1
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Romanuka J, Folkers GE, Gnida M, Kovačič L, Wienk H, Kaptein R, Boelens R. Genetic switching by the Lac repressor is based on two-state Monod-Wyman-Changeux allostery. Proc Natl Acad Sci U S A 2023; 120:e2311240120. [PMID: 38019859 DOI: 10.1073/pnas.2311240120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric Escherichia coli Lac repressor. In the absence of ligands, the dimer exists in a dynamic equilibrium between DNA-bound and inducer-bound conformations. Binding of either effector shifts this equilibrium toward either bound state. Analysis of the ternary complex between repressor, operator DNA, and inducer shows how adding the inducer results in allosteric changes that disrupt the interdomain contacts between the inducer binding and DNA binding domains and how this in turn leads to destabilization of the hinge helices and release of the Lac repressor from the operator. Based on our data, the allosteric mechanism of the induction process is in full agreement with the well-known Monod-Wyman-Changeux model.
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Affiliation(s)
- Julija Romanuka
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Manuel Gnida
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Lidija Kovačič
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Robert Kaptein
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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2
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Corbeski I, Guo X, Eckhardt BV, Fasci D, Wiegant W, Graewert MA, Vreeken K, Wienk H, Svergun DI, Heck AJR, van Attikum H, Boelens R, Sixma TK, Mattiroli F, van Ingen H. Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF. Sci Adv 2022; 8:eabo0517. [PMID: 35895815 PMCID: PMC9328677 DOI: 10.1126/sciadv.abo0517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/10/2022] [Indexed: 05/26/2023]
Abstract
Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B. Here, we show that the acidic domain of DNA repair factor APLF (APLFAD) can assemble the histone octamer in a single step and deposit it on DNA to form nucleosomes. The crystal structure of the APLFAD-histone octamer complex shows that APLFAD tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLFAD affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted.
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Affiliation(s)
- Ivan Corbeski
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Xiaohu Guo
- Division of Biochemistry and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Bruna V. Eckhardt
- Hubrecht Institute—KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Domenico Fasci
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Wouter Wiegant
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Melissa A. Graewert
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Kees Vreeken
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Titia K. Sixma
- Division of Biochemistry and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Francesca Mattiroli
- Hubrecht Institute—KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
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3
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Poelman H, Ippel H, Gürkan B, Boelens R, Vriend G, Veer CV', Lutgens E, Nicolaes GAF. Structural anomalies in a published NMR-derived structure of IRAK-M. J Mol Graph Model 2021; 111:108061. [PMID: 34837785 DOI: 10.1016/j.jmgm.2021.108061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022]
Abstract
Signaling by Toll-Like Receptors and the Interleukin-1 Receptor (IL1-R) involves intracellular binding of MyD88, followed by assembly of IL1-R Associated Kinases (IRAKs) into the so-called Myddosome. Using NMR, Nechama et al. determined the structure of the IRAK-M death domain monomer (PDBid: 5UKE). With this structure, they performed a docking study to model the location of IRAK-M in the Myddosome. Based on this, they present a molecular basis for selectivity of IRAK-M towards IRAK1 over IRAK2 binding. When we attempted to use 5UKE as a homology modeling template, we noticed that our 5UKE-based models had structural issues, such as disallowed torsion angles and solvent exposed tryptophans. We therefore analyzed the NMR ensemble of 5UKE using structure validation tools and we compared 5UKE with homologous high-resolution X-ray structures. We identified several structural anomalies in 5UKE, including packing issues, frayed helices and improbable side chain conformations. We used Yasara to build a homology model, based on two high resolution death domain crystal structures, as an alternative model for the IRAK-M death domain (atomic coordinates, modeling details and validation are available at https://swift.cmbi.umcn.nl/gv/service/5uke/). Our model agrees better with known death domain structure information than 5UKE and also with the chemical shift data that was deposited for 5UKE.
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Affiliation(s)
- Hessel Poelman
- Amsterdam UMC, University of Amsterdam, Medical Biochemistry, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
| | - Hans Ippel
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands
| | - Berke Gürkan
- Amsterdam UMC, University of Amsterdam, Center for Experimental and Molecular Medicine, Amsterdam Infection and Immunity Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Rolf Boelens
- Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Gert Vriend
- BIPS, Poblacion BACO, 5201, Mindoro, Philippines
| | - Cornelis van 't Veer
- Amsterdam UMC, University of Amsterdam, Center for Experimental and Molecular Medicine, Amsterdam Infection and Immunity Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Esther Lutgens
- Amsterdam UMC, University of Amsterdam, Medical Biochemistry, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians Universität, München, Germany & German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80539, Munich, Germany
| | - Gerry A F Nicolaes
- Amsterdam UMC, University of Amsterdam, Medical Biochemistry, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands.
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Boelens R, Ivanov K, Matysik J. Introduction to a special issue of Magnetic Resonance in honour of Robert Kaptein at the occasion of his 80th birthday. Magn Reson (Gott) 2021; 2:465-474. [PMID: 37904778 PMCID: PMC10539797 DOI: 10.5194/mr-2-465-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 11/01/2023]
Abstract
This publication, in honour of Robert Kaptein's 80th birthday, contains contributions from colleagues, many of whom have worked with him, and others who admire his work and have been stimulated by his research. The contributions show current research in biomolecular NMR, spin hyperpolarisation and spin chemistry, including CIDNP (chemically induced dynamic nuclear polarisation), topics to which he has contributed enormously. His proposal of the radical pair mechanism was the birth of the field of spin chemistry, and the laser CIDNP NMR experiment on a protein was a major breakthrough in hyperpolarisation research. He set milestones for biomolecular NMR by developing computational methods for protein structure determination, including restrained molecular dynamics and 3D NMR methodology. With a lac repressor headpiece, he determined one of the first protein structures determined by NMR. His studies of the lac repressor provided the first examples of detailed studies of protein nucleic acid complexes by NMR. This deepened our understanding of protein DNA recognition and led to a molecular model for protein sliding along the DNA. Furthermore, he played a leading role in establishing the cluster of NMR large-scale facilities in Europe. This editorial gives an introduction to the publication and is followed by a biography describing his contributions to magnetic resonance.
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Affiliation(s)
- Rolf Boelens
- Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Konstantin Ivanov
- International Tomography Center, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University,
Novosibirsk 630090, Russia
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04189 Leipzig, Germany
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Boelens R. Meet Our Editorial Board Member. Curr Protein Pept Sci 2020. [DOI: 10.2174/138920372111201203091813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- R. Boelens
- Bijvoet Center for Biomolecular Research Utrecht University Utrecht, Netherlands
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Giassa IC, Vavrinská A, Zelinka J, Šebera J, Sychrovský V, Boelens R, Fiala R, Trantírek L. HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids. Chempluschem 2020; 85:2177-2185. [PMID: 32986260 DOI: 10.1002/cplu.202000505] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Indexed: 11/06/2022]
Abstract
Field-Induced Residual Dipolar Couplings (fiRDC) are a valuable source of long-range information on structure of nucleic acids (NA) in solution. A web application (HERMES) was developed for structure-based prediction and analysis of the (fiRDCs) in NA. fiRDC prediction is based on input 3D model structure(s) of NA and a built-in library of nucleobase-specific magnetic susceptibility tensors and reference geometries. HERMES allows three basic applications: (i) the prediction of fiRDCs for a given structural model of NAs, (ii) the validation of experimental or modeled NA structures using experimentally derived fiRDCs, and (iii) assessment of the oligomeric state of the NA fragment and/or the identification of a molecular NA model that is consistent with experimentally derived fiRDC data. Additionally, the program's built-in routine for rigid body modeling allows the evaluation of relative orientation of domains within NA that is in agreement with experimental fiRDCs.
