51
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Leonarski F, D'Ascenzo L, Auffinger P. Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. RNA (NEW YORK, N.Y.) 2019; 25:173-192. [PMID: 30409785 PMCID: PMC6348993 DOI: 10.1261/rna.068437.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/16/2018] [Indexed: 05/04/2023]
Abstract
Precise knowledge of Mg2+ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg2+ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected since many of those are associated with misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg2+ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg2+ stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ must be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
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52
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Structural Basis of H +-Dependent Conformational Change in a Bacterial MATE Transporter. Structure 2018; 27:293-301.e3. [PMID: 30449688 DOI: 10.1016/j.str.2018.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/07/2018] [Accepted: 10/10/2018] [Indexed: 12/28/2022]
Abstract
Multidrug and toxic compound extrusion (MATE) transporters efflux toxic compounds using a Na+ or H+ gradient across the membrane. Although the structures of MATE transporters have been reported, the cation-coupled substrate transport mechanism remains controversial. Here we report crystal structures of VcmN, a Vibrio cholerae MATE transporter driven by the H+ gradient. High-resolution structures in two distinct conformations associated with different pHs revealed that the rearrangement of the hydrogen-bonding network around the conserved Asp35 induces the bending of transmembrane helix 1, as in the case of the H+-coupled Pyrococcus furiosus MATE transporter. We also determined the crystal structure of the D35N mutant, which captured a unique conformation of TM1 facilitated by an altered hydrogen-bonding network. Based on the present results, we propose a common step in the transport cycle shared among prokaryotic H+-coupled MATE transporters.
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53
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Novel insights into the degradation of β-1,3-glucans by the cellulosome of Clostridium thermocellum revealed by structure and function studies of a family 81 glycoside hydrolase. Int J Biol Macromol 2018; 117:890-901. [DOI: 10.1016/j.ijbiomac.2018.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 11/19/2022]
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54
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Shabalin IG, Porebski PJ, Minor W. Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. CRYSTALLOGR REV 2018; 24:236-262. [PMID: 30416256 DOI: 10.1080/0889311x.2018.1521805] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount sof instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.
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Affiliation(s)
- Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
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55
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van Beusekom B, Joosten K, Hekkelman ML, Joosten RP, Perrakis A. Homology-based loop modeling yields more complete crystallographic protein structures. IUCRJ 2018; 5:585-594. [PMID: 30224962 PMCID: PMC6126648 DOI: 10.1107/s2052252518010552] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and 'graft' these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects.
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Affiliation(s)
- Bart van Beusekom
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands
| | - Krista Joosten
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands
| | - Maarten L. Hekkelman
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands
| | - Robbie P. Joosten
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands
| | - Anastassis Perrakis
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands
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56
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Gunaratne R, Kumar S, Frederiksen JW, Stayrook S, Lohrmann JL, Perry K, Bompiani KM, Chabata CV, Thalji NK, Ho MD, Arepally G, Camire RM, Krishnaswamy S, Sullenger BA. Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass. Nat Biotechnol 2018; 36:606-613. [PMID: 29863725 PMCID: PMC6349032 DOI: 10.1038/nbt.4153] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 03/27/2018] [Indexed: 02/05/2023]
Abstract
Unfractionated heparin (UFH), the standard anticoagulant for cardiopulmonary bypass (CPB) surgery, carries a risk of post-operative bleeding and is potentially harmful in patients with heparin-induced thrombocytopenia-associated antibodies. To improve the activity of an alternative anticoagulant, the RNA aptamer 11F7t, we solved X-ray crystal structures of the aptamer bound to factor Xa (FXa). The finding that 11F7t did not bind the catalytic site suggested that it could complement small-molecule FXa inhibitors. We demonstrate that combinations of 11F7t and catalytic-site FXa inhibitors enhance anticoagulation in purified reaction mixtures and plasma. Aptamer-drug combinations prevented clot formation as effectively as UFH in human blood circulated in an extracorporeal oxygenator circuit that mimicked CPB, while avoiding side effects of UFH. An antidote could promptly neutralize the anticoagulant effects of both FXa inhibitors. Our results suggest that drugs and aptamers with shared targets can be combined to exert more specific and potent effects than either agent alone.
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Affiliation(s)
- Ruwan Gunaratne
- Duke University, Department of Pharmacology and Cancer Biology, Durham, NC 27710
- Duke University, Medical Scientist Training Program, Durham, NC 27710
| | - Shekhar Kumar
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Steven Stayrook
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Kay Perry
- Northeastern Collaborative Access Team (NE-CAT) and Departments of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439
| | | | - Charlene V. Chabata
- Duke University, Department of Pharmacology and Cancer Biology, Durham, NC 27710
| | - Nabil K. Thalji
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | - Michelle D. Ho
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Rodney M. Camire
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | - Sriram Krishnaswamy
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | - Bruce A. Sullenger
- Duke University, Department of Pharmacology and Cancer Biology, Durham, NC 27710
- Duke University, Department of Surgery, Durham, NC 27710
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57
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van Beusekom B, Lütteke T, Joosten RP. Making glycoproteins a little bit sweeter with PDB-REDO. Acta Crystallogr F Struct Biol Commun 2018; 74:463-472. [PMID: 30084395 PMCID: PMC6096482 DOI: 10.1107/s2053230x18004016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/07/2018] [Indexed: 02/04/2023] Open
Abstract
Glycosylation is one of the most common forms of protein post-translational modification, but is also the most complex. Dealing with glycoproteins in structure model building, refinement, validation and PDB deposition is more error-prone than dealing with nonglycosylated proteins owing to limitations of the experimental data and available software tools. Also, experimentalists are typically less experienced in dealing with carbohydrate residues than with amino-acid residues. The results of the reannotation and re-refinement by PDB-REDO of 8114 glycoprotein structure models from the Protein Data Bank are analyzed. The positive aspects of 3620 reannotations and subsequent refinement, as well as the remaining challenges to obtaining consistently high-quality carbohydrate models, are discussed.
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Affiliation(s)
- Bart van Beusekom
- Division of Biochemistry, Netherlands Cancer Insitute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Frankfurter Strasse 100, 35392 Giessen, Germany
| | - Robbie P. Joosten
- Division of Biochemistry, Netherlands Cancer Insitute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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58
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Bar-Zvi S, Lahav A, Harris D, Niedzwiedzki DM, Blankenship RE, Adir N. Structural heterogeneity leads to functional homogeneity in A. marina phycocyanin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:544-553. [DOI: 10.1016/j.bbabio.2018.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/18/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022]
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59
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Croll TI. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D Struct Biol 2018; 74:519-530. [PMID: 29872003 PMCID: PMC6096486 DOI: 10.1107/s2059798318002425] [Citation(s) in RCA: 917] [Impact Index Per Article: 152.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 02/09/2018] [Indexed: 01/19/2023] Open
Abstract
This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
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Affiliation(s)
- Tristan Ian Croll
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
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60
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Svensson O, Gilski M, Nurizzo D, Bowler MW. Multi-position data collection and dynamic beam sizing: recent improvements to the automatic data-collection algorithms on MASSIF-1. Acta Crystallogr D Struct Biol 2018; 74:433-440. [PMID: 29717714 PMCID: PMC5930350 DOI: 10.1107/s2059798318003728] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/03/2018] [Indexed: 12/11/2022] Open
Abstract
Macromolecular crystallography is now a mature and widely used technique that is essential in the understanding of biology and medicine. Increases in computing power combined with robotics have not only enabled large numbers of samples to be screened and characterized but have also enabled better decisions to be taken on data collection itself. This led to the development of MASSIF-1 at the ESRF, the first beamline in the world to run fully automatically while making intelligent decisions taking user requirements into account. Since opening in late 2014, the beamline has processed over 42 000 samples. Improvements have been made to the speed of the sample-handling robotics and error management within the software routines. The workflows initially put into place, while highly innovative at the time, have been expanded to include increased complexity and additional intelligence using the information gathered during characterization; this includes adapting the beam diameter dynamically to match the diffraction volume within the crystal. Complex multi-position and multi-crystal data collections have now also been integrated into the selection of experiments available. This has led to increased data quality and throughput, allowing even the most challenging samples to be treated automatically.
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Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Maciej Gilski
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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61
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Chaudhary SK, Jeyakanthan J, Sekar K. Structural and functional roles of dynamically correlated residues in thymidylate kinase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:341-354. [PMID: 29652261 DOI: 10.1107/s2059798318002267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/07/2018] [Indexed: 11/10/2022]
Abstract
Thymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg2+. In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase from Thermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme. High-resolution X-ray crystal structures of thymidylate kinase in apo and ligand-bound states were solved. This is the first report of structures of binary and ternary complexes of thymidylate kinase with its natural substrates ATP and ATP-TMP, respectively. Distinct conformations of the active-site residues, the P-loop and the LID region observed in the apo and ligand-bound structures revealed that their concerted motion is required for the binding and proper positioning of the substrate TMP. Structural analyses provide an insight into the mode of substrate binding at the active site. The residues involved in communication between the substrates were identified through network analysis using molecular-dynamics simulations. The residues identified showed high sequence conservation across species. Biochemical analyses show that mutations of these residues either resulted in a loss of activity or affected the thermal stability of the protein. Further, molecular-dynamics analyses of mutants suggest that the proper positioning of TMP is important for catalysis. These data also provide an insight into the phosphoryl-transfer mechanism.
