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Prostko P, Pikkemaat J, Selter P, Lukaschek M, Wechselberger R, Khamiakova T, Valkenborg D. R Shiny App for the Automated Deconvolution of NMR Spectra to Quantify the Solid-State Forms of Pharmaceutical Mixtures. Metabolites 2022; 12:metabo12121248. [PMID: 36557287 PMCID: PMC9786300 DOI: 10.3390/metabo12121248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Bioavailability and chemical stability are important characteristics of drug products that are strongly affected by the solid-state structure of the active pharmaceutical ingredient (API). In pharmaceutical development and quality control activities, solid-state NMR (ssNMR) has proved to be an excellent tool for the detection and accurate quantification of undesired solid-state forms. To obtain correct quantitative outcomes, the resulting spectrum of an analytical sample should be deconvoluted into the individual spectra of the pure components. However, the ssNMR deconvolution is particularly challenging due to the following: the relatively large line widths that may lead to severe peak overlap, multiple spinning sidebands as a result of applying Magic Angle Spinning (MAS), and highly irregular peak shapes commonly observed in mixture spectra. To address these challenges, we created a tailored and automated deconvolution approach of ssNMR mixture spectra that involves a linear combination modelling (LCM) of previously acquired reference spectra of pure solid-state components. For optimal model performance, the template and mixture spectra should be acquired under the same conditions and experimental settings. In addition to the parameters controlling the contributions of the components in the mixture, the proposed model includes terms for spectral processing such as phase correction and horizontal shifting that are all jointly estimated via a non-linear, constrained optimisation algorithm. Finally, our novel procedure has been implemented in a fully functional and user-friendly R Shiny webtool (hence no local R installation required) that offers interactive data visualisations, manual adjustments to the automated deconvolution results, and the traceability and reproducibility of analyses.
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Affiliation(s)
- Piotr Prostko
- Data Science Institute, UHasselt—Hasselt University, Agoralaan 1, BE 3590 Diepenbeek, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Agoralaan 1, BE 3590 Diepenbeek, Belgium
| | - Jeroen Pikkemaat
- Janssen Pharmaceutica, Department of Analytical Development, Turnhoutseweg 30, BE 2340 Beerse, Belgium
| | - Philipp Selter
- Janssen Pharmaceutica, Department of Analytical Development, Turnhoutseweg 30, BE 2340 Beerse, Belgium
| | - Michail Lukaschek
- Janssen Pharmaceutica, Department of Analytical Development, Turnhoutseweg 30, BE 2340 Beerse, Belgium
| | - Rainer Wechselberger
- Janssen Pharmaceutica, Department of Analytical Development, Turnhoutseweg 30, BE 2340 Beerse, Belgium
| | - Tatsiana Khamiakova
- Janssen Pharmaceutica, Manufacturing and Applied Statistics, Turnhoutseweg 30, BE 2340 Beerse, Belgium
| | - Dirk Valkenborg
- Data Science Institute, UHasselt—Hasselt University, Agoralaan 1, BE 3590 Diepenbeek, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Agoralaan 1, BE 3590 Diepenbeek, Belgium
- Correspondence:
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2
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Carloni LE, Wechselberger R, De Vijlder T. Characterization of In Vitro G-Quadruplex Formation of Imetelstat Telomerase Inhibitor. Nucleic Acid Ther 2021; 31:341-350. [PMID: 34018844 DOI: 10.1089/nat.2020.0918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Imetelstat (GRN163L) is a potent and specific telomerase inhibitor currently in clinical development for the treatment of hematological malignancies such as myelofibrosis and myelodysplastic syndrome. It is a 13-mer N3'-P5' thio-phosphoramidate oligonucleotide covalently functionalized at the 5'-end with a palmitoyl lipid moiety through an aminoglycerol linker. As a competitive inhibitor of human telomerase, imetelstat directly binds to the telomerase RNA component sequence (hTR) in the catalytic site of the enzyme and acts as a direct competitor of human telomere binding. Administration of imetelstat causes progressive shortening of the telomeres, thereby inhibiting malignant cells' proliferation. We report here the ability of imetelstat to form stable, parallel, intermolecular G-quadruplex structures in vitro. The impact of the ionic environment on the formation and stability of imetelstat higher-order structure was investigated through circular dichroism spectroscopy, thermal denaturation analysis, and size-exclusion chromatography. We demonstrated that different structural elements, such as the 5'-palmitoyl linker and the thio-phosphoramidate backbone, critically contribute to G-quadruplex stability. Experiments further showed that G-quadruplex formation does not hamper binding to the hTR oligonucleotide sequence in vitro.