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Affiliation(s)
| | - Andrea Vavrinská
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Jiří Zelinka
- Department of Mathematics and Statistics, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 166 10, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 166 10, Czech Republic
| | - Rolf Boelens
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Brno
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Brno
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7
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Shahul Hameed D, van Tilburg GBA, Merkx R, Flierman D, Wienk H, El Oualid F, Hofmann K, Boelens R, Ovaa H. Diubiquitin-Based NMR Analysis: Interactions Between Lys6-Linked diUb and UBA Domain of UBXN1. Front Chem 2020; 7:921. [PMID: 32039147 PMCID: PMC6987245 DOI: 10.3389/fchem.2019.00921] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/18/2019] [Indexed: 12/03/2022] Open
Abstract
Ubiquitination is a process in which a protein is modified by the covalent attachment of the C-terminal carboxylic acid of ubiquitin (Ub) to the ε-amine of lysine or N-terminal methionine residue of a substrate protein or another Ub molecule. Each of the seven internal lysine residues and the N-terminal methionine residue of Ub can be linked to the C-terminus of another Ub moiety to form 8 distinct Ub linkages and the resulting differences in linkage types elicit different Ub signaling pathways. Cellular responses are triggered when proteins containing ubiquitin-binding domains (UBDs) recognize and bind to specific polyUb linkage types. To get more insight into the differences between polyUb chains, all of the seven lysine-linked di-ubiquitin molecules (diUbs) were prepared and used as a model to study their structural conformations in solution using NMR spectroscopy. We report the synthesis of diUb molecules, fully 15N-labeled on the distal (N-terminal) Ub moiety and revealed their structural orientation with respect to the proximal Ub. As expected, the diUb molecules exist in different conformations in solution, with multiple conformations known to exist for K6-, K48-, and K63-linked diUb molecules. These multiple conformations allow structural flexibility in binding with UBDs thereby inducing unique responses. One of the well-known but poorly understood UBD-Ub interaction is the recognition of K6 polyubiquitin by the ubiquitin-associated (UBA) domain of UBXN1 in the BRCA-mediated DNA repair pathway. Using our synthetic 15N-labeled diUbs, we establish here how a C-terminally extended UBA domain of UBXN1 confers specificity to K6 diUb while the non-extended version of the domain does not show any linkage preference. We show that the two distinct conformations of K6 diUb that exist in solution converge into a single conformation upon binding to this extended form of the UBA domain of the UBXN1 protein. It is likely that more of such extended UBA domains exist in nature and can contribute to linkage-specificity in Ub signaling. The isotopically labeled diUb compounds described here and the use of NMR to study their interactions with relevant partner molecules will help accelerate our understanding of Ub signaling pathways.
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Affiliation(s)
- Dharjath Shahul Hameed
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Gabrielle B A van Tilburg
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Remco Merkx
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dennis Flierman
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Farid El Oualid
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,UbiQ Bio BV, Amsterdam, Netherlands
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Huib Ovaa
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
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8
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Abstract
Numerous proteins are involved in the multiple pathways of the DNA damage response network and play a key role to protect the genome from the wide variety of damages that can occur to DNA. An example of this is the structure-specific endonuclease ERCC1-XPF. This heterodimeric complex is in particular involved in nucleotide excision repair (NER), but also in double strand break repair and interstrand cross-link repair pathways. Here we review the function of ERCC1-XPF in various DNA repair pathways and discuss human disorders associated with ERCC1-XPF deficiency. We also overview our molecular and structural understanding of XPF-ERCC1.
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Affiliation(s)
- Maryam Faridounnia
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Gert E Folkers
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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9
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Emendato A, Guerrini R, Marzola E, Wienk H, Boelens R, Leone S, Picone D. Disordered Peptides Looking for Their Native Environment: Structural Basis of CB1 Endocannabinoid Receptor Binding to Pepcans. Front Mol Biosci 2018; 5:100. [PMID: 30505835 PMCID: PMC6250848 DOI: 10.3389/fmolb.2018.00100] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/26/2018] [Indexed: 01/15/2023] Open
Abstract
Endocannabinoid peptides, or “pepcans,” are endogenous ligands of the CB1 cannabinoid receptor. Depending on their length, they display diverse activity: For instance, the nona-peptide Pepcan-9, also known as hemopressin, is a powerful inhibitor of CB1, whereas the longer variant Pepcan-12, which extends by only three amino acid residues at the N-terminus, acts on both CB1 and CB2 as an allosteric modulator, although with diverse effects. Despite active research on their pharmacological applications, very little is known about structure-activity relationships of pepcans. Different structures have been proposed for the nona-peptide, which has also been reported to form fibrillar aggregates. This might have affected the outcome and reproducibility of bioactivity studies. In an attempt of elucidating the determinants of both biological activity and aggregation propensity of Pepcan-9 and Pepcan-12, we have performed their structure characterization in solvent systems characterized by different polarity and pH. We have found that, while disordered in aqueous environment, both peptides display helical structure in less polar environment, mimicking the proteic receptor milieu. In the case of Pepcan-9, this structure is fully consistent with the observed modulation of the CB1. For Pepcan-12, whose allosteric binding site is still unknown, the presented structure is compatible with the binding at one of the previously proposed allosteric sites on CB1. These findings open the way to structure-driven design of selective peptide modulators of CB1.
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Affiliation(s)
- Alessandro Emendato
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Erika Marzola
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Hans Wienk
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Serena Leone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
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10
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Corbeski I, Dolinar K, Wienk H, Boelens R, van Ingen H. DNA repair factor APLF acts as a H2A-H2B histone chaperone through binding its DNA interaction surface. Nucleic Acids Res 2018; 46:7138-7152. [PMID: 29905837 PMCID: PMC6101569 DOI: 10.1093/nar/gky507] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 11/20/2017] [Revised: 05/02/2018] [Accepted: 05/22/2018] [Indexed: 01/23/2023] Open
Abstract
Genome replication, transcription and repair require the assembly/disassembly of the nucleosome. Histone chaperones are regulators of this process by preventing formation of non-nucleosomal histone-DNA complexes. Aprataxin and polynucleotide kinase like factor (APLF) is a non-homologous end-joining (NHEJ) DNA repair factor that possesses histone chaperone activity in its acidic domain (APLFAD). Here, we studied the molecular basis of this activity using biochemical and structural methods. We find that APLFAD is intrinsically disordered and binds histone complexes (H3-H4)2 and H2A-H2B specifically and with high affinity. APLFAD prevents unspecific complex formation between H2A-H2B and DNA in a chaperone assay, establishing for the first time its specific histone chaperone function for H2A-H2B. On the basis of a series of nuclear magnetic resonance studies, supported by mutational analysis, we show that the APLFAD histone binding domain uses two aromatic side chains to anchor to the α1-α2 patches on both H2A and H2B, thereby covering most of their DNA-interaction surface. An additional binding site on both APLFAD and H2A-H2B may be involved in the handoff between APLF and DNA or other chaperones. Together, our data support the view that APLF provides not only a scaffold but also generic histone chaperone activity for the NHEJ-complex.
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Affiliation(s)
- Ivan Corbeski
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Klemen Dolinar
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Group for Nano- and Biotechnological applications, Department of Fundamentals of Electrical Engineering, Mathematics and Physics, University of Ljubljana, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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11
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Lancefield CS, Wienk HLJ, Boelens R, Weckhuysen BM, Bruijnincx PCA. Identification of a diagnostic structural motif reveals a new reaction intermediate and condensation pathway in kraft lignin formation. Chem Sci 2018; 9:6348-6360. [PMID: 30310563 PMCID: PMC6115679 DOI: 10.1039/c8sc02000k] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/02/2018] [Indexed: 01/25/2023] Open
Abstract
Kraft lignin, the main by-product of the pulping industry, is an abundant, yet highly underutilized renewable aromatic polymer. During kraft pulping, the lignin undergoes extensive structural modification, with many labile native bonds being replaced by new, more recalcitrant ones. Currently little is known about the nature of those bonds and linkages in kraft lignin, information that is essential for its efficient valorization to renewable fuels, materials or chemicals. Here, we provide detailed new insights into the structure of softwood kraft lignin, identifying and quantifying the major native as well as kraft pulping-derived units as a function of molecular weight. De novo synthetic kraft lignins, generated from (isotope labelled) dimeric and advanced polymeric models, provided key mechanistic understanding of kraft lignin formation, revealing different process dependent reaction pathways to be operating. The discovery of a novel kraft-derived lactone condensation product proved diagnostic for the identification of a previously unknown homovanillin based condensation pathway. The lactone marker is found in various different soft- and hardwood kraft lignins, suggesting the general pertinence of this new condensation mechanism for kraft pulping. These novel structural and mechanistic insights will aid the development of future biomass and lignin valorization technologies.