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Affiliation(s)
| | | | - Kanagaraj Sekar
- Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
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62
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van Beusekom B, Touw WG, Tatineni M, Somani S, Rajagopal G, Luo J, Gilliland GL, Perrakis A, Joosten RP. Homology-based hydrogen bond information improves crystallographic structures in the PDB. Protein Sci 2018; 27:798-808. [PMID: 29168245 PMCID: PMC5818736 DOI: 10.1002/pro.3353] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 01/06/2023]
Abstract
The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB-REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset.
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Affiliation(s)
- Bart van Beusekom
- Department of BiochemistryNetherlands Cancer Institute, Plesmanlaan 121Amsterdam1066 CXThe Netherlands
| | - Wouter G. Touw
- Department of BiochemistryNetherlands Cancer Institute, Plesmanlaan 121Amsterdam1066 CXThe Netherlands
| | - Mahidhar Tatineni
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman DriveLa JollaCalifornia92093‐0505
| | - Sandeep Somani
- Discovery Sciences, Janssen R&D LLCSpring HousePennsylvania
| | | | - Jinquan Luo
- Janssen BioTherapeutics, Janssen R&D LLCSpring HousePennsylvania
| | | | - Anastassis Perrakis
- Department of BiochemistryNetherlands Cancer Institute, Plesmanlaan 121Amsterdam1066 CXThe Netherlands
| | - Robbie P. Joosten
- Department of BiochemistryNetherlands Cancer Institute, Plesmanlaan 121Amsterdam1066 CXThe Netherlands
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63
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Cole JC, Korb O, McCabe P, Read MG, Taylor R. Knowledge-Based Conformer Generation Using the Cambridge Structural Database. J Chem Inf Model 2018; 58:615-629. [PMID: 29425456 DOI: 10.1021/acs.jcim.7b00697] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Fast generation of plausible molecular conformations is central to molecular modeling. This paper presents an approach to conformer generation that makes extensive use of the information available in the Cambridge Structural Database. By using geometric distributions derived from the Cambridge Structural Database, it is possible to create biologically relevant conformations in the majority of cases analyzed. The paper compares the performance of the approach with previously published evaluations, and presents some cases where the method fails. The method appears to show significantly improved performance in reproduction of the conformations of structures observed in the Cambridge Structural Database and the Protein Data Bank as compared to other published methods of a similar speed.
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Affiliation(s)
- Jason C Cole
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Oliver Korb
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Patrick McCabe
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Murray G Read
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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64
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Structure and activity of ChiX: a peptidoglycan hydrolase required for chitinase secretion by Serratia marcescens. Biochem J 2018; 475:415-428. [PMID: 29229757 PMCID: PMC5778951 DOI: 10.1042/bcj20170633] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 11/17/2022]
Abstract
The Gram-negative bacterium Serratia marcescens secretes many proteins that are involved in extracellular chitin degradation. This so-called chitinolytic machinery includes three types of chitinase enzymes and a lytic polysaccharide monooxygenase. An operon has been identified in S. marcescens, chiWXYZ, that is thought to be involved in the secretion of the chitinolytic machinery. Genetic evidence points to the ChiX protein being a key player in the secretion mechanism, since deletion of the chiX gene in S. marcescens led to a mutant strain blocked for secretion of all members of the chitinolytic machinery. In this work, a detailed structural and biochemical characterisation of ChiX is presented. The high-resolution crystal structure of ChiX reveals the protein to be a member of the LAS family of peptidases. ChiX is shown to be a zinc-containing metalloenzyme, and in vitro assays demonstrate that ChiX is an l-Ala d-Glu endopeptidase that cleaves the cross-links in bacterial peptidoglycan. This catalytic activity is shown to be intimately linked with the secretion of the chitinolytic machinery, since substitution of the ChiX Asp-120 residue results in a variant protein that is both unable to digest peptidoglycan and cannot rescue the phenoytype of a chiX mutant strain.
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65
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van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validation of Molecular Simulation: An Overview of Issues. Angew Chem Int Ed Engl 2017; 57:884-902. [PMID: 28682472 DOI: 10.1002/anie.201702945] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Indexed: 12/14/2022]
Abstract
Computer simulation of molecular systems enables structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic, or supra-molecular level. To interpret results of such simulations appropriately, the quality of the calculated properties must be evaluated. This depends on the way the simulations are performed and on the way they are validated by comparison to values Qexp of experimentally observable quantities Q. One must consider 1) the accuracy of Qexp , 2) the accuracy of the function Q(rN ) used to calculate a Q-value based on a molecular configuration rN of N particles, 3) the sensitivity of the function Q(rN ) to the configuration rN , 4) the relative time scales of the simulation and experiment, 5) the degree to which the calculated and experimental properties are equivalent, and 6) the degree to which the system simulated matches the experimental conditions. Experimental data is limited in scope and generally corresponds to averages over both time and space. A critical analysis of the various factors influencing the apparent degree of (dis)agreement between simulations and experiment is presented and illustrated using examples from the literature. What can be done to enhance the validation of molecular simulation is also discussed.
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Affiliation(s)
- Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autonoma de Barcelona, UAB, 08193, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, ICREA, 08010, Barcelona, Spain
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569, Stuttgart, Germany
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Lorna J Smith
- Department of Chemistry, Inorganic Chemistry, Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
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66
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van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validierung von molekularen Simulationen: eine Übersicht verschiedener Aspekte. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wilfred F. van Gunsteren
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine; Universitat Autònoma de Barcelona; Spanien
- Catalan Institution for Research and Advanced Studies, ICREA; Barcelona Spanien
| | - Niels Hansen
- Institut für Technische Thermodynamik und Thermische Verfahrenstechnik; Universität Stuttgart; Deutschland
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences; University of Queensland; St. Lucia Australien
| | - Chris Oostenbrink
- Institut für Molekulare Modellierung und Simulation; Universität für Bodenkultur Wien; Österreich
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Lorna J. Smith
- Inorganic Chemistry Laboratory; Department of Chemistry; University of Oxford; Großbritannien
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67
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Amata E, Rescifina A, Prezzavento O, Arena E, Dichiara M, Pittalà V, Montilla-García Á, Punzo F, Merino P, Cobos EJ, Marrazzo A. (+)-Methyl (1R,2S)-2-{[4-(4-Chlorophenyl)-4-hydroxypiperidin-1-yl]methyl}-1-phenylcyclopropanecarboxylate [(+)-MR200] Derivatives as Potent and Selective Sigma Receptor Ligands: Stereochemistry and Pharmacological Properties. J Med Chem 2017; 61:372-384. [PMID: 29220177 DOI: 10.1021/acs.jmedchem.7b01584] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Methoxycarbonyl-1-phenyl-2-cyclopropylmethyl based derivatives cis-(+)-1a [cis-(+)-MR200], cis-(-)-1a [cis-(-)-MR201], and trans-(±)-1a [trans-(±)-MR204], have been identified as new potent sigma (σ) receptor ligands. In the present paper, novel enantiomerically pure analogues were synthesized and optimized for their σ receptor affinity and selectivity. Docking studies rationalized the results obtained in the radioligand binding assay. Absolute stereochemistry was unequivocally established by X-ray analysis of precursor trans-(+)-5a as camphorsulfonyl derivative 9. The most promising compound, trans-(+)-1d, showed remarkable selectivity over a panel of more than 15 receptors as well as good chemical and enzymatic stability in human plasma. An in vivo evaluation evidenced that trans-(+)-1d, in contrast to trans-(-)-1d, cis-(+)-1d, or cis-(-)-1d, which behave as σ1 antagonists, exhibited a σ1 agonist profile. These data clearly demonstrated that compound trans-(+)-1d, due to its σ1 agonist activity and favorable receptor selectivity and stability, provided an useful tool for the study of σ1 receptors.