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Affiliation(s)
- Laure-Elie Carloni
- Small Molecule Pharmaceutical Development, Janssen Research & Development, Beerse, Belgium
| | - Rainer Wechselberger
- Small Molecule Pharmaceutical Development, Janssen Research & Development, Beerse, Belgium
| | - Thomas De Vijlder
- Small Molecule Pharmaceutical Development, Janssen Research & Development, Beerse, Belgium
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Capaldi D, Akhtar N, Atherton T, Benstead D, Charaf A, De Vijlder T, Heatherington C, Hoernschemeyer J, Jiang H, Rieder U, Ring F, Peter R, Stolee JA, Wechselberger R. Strategies for Identity Testing of Therapeutic Oligonucleotide Drug Substances and Drug Products. Nucleic Acid Ther 2020; 30:249-264. [PMID: 32857010 DOI: 10.1089/nat.2020.0878] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A risk-based approach for routine identity testing of therapeutic oligonucleotide drug substances and drug products is described. Risk analysis of solid-phase oligonucleotide synthesis indicates that intact mass measurement is a powerful technique for confirming synthesis of the intended oligonucleotide. Further risk assessment suggests that the addition of a second, sequence-sensitive identity test, which relies on a comparison of some property of the sample to a reference standard of proven identity, results in a sufficient test of identity for most oligonucleotide drug substances and products. Alternative strategies for drug product identity testing are presented. The analysis creates a common way to communicate risk and should result in a harmonized approach to identity testing that avoids the unnecessary analytical burden associated with routine de novo sequencing, without compromising quality or patient safety.
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Affiliation(s)
- Daniel Capaldi
- Development Chemistry, Ionis Pharmaceuticals Inc., Carlsbad, California, USA
| | - Nadim Akhtar
- New Modalities and Parenteral Development and Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | - Tom Atherton
- Structure and Function Characterization, CMC Analytical, GlaxoSmithKline, Stevenage, United Kingdom
| | - David Benstead
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | - Ayman Charaf
- Research and Development Tides, Pharmaceutical Development Platform, Sanofi-Aventis GmbH, Frankfurt am Main, Germany
| | - Thomas De Vijlder
- Analytical Development, Small Molecule Development, Janssen Pharmaceutical Companies of Johnson and Johnson, Beerse, Belgium
| | - Carl Heatherington
- Drug Substance and Product Analysis UK, CMC Analytical, GlaxoSmithKline, Stevenage, United Kingdom
| | | | - Hong Jiang
- Analytical Development, Biogen, Cambridge, Massachusetts, USA
| | - Ulrike Rieder
- Technical Research and Development, Global Drug Development, Novartis Pharma, Basel, Switzerland
| | - Francis Ring
- Development Chemistry, Ionis Pharmaceuticals Inc., Carlsbad, California, USA
| | - Robert Peter
- Analytical Research and Development, Synthetic Molecules Technical Development, F. Hoffmann-La Roche, Basel, Switzerland
| | | | - Rainer Wechselberger
- Analytical Development, Small Molecule Development, Janssen Pharmaceutical Companies of Johnson and Johnson, Beerse, Belgium
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Abstract
3D domain swapping (3D‐DS) is a complex protein aggregation process for which no unique mechanism exists. We report an analysis of 3D‐DS in bovine seminal ribonuclease, a homodimeric protein whose subunits are linked by two disulfide bridges, based on NMR and biochemical studies. The presence of the covalent bonds between the subunits stabilizes the unswapped dimer, and allows distinct evaluation of the structural and dynamic effects of the swapping with respect to the dimerization process. In comparison with the monomeric subunit, which, in solution has a compact structure without any propensity for local unfolding, both swapped and unswapped dimers show increased flexibility. NMR analysis, together with urea denaturation and hydrogen–deuterium exchange data, indicates that the two dimers have increased conformational fluctuations. Furthermore, we found that the rate‐limiting step of both the swapping and unswapping pathways is the detachment of the N‐terminal helices from the monomers. These results suggest a new general mechanism in which a dimeric intermediate could facilitate 3D‐DS in globular proteins. Structured digital abstract http://www.uniprot.org/uniprot/P00669 and http://www.uniprot.org/uniprot/P00669 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0407 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0077 (http://www.ebi.ac.uk/intact/interaction/EBI-8870415)
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Oyen D, Wechselberger R, Srinivasan V, Steyaert J, Barlow JN. Mechanistic analysis of allosteric and non-allosteric effects arising from nanobody binding to two epitopes of the dihydrofolate reductase of Escherichia coli. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2013; 1834:2147-57. [DOI: 10.1016/j.bbapap.2013.07.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/22/2013] [Accepted: 07/24/2013] [Indexed: 11/16/2022]
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Stötzel S, Schurink M, Wienk H, Siebler U, Burg-Roderfeld M, Eckert T, Kulik B, Wechselberger R, Sewing J, Steinmeyer J, Oesser S, Boelens R, Siebert HC. Cover Picture: Molecular Organization of Various Collagen Fragments as Revealed by Atomic Force Microscopy and Diffusion-Ordered NMR Spectroscopy (ChemPhysChem 13/2012). Chemphyschem 2012. [DOI: 10.1002/cphc.201290060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Stötzel S, Schurink M, Wienk H, Siebler U, Burg-Roderfeld M, Eckert T, Kulik B, Wechselberger R, Sewing J, Steinmeyer J, Oesser S, Boelens R, Siebert HC. Molecular Organization of Various Collagen Fragments as Revealed by Atomic Force Microscopy and Diffusion-Ordered NMR Spectroscopy. Chemphyschem 2012; 13:3117-25. [DOI: 10.1002/cphc.201200284] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Indexed: 12/22/2022]
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8
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Spadaccini R, Ercole C, Gentile MA, Sanfelice D, Boelens R, Wechselberger R, Batta G, Bernini A, Niccolai N, Picone D. NMR studies on structure and dynamics of the monomeric derivative of BS-RNase: new insights for 3D domain swapping. PLoS One 2012; 7:e29076. [PMID: 22253705 PMCID: PMC3257227 DOI: 10.1371/journal.pone.0029076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 11/20/2011] [Indexed: 11/18/2022] Open
Abstract