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Affiliation(s)
- Christopher S Lancefield
- Inorganic Chemistry and Catalysis , Debye Institute for Nanomaterials Science , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Hans L J Wienk
- NMR Spectroscopy , Bijvoet Center for Biomolecular Research , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy , Bijvoet Center for Biomolecular Research , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Bert M Weckhuysen
- Inorganic Chemistry and Catalysis , Debye Institute for Nanomaterials Science , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Pieter C A Bruijnincx
- Inorganic Chemistry and Catalysis , Debye Institute for Nanomaterials Science , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
- Organic Chemistry and Catalysis , Debye Institute for Nanomaterials Science , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands
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12
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Kaptein R, Boelens R, Luchinat C. Nicolaas Bloembergen: a pioneer in magnetic resonance and in maser and laser physics. J Biomol NMR 2017; 69:181-182. [PMID: 29134388 DOI: 10.1007/s10858-017-0143-4] [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] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Rob Kaptein
- Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Rolf Boelens
- Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Claudio Luchinat
- CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
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13
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Boelens R. Meet Our Editorial Board Member. Curr Protein Pept Sci 2017. [DOI: 10.2174/138920371806170418222519] [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: 11/22/2022]
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14
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Das D, Faridounnia M, Kovacic L, Kaptein R, Boelens R, Folkers GE. Single-stranded DNA Binding by the Helix-Hairpin-Helix Domain of XPF Protein Contributes to the Substrate Specificity of the ERCC1-XPF Protein Complex. J Biol Chem 2016; 292:2842-2853. [PMID: 28028171 DOI: 10.1074/jbc.m116.747857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 12/24/2016] [Indexed: 11/06/2022] Open
Abstract
The nucleotide excision repair protein complex ERCC1-XPF is required for incision of DNA upstream of DNA damage. Functional studies have provided insights into the binding of ERCC1-XPF to various DNA substrates. However, because no structure for the ERCC1-XPF-DNA complex has been determined, the mechanism of substrate recognition remains elusive. Here we biochemically characterize the substrate preferences of the helix-hairpin-helix (HhH) domains of XPF and ERCC-XPF and show that the binding to single-stranded DNA (ssDNA)/dsDNA junctions is dependent on joint binding to the DNA binding domain of ERCC1 and XPF. We reveal that the homodimeric XPF is able to bind various ssDNA sequences but with a clear preference for guanine-containing substrates. NMR titration experiments and in vitro DNA binding assays also show that, within the heterodimeric ERCC1-XPF complex, XPF specifically recognizes ssDNA. On the other hand, the HhH domain of ERCC1 preferentially binds dsDNA through the hairpin region. The two separate non-overlapping DNA binding domains in the ERCC1-XPF heterodimer jointly bind to an ssDNA/dsDNA substrate and, thereby, at least partially dictate the incision position during damage removal. Based on structural models, NMR titrations, DNA-binding studies, site-directed mutagenesis, charge distribution, and sequence conservation, we propose that the HhH domain of ERCC1 binds to dsDNA upstream of the damage, and XPF binds to the non-damaged strand within a repair bubble.
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Affiliation(s)
- Devashish Das
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Maryam Faridounnia
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Lidija Kovacic
- the Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Robert Kaptein
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Rolf Boelens
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Gert E Folkers
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
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15
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Oliveira LC, Souza DP, Oka GU, Lima FDS, Oliveira RJ, Favaro DC, Wienk H, Boelens R, Farah CS, Salinas RK. VirB7 and VirB9 Interactions Are Required for the Assembly and Antibacterial Activity of a Type IV Secretion System. Structure 2016; 24:1707-1718. [PMID: 27594685 DOI: 10.1016/j.str.2016.07.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/16/2022]
Abstract
The type IV secretion system (T4SS) from the phytopathogen Xanthomonas citri (Xac) is a bactericidal nanomachine. The T4SS core complex is a ring composed of multiple copies of VirB7-VirB9-VirB10 subunits. Xac-VirB7 contains a disordered N-terminal tail (VirB7NT) that recognizes VirB9, and a C-terminal domain (VirB7CT) involved in VirB7 self-association. Here, we show that VirB7NT forms a short β strand upon binding to VirB9 and stabilizes it. A tight interaction between them is essential for T4SS assembly and antibacterial activity. Abolishing VirB7 self-association or deletion of the VirB7 C-terminal domain impairs this antibacterial activity without disturbing T4SS assembly. These findings reveal protein interactions within the core complex that are critical for the stability and activity of a T4SS.
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Affiliation(s)
- Luciana Coutinho Oliveira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Diorge Paulo Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil.
| | - Gabriel Umaji Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Filipe da Silva Lima
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Ronaldo Junio Oliveira
- Departamento de Física, Instituto de Ciências Exatas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais 38064-200, Brazil
| | - Denize Cristina Favaro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584-CH, the Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584-CH, the Netherlands
| | - Chuck Shaker Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil.
| | - Roberto Kopke Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil.
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16
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Dongre R, Folkers GE, Gualerzi CO, Boelens R, Wienk H. A model for the interaction of the G3-subdomain of Geobacillus stearothermophilus IF2 with the 30S ribosomal subunit. Protein Sci 2016; 25:1722-33. [PMID: 27364543 DOI: 10.1002/pro.2977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 11/10/2022]
Abstract
Bacterial translation initiation factor IF2 complexed with GTP binds to the 30S ribosomal subunit, promotes ribosomal binding of fMet-tRNA, and favors the joining of the small and large ribosomal subunits yielding a 70S initiation complex ready to enter the translation elongation phase. Within the IF2 molecule subdomain G3, which is believed to play an important role in the IF2-30S interaction, is positioned between the GTP-binding G2 and the fMet-tRNA binding C-terminal subdomains. In this study the solution structure of subdomain G3 of Geobacillus stearothermophilus IF2 has been elucidated. G3 forms a core structure consisting of two β-sheets with each four anti-parallel strands, followed by a C-terminal α-helix. In line with its role as linker between G3 and subdomain C1, this helix has no well-defined orientation but is endowed with a dynamic nature. The structure of the G3 core is that of a typical OB-fold module, similar to that of the corresponding subdomain of Thermus thermophilus IF2, and to that of other known RNA-binding modules such as IF2-C2, IF1 and subdomains II of elongation factors EF-Tu and EF-G. Structural comparisons have resulted in a model that describes the interaction between IF2-G3 and the 30S ribosomal subunit.
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Affiliation(s)
- Ramachandra Dongre
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Gert E Folkers
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Claudio O Gualerzi
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, Italy
| | - Rolf Boelens
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Hans Wienk
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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17
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Tuppo L, Spadaccini R, Alessandri C, Wienk H, Boelens R, Giangrieco I, Tamburrini M, Mari A, Picone D, Ciardiello MA. Structure, stability, and IgE binding of the peach allergen Peamaclein (Pru p 7). Biopolymers 2016; 102:416-25. [PMID: 25130872 DOI: 10.1002/bip.22530] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 06/06/2014] [Accepted: 07/22/2014] [Indexed: 12/20/2022]
Abstract
Knowledge of the structural properties of allergenic proteins is a necessary prerequisite to better understand the molecular bases of their action, and also to design targeted structural/functional modifications. Peamaclein is a recently identified 7 kDa peach allergen that has been associated with severe allergic reactions in sensitive subjects. This protein represents the first component of a new allergen family, which has no 3D structure available yet. Here, we report the first experimental data on the 3D-structure of Peamaclein. Almost 75% of the backbone resonances, including two helical stretches in the N-terminal region, and four out of six cysteine pairs have been assigned by 2D-NMR using a natural protein sample. Simulated gastrointestinal digestion experiments have highlighted that Peamaclein is even more resistant to digestion than the peach major allergen Pru p 3. Only the heat-denatured protein becomes sensitive to intestinal proteases. Similar to Pru p 3, Peamaclein keeps its native 3D-structure up to 90°C, but it becomes unfolded at temperatures of 100-120°C. Heat denaturation affects the immunological properties of both peach allergens, which lose at least partially their IgE-binding epitopes. In conclusion, the data collected in this study provide a first set of information on the molecular properties of Peamaclein. Future studies could lead to the possible use of the denatured form of this protein as a vaccine, and of the inclusion of cooked peach in the diet of subjects allergic to Peamaclein.