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Affiliation(s)
- Emanuele Amata
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Antonio Rescifina
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Orazio Prezzavento
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Emanuela Arena
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Maria Dichiara
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Valeria Pittalà
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Ángeles Montilla-García
- Institute of Neuroscience and Department of Pharmacology, Faculty of Medicine, University of Granada , Avenida de Madrid 11, E-18012 Granada, Spain
| | - Francesco Punzo
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
| | - Pedro Merino
- Laboratorio de Síntesis Asimétrica, Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC , Campus San Francisco, E-50009 Zaragoza, Aragón, Spain
| | - Enrique J Cobos
- Institute of Neuroscience and Department of Pharmacology, Faculty of Medicine, University of Granada , Avenida de Madrid 11, E-18012 Granada, Spain
| | - Agostino Marrazzo
- Dipartimento di Scienze del Farmaco, Università di Catania , Viale A. Doria 6, 95125 Catania, Italy
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68
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Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus. Nat Commun 2017; 8:2196. [PMID: 29259165 PMCID: PMC5736709 DOI: 10.1038/s41467-017-02109-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 11/07/2017] [Indexed: 02/08/2023] Open
Abstract
Ruminococcus gnavus is a human gut symbiont wherein the ability to degrade mucins is mediated by an intramolecular trans-sialidase (RgNanH). RgNanH comprises a GH33 catalytic domain and a sialic acid-binding carbohydrate-binding module (CBM40). Here we used glycan arrays, STD NMR, X-ray crystallography, mutagenesis and binding assays to determine the structure and function of RgNanH_CBM40 (RgCBM40). RgCBM40 displays the canonical CBM40 β-sandwich fold and broad specificity towards sialoglycans with millimolar binding affinity towards α2,3- or α2,6-sialyllactose. RgCBM40 binds to mucus produced by goblet cells and to purified mucins, providing direct evidence for a CBM40 as a novel bacterial mucus adhesin. Bioinformatics data show that RgCBM40 canonical type domains are widespread among Firmicutes. Furthermore, binding of R. gnavus ATCC 29149 to intestinal mucus is sialic acid mediated. Together, this study reveals novel features of CBMs which may contribute to the biogeography of symbiotic bacteria in the gut. The mucus layer is an important physical niche within the gut which harbours a distinct microbial community. Here the authors show that specific carbohydrate-binding modules associated with bacterial carbohydrate-active enzymes are mucus adhesins that target regions of the distal colon rich in sialomucins.
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69
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Delbart F, Brams M, Gruss F, Noppen S, Peigneur S, Boland S, Chaltin P, Brandao-Neto J, von Delft F, Touw WG, Joosten RP, Liekens S, Tytgat J, Ulens C. An allosteric binding site of the α7 nicotinic acetylcholine receptor revealed in a humanized acetylcholine-binding protein. J Biol Chem 2017; 293:2534-2545. [PMID: 29237730 PMCID: PMC5818190 DOI: 10.1074/jbc.m117.815316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/24/2017] [Indexed: 11/06/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) belong to the family of pentameric ligand-gated ion channels and mediate fast excitatory transmission in the central and peripheral nervous systems. Among the different existing receptor subtypes, the homomeric α7 nAChR has attracted considerable attention because of its possible implication in several neurological and psychiatric disorders, including cognitive decline associated with Alzheimer's disease or schizophrenia. Allosteric modulators of ligand-gated ion channels are of particular interest as therapeutic agents, as they modulate receptor activity without affecting normal fluctuations of synaptic neurotransmitter release. Here, we used X-ray crystallography and surface plasmon resonance spectroscopy of α7-acetylcholine-binding protein (AChBP), a humanized chimera of a snail AChBP, which has 71% sequence similarity with the extracellular ligand-binding domain of the human α7 nAChR, to investigate the structural determinants of allosteric modulation. We extended previous observations that an allosteric site located in the vestibule of the receptor offers an attractive target for receptor modulation. We introduced seven additional humanizing mutations in the vestibule-located binding site of AChBP to improve its suitability as a model for studying allosteric binding. Using a fragment-based screening approach, we uncovered an allosteric binding site located near the β8-β9 loop, which critically contributes to coupling ligand binding to channel opening in human α7 nAChR. This work expands our understanding of the topology of allosteric binding sites in AChBP and, by extrapolation, in the human α7 nAChR as determined by electrophysiology measurements. Our insights pave the way for drug design strategies targeting nAChRs involved in ion channel-mediated disorders.
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Affiliation(s)
- Florian Delbart
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Marijke Brams
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Fabian Gruss
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Sam Noppen
- the Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Steve Peigneur
- the Laboratory of Toxicology and Pharmacology, Faculty of Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Sandro Boland
- the Center for Innovation and Stimulation of Drug Discovery Leuven, Cistim Leuven vzw, 3001 Heverlee, Belgium
| | - Patrick Chaltin
- the Center for Innovation and Stimulation of Drug Discovery Leuven, Cistim Leuven vzw, 3001 Heverlee, Belgium.,the Center for Innovation and Stimulation of Drug Discovery Leuven and Center for Drug Design and Discovery, KU Leuven, 3001 Heverlee, Belgium
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom, and
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom, and
| | - Wouter G Touw
- the Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Robbie P Joosten
- the Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Sandra Liekens
- the Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Jan Tytgat
- the Laboratory of Toxicology and Pharmacology, Faculty of Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Chris Ulens
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium,
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70
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Floresta G, Pistarà V, Amata E, Dichiara M, Damigella A, Marrazzo A, Prezzavento O, Punzo F, Rescifina A. Molecular modeling studies of pseudouridine isoxazolidinyl nucleoside analogues as potential inhibitors of the pseudouridine 5'-monophosphate glycosidase. Chem Biol Drug Des 2017; 91:519-525. [PMID: 28941159 DOI: 10.1111/cbdd.13113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/25/2017] [Accepted: 09/02/2017] [Indexed: 12/14/2022]
Abstract
In this paper, we investigated the hypothesis that pseudouridine isoxazolidinyl nucleoside analogues could act as potential inhibitors of the pseudouridine 5'-monophosphate glycosidase. This purpose was pursued using molecular modeling and in silico ADME-Tox profiling. From these studies emerged that the isoxazolidinyl derivative 1 5'-monophosphate can be effectively accommodated within the active site of the enzyme with a ligand efficiency higher than that of the natural substrate. In this context, the poor nucleofugality of the N-protonated isoxazolidine prevents or slows down, the first mechanistic step proposed for the degradation of the pseudouridine 5'-monophosphate glycosidase, leading to the enzyme inhibition. Finally, the results of the physicochemical and ADME-Tox informative analysis pointed out that compound 1 is weakly bounded to plasma protein, only moderately permeate the blood-brain barrier, and is non-carcinogen in rat and mouse. To the best of our knowledge, this is the first paper that introduces the possibility of inhibition of pseudouridine 5'-monophosphate glycosidase by a molecule that competing with the natural substrate hinders the glycosidic C-C bond cleavage.
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Affiliation(s)
- Giuseppe Floresta
- Dipartimento di Scienze del Farmaco, Università di Catania, Catania, Italy.,Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
| | - Venerando Pistarà
- Dipartimento di Scienze del Farmaco, Università di Catania, Catania, Italy
| | - Emanuele Amata
- Dipartimento di Scienze del Farmaco, Università di Catania, Catania, Italy
| | - Maria Dichiara
- Dipartimento di Scienze del Farmaco, Università di Catania, Catania, Italy
| | | | - Agostino Marrazzo
- Dipartimento di Scienze del Farmaco, Università di Catania, Catania, Italy
| | - Orazio Prezzavento
- Dipartimento di Scienze del Farmaco, Università di Catania, Catania, Italy
| | - Francesco Punzo
- Dipartimento di Scienze del Farmaco, Università di Catania, Catania, Italy
| | - Antonio Rescifina
- Dipartimento di Scienze del Farmaco, Università di Catania, Catania, Italy
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71
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Yom-Tov G, Barak R, Matalon O, Barda-Saad M, Guez-Haddad J, Opatowsky Y. Robo Ig4 Is a Dimerization Domain. J Mol Biol 2017; 429:3606-3616. [PMID: 29017837 DOI: 10.1016/j.jmb.2017.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/02/2017] [Accepted: 10/02/2017] [Indexed: 01/06/2023]
Abstract
Robo receptors play pivotal roles in axonal guidance as well as in neurogenesis, angiogenesis, cell migration, and cancer progression and invasiveness. They are considered to be attractive drug targets for the treatment of cancer, ocular neovascular disorders, chronic kidney diseases, and more. Despite their great importance, the mechanisms by which Robo receptors switch from their "off" to "on" states remain obscure. One possibility involves a monomer-to-dimer or dimer-to-monomer transition that facilitates the recruitment and activation of enzymatic effectors to instigate intracellular signaling. However, it is not known which domains mediate Robo dimerization, or the structural properties of the dimeric interactions. Here, we identify the extracellular Ig4 (D4) as a Robo dimerization domain. We have determined the crystal structure of the tandem Ig4-5 domains (D4-5) of human Robo2 and found that a hydrophobic surface on D4 mediates close homotypic contacts with a reciprocal D4. Analytical ultracentrifugation measurements of intact and mutated D4-5 shows that dimerization through the D4 interface is specific and has a dimerization dissociation constant of 16.9μM in solution. Direct fluorescence resonance energy transfer dimerization measurements in HEK293 cells corroborate the dimerization of transmembrane hRobo2 through D4, and a functional COS-7 cell collapse assay links D4-mediated dimerization with Robo intracellular signaling. The high level of conservation in the D4 dimerization interface throughout all Robo orthologs and paralogs implies that D4-mediated dimerization is a central hallmark in Robo activation and signaling.