Three-dimensional domain swapping is a common phenomenon in pancreatic-like ribonucleases. In the aggregated state, these proteins acquire new biological functions, including selective cytotoxicity against tumour cells. RNase A is able to dislocate both N- and C-termini, but usually this process requires denaturing conditions. In contrast, bovine seminal ribonuclease (BS-RNase), which is a homo-dimeric protein sharing 80% of sequence identity with RNase A, occurs natively as a mixture of swapped and unswapped isoforms. The presence of two disulfides bridging the subunits, indeed, ensures a dimeric structure also to the unswapped molecule. In vitro, the two BS-RNase isoforms interconvert under physiological conditions. Since the tendency to swap is often related to the instability of the monomeric proteins, in these paper we have analysed in detail the stability in solution of the monomeric derivative of BS-RNase (mBS) by a combination of NMR studies and Molecular Dynamics Simulations. The refinement of NMR structure and relaxation data indicate a close similarity with RNase A, without any evidence of aggregation or partial opening. The high compactness of mBS structure is confirmed also by H/D exchange, urea denaturation, and TEMPOL mapping of the protein surface. The present extensive structural and dynamic investigation of (monomeric) mBS did not show any experimental evidence that could explain the known differences in swapping between BS-RNase and RNase A. Hence, we conclude that the swapping in BS-RNase must be influenced by the distinct features of the dimers, suggesting a prominent role for the interchain disulfide bridges.
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Affiliation(s)
- Roberta Spadaccini
- Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Benevento, Italy
| | - Carmine Ercole
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Maria A. Gentile
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Domenico Sanfelice
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Rolf Boelens
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Rainer Wechselberger
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Gyula Batta
- Institute of Chemistry, University of Debrecen, Debrecen, Hungary
| | - Andrea Bernini
- Dipartimento di Biotecnologie, Università degli Studi di Siena, Siena, Italy
| | - Neri Niccolai
- Dipartimento di Biotecnologie, Università degli Studi di Siena, Siena, Italy
| | - Delia Picone
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- * E-mail:
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Sette M, Wechselberger R, Crestini C. Elucidation of Lignin Structure by Quantitative 2D NMR. Chemistry 2011; 17:9529-35. [DOI: 10.1002/chem.201003045] [Citation(s) in RCA: 211] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 04/14/2011] [Indexed: 11/06/2022]
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10
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Lemaire S, Houpis I, Wechselberger R, Langens J, Vermeulen WAA, Smets N, Nettekoven U, Wang Y, Xiao T, Qu H, Liu R, Jonckers TH, Raboisson P, Vandyck K, Nilsson KM, Farina V. Practical Synthesis of (2′R)-2′-Deoxy-2′-C-methyluridine by Highly Diastereoselective Homogeneous Hydrogenation. J Org Chem 2010; 76:297-300. [DOI: 10.1021/jo101822j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sébastien Lemaire
- Johnson and Johnson Pharmaceutical Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Ioannis Houpis
- Johnson and Johnson Pharmaceutical Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Rainer Wechselberger
- Johnson and Johnson Pharmaceutical Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Jaak Langens
- Johnson and Johnson Pharmaceutical Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Wim A. A. Vermeulen
- Johnson and Johnson Pharmaceutical Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Nico Smets
- Johnson and Johnson Pharmaceutical Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | | | - Youchu Wang
- WuXi PharmaTech Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, PR China
| | - Tingting Xiao
- WuXi PharmaTech Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, PR China
| | - Haisheng Qu
- WuXi PharmaTech Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, PR China
| | - Renmao Liu
- WuXi PharmaTech Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, PR China
| | - Tim H.M. Jonckers
- Tibotec BVBA, Medicinal Chemistry, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Pierre Raboisson
- Tibotec BVBA, Medicinal Chemistry, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Koen Vandyck
- Tibotec BVBA, Medicinal Chemistry, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | | | - Vittorio Farina
- Johnson and Johnson Pharmaceutical Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
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11
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Siebert HC, Burg-Roderfeld M, Eckert T, Stötzel S, Kirch U, Diercks T, Humphries MJ, Frank M, Wechselberger R, Tajkhorshid E, Oesser S. Interaction of the α2A domain of integrin with small collagen fragments. Protein Cell 2010; 1:393-405. [PMID: 21203951 DOI: 10.1007/s13238-010-0038-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 03/27/2010] [Indexed: 11/29/2022] Open
Abstract
We here present a detailed study of the ligand-receptor interactions between single and triple-helical strands of collagen and the α2A domain of integrin (α2A), providing valuable new insights into the mechanisms and dynamics of collagen-integrin binding at a sub-molecular level. The occurrence of single and triple-helical strands of the collagen fragments was scrutinized with atom force microscopy (AFM) techniques. Strong interactions of the triple-stranded fragments comparable to those of collagen can only be detected for the 42mer triple-helical collagen-like peptide under study (which contains 42 amino acid residues per strand) by solid phase assays as well as by surface plasmon resonance (SPR) measurements. However, changes in NMR signals during titration and characteristic saturation transfer difference (STD) NMR signals are also detectable when α2A is added to a solution of the 21mer single-stranded collagen fragment. Molecular dynamics (MD) simulations employing different sets of force field parameters were applied to study the interaction between triple-helical or single-stranded collagen fragments with α2A. It is remarkable that even single-stranded collagen fragments can form various complexes with α2A showing significant differences in the complex stability with identical ligands. The results of MD simulations are in agreement with the signal alterations in our NMR experiments, which are indicative of the formation of weak complexes between single-stranded collagen and α2A in solution. These results provide useful information concerning possible interactions of α2A with small collagen fragments that are of relevance to the design of novel therapeutic A-domain inhibitors.