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Affiliation(s)
- Lisa Tuppo
- Institute of Biosciences and BioResources, CNR, Via Pietro Castellino 111, Naples, I-80131, Italy
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18
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Zhang R, Loers G, Schachner M, Boelens R, Wienk H, Siebert S, Eckert T, Kraan S, Rojas-Macias MA, Lütteke T, Galuska SP, Scheidig A, Petridis AK, Liang S, Billeter M, Schauer R, Steinmeyer J, Schröder JM, Siebert HC. Molecular Basis of the Receptor Interactions of Polysialic Acid (polySia), polySia Mimetics, and Sulfated Polysaccharides. ChemMedChem 2016; 11:990-1002. [PMID: 27136597 DOI: 10.1002/cmdc.201500609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 03/01/2016] [Indexed: 02/05/2023]
Abstract
Polysialic acid (polySia) and polySia glycomimetic molecules support nerve cell regeneration, differentiation, and neuronal plasticity. With a combination of biophysical and biochemical methods, as well as data mining and molecular modeling techniques, it is possible to correlate specific ligand-receptor interactions with biochemical processes and in vivo studies that focus on the potential therapeutic impact of polySia, polySia glycomimetics, and sulfated polysaccharides in neuronal diseases. With this strategy, the receptor interactions of polySia and polySia mimetics can be understood on a submolecular level. As the HNK-1 glycan also enhances neuronal functions, we tested whether similar sulfated oligo- and polysaccharides from seaweed could be suitable, in addition to polySia, for finding potential new routes into patient care focusing on an improved cure for various neuronal diseases. The knowledge obtained here on the structural interplay between polySia or sulfated polysaccharides and their receptors can be exploited to develop new drugs and application routes for the treatment of neurological diseases and dysfunctions.
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Affiliation(s)
- Ruiyan Zhang
- RI-B-NT: Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148, Kiel, Germany
- Zoological Institute, Department of Structural Biology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Gabriele Loers
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, University of Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - Melitta Schachner
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, University of Hamburg, Falkenried 94, 20251, Hamburg, Germany
- Center for Neuroscience, Shantou University Medical College, 22 Xin Ling Road, Shantou, Guangdong, 515041, China
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hans Wienk
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Simone Siebert
- RI-B-NT: Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148, Kiel, Germany
| | - Thomas Eckert
- Institute of Veterinary Physiology and Biochemistry, Fachbereich Veterinärmedizin, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals, Justus-Liebig-Universität Gießen, Frankfurter Str. 106, 35392, Gießen, Germany
| | - Stefan Kraan
- Ocean Harvest Technology Ltd., N17 Business Park, Milltown, County Galway, Ireland
| | - Miguel A Rojas-Macias
- Institute of Veterinary Physiology and Biochemistry, Fachbereich Veterinärmedizin, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Fachbereich Veterinärmedizin, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
| | - Sebastian P Galuska
- Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-Universität Gießen, Friedrichstr. 24, 35392, Gießen, Germany
| | - Axel Scheidig
- Zoological Institute, Department of Structural Biology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Athanasios K Petridis
- Neurosurgery Clinic, University Düsseldorf, Moorenstraße 5, 40255, Düsseldorf, Germany
| | - Songping Liang
- College of Life Sciences, Hunan Normal University, 410081, Changsha, China
| | - Martin Billeter
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 100, 40530, Gothenburg, Sweden
| | - Roland Schauer
- Institute of Biochemistry, Kiel University, Olshausenstr. 40, 24098, Kiel, Germany
| | - Jürgen Steinmeyer
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University Hospital Giessen and Marburg GmbH, Paul-Meimberg-Str. 3, 35392, Gießen, Germany
| | - Jens-Michael Schröder
- Department of Dermatology, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Hans-Christian Siebert
- RI-B-NT: Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148, Kiel, Germany.
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Vavrinská A, Zelinka J, Šebera J, Sychrovský V, Fiala R, Boelens R, Sklenář V, Trantírek L. Erratum to: Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. J Biomol NMR 2016; 65:49. [PMID: 27215413 PMCID: PMC4969947 DOI: 10.1007/s10858-016-0034-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- Andrea Vavrinská
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jiří Zelinka
- Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 542/2, 166 10, Praha 6, Czech Republic
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 542/2, 166 10, Praha 6, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Vladimír Sklenář
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
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20
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Nooren IM, Folkers GE, Kaptein R, Sauer RT, Boelens R. Structure and dynamics of the tetrameric mnt repressor and a model for its DNA complex. J Biomol Struct Dyn 2016; 17 Suppl 1:113-22. [PMID: 22607414 DOI: 10.1080/07391102.2000.10506611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract The tetrameric Mnt repressor of bacteriophage P22 consists of two dimeric DNA-binding domains and a tetramerization domain. The NOE and chemical shift data demonstrate that the structures of the domains in the wild-type repressor protein are similar to those of the separate domains, the three-dimensional structures of which have been determined previously. (15)N relaxation measurements show that the linker that connects the anti-parallel four-helix bundle with the two β-sheet DNA-binding dimers is highly flexible. No evidence was found for interactions between the distinct modules. The (15)N relaxation properties of the two domains differ substantially, confirming their structural independence. A model in which one two-stranded coiled coil of the four-helix bundle is attached to one N-terminal dimer is most consistent with the biochemical data and (15)N relaxation data. For the Mnt-DNA complex this geometry fits with a model in which the two β-sheet DNA-binding domains are bound at two successive major grooves of the Mnt operator and the tetramerization domain is packed between these two DNA-bound dimers. In such a model the two-fold symmetry axis of the four-helix bundle coincides with that of the operator sequence and the two bound dimers. Bending of the Mnt operator of approximately 30° upon binding of the tetramer, as measured by gel-shift assays, is in agreement with this model of the Mnt-DNA complex.
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Affiliation(s)
- I M Nooren
- a Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research , Utrecht University , Padualaan 8 , 3584 , CH Utrecht , The Netherlands
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21
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Vavrinská A, Zelinka J, Šebera J, Sychrovský V, Fiala R, Boelens R, Sklenář V, Trantírek L. Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. J Biomol NMR 2016; 64:53-62. [PMID: 26685997 PMCID: PMC4742510 DOI: 10.1007/s10858-015-0005-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/06/2015] [Indexed: 06/05/2023]
Abstract
Heteronuclear and homonuclear direct (D) and indirect (J) spin-spin interactions are important sources of structural information about nucleic acids (NAs). The Hamiltonians for the D and J interactions have the same functional form; thus, the experimentally measured apparent spin-spin coupling constant corresponds to a sum of J and D. In biomolecular NMR studies, it is commonly presumed that the dipolar contributions to Js are effectively canceled due to random molecular tumbling. However, in strong magnetic fields, such as those employed for NMR analysis, the tumbling of NA fragments is anisotropic because the inherent magnetic susceptibility of NAs causes an interaction with the external magnetic field. This motional anisotropy is responsible for non-zero D contributions to Js. Here, we calculated the field-induced D contributions to 33 structurally relevant scalar coupling constants as a function of magnetic field strength, temperature and NA fragment size. We identified two classes of Js, namely (1)JCH and (3)JHH couplings, whose quantitative interpretation is notably biased by NA motional anisotropy. For these couplings, the magnetic field-induced dipolar contributions were found to exceed the typical experimental error in J-coupling determinations by a factor of two or more and to produce considerable over- or under-estimations of the J coupling-related torsion angles, especially at magnetic field strengths >12 T and for NA fragments longer than 12 bp. We show that if the non-zero D contributions to J are not properly accounted for, they might cause structural artifacts/bias in NA studies that use solution NMR spectroscopy.
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Affiliation(s)
- Andrea Vavrinská
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jiří Zelinka
- Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 542/2, 166 10, Praha 6, Czech Republic
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 542/2, 166 10, Praha 6, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Vladimír Sklenář
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
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Nieto L, Tharun IM, Balk M, Wienk H, Boelens R, Ottmann C, Milroy LG, Brunsveld L. Estrogen Receptor Folding Modulates cSrc Kinase SH2 Interaction via a Helical Binding Mode. ACS Chem Biol 2015; 10:2624-32. [PMID: 26352092 DOI: 10.1021/acschembio.5b00568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The estrogen receptors (ERs) feature, next to their transcriptional role, important nongenomic signaling actions, with emerging clinical relevance. The Src Homology 2 (SH2) domain mediated interaction between cSrc kinase and ER plays a key role in this; however the molecular determinants of this interaction have not been elucidated. Here, we used phosphorylated ER peptide and semisynthetic protein constructs in a combined biochemical and structural study to, for the first time, provide a quantitative and structural characterization of the cSrc SH2-ER interaction. Fluorescence polarization experiments delineated the SH2 binding motif in the ER sequence. Chemical shift perturbation analysis by nuclear magnetic resonance (NMR) together with molecular dynamics (MD) simulations allowed us to put forward a 3D model of the ER-SH2 interaction. The structural basis of this protein-protein interaction has been compared with that of the high affinity SH2 binding sequence GpYEEI. The ER features a different binding mode from that of the "two-pronged plug two-hole socket" model in the so-called specificity determining region. This alternative binding mode is modulated via the folding of ER helix 12, a structural element directly C-terminal of the key phosphorylated tyrosine. The present findings provide novel molecular entries for understanding nongenomic ER signaling and targeting the corresponding disease states.