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Affiliation(s)
- Galit Yom-Tov
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Reut Barak
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Omri Matalon
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Mira Barda-Saad
- 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
| | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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72
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Zagni C, Pistarà V, Oliveira LA, Castilho RM, Romeo G, Chiacchio U, Rescifina A. Serendipitous discovery of potent human head and neck squamous cell carcinoma anti-cancer molecules: A fortunate failure of a rational molecular design. Eur J Med Chem 2017; 141:188-196. [PMID: 29031066 DOI: 10.1016/j.ejmech.2017.09.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/01/2017] [Accepted: 09/29/2017] [Indexed: 01/21/2023]
Abstract
Histone deacetylase inhibitors (HDACis) play an important role as valuable drugs targeted to cancer therapy: several HDACis are currently being tested in clinical trials. Two new potential HDACis 1a and 1d, characterized by the presence of a biphenyl-4-sulfonamide group as a connection unit between the N-{4-[(E)-(2-formylhydrazinylidene)methyl]-3-hydroxyphenyl} and the 2-hydroxy-N-(trifluoroacetyl)benzamide moiety, respectively, as two zinc-binding group (ZBG), have been designed, synthesized and tested for their biological activity. Surprisingly, compounds 1a and 12, this last exclusively obtained in place of 1d, exhibited a very low HDAC inhibitory activity. A serendipitous assay of these two compounds, conducted on three chemoresistant cell lines of head and neck squamous cell carcinoma (HNSCC), showed their antiproliferative activity at low nanomolar concentrations, better than cisplatin. In vitro, biological assays indicated that compounds 1a and 12 are able to increase acetylation of histone H3 and to interfere with the PI3K/Akt/mTOR pathway by inducing the accumulation of PTEN protein.
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Affiliation(s)
- Chiara Zagni
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Venerando Pistarà
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, V.le A. Doria, 95125 Catania, Italy
| | - Luciana A Oliveira
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109-1078, USA
| | - Rogerio M Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109-1078, USA
| | - Giovanni Romeo
- Dipartimento Farmaco-Chimico, Università di Messina, Viale SS. Annunziata, Messina 98168, Italy
| | - Ugo Chiacchio
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, V.le A. Doria, 95125 Catania, Italy
| | - Antonio Rescifina
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, V.le A. Doria, 95125 Catania, Italy.
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73
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Devi S, Abdul Rehman SA, Tarique KF, Gourinath S. Structural characterization and functional analysis of cystathionine β-synthase: an enzyme involved in the reverse transsulfuration pathway of Bacillus anthracis. FEBS J 2017; 284:3862-3880. [PMID: 28921884 DOI: 10.1111/febs.14273] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/31/2017] [Accepted: 09/13/2017] [Indexed: 01/29/2023]
Abstract
The reverse transsulfuration pathway has been reported to produce cysteine from homocysteine in eukaryotes ranging from protozoans to mammals while bacteria and plants produce cysteine via a de novo pathway. Interestingly, the bacterium Bacillus anthracis includes enzymes of the reverse transsulfuration pathway viz. cystathionine β-synthase [BaCBS, previously annotated to be an O-acetylserine sulfhydrylase (OASS)] and cystathionine γ-lyase. Here, we report the structure of BaCBS at a resolution of 2.2 Å. The enzyme was found to show CBS activity only with activated serine (O-acetylserine) and not with serine, and was also observed to display OASS activity but not serine sulfhydrylase activity. BaCBS was also found to produce hydrogen sulfide (H2 S) upon reaction of cysteine and homocysteine. A mutational study revealed Glu 220, conserved in CBS, to be necessary for generating H2 S. Structurally, BaCBS display a considerably more open active site than has been found for any other CBS or OASS, which was attributed to the presence of a helix at the junction of the C- and N-terminal domains. The root-mean-square deviation (RMSD) between the backbone Cα carbon atoms of BaCBS and those of other CBSs and OASSs were calculated to be greater than 3.0 Å. The pyridoxal 5'-phosphate at the active site was not traced, and appeared to be highly flexible due to the active site being wide open. Phylogenetic analysis revealed the presence of an O-acetylserine-dependent CBS in the bacterial domain and making separate clade from CBS and OASS indicating its evolution for specific function. DATABASE Structural data are available in the PDB under the accession number 5XW3.
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Affiliation(s)
- Suneeta Devi
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Syed A Abdul Rehman
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.,MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Khaja F Tarique
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.,Public Health Research Institute, Rutgers, Newark, NJ, USA
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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74
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Lobner E, Humm AS, Mlynek G, Kubinger K, Kitzmüller M, Traxlmayr MW, Djinović-Carugo K, Obinger C. Two-faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 Å crystal structure of the complex. MAbs 2017; 9:1088-1104. [PMID: 28816592 PMCID: PMC5627596 DOI: 10.1080/19420862.2017.1364825] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Fcabs (Fc domain with antigen-binding sites) are promising novel therapeutics. By engineering of the C-terminal loops of the CH3 domains, 2 antigen binding sites can be inserted in close proximity. To elucidate the binding mode(s) between homodimeric Fcabs and small homodimeric antigens, the interaction between the Fcabs 448 and CT6 (having the AB, CD and EF loops and the C-termini engineered) with homodimeric VEGF was investigated. The crystal structures of these Fcabs, which form polymers with the antigen VEGF in solution, were determined. However, construction of heterodimeric Fcabs (JanusFcabs: one chain Fc-wt, one chain VEGF-binding) results in formation of distinct JanusFcab–VEGF complexes (2:1), which allowed elucidation of the crystal structure of the JanusCT6–VEGF complex at 2.15 Å resolution. VEGF binding to Janus448 and JanusCT6 is shown to be entropically unfavorable, but enthalpically favorable. Structure-function relationships are discussed with respect to Fcab design and engineering strategies.
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Affiliation(s)
- Elisabeth Lobner
- a Christian Doppler Laboratory for Antibody Engineering , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria.,b Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria
| | - Anne-Sophie Humm
- a Christian Doppler Laboratory for Antibody Engineering , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria.,c Department for Structural and Computational Biology , Max F. Perutz Laboratories, University of Vienna , Dr. Bohr-Gasse 9, Vienna , Austria
| | - Georg Mlynek
- c Department for Structural and Computational Biology , Max F. Perutz Laboratories, University of Vienna , Dr. Bohr-Gasse 9, Vienna , Austria
| | - Konstantin Kubinger
- a Christian Doppler Laboratory for Antibody Engineering , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria.,b Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria
| | - Michael Kitzmüller
- a Christian Doppler Laboratory for Antibody Engineering , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria.,b Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria
| | - Michael W Traxlmayr
- a Christian Doppler Laboratory for Antibody Engineering , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria.,b Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria
| | - Kristina Djinović-Carugo
- c Department for Structural and Computational Biology , Max F. Perutz Laboratories, University of Vienna , Dr. Bohr-Gasse 9, Vienna , Austria.,d Department of Biochemistry, Faculty of Chemistry and Chemical Technology , University of Ljubljana , Večna pot 113, Ljubljana , Slovenia
| | - Christian Obinger
- a Christian Doppler Laboratory for Antibody Engineering , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria.,b Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18, Vienna , Austria
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75
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Argenzio E, Moolenaar WH. Emerging biological roles of Cl- intracellular channel proteins. J Cell Sci 2017; 129:4165-4174. [PMID: 27852828 DOI: 10.1242/jcs.189795] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cl- intracellular channels (CLICs) are a family of six evolutionary conserved cytosolic proteins that exist in both soluble and membrane-associated forms; however, their functions have long been elusive. Soluble CLICs adopt a glutathione S-transferase (GST)-fold, can induce ion currents in artificial membranes and show oxidoreductase activity in vitro, but there is no convincing evidence of CLICs having such activities in vivo. Recent studies have revealed a role for CLIC proteins in Rho-regulated cortical actin dynamics as well as vesicular trafficking and integrin recycling, the latter of which are under the control of Rab GTPases. In this Commentary, we discuss the emerging roles of CLIC proteins in these processes and the lessons learned from gene-targeting studies. We also highlight outstanding questions regarding the molecular function(s) of these important but still poorly understood proteins.
