaining heavy-atom derivatives, were overcome. Many different subunits of the same fold class were distinguished at low resolution aided by combinatorial selenomethionine labelling. As an example of how challenging projects can be approached, the structure determination of CSN is described as it unfolded using cluster-compound MIRAS phasing, MR-SAD with electron-density models and cross-crystal averaging exploiting non-isomorphism among unit-cell variants of the same crystal form.
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Affiliation(s)
- Richard D. Bunker
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 10, 4003 Basel, Switzerland
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10
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Karplus PA, Diederichs K. Assessing and maximizing data quality in macromolecular crystallography. Curr Opin Struct Biol 2015. [PMID: 26209821 DOI: 10.1016/j.sbi.2015.07.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The quality of macromolecular crystal structures depends, in part, on the quality and quantity of the data used to produce them. Here, we review recent shifts in our understanding of how to use data quality indicators to select a high resolution cutoff that leads to the best model, and of the potential to greatly increase data quality through the merging of multiple measurements from multiple passes of single crystals or from multiple crystals. Key factors supporting this shift are the introduction of more robust correlation coefficient based indicators of the precision of merged data sets as well as the recognition of the substantial useful information present in extensive amounts of data once considered too weak to be of value.
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Affiliation(s)
- P Andrew Karplus
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA.
| | - Kay Diederichs
- University of Konstanz, Faculty of Biology, Box 647, D-78457 Konstanz, Germany.
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11
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Rice SL, Boucher LE, Schlessman JL, Preimesberger MR, Bosch J, Lecomte JTJ. Structure of Chlamydomonas reinhardtii THB1, a group 1 truncated hemoglobin with a rare histidine-lysine heme ligation. Acta Crystallogr F Struct Biol Commun 2015; 71:718-25. [PMID: 26057801 PMCID: PMC4461336 DOI: 10.1107/s2053230x15006949] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/07/2015] [Indexed: 04/05/2023] Open
Abstract
THB1 is one of several group 1 truncated hemoglobins (TrHb1s) encoded in the genome of the unicellular green alga Chlamydomonas reinhardtii. THB1 expression is under the control of NIT2, the master regulator of nitrate assimilation, which also controls the expression of the only nitrate reductase in the cell, NIT1. In vitro and physiological evidence suggests that THB1 converts the nitric oxide generated by NIT1 into nitrate. To aid in the elucidation of the function and mechanism of THB1, the structure of the protein was solved in the ferric state. THB1 resembles other TrHb1s, but also exhibits distinct features associated with the coordination of the heme iron by a histidine (proximal) and a lysine (distal). The new structure illustrates the versatility of the TrHb1 fold, suggests factors that stabilize the axial ligation of a lysine, and highlights the difficulty of predicting the identity of the distal ligand, if any, in this group of proteins.
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Affiliation(s)
- Selena L. Rice
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Lauren E. Boucher
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
- Johns Hopkins Malaria Research Institute, Johns Hopkins University, Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jamie L. Schlessman
- Chemistry Department, US Naval Academy, 572 Holloway Road, Annapolis, MD 21402, USA
| | - Matthew R. Preimesberger
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Jürgen Bosch
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
- Johns Hopkins Malaria Research Institute, Johns Hopkins University, Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
| | - Juliette T. J. Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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12
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Weichenberger CX, Afonine PV, Kantardjieff K, Rupp B. The solvent component of macromolecular crystals. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1023-38. [PMID: 25945568 PMCID: PMC4427195 DOI: 10.1107/s1399004715006045] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/25/2015] [Indexed: 11/10/2022]
Abstract
The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.
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Affiliation(s)
- Christian X. Weichenberger
- Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, Bozen/Bolzano, I-39100 Südtirol/Alto Adige, Italy
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mail Stop 64R0121, Berkeley, CA 94720, USA
| | - Katherine Kantardjieff
- College of Science and Mathematics, California State University, San Marcos, CA 92078, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
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13
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McPhee SA, Huang L, Lilley DMJ. A critical base pair in k-turns that confers folding characteristics and correlates with biological function. Nat Commun 2014; 5:5127. [PMID: 25351101 PMCID: PMC4382518 DOI: 10.1038/ncomms6127] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 09/02/2014] [Indexed: 12/28/2022] Open
Abstract
Kink turns (k-turns) are widespread elements in RNA that mediate tertiary contacts by kinking the helical axis. We have found that the ability of k-turns to undergo ion-induced folding is conferred by a single base pair that follows the conserved A·G pairs, that is, the 3b·3n position. A Watson–Crick pair leads to an inability to fold in metal ions alone, while 3n=G or 3b=C (but not both) permits folding. Crystallographic study reveals two hydrated metal ions coordinated to O6 of G3n and G2n of Kt-7. Removal of either atom impairs Mg2+-induced folding in solution. While SAM-I riboswitches have 3b·3n sequences that would predispose them to ion-induced folding, U4 snRNA are strongly biased to an inability to such folding. Thus riboswitch sequences allow folding to occur independently of protein binding, while U4 should remain unfolded until bound by protein. The empirical rules deduced for k-turn folding have strong predictive value. The k-turn is a widespread RNA element that adopts a kinked structure that mediates tertiary contacts and frequently binds specific proteins. Here, McPhee et al. show that the ability of a given k-turn to fold in the presence of metal ions alone—or to otherwise require protein binding—is attributable to a specific base pair.