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Affiliation(s)
- Hans-Christian Siebert
- Institut für Biochemie und Endokrinologie, Veterinärmedizinische Fakultät, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany.
| | - Monika Burg-Roderfeld
- Institut für Biochemie und Endokrinologie, Veterinärmedizinische Fakultät, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
| | - Thomas Eckert
- Institut für Biochemie und Endokrinologie, Veterinärmedizinische Fakultät, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
| | - Sabine Stötzel
- Institut für Biochemie und Endokrinologie, Veterinärmedizinische Fakultät, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
| | - Ulrike Kirch
- Institut für Biochemie und Endokrinologie, Veterinärmedizinische Fakultät, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
| | - Tammo Diercks
- CiC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160, Derio, Spain.,Utrecht Facility for High-resolution NMR, Bijvoetcenter for Biomolecular Research Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, University of Manchester, 2.205 Stopford Building, Oxford Road, Manchester, M13 9PT, UK
| | - Martin Frank
- Molecular Structure Analysis Core Facility, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Rainer Wechselberger
- Utrecht Facility for High-resolution NMR, Bijvoetcenter for Biomolecular Research Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Emad Tajkhorshid
- Department of Biochemistry, Beckman Institute, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Steffen Oesser
- Collagen Research Institute, Schauenburgerstr. 116, D-24118, Kiel, Germany
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Bhunia A, Vivekanandan S, Eckert T, Burg-Roderfeld M, Wechselberger R, Romanuka J, Bächle D, Kornilov AV, von der Lieth CW, Jiménez-Barbero J, Nifantiev NE, Schachner M, Sewald N, Lütteke T, Gabius HJ, Siebert HC. Why Structurally Different Cyclic Peptides Can Be Glycomimetics of the HNK-1 Carbohydrate Antigen []. J Am Chem Soc 2010. [DOI: 10.1021/ja100344v] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Bhunia A, Vivekanandan S, Eckert T, Burg-Roderfeld M, Wechselberger R, Romanuka J, Bächle D, Kornilov AV, von der Lieth CW, Jiménez-Barbero J, Nifantiev NE, Schachner M, Sewald N, Lütteke T, Hans-Joachim G, Siebert HC. Why structurally different cyclic peptides can be glycomimetics of the HNK-1 carbohydrate antigen. J Am Chem Soc 2010; 132:96-105. [PMID: 19958024 DOI: 10.1021/ja904334s] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The cyclic peptides c-(LSETTl) and c-(RTLPFS) are of potential clinical interest--they stimulate neurite outgrowth in a way that is similar to the effects of the HNK-1 (human natural killer cell-1) antigenic carbohydrate chains, which are terminated by 3'-sulfated glucuronic acid attached to an N-acetyllactosamine unit. To investigate the structure-activity relationships of the ability of the cyclic peptides to mimic HNK-1 carbohydrates, conformational analysis and examination of hydrophobic and hydrophilic patterns were performed and compared with the characteristics of a synthetic HNK-1 trisaccharide derivative. Data obtained demonstrate that both the trisaccharide and the glycomimetic peptide c-(LSETTl) exhibit a similar relationship between their hydrophobic moieties and their negatively charged sites. However, the second cyclic glycomimetic peptide investigated here, c-(RTLPFS), has a positively charged group as a potential contact point due to its Arg residue. Therefore, we studied the amino acid composition of all known receptor structures in the Protein Data Bank that are in contact with uronic acid and/or sulfated glycans. Interactions of the HNK-1 trisaccharide, c-(LSETTl), and c-(RTLPFS) with a laminin fragment involved in HNK-1 carbohydrate binding (i.e., the 21mer peptide: KGVSSRSYVGCIKNLEISRST) were also analyzed. Because the structure of the HNK-1-binding laminin domain is not available in the Protein Data Bank, we used the HNK-1-binding 21mer peptide fragment of laminin for the construction of a model receptor that enabled us to compare the molecular interplay of the HNK-1 trisaccharide and the two cyclopeptides c-(LSETTl) and c-(RTLPFS) with a reliable receptor structure in considerable detail.