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Affiliation(s)
- Elisabetta Argenzio
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Wouter H Moolenaar
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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76
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Peach ML, Cachau RE, Nicklaus MC. Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. J Mol Recognit 2017; 30:10.1002/jmr.2618. [PMID: 28233410 PMCID: PMC5553890 DOI: 10.1002/jmr.2618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 12/25/2022]
Abstract
In this review, we address a fundamental question: What is the range of conformational energies seen in ligands in protein-ligand crystal structures? This value is important biophysically, for better understanding the protein-ligand binding process; and practically, for providing a parameter to be used in many computational drug design methods such as docking and pharmacophore searches. We synthesize a selection of previously reported conflicting results from computational studies of this issue and conclude that high ligand conformational energies really are present in some crystal structures. The main source of disagreement between different analyses appears to be due to divergent treatments of electrostatics and solvation. At the same time, however, for many ligands, a high conformational energy is in error, due to either crystal structure inaccuracies or incorrect determination of the reference state. Aside from simple chemistry mistakes, we argue that crystal structure error may mainly be because of the heuristic weighting of ligand stereochemical restraints relative to the fit of the structure to the electron density. This problem cannot be fixed with improvements to electron density fitting or with simple ligand geometry checks, though better metrics are needed for evaluating ligand and binding site chemistry in addition to geometry during structure refinement. The ultimate solution for accurately determining ligand conformational energies lies in ultrahigh-resolution crystal structures that can be refined without restraints.
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Affiliation(s)
- Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Raul E Cachau
- Data Science and Information Technology Program, Advanced Biomedical Computing Center, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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77
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Hiruma Y, Koch A, Hazraty N, Tsakou F, Medema RH, Joosten RP, Perrakis A. Understanding inhibitor resistance in Mps1 kinase through novel biophysical assays and structures. J Biol Chem 2017; 292:14496-14504. [PMID: 28726638 DOI: 10.1074/jbc.m117.783555] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/06/2017] [Indexed: 01/09/2023] Open
Abstract
Monopolar spindle 1 (Mps1/TTK) is a protein kinase essential in mitotic checkpoint signaling, preventing anaphase until all chromosomes are properly attached to spindle microtubules. Mps1 has emerged as a potential target for cancer therapy, and a variety of compounds have been developed to inhibit its kinase activity. Mutations in the catalytic domain of Mps1 that give rise to inhibitor resistance, but retain catalytic activity and do not display cross-resistance to other Mps1 inhibitors, have been described. Here we characterize the interactions of two such mutants, Mps1 C604Y and C604W, which raise resistance to two closely related compounds, NMS-P715 and its derivative Cpd-5, but not to the well characterized Mps1 inhibitor, reversine. We show that estimates of the IC50 (employing a novel specific and efficient assay that utilizes a fluorescently labeled substrate) and the binding affinity (KD ) indicate that, in both mutants, Cpd-5 should be better tolerated than the closely related NMS-P715. To gain further insight, we determined the crystal structure of the Mps1 kinase mutants bound to Cpd-5 and NMS-P715 and compared the binding modes of Cpd-5, NMS-P715, and reversine. The difference in steric hindrance between Tyr/Trp604 and the trifluoromethoxy moiety of NMS-P715, the methoxy moiety of Cpd-5, and complete absence of such a group in reversine, account for differences we observe in vitro Our analysis enforces the notion that inhibitors targeting Mps1 drug-resistant mutations can emerge as a feasible intervention strategy based on existing scaffolds, if the clinical need arises.
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Affiliation(s)
| | - Andre Koch
- Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | | | | | - René H Medema
- Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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78
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Panneerselvam S, Kumpula EP, Kursula I, Burkhardt A, Meents A. Rapid cadmium SAD phasing at the standard wavelength (1 Å). Acta Crystallogr D Struct Biol 2017; 73:581-590. [PMID: 28695858 PMCID: PMC5505155 DOI: 10.1107/s2059798317006970] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/10/2017] [Indexed: 12/26/2022] Open
Abstract
Cadmium ions can be effectively used to promote crystal growth and for experimental phasing. Here, the use of cadmium ions as a suitable anomalous scatterer at the standard wavelength of 1 Å is demonstrated. The structures of three different proteins were determined using cadmium single-wavelength anomalous dispersion (SAD) phasing. Owing to the strong anomalous signal, the structure of lysozyme could be automatically phased and built using a very low anomalous multiplicity (1.1) and low-completeness (77%) data set. Additionally, it is shown that cadmium ions can easily substitute divalent ions in ATP-divalent cation complexes. This property could be generally applied for phasing experiments of a wide range of nucleotide-binding proteins. Improvements in crystal growth and quality, good anomalous signal at standard wavelengths (i.e. no need to change photon energy) and rapid phasing and refinement using a single data set are benefits that should allow cadmium ions to be widely used for experimental phasing.
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Affiliation(s)
| | - Esa-Pekka Kumpula
- Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Inari Kursula
- Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Anja Burkhardt
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alke Meents
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
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79
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Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARA/Endofin with HD-PTP. Structure 2017; 25:1011-1024.e4. [PMID: 28602823 PMCID: PMC5501724 DOI: 10.1016/j.str.2017.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/03/2017] [Accepted: 05/10/2017] [Indexed: 01/17/2023]
Abstract
SARA and endofin are endosomal adaptor proteins that drive Smad phosphorylation by ligand-activated transforming growth factor β/bone morphogenetic protein (TGFβ/BMP) receptors. We show in this study that SARA and endofin also recruit the tumor supressor HD-PTP, a master regulator of endosomal sorting and ESCRT-dependent receptor downregulation. High-affinity interactions occur between the SARA/endofin N termini, and the conserved hydrophobic region in the HD-PTP Bro1 domain that binds CHMP4/ESCRT-III. CHMP4 engagement is a universal feature of Bro1 proteins, but SARA/endofin binding is specific to HD-PTP. Crystallographic structures of HD-PTPBro1 in complex with SARA, endofin, and three CHMP4 isoforms revealed that all ligands bind similarly to the conserved site but, critically, only SARA/endofin interact at a neighboring pocket unique to HD-PTP. The structures, together with mutagenesis and binding analysis, explain the high affinity and specific binding of SARA/endofin, and why they compete so effectively with CHMP4. Our data invoke models for how endocytic regulation of TGFβ/BMP signaling is controlled.
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80
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Fcab-HER2 Interaction: a Ménage à Trois. Lessons from X-Ray and Solution Studies. Structure 2017; 25:878-889.e5. [PMID: 28528777 DOI: 10.1016/j.str.2017.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/10/2017] [Accepted: 04/28/2017] [Indexed: 01/07/2023]
Abstract
The crystallizable fragment (Fc) of the immunoglobulin class G (IgG) is an attractive scaffold for the design of novel therapeutics. Upon engineering the C-terminal loops in the CH3 domains, Fcabs (Fc domain with antigen-binding sites) can be designed. We present the first crystal structures of Fcabs, i.e., of the HER2-binding clone H10-03-6 having the AB and EF loop engineered and the stabilized version STAB19 derived by directed evolution. Comparison with the crystal structure of the Fc wild-type protein reveals conservation of the overall domain structures but significant differences in EF-loop conformations. Furthermore, we present the first Fcab-antigen complex structures demonstrating the interaction between the engineered Fcab loops with domain IV of HER2. The crystal structures of the STAB19-HER2 and H10-03-6-HER2 complexes together with analyses by isothermal titration calorimetry, SEC-MALS, and fluorescence correlation spectroscopy show that one homodimeric Fcab binds two HER2 molecules following a negative cooperative binding behavior.
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81
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Stanek KA, Patterson-West J, Randolph PS, Mura C. Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode. Acta Crystallogr D Struct Biol 2017; 73:294-315. [PMID: 28375142 PMCID: PMC5379935 DOI: 10.1107/s2059798317000031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/02/2017] [Indexed: 11/10/2022] Open
Abstract
The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus (Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore, Aae Hfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures of Aae Hfq were determined in space groups P1 and P6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.
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Affiliation(s)
- Kimberly A. Stanek
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Jennifer Patterson-West
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Peter S. Randolph
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
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82
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Novel insights into the interaction of UBA5 with UFM1 via a UFM1-interacting sequence. Sci Rep 2017; 7:508. [PMID: 28360427 PMCID: PMC5428781 DOI: 10.1038/s41598-017-00610-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/06/2017] [Indexed: 02/06/2023] Open
Abstract
The modification of proteins by ubiquitin-fold modifier 1 (UFM1) is implicated in many human diseases. Prior to conjugation, UFM1 undergoes activation by its cognate activating enzyme, UBA5. UBA5 is a non-canonical E1 activating enzyme that possesses an adenylation domain but lacks a distinct cysteine domain. Binding of UBA5 to UFM1 is mediated via an amino acid sequence, known as the UFM1-interacting sequence (UIS), located outside the adenylation domain that is required for UFM1 activation. However, the precise boundaries of the UIS are yet not clear and are still under debate. Here we revisit the interaction of UFM1 with UBA5 by determining the crystal structure of UFM1 fused to 13 amino acids of human UBA5. Using binding and activity assays, we found that His 336 of UBA5, previously not reported to be part of the UIS, occupies a negatively charged pocket on UFM1’s surface. This His is involved in UFM1 binding and if mutated perturbs activation of UFM1. Surprisingly, we also found that the interaction between two UFM1 molecules mimics how the UIS binds UFM1. Specifically, UFM1 His 70 resembles UBA5 His336 and enters a negatively charged pocked on the other UFM1 molecule. Our results refine our understanding of UFM1-UBA5 binding.