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Affiliation(s)
- Lidia Nieto
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Inga M. Tharun
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Mark Balk
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Hans Wienk
- Bijvoet
Center for Biomolecular Research, NMR Spectroscopy Utrecht University, 3584CH Utrecht, The Netherlands
| | - Rolf Boelens
- Bijvoet
Center for Biomolecular Research, NMR Spectroscopy Utrecht University, 3584CH Utrecht, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
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Furse S, Wienk H, Boelens R, de Kroon AIPM, Killian JA. E. coli MG1655 modulates its phospholipid composition through the cell cycle. FEBS Lett 2015; 589:2726-30. [PMID: 26272829 DOI: 10.1016/j.febslet.2015.07.043] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/07/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
Abstract
This paper describes a study of the phospholipid profile of Escherichia coli MG1655 cultures at the B and D periods of the cell cycle. The results indicate that the phosphatidyl glycerol fraction grows relatively rapidly and that the size of the cardiolipin (CL) fraction does not grow at all during cell elongation. This is consistent with observations that CL is located preferentially at the poles of E. coli. It also suggests that lipid production is controlled as a function of the cell cycle.
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Affiliation(s)
- Samuel Furse
- Membrane Biochemistry and Biophysics, Department of Chemistry, Universiteit Utrecht, Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Universiteit Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Universiteit Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Anton I P M de Kroon
- Membrane Biochemistry and Biophysics, Department of Chemistry, Universiteit Utrecht, Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Department of Chemistry, Universiteit Utrecht, Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands
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24
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Faridounnia M, Wienk H, Kovačič L, Folkers GE, Jaspers NGJ, Kaptein R, Hoeijmakers JHJ, Boelens R. The Cerebro-oculo-facio-skeletal Syndrome Point Mutation F231L in the ERCC1 DNA Repair Protein Causes Dissociation of the ERCC1-XPF Complex. J Biol Chem 2015; 290:20541-55. [PMID: 26085086 DOI: 10.1074/jbc.m114.635169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Indexed: 12/15/2022] Open
Abstract
The ERCC1-XPF heterodimer, a structure-specific DNA endonuclease, is best known for its function in the nucleotide excision repair (NER) pathway. The ERCC1 point mutation F231L, located at the hydrophobic interaction interface of ERCC1 (excision repair cross-complementation group 1) and XPF (xeroderma pigmentosum complementation group F), leads to severe NER pathway deficiencies. Here, we analyze biophysical properties and report the NMR structure of the complex of the C-terminal tandem helix-hairpin-helix domains of ERCC1-XPF that contains this mutation. The structures of wild type and the F231L mutant are very similar. The F231L mutation results in only a small disturbance of the ERCC1-XPF interface, where, in contrast to Phe(231), Leu(231) lacks interactions stabilizing the ERCC1-XPF complex. One of the two anchor points is severely distorted, and this results in a more dynamic complex, causing reduced stability and an increased dissociation rate of the mutant complex as compared with wild type. These data provide a biophysical explanation for the severe NER deficiencies caused by this mutation.
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Affiliation(s)
- Maryam Faridounnia
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hans Wienk
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Lidija Kovačič
- the Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia, and
| | - Gert E Folkers
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nicolaas G J Jaspers
- the Department of Genetics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Robert Kaptein
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jan H J Hoeijmakers
- the Department of Genetics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Rolf Boelens
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands,
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25
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Sinnige T, Weingarth M, Daniëls M, Boelens R, Bonvin AMJJ, Houben K, Baldus M. Conformational Plasticity of the POTRA 5 Domain in the Outer Membrane Protein Assembly Factor BamA. Structure 2015; 23:1317-24. [PMID: 26027731 DOI: 10.1016/j.str.2015.04.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/03/2015] [Accepted: 04/09/2015] [Indexed: 12/22/2022]
Abstract
BamA is the main component of the β-barrel assembly machinery (BAM) that folds and inserts outer membrane proteins in Gram-negative bacteria. Crystal structures have suggested that this process involves conformational changes in the transmembrane β-barrel of BamA that allow for lateral opening, as well as large overall rearrangements of its periplasmic POTRA domains. Here, we identify local dynamics of the BamA POTRA 5 domain by solution and solid-state nuclear magnetic resonance. The protein region undergoing conformational exchange is highly conserved and contains residues critical for interaction with BamD and correct β-barrel assembly in vivo. We show that mutations known to affect the latter processes influence the conformational equilibrium, suggesting that the plasticity of POTRA 5 is related to its interaction with BamD and possibly to substrate binding. Taken together, a view emerges in which local protein plasticity may be critically involved in the different stages of outer membrane protein folding and insertion.
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Affiliation(s)
- Tessa Sinnige
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Mark Daniëls
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Alexandre M J J Bonvin
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Klaartje Houben
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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26
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Sinnige T, Houben K, Pritisanac I, Renault M, Boelens R, Baldus M. Insight into the conformational stability of membrane-embedded BamA using a combined solution and solid-state NMR approach. J Biomol NMR 2015; 61:321-332. [PMID: 25567766 DOI: 10.1007/s10858-014-9891-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
The β-barrel assembly machinery (BAM) is involved in folding and insertion of outer membrane proteins in Gram-negative bacteria, a process that is still poorly understood. With its 790 residues, BamA presents a challenge to current NMR methods. We utilized a "divide and conquer" approach in which we first obtained resonance assignments for BamA's periplasmic POTRA domains 4 and 5 by solution NMR. Comparison of these assignments to solid-state NMR (ssNMR) data obtained on two BamA constructs including the transmembrane domain and one or two soluble POTRA domains suggested that the fold of POTRA domain 5 critically depends on the interface with POTRA 4. Using specific labeling schemes we furthermore obtained ssNMR resonance assignments for residues in the extracellular loop 6 that is known to be crucial for BamA-mediated substrate folding and insertion. Taken together, our data provide novel insights into the conformational stability of membrane-embedded, non-crystalline BamA.
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Affiliation(s)
- Tessa Sinnige
- NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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27
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Deckers R, Sprinkhuizen SM, Crielaard BJ, Ippel JH, Boelens R, Bakker CJG, Storm G, Lammers T, Bartels LW. Absolute MR thermometry using nanocarriers. Contrast Media Mol Imaging 2014; 9:283-90. [PMID: 24706612 DOI: 10.1002/cmmi.1572] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/16/2013] [Accepted: 09/04/2013] [Indexed: 11/06/2022]
Abstract
Accurate time-resolved temperature mapping is crucial for the safe use of hyperthermia-mediated drug delivery. We here propose a magnetic resonance imaging temperature mapping method in which drug delivery systems serve not only to improve tumor targeting, but also as an accurate and absolute nano-thermometer. This method is based on the temperature-dependent chemical shift difference between water protons and the protons in different groups of drug delivery systems. We show that the chemical shift of the protons in the ethylene oxide group in polyethylene glycol (PEG) is temperature-independent, whereas the proton resonance of water decreases with increasing temperature. The frequency difference between both resonances is linear and does not depend on pH and physiological salt conditions. In addition, we show that the proton resonance of the methyl group in N-(2-hydroxypropyl)-methacrylamide (HPMA) is temperature-independent. Therefore, PEGylated liposomes, polymeric mPEG-b-pHPMAm-Lac2 micelles and HPMA copolymers can provide a temperature-independent reference frequency for absolute magnetic resonance (MR) thermometry. Subsequently, we show that multigradient echo MR imaging with PEGylated liposomes in situ allows accurate, time-resolved temperature mapping. In conclusion, nanocarrier materials may serve as highly versatile tools for tumor-targeted drug delivery, acting not only as hyperthermia-responsive drug delivery systems, but also as accurate and precise nano-thermometers.