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Affiliation(s)
- Anirban Bhunia
- Institut für Biochemie und Endokrinologie, Veterinrmedizinische Fakultät, Justus-Liebig-Universität Giessen, Frankfurter Str. 100, 35392 Giessen, Germany
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14
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Siebert HC, Lu SY, Wechselberger R, Born K, Eckert T, Liang S, der Lieth CWV, Jiménez-Barbero J, Schauer R, G Vliegenthart JF, Lütteke T, André S, Kaltner H, Gabius HJ, Kožár T. WITHDRAWN: Corrigendum to "A lectin from the Chinese bird-hunting spider binds sialic acids". Carbohydr Res 2010:S0008-6215(09)00625-9. [PMID: 20176345 DOI: 10.1016/j.carres.2009.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published, doi: 10.1016/j.carres.2010.01.003. The duplicate article has therefore been withdrawn.
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Affiliation(s)
- Hans-Christian Siebert
- Institut für Biochemie und Endokrinologie, Fachbereich für Veterinärmedizin, Justus-Liebig Universität Giessen, Frankfurter Strasse 100, 35392 Giessen, Germany
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15
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Pukin AV, Weijers CA, van Lagen B, Wechselberger R, Sun B, Gilbert M, Karwaski MF, Florack DE, Jacobs BC, Tio-Gillen AP, van Belkum A, Endtz HP, Visser GM, Zuilhof H. GM3, GM2 and GM1 mimics designed for biosensing: chemoenzymatic synthesis, target affinities and 900MHz NMR analysis. Carbohydr Res 2008; 343:636-50. [DOI: 10.1016/j.carres.2008.01.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2007] [Revised: 12/24/2007] [Accepted: 01/07/2008] [Indexed: 11/30/2022]
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Duarte AMS, de Jong ER, Wechselberger R, van Mierlo CPM, Hemminga MA. Segment TM7 from the cytoplasmic hemi-channel from VO-H+-V-ATPase includes a flexible region that has a potential role in proton translocation. Biochimica et Biophysica Acta (BBA) - Biomembranes 2007; 1768:2263-70. [PMID: 17573038 DOI: 10.1016/j.bbamem.2007.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 04/23/2007] [Accepted: 05/11/2007] [Indexed: 11/25/2022]
Abstract
A 900-MHz NMR study is reported of peptide sMTM7 that mimics the cytoplasmic proton hemi-channel domain of the seventh transmembrane segment (TM7) from subunit a of H(+)-V-ATPase from Saccharomyces cerevisiae. The peptide encompasses the amino acid residues known to actively participate in proton translocation. In addition, peptide sMTM7 contains the amino acid residues that upon mutation cause V-ATPase to become resistant against the inhibitor bafilomycin. 2D TOCSY and NOESY (1)H-(1)H NMR spectra are obtained of sMTM7 dissolved in d(6)-DMSO and are used to calculate the three-dimensional structure of the peptide. The NMR-based structures and corresponding dynamical features of peptide sMTM7 show that sMTM7 is composed of two alpha-helical regions. These regions are separated by a flexible hinge of two residues. The hinge acts as a ball-and-joint socket and both helical segments move independently with respect to one another. This movement in TM7 is suggested to cause the opening and closing of the cytoplasmic proton hemi-channel and enables proton translocation.
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Affiliation(s)
- Afonso M S Duarte
- Laboratory of Biophysics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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17
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Tomaselli S, Crescenzi O, Sanfelice D, Ab E, Wechselberger R, Angeli S, Scaloni A, Boelens R, Tancredi T, Pelosi P, Picone D. Solution structure of a chemosensory protein from the desert locust Schistocerca gregaria. Biochemistry 2006; 45:10606-13. [PMID: 16939212 DOI: 10.1021/bi060998w] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical stimuli, generally constituted by small volatile organic molecules, are extremely important for the survival of different insect species. In the course of evolution, insects have developed very sophisticated biochemical systems for the binding and the delivery of specific semiochemicals to their cognate membrane-bound receptors. Chemosensory proteins (CSPs) are a class of small soluble proteins present at high concentration in insect chemosensory organs; they are supposed to be involved in carrying the chemical messages from the environment to the chemosensory receptors. In this paper, we report on the solution structure of CSPsg4, a chemosensory protein from the desert locust Schistocerca gregaria, which is expressed in the antennae and other chemosensory organs. The 3D NMR structure revealed an overall fold consisting of six alpha-helices, spanning residues 13-18, 20-31, 40-54, 62-78, 80-90, and 97-103, connected by loops which in some cases show dihedral angles typical of beta-turns. As in the only other chemosensory protein whose structure has been solved so far, namely, CSP from the moth Mamestra brassicae, four helices are arranged to form a V-shaped motif; another helix runs across the two V's, and the last one is packed against the external face. Analysis of the tertiary structure evidenced multiple hydrophobic cavities which could be involved in ligand binding. In fact, incubation of the protein with a natural ligand, namely, oleamide, produced substantial changes to the NMR spectra, suggesting extensive conformational transitions upon ligand binding.