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83
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Crystal structures of an archaeal thymidylate kinase from Sulfolobus tokodaii provide insights into the role of a conserved active site Arginine residue. J Struct Biol 2017; 197:236-249. [DOI: 10.1016/j.jsb.2016.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 11/22/2022]
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84
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Krojer T, Talon R, Pearce N, Collins P, Douangamath A, Brandao-Neto J, Dias A, Marsden B, von Delft F. The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination. Acta Crystallogr D Struct Biol 2017; 73:267-278. [PMID: 28291762 PMCID: PMC5349439 DOI: 10.1107/s2059798316020234] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/20/2016] [Indexed: 11/11/2022] Open
Abstract
XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.
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Affiliation(s)
- Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Romain Talon
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Nicholas Pearce
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Patrick Collins
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Alice Douangamath
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Jose Brandao-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Alexandre Dias
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Brian Marsden
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, England
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
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85
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Werner JP, Mitchell JM, Taracila MA, Bonomo RA, Powers RA. Exploring the potential of boronic acids as inhibitors of OXA-24/40 β-lactamase. Protein Sci 2017; 26:515-526. [PMID: 27997706 DOI: 10.1002/pro.3100] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/08/2016] [Accepted: 12/08/2016] [Indexed: 01/01/2023]
Abstract
β-lactam antibiotics are crucial to the management of bacterial infections in the medical community. Due to overuse and misuse, clinically significant bacteria are now resistant to many commercially available antibiotics. The most widespread resistance mechanism to β-lactams is the expression of β-lactamase enzymes. To overcome β-lactamase mediated resistance, inhibitors were designed to inactivate these enzymes. However, current inhibitors (clavulanic acid, tazobactam, and sulbactam) for β-lactamases also contain the characteristic β-lactam ring, making them susceptible to resistance mechanisms employed by bacteria. This presents a critical need for novel, non-β-lactam inhibitors that can circumvent these resistance mechanisms. The carbapenem-hydrolyzing class D β-lactamases (CHDLs) are of particular concern, given that they efficiently hydrolyze potent carbapenem antibiotics. Unfortunately, these enzymes are not inhibited by clinically available β-lactamase inhibitors, nor are they effectively inhibited by the newest, non-β-lactam inhibitor, avibactam. Boronic acids are known transition state analog inhibitors of class A and C β-lactamases, and are not extensively characterized as inhibitors of class D β-lactamases. Importantly, boronic acids provide a novel way to potentially inhibit class D β-lactamases. Sixteen boronic acids were selected and tested for inhibition of the CHDL OXA-24/40. Several compounds were identified as effective inhibitors of OXA-24/40, with Ki values as low as 5 μM. The X-ray crystal structures of OXA-24/40 in complex with BA3, BA4, BA8, and BA16 were determined and revealed the importance of interactions with hydrophobic residues Tyr112 and Trp115. These boronic acids serve as progenitors in optimization efforts of a novel series of inhibitors for class D β-lactamases.
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Affiliation(s)
- Josephine P Werner
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | - Joshua M Mitchell
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | - Magdalena A Taracila
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, 44106.,Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio, 44106
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, 44106.,Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio, 44106
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
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86
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Guan R, Aiyer S, Cote ML, Xiao R, Jiang M, Acton TB, Roth MJ, Montelione GT. X-ray crystal structure of the N-terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition. Proteins 2017; 85:647-656. [PMID: 28066922 DOI: 10.1002/prot.25245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/15/2016] [Accepted: 11/23/2016] [Indexed: 01/26/2023]
Abstract
The retroviral integrase (IN) carries out the integration of a dsDNA copy of the viral genome into the host DNA, an essential step for viral replication. All IN proteins have three general domains, the N-terminal domain (NTD), the catalytic core domain, and the C-terminal domain. The NTD includes an HHCC zinc finger-like motif, which is conserved in all retroviral IN proteins. Two crystal structures of Moloney murine leukemia virus (M-MuLV) IN N-terminal region (NTR) constructs that both include an N-terminal extension domain (NED, residues 1-44) and an HHCC zinc-finger NTD (residues 45-105), in two crystal forms are reported. The structures of IN NTR constructs encoding residues 1-105 (NTR1-105 ) and 8-105 (NTR8-105 ) were determined at 2.7 and 2.15 Å resolution, respectively and belong to different space groups. While both crystal forms have similar protomer structures, NTR1-105 packs as a dimer and NTR8-105 packs as a tetramer in the asymmetric unit. The structure of the NED consists of three anti-parallel β-strands and an α-helix, similar to the NED of prototype foamy virus (PFV) IN. These three β-strands form an extended β-sheet with another β-strand in the HHCC Zn2+ binding domain, which is a unique structural feature for the M-MuLV IN. The HHCC Zn2+ binding domain structure is similar to that in HIV and PFV INs, with variations within the loop regions. Differences between the PFV and MLV IN NEDs localize at regions identified to interact with the PFV LTR and are compared with established biochemical and virological data for M-MuLV. Proteins 2017; 85:647-656. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rongjin Guan
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Sriram Aiyer
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Marie L Cote
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, New Jersey, 08854
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Mei Jiang
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Thomas B Acton
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Monica J Roth
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, New Jersey, 08854
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87
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Steiner RA, Tucker JA. Keep it together: restraints in crystallographic refinement of macromolecule-ligand complexes. Acta Crystallogr D Struct Biol 2017; 73:93-102. [PMID: 28177305 PMCID: PMC5297912 DOI: 10.1107/s2059798316017964] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/08/2016] [Indexed: 01/23/2023] Open
Abstract
A short introduction is provided to the concept of restraints in macromolecular crystallographic refinement. A typical ligand restraint-generation process is then described, covering types of input, the methodology and the mechanics behind the software in general terms, how this has evolved over recent years and what to look for in the output. Finally, the currently available restraint-generation software is compared, concluding with some thoughts for the future.
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Affiliation(s)
- Roberto A. Steiner
- Randall Division of Cell and Molecular Biophysics, King’s College London, London SE1 1UL, England
| | - Julie A. Tucker
- Northern Institute for Cancer Research, Paul O’Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, England
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88
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Long F, Nicholls RA, Emsley P, Gražulis S, Merkys A, Vaitkus A, Murshudov GN. AceDRG: a stereochemical description generator for ligands. Acta Crystallogr D Struct Biol 2017; 73:112-122. [PMID: 28177307 PMCID: PMC5297914 DOI: 10.1107/s2059798317000067] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/03/2017] [Indexed: 11/11/2022] Open
Abstract
The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the `ideal' bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files.
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Affiliation(s)
- Fei Long
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Paul Emsley
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Saulius Gražulis
- Institute of Biotechnology, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania
| | - Andrius Merkys
- Institute of Biotechnology, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania
| | - Antanas Vaitkus
- Institute of Biotechnology, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
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89
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Long F, Nicholls RA, Emsley P, Gražulis S, Merkys A, Vaitkus A, Murshudov GN. Validation and extraction of molecular-geometry information from small-molecule databases. Acta Crystallogr D Struct Biol 2017; 73:103-111. [PMID: 28177306 PMCID: PMC5297913 DOI: 10.1107/s2059798317000079] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/03/2017] [Indexed: 11/18/2022] Open
Abstract
A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation. The selection criteria made sure that the crystal structures used to derive atom types, bond and angle classes are of sufficiently high quality. Any suspicious entries at a crystal or molecular level were removed from further consideration. The selection criteria included (i) the resolution of the data used for refinement (entries solved at 0.84 Å resolution or higher) and (ii) the structure-solution method (structures must be from a single-crystal experiment and all atoms of generated molecules must have full occupancies), as well as basic sanity checks such as (iii) consistency between the valences and the number of connections between atoms, (iv) acceptable bond-length deviations from the expected values and (v) detection of atomic collisions. The derived atom types and bond classes were then validated using high-order moment-based statistical techniques. The results of the statistical analyses were fed back to fine-tune the atom typing. The developed procedure was repeated four times, resulting in fine-grained atom typing, bond and angle classes. The procedure will be repeated in the future as and when new entries are deposited in the COD. The whole procedure can also be applied to any source of small-molecule structures, including the Cambridge Structural Database and the ZINC database.