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Affiliation(s)
- Roel Deckers
- Image Sciences Institute, University Medical Center Utrecht, Utrecht, Netherlands
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28
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Ferguson FM, Dias DM, Rodrigues JPGLM, Wienk H, Boelens R, Bonvin AMJJ, Abell C, Ciulli A. Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking. Biochemistry 2014; 53:6706-16. [PMID: 25266743 DOI: 10.1021/bi500909d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Bromodomains are epigenetic reader domains, which have come under increasing scrutiny both from academic and pharmaceutical research groups. Effective targeting of the BAZ2B bromodomain by small molecule inhibitors has been recently reported, but no structural information is yet available on the interaction with its natural binding partner, acetylated histone H3K14ac. We have assigned the BAZ2B bromodomain and studied its interaction with H3K14ac acetylated peptides by NMR spectroscopy using both chemical shift perturbation (CSP) data and clean chemical exchange (CLEANEX-PM) NMR experiments. The latter was used to characterize water molecules known to play an important role in mediating interactions. Besides the anticipated Kac binding site, we consistently found the bromodomain BC loop as hotspots for the interaction. This information was used to create a data-driven model for the complex using HADDOCK. Our findings provide both structure and dynamics characterization that will be useful in the quest for potent and selective inhibitors to probe the function of the BAZ2B bromodomain.
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Affiliation(s)
- Fleur M Ferguson
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, U.K
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29
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Khan F, Daniëls MA, Folkers GE, Boelens R, Saqlan Naqvi SM, van Ingen H. Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function. Nucleic Acids Res 2014; 42:8705-18. [PMID: 24957607 PMCID: PMC4117745 DOI: 10.1093/nar/gku468] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 10/15/2013] [Revised: 04/30/2014] [Accepted: 05/12/2014] [Indexed: 12/30/2022] Open
Abstract
Glycine-rich RNA-binding proteins (GR-RBPs) are involved in cold shock response of plants as RNA chaperones facilitating mRNA transport, splicing and translation. GR-RBPs are bipartite proteins containing a RNA recognition motif (RRM) followed by a glycine-rich region. Here, we studied the structural basis of nucleic acid binding of full-length Nicotiana tabacum GR-RBP1. NMR studies of NtGR-RBP1 show that the glycine-rich domain, while intrinsically disordered, is responsible for mediating self-association by transient interactions with its RRM domain (NtRRM). Both NtGR-RBP1 and NtRRM bind specifically and with low micromolar affinity to RNA and single-stranded DNA. The solution structure of NtRRM shows that it is a canonical RRM domain. A HADDOCK model of the NtRRM-RNA complex, based on NMR chemical shift and NOE data, shows that nucleic acid binding results from a combination of stacking and electrostatic interactions with conserved RRM residues. Finally, DNA melting experiments demonstrate that NtGR-RBP1 is more efficient in melting CTG containing nucleic acids than isolated NtRRM. Together, our study supports the model that self-association of GR-RBPs by the glycine-rich region results in cooperative unfolding of non-native substrate structures, thereby enhancing its chaperone function.
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Affiliation(s)
- Fariha Khan
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Department of Biochemistry, PMAS Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan
| | - Mark A Daniëls
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - S M Saqlan Naqvi
- Department of Biochemistry, PMAS Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan
| | - Hugo van Ingen
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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30
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Scheepstra M, Nieto L, Hirsch AKH, Fuchs S, Leysen S, Lam CV, in het Panhuis L, van Boeckel CAA, Wienk H, Boelens R, Ottmann C, Milroy L, Brunsveld L. A Natural‐Product Switch for a Dynamic Protein Interface. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403773] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Marcel Scheepstra
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Lidia Nieto
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Anna K. H. Hirsch
- Stratingh Institue for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen (The Netherlands)
| | - Sascha Fuchs
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Seppe Leysen
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Chan Vinh Lam
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Leslie in het Panhuis
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Constant A. A. van Boeckel
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Hans Wienk
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584CH Utrecht (The Netherlands)
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584CH Utrecht (The Netherlands)
| | - Christian Ottmann
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Lech‐Gustav Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
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31
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Scheepstra M, Nieto L, Hirsch AKH, Fuchs S, Leysen S, Lam CV, in het Panhuis L, van Boeckel CAA, Wienk H, Boelens R, Ottmann C, Milroy LG, Brunsveld L. A natural-product switch for a dynamic protein interface. Angew Chem Int Ed Engl 2014; 53:6443-8. [PMID: 24821627 DOI: 10.1002/anie.201403773] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Indexed: 01/11/2023]
Abstract
Small ligands are a powerful way to control the function of protein complexes via dynamic binding interfaces. The classic example is found in gene transcription where small ligands regulate nuclear receptor binding to coactivator proteins via the dynamic activation function 2 (AF2) interface. Current ligands target the ligand-binding pocket side of the AF2. Few ligands are known, which selectively target the coactivator side of the AF2, or which can be selectively switched from one side of the interface to the other. We use NMR spectroscopy and modeling to identify a natural product, which targets the retinoid X receptor (RXR) at both sides of the AF2. We then use chemical synthesis, cellular screening and X-ray co-crystallography to split this dual activity, leading to a potent and molecularly efficient RXR agonist, and a first-of-kind inhibitor selective for the RXR/coactivator interaction. Our findings justify future exploration of natural products at dynamic protein interfaces.
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Affiliation(s)
- Marcel Scheepstra
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
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32
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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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33
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Weiss J, Wienk H, Boelens R, Laschewsky A. Block Copolymer Micelles with an Intermediate Star-/Flower-Like Structure Studied by1H NMR Relaxometry. MACROMOL CHEM PHYS 2014. [DOI: 10.1002/macp.201300753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jan Weiss
- Institute Charles Sadron; UPR22-CNRS; 23 Rue de Loess 67034 Strasbourg Cedex 2 France
| | - Hans Wienk
- NMR Spectroscopy; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584CH Utrecht The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584CH Utrecht The Netherlands
| | - André Laschewsky
- Department of Chemistry; University of Potsdam; Karl-Liebknecht-Strasse 24-25 14476 Potsdam-Golm Germany
- Fraunhofer Institute for Applied Polymer Research; Geiselbergstrasse 69 14476 Potsdam-Golm Germany
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34
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Karagöz GE, Duarte AMS, Akoury E, Ippel H, Biernat J, Morán Luengo T, Radli M, Didenko T, Nordhues BA, Veprintsev DB, Dickey CA, Mandelkow E, Zweckstetter M, Boelens R, Madl T, Rüdiger SGD. Hsp90-Tau complex reveals molecular basis for specificity in chaperone action. Cell 2014; 156:963-74. [PMID: 24581495 PMCID: PMC4263503 DOI: 10.1016/j.cell.2014.01.037] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/11/2013] [Accepted: 01/15/2014] [Indexed: 12/11/2022]
Abstract
Protein folding in the cell relies on the orchestrated action of conserved families of molecular chaperones, the Hsp70 and Hsp90 systems. Hsp70 acts early and Hsp90 late in the folding path, yet the molecular basis of this timing is enigmatic, mainly because the substrate specificity of Hsp90 is poorly understood. Here, we obtained a structural model of Hsp90 in complex with its natural disease-associated substrate, the intrinsically disordered Tau protein. Hsp90 binds to a broad region in Tau that includes the aggregation-prone repeats. Complementarily, a 106-Å-long substrate-binding interface in Hsp90 enables many low-affinity contacts. This allows recognition of scattered hydrophobic residues in late folding intermediates that remain after early burial of the Hsp70 sites. Our model resolves the paradox of how Hsp90 specifically selects for late folding intermediates but also for some intrinsically disordered proteins-through the eyes of Hsp90 they look the same.