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Affiliation(s)
- Scott A McPhee
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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14
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Moreno-Morcillo M, Taylor NMI, Gruene T, Legrand P, Rashid UJ, Ruiz FM, Steuerwald U, Müller CW, Fernández-Tornero C. Solving the RNA polymerase I structural puzzle. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2570-82. [PMID: 25286842 PMCID: PMC4188003 DOI: 10.1107/s1399004714015788] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/06/2014] [Indexed: 11/28/2022]
Abstract
Knowing the structure of multi-subunit complexes is critical to understand basic cellular functions. However, when crystals of these complexes can be obtained they rarely diffract beyond 3 Å resolution, which complicates X-ray structure determination and refinement. The crystal structure of RNA polymerase I, an essential cellular machine that synthesizes the precursor of ribosomal RNA in the nucleolus of eukaryotic cells, has recently been solved. Here, the crucial steps that were undertaken to build the atomic model of this multi-subunit enzyme are reported, emphasizing how simple crystallographic experiments can be used to extract relevant biological information. In particular, this report discusses the combination of poor molecular replacement and experimental phases, the application of multi-crystal averaging and the use of anomalous scatterers as sequence markers to guide tracing and to locate the active site. The methods outlined here will likely serve as a reference for future structural determination of large complexes at low resolution.
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Affiliation(s)
- María Moreno-Morcillo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Nicholas M. I. Taylor
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Tim Gruene
- Department of Structural Chemistry, Georg-August-University, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Pierre Legrand
- SOLEIL Synchrotron, L’Orme de Merisiers, Saint Aubin, Gif-sur-Yvette, France
| | - Umar J. Rashid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Federico M. Ruiz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ulrich Steuerwald
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christoph W. Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Carlos Fernández-Tornero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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15
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Weichenberger CX, Rupp B. Ten years of probabilistic estimates of biocrystal solvent content: new insights via nonparametric kernel density estimate. ACTA ACUST UNITED AC 2014; 70:1579-88. [PMID: 24914969 DOI: 10.1107/s1399004714005550] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/11/2014] [Indexed: 11/10/2022]
Abstract
The probabilistic estimate of the solvent content (Matthews probability) was first introduced in 2003. Given that the Matthews probability is based on prior information, revisiting the empirical foundation of this widely used solvent-content estimate is appropriate. The parameter set for the original Matthews probability distribution function employed in MATTPROB has been updated after ten years of rapid PDB growth. A new nonparametric kernel density estimator has been implemented to calculate the Matthews probabilities directly from empirical solvent-content data, thus avoiding the need to revise the multiple parameters of the original binned empirical fit function. The influence and dependency of other possible parameters determining the solvent content of protein crystals have been examined. Detailed analysis showed that resolution is the primary and dominating model parameter correlated with solvent content. Modifications of protein specific density for low molecular weight have no practical effect, and there is no correlation with oligomerization state. A weak, and in practice irrelevant, dependency on symmetry and molecular weight is present, but cannot be satisfactorily explained by simple linear or categorical models. The Bayesian argument that the observed resolution represents only a lower limit for the true diffraction potential of the crystal is maintained. The new kernel density estimator is implemented as the primary option in the MATTPROB web application at http://www.ruppweb.org/mattprob/.
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Affiliation(s)
- Christian X Weichenberger
- Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, I-39100 Bozen/Bolzano, Italy
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
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16
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Dauter Z, Wlodawer A, Minor W, Jaskolski M, Rupp B. Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. IUCRJ 2014; 1:179-93. [PMID: 25075337 PMCID: PMC4086436 DOI: 10.1107/s2052252514005442] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/10/2014] [Indexed: 05/20/2023]
Abstract
Whereas the vast majority of the more than 85 000 crystal structures of macromolecules currently deposited in the Protein Data Bank are of high quality, some suffer from a variety of imperfections. Although this fact has been pointed out in the past, it is still worth periodic updates so that the metadata obtained by global analysis of the available crystal structures, as well as the utilization of the individual structures for tasks such as drug design, should be based on only the most reliable data. Here, selected abnormal deposited structures have been analysed based on the Bayesian reasoning that the correctness of a model must be judged against both the primary evidence as well as prior knowledge. These structures, as well as information gained from the corresponding publications (if available), have emphasized some of the most prevalent types of common problems. The errors are often perfect illustrations of the nature of human cognition, which is frequently influenced by preconceptions that may lead to fanciful results in the absence of proper validation. Common errors can be traced to negligence and a lack of rigorous verification of the models against electron density, creation of non-parsimonious models, generation of improbable numbers, application of incorrect symmetry, illogical presentation of the results, or violation of the rules of chemistry and physics. Paying more attention to such problems, not only in the final validation stages but during the structure-determination process as well, is necessary not only in order to maintain the highest possible quality of the structural repositories and databases but most of all to provide a solid basis for subsequent studies, including large-scale data-mining projects. For many scientists PDB deposition is a rather infrequent event, so the need for proper training and supervision is emphasized, as well as the need for constant alertness of reason and critical judgment as absolutely necessary safeguarding measures against such problems. Ways of identifying more problematic structures are suggested so that their users may be properly alerted to their possible shortcomings.
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Affiliation(s)
- Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, NCI, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics, USA
- New York Structural Genomics Consortium, USA
- Center for Structural Genomics of Infectious Diseases, USA
- Enzyme Function Initiative, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Bernhard Rupp
- k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Innsbruck Medical University, Schöpfstrasse 41, A-6020 Innsbruck, Austria
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