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Affiliation(s)
- Fei Long
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Paul Emsley
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Saulius Gražulis
- Institute of Biotechnology, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania
| | - Andrius Merkys
- Institute of Biotechnology, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania
| | - Antanas Vaitkus
- Institute of Biotechnology, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
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90
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Leonarski F, D'Ascenzo L, Auffinger P. Mg2+ ions: do they bind to nucleobase nitrogens? Nucleic Acids Res 2017; 45:987-1004. [PMID: 27923930 PMCID: PMC5314772 DOI: 10.1093/nar/gkw1175] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 01/28/2023] Open
Abstract
Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for divalent metals. Further, Mg2+ coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg2+ assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na+, K+, NH4+ ions, water molecules or spurious density peaks. Consequently, apart from few documented exceptions, Mg2+ ions do not bind to N7 atoms. Without much of a surprise, Mn2+, Zn2+ and Cd2+, which have a higher affinity for nitrogens, may contact N7 atoms when present in crystallization buffers. In this respect, we describe for the first time a potential Zn2+ ribosomal binding site involving two purine N7 atoms. Further, we provide a set of guidelines to help in the assignment of Mg2+ in crystallographic, cryo-EM, NMR and model building practices and discuss implications of our findings related to ion substitution experiments.
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Affiliation(s)
- Filip Leonarski
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Luigi D'Ascenzo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
| | - Pascal Auffinger
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
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91
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De March M, Merino N, Barrera-Vilarmau S, Crehuet R, Onesti S, Blanco FJ, De Biasio A. Structural basis of human PCNA sliding on DNA. Nat Commun 2017; 8:13935. [PMID: 28071730 PMCID: PMC5234079 DOI: 10.1038/ncomms13935] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/14/2016] [Indexed: 02/06/2023] Open
Abstract
Sliding clamps encircle DNA and tether polymerases and other factors to the genomic template. However, the molecular mechanism of clamp sliding on DNA is unknown. Using crystallography, NMR and molecular dynamics simulations, here we show that the human clamp PCNA recognizes DNA through a double patch of basic residues within the ring channel, arranged in a right-hand spiral that matches the pitch of B-DNA. We propose that PCNA slides by tracking the DNA backbone via a ‘cogwheel' mechanism based on short-lived polar interactions, which keep the orientation of the clamp invariant relative to DNA. Mutation of residues at the PCNA–DNA interface has been shown to impair the initiation of DNA synthesis by polymerase δ (pol δ). Therefore, our findings suggest that a clamp correctly oriented on DNA is necessary for the assembly of a replication-competent PCNA-pol δ holoenzyme. DNA sliding clamps are ring-shaped proteins that encircle DNA and harbour polymerases and other factors that promote processive DNA replication. Here the authors use X-ray crystallography, NMR and MD simulations to propose a model for a PCNA sliding mechanism that relies on short-lived polar interactions.
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Affiliation(s)
- Matteo De March
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
| | - Nekane Merino
- CIC bioGUNE, Parque Tecnologico de Bizkaia Edificio 800, 48160 Derio, Spain
| | - Susana Barrera-Vilarmau
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ramon Crehuet
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
| | - Francisco J Blanco
- CIC bioGUNE, Parque Tecnologico de Bizkaia Edificio 800, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Alfredo De Biasio
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
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92
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Ray L, Valentic TR, Miyazawa T, Withall DM, Song L, Milligan JC, Osada H, Takahashi S, Tsai SC, Challis GL. A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units. Nat Commun 2016; 7:13609. [PMID: 28000660 PMCID: PMC5187497 DOI: 10.1038/ncomms13609] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 10/19/2016] [Indexed: 11/12/2022] Open
Abstract
Type I modular polyketide synthases assemble diverse bioactive natural products. Such multienzymes typically use malonyl and methylmalonyl-CoA building blocks for polyketide chain assembly. However, in several cases more exotic alkylmalonyl-CoA extender units are also known to be incorporated. In all examples studied to date, such unusual extender units are biosynthesized via reductive carboxylation of α, β-unsaturated thioesters catalysed by crotonyl-CoA reductase/carboxylase (CCRC) homologues. Here we show using a chemically-synthesized deuterium-labelled mechanistic probe, and heterologous gene expression experiments that the unusual alkylmalonyl-CoA extender units incorporated into the stambomycin family of polyketide antibiotics are assembled by direct carboxylation of medium chain acyl-CoA thioesters. X-ray crystal structures of the unusual β-subunit of the acyl-CoA carboxylase (YCC) responsible for this reaction, alone and in complex with hexanoyl-CoA, reveal the molecular basis for substrate recognition, inspiring the development of methodology for polyketide bio-orthogonal tagging via incorporation of 6-azidohexanoic acid and 8-nonynoic acid into novel stambomycin analogues.
Polyketides are typically assembled from a starter unit and malonyl- and/or methylmalonyl-CoA-derived extender units, but the macrolide antibiotics stambomycins incorporate non-standard alkylmalonyl-CoA extender units. Here, the authors describe the biosynthetic pathway responsible for this unusual synthesis.
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Affiliation(s)
- Lauren Ray
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Timothy R Valentic
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Takeshi Miyazawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - David M Withall
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Jacob C Milligan
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shunji Takahashi
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Shiou-Chuan Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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93
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Bohari MH, Yu X, Zick Y, Blanchard H. Structure-based rationale for differential recognition of lacto- and neolacto- series glycosphingolipids by the N-terminal domain of human galectin-8. Sci Rep 2016; 6:39556. [PMID: 28000747 PMCID: PMC5175137 DOI: 10.1038/srep39556] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/23/2016] [Indexed: 12/19/2022] Open
Abstract
Glycosphingolipids are ubiquitous cell surface molecules undertaking fundamental cellular processes. Lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT) are the representative core structures for lacto- and neolacto-series glycosphingolipids. These glycolipids are the carriers to the blood group antigen and human natural killer antigens mainly found on blood cells, and are also principal components in human milk, contributing to infant health. The β-galactoside recognising galectins mediate various cellular functions of these glycosphingolipids. We report crystallographic structures of the galectin-8 N-terminal domain (galectin-8N) in complex with LNT and LNnT. We reveal the first example in which the non-reducing end of LNT binds to the primary binding site of a galectin, and provide a structure-based rationale for the significant ten-fold difference in binding affinities of galectin-8N toward LNT compared to LNnT, such a magnitude of difference not being observed for any other galectin. In addition, the LNnT complex showed that the unique Arg59 has ability to adopt a new orientation, and comparison of glycerol- and lactose-bound galectin-8N structures reveals a minimum atomic framework for ligand recognition. Overall, these results enhance our understanding of glycosphingolipids interactions with galectin-8N, and highlight a structure-based rationale for its significantly different affinity for components of biologically relevant glycosphingolipids.
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Affiliation(s)
- Mohammad H. Bohari
- Institute for Glycomics, Griffith University, Gold Coast Campus, 4222, Australia
| | - Xing Yu
- Institute for Glycomics, Griffith University, Gold Coast Campus, 4222, Australia
| | - Yehiel Zick
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Helen Blanchard
- Institute for Glycomics, Griffith University, Gold Coast Campus, 4222, Australia
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94
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van Gunsteren WF, Allison JR, Daura X, Dolenc J, Hansen N, Mark AE, Oostenbrink C, Rusu VH, Smith LJ. Bestimmung von Strukturinformation aus experimentellen Messdaten für Biomoleküle. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601828] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Wilfred F. van Gunsteren
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Jane R. Allison
- Centre for Theor. Chem. and Phys. & Institute of Natural and Mathematical Sciences; Massey Univ.; Auckland Neuseeland
- Biomolecular Interaction Centre; University of Canterbury, Christchurch; Neuseeland
- Maurice Wilkins Centre for Molecular Biodiscovery; Neuseeland
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine; Universitat Autònoma de Barcelona (UAB); 08193 Barcelona Spanien
- Catalan Institution for Research and Advanced Studies (ICREA); 08010 Barcelona Spanien
| | - Jožica Dolenc
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Niels Hansen
- Institut für Technische Thermodynamik und Thermische Verfahrenstechnik; Universität Stuttgart; Pfaffenwaldring 9 70569 Stuttgart Deutschland
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences; University of Queensland; St. Lucia QLD 4072 Australien
| | - Chris Oostenbrink
- Institut für Molekulare Modellierung und Simulation; Universität für Bodenkultur Wien; Wien Österreich
| | - Victor H. Rusu
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Lorna J. Smith
- Department of Chemistry; University of Oxford, Inorganic Chemistry Laboratory; South Parks Road Oxford OX1 3QR Großbritannien
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95
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van Gunsteren WF, Allison JR, Daura X, Dolenc J, Hansen N, Mark AE, Oostenbrink C, Rusu VH, Smith LJ. Deriving Structural Information from Experimentally Measured Data on Biomolecules. Angew Chem Int Ed Engl 2016; 55:15990-16010. [PMID: 27862777 DOI: 10.1002/anie.201601828] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/08/2016] [Indexed: 12/27/2022]
Abstract
During the past half century, the number and accuracy of experimental techniques that can deliver values of observables for biomolecular systems have been steadily increasing. The conversion of a measured value Qexp of an observable quantity Q into structural information is, however, a task beset with theoretical and practical problems: 1) insufficient or inaccurate values of Qexp , 2) inaccuracies in the function Q(r→) used to relate the quantity Q to structure r→ , 3) how to account for the averaging inherent in the measurement of Qexp , 4) how to handle the possible multiple-valuedness of the inverse r→(Q) of the function Q(r→) , to mention a few. These apply to a variety of observable quantities Q and measurement techniques such as X-ray and neutron diffraction, small-angle and wide-angle X-ray scattering, free-electron laser imaging, cryo-electron microscopy, nuclear magnetic resonance, electron paramagnetic resonance, infrared and Raman spectroscopy, circular dichroism, Förster resonance energy transfer, atomic force microscopy and ion-mobility mass spectrometry. The process of deriving structural information from measured data is reviewed with an eye to non-experts and newcomers in the field using examples from the literature of the effect of the various choices and approximations involved in the process. A list of choices to be avoided is provided.