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Affiliation(s)
- G Elif Karagöz
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Afonso M S Duarte
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Elias Akoury
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Hans Ippel
- Biomolecular NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; CARIM School for Cardiovascular Diseases, Biochemistry Group, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Jacek Biernat
- DZNE, German Center for Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Tania Morán Luengo
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Martina Radli
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Tatiana Didenko
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bryce A Nordhues
- Department of Pharmaceutical Sciences and Department of Molecular Medicine, University of South Florida Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL 33613, USA
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland and Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Chad A Dickey
- Department of Pharmaceutical Sciences and Department of Molecular Medicine, University of South Florida Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL 33613, USA
| | - Eckhard Mandelkow
- DZNE, German Center for Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany; CAESAR Research Center, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Markus Zweckstetter
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany; Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center, 37073 Göttingen, Germany
| | - Rolf Boelens
- Biomolecular NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Tobias Madl
- Biomolecular NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Institute of Structural Biology, Helmholtz Zentrum München Neuherberg and Biomolecular NMR-Spectroscopy, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany; Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria.
| | - Stefan G D Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Popovic M, Wienk H, Coglievina M, Boelens R, Pongor S, Pintar A. The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA. Proteins 2014; 82:537-45. [DOI: 10.1002/prot.24507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/19/2013] [Accepted: 01/06/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Matija Popovic
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
| | - Hans Wienk
- Bijvoet Center for Biomolecular Research, Utrecht University; 3584 CH Utrecht the Netherlands
| | - Maristella Coglievina
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University; 3584 CH Utrecht the Netherlands
| | - Sándor Pongor
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
| | - Alessandro Pintar
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
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36
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De Vlieg J, Boelens R, Scheek RM, Kaptein R, van Gunsteren WF. Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data: ALacRepressor Headpiece Structure Based on Information on J-coupling and from Presence and Absence of NOE's. Isr J Chem 2013. [DOI: 10.1002/ijch.198600027] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [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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37
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Stob S, Scheek RM, Boelens R, Dukstra K, Kaptein R. Applications of Two-Dimensional1H NMR Methods to Photo-Chemically Induced Dynamic Nuclear Polarisation Spectroscopy. Isr J Chem 2013. [DOI: 10.1002/ijch.198800043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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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38
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Augustyniak W, Wienk H, Boelens R, Reetz MT. ¹H, ¹³C and ¹⁵N resonance assignments of wild-type Bacillus subtilis Lipase A and its mutant evolved towards thermostability. Biomol NMR Assign 2013; 7:249-252. [PMID: 22996591 DOI: 10.1007/s12104-012-9420-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/05/2012] [Indexed: 06/01/2023]
Abstract
Previously, we evolved Lipase A from Bacillus subtilis towards increased thermostability. The resulting mutant retains significant catalytic activity upon heating above 60 °C (and up to 100 °C) and cooling down, whereas wild-type lipase precipitates irreversibly and does not show significant activity in these conditions. Kinetic thermostability of proteins has not been characterized well on the molecular structure level so far, therefore our aim is to study it using NMR spectroscopy. Here, nearly complete (1)H, (13)C and (15)N resonance assignments are reported for wild-type and mutant Lipase A. Chemical shifts were used to predict secondary structure elements of both Lipase A variants.
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Affiliation(s)
- Wojciech Augustyniak
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
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39
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Wienk H, Slootweg JC, Speerstra S, Kaptein R, Boelens R, Folkers GE. The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition. Nucleic Acids Res 2013; 41:6739-49. [PMID: 23661679 PMCID: PMC3711432 DOI: 10.1093/nar/gkt354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
To maintain the integrity of the genome, multiple DNA repair systems exist to repair damaged DNA. Recognition of altered DNA, including bulky adducts, pyrimidine dimers and interstrand crosslinks (ICL), partially depends on proteins containing helix-hairpin-helix (HhH) domains. To understand how ICL is specifically recognized by the Fanconi anemia proteins FANCM and FAAP24, we determined the structure of the HhH domain of FAAP24. Although it resembles other HhH domains, the FAAP24 domain contains a canonical hairpin motif followed by distorted motif. The HhH domain can bind various DNA substrates; using nuclear magnetic resonance titration experiments, we demonstrate that the canonical HhH motif is required for double-stranded DNA (dsDNA) binding, whereas the unstructured N-terminus can interact with single-stranded DNA. Both DNA binding surfaces are used for binding to ICL-like single/double-strand junction-containing DNA substrates. A structural model for FAAP24 bound to dsDNA has been made based on homology with the translesion polymerase iota. Site-directed mutagenesis, sequence conservation and charge distribution support the dsDNA-binding model. Analogous to other HhH domain-containing proteins, we suggest that multiple FAAP24 regions together contribute to binding to single/double-strand junction, which could contribute to specificity in ICL DNA recognition.
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Affiliation(s)
- Hans Wienk
- Bijvoet Center For Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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40
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van Nuland R, van Schaik FM, Simonis M, van Heesch S, Cuppen E, Boelens R, Timmers HM, van Ingen H. Nucleosomal DNA binding drives the recognition of H3K36-methylated nucleosomes by the PSIP1-PWWP domain. Epigenetics Chromatin 2013; 6:12. [PMID: 23656834 PMCID: PMC3663649 DOI: 10.1186/1756-8935-6-12] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 04/16/2013] [Indexed: 12/31/2022] Open
Abstract
Background Recognition of histone modifications by specialized protein domains is a key step in the regulation of DNA-mediated processes like gene transcription. The structural basis of these interactions is usually studied using histone peptide models, neglecting the nucleosomal context. Here, we provide the structural and thermodynamic basis for the recognition of H3K36-methylated (H3K36me) nucleosomes by the PSIP1-PWWP domain, based on extensive mutational analysis, advanced nuclear magnetic resonance (NMR), and computational approaches. Results The PSIP1-PWWP domain binds H3K36me3 peptide and DNA with low affinity, through distinct, adjacent binding surfaces. PWWP binding to H3K36me nucleosomes is enhanced approximately 10,000-fold compared to a methylated peptide. Based on mutational analyses and NMR data, we derive a structure of the complex showing that the PWWP domain is bound to H3K36me nucleosomes through simultaneous interactions with both methylated histone tail and nucleosomal DNA. Conclusion Concerted binding to the methylated histone tail and nucleosomal DNA underlies the high- affinity, specific recognition of H3K36me nucleosomes by the PSIP1-PWWP domain. We propose that this bipartite binding mechanism is a distinctive and general property in the recognition of histone modifications close to the nucleosome core.
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Affiliation(s)
- Rick van Nuland
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University Utrecht, Padualaan 8, Utrecht, CH, 3854, The Netherlands.
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41
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Koharudin LMI, Boelens R, Kaptein R, Gronenborn AM. A NMR guided approach for CsrA-RNA crystallization. J Biomol NMR 2013; 56:31-39. [PMID: 23359257 DOI: 10.1007/s10858-013-9712-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/21/2013] [Indexed: 06/01/2023]
Abstract
Structure determination of protein-nucleic acid complexes remains a challenging task. Here we present a simple method for generating crystals of a CsrA-nucleic acid complex, guided entirely by results from nuclear magnetic resonances spectroscopy (NMR) spectroscopy. Using a construct that lacks thirteen non-essential C-terminal residues, efficient binding to DNA could be demonstrated. One CsrA dimer interacts with two DNA oligonucleotides, similar to previous findings with RNA. Furthermore, the NMR study of the CsrA-DNA complex was the basis for successfully homing in on conditions that were suitable for obtaining crystals of the CsrA-DNA complex. Our results may be useful for those cases where RNA in protein-nucleic acid complexes may be replaced by DNA.
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Affiliation(s)
- Leonardus M I Koharudin
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, BST3/Rm1050, Pittsburgh, PA 15260, USA
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Loth K, Gnida M, Romanuka J, Kaptein R, Boelens R. Sliding and target location of DNA-binding proteins: an NMR view of the lac repressor system. J Biomol NMR 2013; 56:41-49. [PMID: 23568265 DOI: 10.1007/s10858-013-9723-0] [Citation(s) in RCA: 7] [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] [Received: 12/23/2012] [Accepted: 03/15/2013] [Indexed: 06/02/2023]
Abstract
In non-specific lac headpiece-DNA complexes selective NMR line broadening is observed that strongly depends on length and composition of the DNA fragments. This broadening involves amide protons found in the non-specific lac-DNA structure to be interacting with the DNA phosphate backbone, and can be ascribed to DNA sliding of the protein along the DNA. This NMR exchange broadening has been used to estimate the 1D diffusion constant for sliding along non-specific DNA. The observed 1D diffusion constant of 4×10(-12) cm(2)/s is two orders of magnitude smaller than derived from previous kinetic experiments, but falls in the range of values determined more recently using single molecule methods. This strongly supports the notion that sliding could play at most a minor role in the association kinetics of binding of lac repressor to lac operator and that other processes such as hopping and intersegment transfer contribute to facilitate the DNA recognition process.