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Affiliation(s)
- Simona Tomaselli
- Department of Chemistry, University of Naples Federico II, 80126 Napoli, Italy
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18
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Singh S, Folkers G, Bonvin A, Boelens R, Wechselberger R, Niztayev A, Kaptein R. Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli. EMBO J 2002; 21:6257-66. [PMID: 12426397 PMCID: PMC137216 DOI: 10.1093/emboj/cdf627] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5' incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix-hairpin-helix (HhH) motifs connected by a small connector helix. The UvrC CTD is shown to mediate structure-specific DNA binding. The domain binds to a single-stranded-double-stranded junction DNA, with a strong specificity towards looped duplex DNA that contains at least six unpaired bases per loop ("bubble DNA"). Using chemical shift perturbation experiments, the DNA-binding surface is mapped to the first hairpin region encompassing the conserved glycine-valine-glycine residues followed by lysine-arginine-arginine, a positively charged surface patch and the second hairpin region consisting of glycine-isoleucine-serine. A model for the protein-DNA complex is proposed that accounts for this specificity.
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Affiliation(s)
| | | | | | | | | | | | - R. Kaptein
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Corresponding author e-mail:
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19
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Augustijn KD, Duval DL, Wechselberger R, Kaptein R, Gutierrez-Hartmann A, van der Vliet PC. Structural characterization of the PIT-1/ETS-1 interaction: PIT-1 phosphorylation regulates PIT-1/ETS-1 binding. Proc Natl Acad Sci U S A 2002; 99:12657-62. [PMID: 12242337 PMCID: PMC130516 DOI: 10.1073/pnas.192693499] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The POU-domain transcription factor Pit-1 and Ets-1, a member of the ETS family of transcription factors, can associate in solution and synergistically activate the prolactin promoter by binding to a composite response element in the prolactin promoter. We mapped the minimal region of Ets-1 required for the interaction with the Pit-1 POU-homeodomain. Here, we describe a detailed NMR study of the interaction between the POU-homeodomain of Pit-1 and the minimal interacting region of Ets-1. By using heteronuclear single quantum coherence titration experiments, we were able to map exact residues on the POU-homeodomain that are involved in the interaction with this minimal Ets-1 interaction domain. By using our NMR data, we generated point mutants in the POU-homeodomain and tested their effect on the interaction with Ets-1. Our results show that phosphorylation of Pit-1 can regulate the interaction with Ets-1.
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Affiliation(s)
- Kevin D Augustijn
- Department of Physiological Chemistry, University Medical Center Utrecht and Center for Biomedical Genetics, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
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20
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Siebert HC, Lü SY, Frank M, Kramer J, Wechselberger R, Joosten J, André S, Rittenhouse-Olson K, Roy R, von der Lieth CW, Kaptein R, Vliegenthart JFG, Heck AJR, Gabius HJ. Analysis of protein-carbohydrate interaction at the lower size limit of the protein part (15-mer peptide) by NMR spectroscopy, electrospray ionization mass spectrometry, and molecular modeling. Biochemistry 2002; 41:9707-17. [PMID: 12135393 DOI: 10.1021/bi025891x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structural analysis of minimally sized lectins will offer insights into fundamentals of intermolecular recognition and potential for biomedical applications. We thus moved significantly beyond the natural limit of lectin size to determine the structure of synthetic mini-lectins in solution, their carbohydrate selectivity and the impact of ligand binding on their conformational behavior. Using three disaccharide (Thomsen-Friedenreich antigen; Gal beta 1,3GalNAc alpha 1,R)-binding pentadecapeptides without internal disulfide bridges as role models, we successfully tested a combined strategy with different techniques of NMR spectroscopy, electrospray ionization mass spectrometry, and molecular modeling. In solution, the peptides invariably displayed flexibility with rather limited restrictions, shown by NMR experiments including nearly complete resonance assignments and molecular dynamics simulations. The occurrence of aromatic/nonpolar amino acids in the sequence did not lead to formation of a hydrophobic core known from microbial chitinase modules. Selectivity of disaccharide binding was independently observed by mass spectrometry and NMR analysis. Specific ligand interaction yielded characteristic NMR signal alterations but failed to reduce conformational flexibility significantly. We have thereby proven effectiveness of our approach to analyze even low-affinity interactions (not restricted to carbohydrates as ligands). It will be useful to evaluate the impact of rational manipulation of lead peptide sequences.
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Affiliation(s)
- Hans-Christian Siebert
- Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität München, Veterinärstrasse 13, 80539 München, Germany.
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21
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Kalodimos CG, Bonvin AM, Salinas RK, Wechselberger R, Boelens R, Kaptein R. Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. EMBO J 2002; 21:2866-76. [PMID: 12065400 PMCID: PMC126071 DOI: 10.1093/emboj/cdf318] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The lac repressor-operator system is a model system for understanding protein-DNA interactions and allosteric mechanisms in gene regulation. Despite the wealth of biochemical data provided by extensive mutations of both repressor and operator, the specific recognition mechanism of the natural lac operators by lac repressor has remained elusive. Here we present the first high-resolution structure of a dimer of the DNA-binding domain of lac repressor bound to its natural operator 01. The global positioning of the dimer on the operator is dramatically asymmetric, which results in a different pattern of specific contacts between the two sites. Specific recognition is accomplished by a combination of elongation and twist by 48 degrees of the right lac subunit relative to the left one, significant rearrangement of many side chains as well as sequence-dependent deformability of the DNA. The set of recognition mechanisms involved in the lac repressor-operator system is unique among other protein-DNA complexes and presents a nice example of the adaptability that both proteins and DNA exhibit in the context of their mutual interaction.