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Affiliation(s)
- Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Jane R Allison
- Centre for Theor. Chem. and Phys. & Institute of Natural and Mathematical Sciences, Massey Univ., Auckland, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona (UAB), 08193, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
| | - Jožica Dolenc
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569, Stuttgart, Germany
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Victor H Rusu
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Lorna J Smith
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
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96
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Joosten RP, Lütteke T. Carbohydrate 3D structure validation. Curr Opin Struct Biol 2016; 44:9-17. [PMID: 27816840 DOI: 10.1016/j.sbi.2016.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 12/11/2022]
Abstract
Glycoproteins and protein-carbohydrate complexes in the worldwide Protein Data Bank (wwPDB) can be an excellent source of information for glycoscientists. Unfortunately, a rather large number of errors and inconsistencies is found in the glycan moieties of these 3D structures. This review illustrates frequent problems of carbohydrate moieties in wwPDB entries, such as nomenclature issues, incorrect N-glycan core structures, missing or erroneous linkages, or poor glycan geometry, and describes the carbohydrate-specific validation tools that are designed to identify such problems. Recommendations how to avoid these issues or how to rectify incorrect structures are also given.
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Affiliation(s)
- Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Frankfurter Str. 100, 35392 Giessen, Germany.
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97
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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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98
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Freire F, Verma A, Bule P, Alves VD, Fontes CMGA, Goyal A, Najmudin S. Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) from Clostridium thermocellum. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:1162-1173. [PMID: 27841749 DOI: 10.1107/s2059798316014376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/09/2016] [Indexed: 11/10/2022]
Abstract
Glucuronoxylan endo-β-1,4-xylanases cleave the xylan chain specifically at sites containing 4-O-methylglucuronic acid substitutions. These enzymes have recently received considerable attention owing to their importance in the cooperative hydrolysis of heteropolysaccharides. However, little is known about the hydrolysis of glucuronoxylans in extreme environments. Here, the structure of a thermostable family 30 glucuronoxylan endo-β-1,4-xylanase (CtXyn30A) from Clostridium thermocellum is reported. CtXyn30A is part of the cellulosome, a highly elaborate multi-enzyme complex secreted by the bacterium to efficiently deconstruct plant cell-wall carbohydrates. CtXyn30A preferably hydrolyses glucuronoxylans and displays maximum activity at pH 6.0 and 70°C. The structure of CtXyn30A displays a (β/α)8 TIM-barrel core with a side-associated β-sheet domain. Structural analysis of the CtXyn30A mutant E225A, solved in the presence of xylotetraose, revealed xylotetraose-cleavage oligosaccharides partially occupying subsites -3 to +2. The sugar ring at the +1 subsite is held in place by hydrophobic stacking interactions between Tyr139 and Tyr200 and hydrogen bonds to the OH group of Tyr227. Although family 30 glycoside hydrolases are retaining enzymes, the xylopyranosyl ring at the -1 subsite of CtXyn30A-E225A appears in the α-anomeric configuration. A set of residues were found to be strictly conserved in glucuronoxylan endo-β-1,4-xylanases and constitute the molecular determinants of the restricted specificity displayed by these enzymes. CtXyn30A is the first thermostable glucuronoxylan endo-β-1,4-xylanase described to date. This work reveals that substrate recognition by both thermophilic and mesophilic glucuronoxylan endo-β-1,4-xylanases is modulated by a conserved set of residues.
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Affiliation(s)
- Filipe Freire
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Anil Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Pedro Bule
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Victor D Alves
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Arun Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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99
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Correia MAS, Otrelo-Cardoso AR, Schwuchow V, Sigfridsson Clauss KGV, Haumann M, Romão MJ, Leimkühler S, Santos-Silva T. The Escherichia coli Periplasmic Aldehyde Oxidoreductase Is an Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes. ACS Chem Biol 2016; 11:2923-2935. [PMID: 27622978 DOI: 10.1021/acschembio.6b00572] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The xanthine oxidase (XO) family comprises molybdenum-dependent enzymes that usually form homodimers (or dimers of heterodimers/trimers) organized in three domains that harbor two [2Fe-2S] clusters, one FAD, and a Mo cofactor. In this work, we crystallized an unusual member of the family, the periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli. This is the first example of an E. coli protein containing a molybdopterin-cytosine-dinucleotide cofactor and is the only heterotrimer of the XO family so far structurally characterized. The crystal structure revealed the presence of an unexpected [4Fe-4S] cluster, anchored to an additional 40 residues subdomain. According to phylogenetic analysis, proteins containing this cluster are widely spread in many bacteria phyla, putatively through repeated gene transfer events. The active site of PaoABC is highly exposed to the surface with no aromatic residues and an arginine (PaoC-R440) making a direct interaction with PaoC-E692, which acts as a base catalyst. In order to understand the importance of R440, kinetic assays were carried out, and the crystal structure of the PaoC-R440H variant was also determined.
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Affiliation(s)
- Márcia A. S. Correia
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Rita Otrelo-Cardoso
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Viola Schwuchow
- Institut
für Biologie und Biochemie, Universität Potsdam, Am Neuen Palais
10, 14469 Potsdam, Deutschland
| | | | - Michael Haumann
- Freie Universität Berlin, Fachbereich Physik, 14195 Berlin, Germany
| | - Maria João Romão
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Silke Leimkühler
- Institut
für Biologie und Biochemie, Universität Potsdam, Am Neuen Palais
10, 14469 Potsdam, Deutschland
| | - Teresa Santos-Silva
- UCIBIO/Requimte,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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100
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Nogly P, Panneels V, Nelson G, Gati C, Kimura T, Milne C, Milathianaki D, Kubo M, Wu W, Conrad C, Coe J, Bean R, Zhao Y, Båth P, Dods R, Harimoorthy R, Beyerlein KR, Rheinberger J, James D, DePonte D, Li C, Sala L, Williams GJ, Hunter MS, Koglin JE, Berntsen P, Nango E, Iwata S, Chapman HN, Fromme P, Frank M, Abela R, Boutet S, Barty A, White TA, Weierstall U, Spence J, Neutze R, Schertler G, Standfuss J. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography. Nat Commun 2016; 7:12314. [PMID: 27545823 PMCID: PMC4996941 DOI: 10.1038/ncomms12314] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/22/2016] [Indexed: 01/12/2023] Open
Abstract
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
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Affiliation(s)
- Przemyslaw Nogly
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Valerie Panneels
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Tetsunari Kimura
- Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | | | - Despina Milathianaki
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Minoru Kubo
- Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan.,PRESTO, JST, Saitama 332-0012, Japan
| | - Wenting Wu
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Chelsie Conrad
- Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Jesse Coe
- Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Richard Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Kenneth R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Jan Rheinberger
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Daniel James
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Daniel DePonte
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Leonardo Sala
- SwissFEL, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Garth J Williams
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Eriko Nango
- SACLA Science Research Group, RIKEN/SPring-8 Center, Hyogo 679-5148, Japan
| | - So Iwata
- SACLA Science Research Group, RIKEN/SPring-8 Center, Hyogo 679-5148, Japan.,Department of Cell Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Department of Physics, University of Hamburg, 22761 Hamburg, Germany.,Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Petra Fromme
- Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore 94550, USA
| | - Rafael Abela
- SwissFEL, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - John Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Gebhard Schertler
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland.,Department of Biology, ETH Zurich, Zürich 8093, Switzerland
| | - Jörg Standfuss
- Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
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