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Affiliation(s)
- Karine Loth
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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43
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Petrel C, Hocking HG, Reynaud M, Upert G, Favreau P, Biass D, Paolini-Bertrand M, Peigneur S, Tytgat J, Gilles N, Hartley O, Boelens R, Stocklin R, Servent D. Identification, structural and pharmacological characterization of τ-CnVA, a conopeptide that selectively interacts with somatostatin sst3 receptor. Biochem Pharmacol 2013; 85:1663-71. [PMID: 23567999 DOI: 10.1016/j.bcp.2013.03.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 03/14/2013] [Accepted: 03/14/2013] [Indexed: 11/24/2022]
Abstract
Conopeptides are a diverse array of small linear and reticulated peptides that interact with high potency and selectivity with a large diversity of receptors and ion channels. They are used by cone snails for prey capture or defense. Recent advances in venom gland transcriptomic and venom peptidomic/proteomic technologies combined with bioactivity screening approaches lead to the identification of new toxins with original pharmacological profiles. Here, from transcriptomic/proteomic analyses of the Conus consors cone snail, we identified a new conopeptide called τ-CnVA, which displays the typical cysteine framework V of the T1-conotoxin superfamily. This peptide was chemically synthesized and its three-dimensional structure was solved by NMR analysis and compared to that of TxVA belonging to the same family, revealing very few common structural features apart a common orientation of the intercysteine loop. Because of the lack of a clear biological function associated with the T-conotoxin family, τ-CnVA was screened against more than fifty different ion channels and receptors, highlighting its capacity to interact selectively with the somatostatine sst3 receptor. Pharmacological and functional studies show that τ-CnVA displays a micromolar (Ki of 1.5μM) antagonist property for the sst3 receptor, being currently the only known toxin to interact with this GPCR subfamily.
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Affiliation(s)
- C Petrel
- CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, Laboratoire de Toxinologie Moléculaire et Biotechnologies, Gif-sur-Yvette, France
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van der Kolk JH, Boelens R, Halkes SB, Wijnberg ID, de Sain-van der Velden MG, Ippel JH. Some notes on fatal acquired multiple acyl-CoA dehydrogenase deficiency (MADD) in a two-year-old warmblood stallion and European tar spot (Rhytisma acerinum). Vet Q 2013; 33:47-51. [DOI: 10.1080/01652176.2012.758904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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45
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Putker M, Madl T, Vos HR, de Ruiter H, Visscher M, van den Berg MCW, Kaplan M, Korswagen HC, Boelens R, Vermeulen M, Burgering BMT, Dansen TB. Redox-dependent control of FOXO/DAF-16 by transportin-1. Mol Cell 2013; 49:730-42. [PMID: 23333309 DOI: 10.1016/j.molcel.2012.12.014] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 10/07/2012] [Accepted: 12/14/2012] [Indexed: 11/19/2022]
Abstract
Forkhead box O (FOXO; DAF-16 in worms) transcription factors, which are of vital importance in cell-cycle control, stress resistance, tumor suppression, and organismal lifespan, are largely regulated through nucleo-cytoplasmic shuttling. Insulin signaling keeps FOXO/DAF-16 cytoplasmic, and hence transcriptionally inactive. Conversely, as in loss of insulin signaling, reactive oxygen species (ROS) can activate FOXO/DAF-16 through nuclear accumulation. How ROS regulate the nuclear translocation of FOXO/DAF-16 is largely unknown. Cysteine oxidation can stabilize protein-protein interactions through the formation of disulfide-bridges when cells encounter ROS. Using a proteome-wide screen that identifies ROS-induced mixed disulfide-dependent complexes, we discovered several interaction partners of FOXO4, one of which is the nuclear import receptor transportin-1. We show that disulfide formation with transportin-1 is required for nuclear localization and the activation of FOXO4/DAF-16 induced by ROS, but not by the loss of insulin signaling. This molecular mechanism for nuclear shuttling is conserved in C. elegans and directly connects redox signaling to the longevity protein FOXO/DAF-16.
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Affiliation(s)
- Marrit Putker
- Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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Hocking HG, Gerwig GJ, Dutertre S, Violette A, Favreau P, Stöcklin R, Kamerling JP, Boelens R. Structure of the O-glycosylated conopeptide CcTx from Conus consors venom. Chemistry 2012; 19:870-9. [PMID: 23281027 DOI: 10.1002/chem.201202713] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Indexed: 01/30/2023]
Abstract
The glycopeptide CcTx, isolated from the venom of the piscivorous cone snail Conus consors, belongs to the κA-family of conopeptides. These toxins elicit excitotoxic responses in the prey by acting on voltage-gated sodium channels. The structure of CcTx, a first in the κA-family, has been determined by high-resolution NMR spectroscopy together with the analysis of its O-glycan at Ser7. A new type of glycopeptide O-glycan core structure, here registered as core type 9, containing two terminal L-galactose units {α-L-Galp-(1→4)-α-D-GlcpNAc-(1→6)-[α-L-Galp-(1→2)-β-D-Galp-(1→3)-]α-D-GalpNAc-(1→O)}, is highlighted. A sequence comparison to other putative members of the κA-family suggests that O-linked glycosylation might be more common than previously thought. This observation alone underlines the requirement for more careful and in-depth investigations into this type of post-translational modification in conotoxins.
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Affiliation(s)
- Henry G Hocking
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S. In support of the BMRB. Nat Struct Mol Biol 2012; 19:854-60. [PMID: 22955930 DOI: 10.1038/nsmb.2371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- John L Markley
- University of Wisconsin-Madison, Madison, Wisconsin, USA
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Favreau P, Benoit E, Hocking HG, Carlier L, D' hoedt D, Leipold E, Markgraf R, Schlumberger S, Córdova MA, Gaertner H, Paolini-Bertrand M, Hartley O, Tytgat J, Heinemann SH, Bertrand D, Boelens R, Stöcklin R, Molgó J. A novel µ-conopeptide, CnIIIC, exerts potent and preferential inhibition of NaV1.2/1.4 channels and blocks neuronal nicotinic acetylcholine receptors. Br J Pharmacol 2012; 166:1654-68. [PMID: 22229737 DOI: 10.1111/j.1476-5381.2012.01837.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND AND PURPOSE The µ-conopeptide family is defined by its ability to block voltage-gated sodium channels (VGSCs), a property that can be used for the development of myorelaxants and analgesics. We characterized the pharmacology of a new µ-conopeptide (µ-CnIIIC) on a range of preparations and molecular targets to assess its potential as a myorelaxant. EXPERIMENTAL APPROACH µ-CnIIIC was sequenced, synthesized and characterized by its direct block of elicited twitch tension in mouse skeletal muscle and action potentials in mouse sciatic and pike olfactory nerves. µ-CnIIIC was also studied on HEK-293 cells expressing various rodent VGSCs and also on voltage-gated potassium channels and nicotinic acetylcholine receptors (nAChRs) to assess cross-interactions. Nuclear magnetic resonance (NMR) experiments were carried out for structural data. KEY RESULTS Synthetic µ-CnIIIC decreased twitch tension in mouse hemidiaphragms (IC(50) = 150 nM), and displayed a higher blocking effect in mouse extensor digitorum longus muscles (IC = 46 nM), compared with µ-SIIIA, µ-SmIIIA and µ-PIIIA. µ-CnIIIC blocked Na(V)1.4 (IC(50) = 1.3 nM) and Na(V)1.2 channels in a long-lasting manner. Cardiac Na(V)1.5 and DRG-specific Na(V)1.8 channels were not blocked at 1 µM. µ-CnIIIC also blocked the α3β2 nAChR subtype (IC(50) = 450 nM) and, to a lesser extent, on the α7 and α4β2 subtypes. Structure determination of µ-CnIIIC revealed some similarities to α-conotoxins acting on nAChRs. CONCLUSION AND IMPLICATIONS µ-CnIIIC potently blocked VGSCs in skeletal muscle and nerve, and hence is applicable to myorelaxation. Its atypical pharmacological profile suggests some common structural features between VGSCs and nAChR channels.
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Hospes M, Ippel JH, Boelens R, Hellingwerf KJ, Hendriks J. Binding of Hydrogen-Citrate to Photoactive Yellow Protein Is Affected by the Structural Changes Related to Signaling State Formation. J Phys Chem B 2012; 116:13172-82. [DOI: 10.1021/jp306891s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marijke Hospes
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences and Netherlands Institute for Systems Biology, Amsterdam, The Netherlands
| | - Johannes H. Ippel
- Bijvoet Center for Biomolecular
Research, Science Faculty, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Rolf Boelens
- Bijvoet Center for Biomolecular
Research, Science Faculty, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Klaas J. Hellingwerf
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences and Netherlands Institute for Systems Biology, Amsterdam, The Netherlands
| | - Johnny Hendriks
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences and Netherlands Institute for Systems Biology, Amsterdam, The Netherlands
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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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