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Affiliation(s)
| | | | | | | | | | - Robert Kaptein
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
Corresponding author e-mail:
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22
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Campanacci V, Mosbah A, Bornet O, Wechselberger R, Jacquin-Joly E, Cambillau C, Darbon H, Tegoni M. Chemosensory protein from the moth Mamestra brassicae. Expression and secondary structure from 1H and 15N NMR. Eur J Biochem 2001; 268:4731-9. [PMID: 11532009 DOI: 10.1046/j.1432-1327.2001.02398.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A group of ubiquitous small proteins (average 13 kDa) has been isolated from several sensory organs of a wide range of insect species. They are believed to be involved in chemical communication and perception (olfaction or taste) and have therefore been called chemo-sensory proteins (CSPs). Several CSPs have been identified in the antennae and proboscis of the moth Mamestra brassicae. We have expressed one of the antennal proteins (CSPMbraA6) in large quantities as a soluble recombinant protein in Escherichia coli periplasm. This 112-residue protein is a highly soluble monomer of 13 072 Da with a pI of 5.5. NMR data (1H and 15N) indicate that CSPMbraA6 is well folded and contains seven alpha helices (59 amino acids) and two short extended structures (12 amino acids) from positions 5 to 10 and from 107 to 112. Thirty-seven amino acids are involved in beta turns and coiled segments and four amino acids are not assigned in the NMR spectra (the N-terminus and the residue 52 in the loop 48-53), probably due to their mobility. This is the first report on the expression and structural characterization of a recombinant CSP.
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Affiliation(s)
- V Campanacci
- AFMB, UMR 6098-CNRS and Universités d'Aix-Marseille I and II, Marseille, France
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23
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Eijkelenboom AP, van den Ent FM, Wechselberger R, Plasterk RH, Kaptein R, Boelens R. Refined solution structure of the dimeric N-terminal HHCC domain of HIV-2 integrase. J Biomol NMR 2000; 18:119-128. [PMID: 11101216 DOI: 10.1023/a:1008342312269] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The solution structure of the dimeric N-terminal domain of HIV-2 integrase (residues 1-55, named IN(1-55)) has been determined using NMR spectroscopy. The structure of the monomer, which was already reported previously [Eijkelenboom et al. (1997) Curr. Biol., 7, 739-746], consists of four alpha-helices and is well defined. Helices alpha1, alpha2 and alpha3 form a three-helix bundle that is stabilized by zinc binding to His12, His16, Cys40 and Cys43. The dimer interface is formed by the N-terminal tail and the first half of helix alpha3. The orientation of the two monomeric units with respect to each other shows considerable variation. 15N relaxation studies have been used to characterize the nature of the intermonomeric disorder. Comparison of the dimer interface with that of the well-defined dimer interface of HIV-1 IN(1-55) shows that the latter is stabilized by additional hydrophobic interactions and a potential salt bridge. Similar interactions cannot be formed in HIV-2 IN(1-55) [Cai et al. (1997) Nat. Struct. Biol., 4, 567-577], where the corresponding residues are positively charged and neutral ones.
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Affiliation(s)
- A P Eijkelenboom
- Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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24
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Meunier S, Spurio R, Czisch M, Wechselberger R, Guenneugues M, Gualerzi CO, Boelens R. Structure of the fMet-tRNA(fMet)-binding domain of B. stearothermophilus initiation factor IF2. EMBO J 2000; 19:1918-26. [PMID: 10775275 PMCID: PMC302012 DOI: 10.1093/emboj/19.8.1918] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The three-dimensional structure of the fMet-tRNA(fMet) -binding domain of translation initiation factor IF2 from Bacillus stearothermophilus has been determined by heteronuclear NMR spectroscopy. Its structure consists of six antiparallel beta-strands, connected via loops, and forms a closed beta-barrel similar to domain II of elongation factors EF-Tu and EF-G, despite low sequence homology. Two structures of the ternary complexes of the EF-Tu small middle dotaminoacyl-tRNA small middle dot GDP analogue have been reported and were used to propose and discuss the possible fMet-tRNA(fMet)-binding site of IF2.
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Affiliation(s)
- S Meunier
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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25
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Whittaker SB, Czisch M, Wechselberger R, Kaptein R, Hemmings AM, James R, Kleanthous C, Moore GR. Slow conformational dynamics of an endonuclease persist in its complex with its natural protein inhibitor. Protein Sci 2000; 9:713-20. [PMID: 10794413 PMCID: PMC2144623 DOI: 10.1110/ps.9.4.713] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The bacterial toxin colicin E9 is secreted by producing Escherichia coli cells with its 9.5 kDa inhibitor protein Im9 bound tightly to its 14.5 kDa C-terminal DNase domain. Double- and triple-resonance NMR spectra of the isolated DNase domain uniformly labeled with 13C/15N bound to unlabeled Im9 contain more signals than expected for a single DNase conformer, consistent with the bound DNase being present in more than one form. The presence of chemical exchange cross peaks in 750 MHz 15N-1H-15N HSQC-NOESY-HSQC spectra for backbone NH groups of Asp20, Lys21, Trp22, Leu23, Lys69, and Asn70 showed that the bound DNase was in dynamic exchange. The rate of exchange from the major to the minor form was determined to be 1.1 +/- 0.2 s(-1) at 298 K. Previous NMR studies have shown that the free DNase interchanges between two conformers with a forward rate constant of 1.61 +/- 0.11 s(-1) at 288 K, and that the bound Im9 is fixed in one conformation. The NMR studies of the bound DNase show that Im9 binds similarly to both conformers of the DNase and that the buried Trp22 is involved in the dynamic process. For the free DNase, all NH groups within a 9 A radius of any point of the Trp22 ring exhibit heterogeneity suggesting that a rearrangement of the position of this side chain is connected with the conformational interchange. The possible functional significance of this feature of the DNase is discussed.
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Affiliation(s)
- S B Whittaker
- School of Chemical Sciences, University of East Anglia, Norwich, United Kingdom
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26
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Spronk CA, Folkers GE, Noordman AM, Wechselberger R, van den Brink N, Boelens R, Kaptein R. Hinge-helix formation and DNA bending in various lac repressor-operator complexes. EMBO J 1999; 18:6472-80. [PMID: 10562559 PMCID: PMC1171710 DOI: 10.1093/emboj/18.22.6472] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The hinge-region of the lac repressor plays an important role in the models for induction and DNA looping in the lac operon. When lac repressor is bound to a tight-binding symmetric operator, this region forms an alpha-helix that induces bending of the operator. The presence of the hinge-helices is questioned by previous data that suggest that the repressor does not bend the wild-type operator. We show that in the wild-type complex the hinge-helices are formed and the DNA is bent, similar to the symmetric complex. Furthermore, our data show differences in the binding of the DNA binding domains to the half-sites of the wild-type operator and reveal the role of the central base-pair of the wild-type operator in the repressor-operator interaction. The differences in binding to the operator half-sites are incorporated into a model that explains the relative affinities of the repressor for various lac operator sequences that contain left and right half-sites with different spacer lengths.
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Affiliation(s)
- C A Spronk
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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27
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Werten S, Wechselberger R, Boelens R, van der Vliet PC, Kaptein R. Identification of the single-stranded DNA binding surface of the transcriptional coactivator PC4 by NMR. J Biol Chem 1999; 274:3693-9. [PMID: 9920920 DOI: 10.1074/jbc.274.6.3693] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The C-terminal domain of the eukaryotic transcriptional cofactor PC4 (PC4CTD) is known to bind with nanomolar affinity to single-stranded (ss)DNA. Here, NMR is used to study DNA binding by this domain in more detail. Amide resonance shifts that were observed in a 1H15N-HSQC-monitored titration of 15N-labeled protein with the oligonucleotide dT18 indicate that binding of the nucleic acid occurs by means of two anti-parallel channels that were previously identified in the PC4CTD crystal structure. The beta-sheets and loops that make up these channels exhibit above average flexibility in the absence of ssDNA, which is reflected in higher values of T1rho, reduced heteronuclear nuclear Overhauser effects and faster deuterium exchange rates for the amides in this region. Upon ssDNA binding, this excess flexibility is significantly reduced. The binding of ssDNA by symmetry-related channels reported here provides a structural rationale for the preference of PC4CTD for juxtaposed single-stranded regions (e.g. in heteroduplexes) observed in earlier work.
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Affiliation(s)
- S Werten
- Laboratorium voor Fysiologische Chemie, Universiteit Utrecht, Stratenum, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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28
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Haris PI, Wechselberger R, Czisch M. Structure of the S4 and S4-S5 loop region of a voltage-gated potassium channel. Biochem Soc Trans 1998; 26:S358. [PMID: 10047872 DOI: 10.1042/bst026s358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- P I Haris
- Dept. of Biological Sciences, De Montfort University, The Gateway, Leicester, UK
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29
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Schwalbe H, Marino JP, King GC, Wechselberger R, Bermel W, Griesinger C. Determination of a complete set of coupling constants in 13C-labeled oligonucleotides. J Biomol NMR 1994; 4:631-44. [PMID: 7919950 DOI: 10.1007/bf00404274] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Three experiments are introduced to determine a complete set of coupling constants in RNA oligomers. In the HCCH-E.COSY experiment, the vicinal proton-proton coupling constants can be measured with high accuracy. In the P-FIDS-CT-HSQC experiment, vicinal proton-phosphorus and carbon-phosphorus couplings are measured that depend on the phosphodiester backbone torsion angles beta and epsilon. In the refocussed HMBC experiment, vicinal carbon-proton couplings are measured that depend on the glycosidic torsion angle chi.
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Affiliation(s)
- H Schwalbe
- Institut für Organische Chemie, Universität Frankfurt, Germany
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