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Chakrabortty A, Mondal S, Bandyopadhyay S. Conformational Properties of Poly(A)-Binding Protein Complexed with Poly(A) RNA. J Phys Chem B 2024; 128:6449-6462. [PMID: 38941243 DOI: 10.1021/acs.jpcb.4c00704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Microscopic understanding of protein-RNA interactions is important for different biological activities, such as RNA transport, translation, splicing, silencing, etc. Polyadenine (Poly(A)) binding proteins (PABPs) make up a class of regulatory proteins that play critical roles in protecting the poly(A) tails of cellular mRNAs from nuclease degradation. In this work, we performed molecular dynamics simulations to investigate the conformational modifications of human PABP protein and poly(A) RNA that occur during complexation. It is demonstrated that the intermediate linker domain of the protein transforms from a disordered coil-like structure to a helical form during the recognition process, leading to the formation of the complex. On the other hand, disordered collapsed coil-like RNA on complexation has been found to transform into a rigid extended conformation. Importantly, the binding free energy calculation showed that the thermodynamic stability of the complex is primarily guided by favorable hydrophobic interactions between the protein and the RNA.
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Affiliation(s)
- Arun Chakrabortty
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur - 721302, India
| | - Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur - 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur - 721302, India
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Aladin V, Sreemantula AK, Biedenbänder T, Marchanka A, Corzilius B. Specific Signal Enhancement on an RNA-Protein Interface by Dynamic Nuclear Polarization. Chemistry 2023; 29:e202203443. [PMID: 36533705 DOI: 10.1002/chem.202203443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
Sensitivity and specificity are both crucial for the efficient solid-state NMR structure determination of large biomolecules. We present an approach that features both advantages by site-specific enhancement of NMR spectroscopic signals from the protein-RNA binding site within a ribonucleoprotein (RNP) by dynamic nuclear polarization (DNP). This approach uses modern biochemical techniques for sparse isotope labeling and exploits the molecular dynamics of 13 C-labeled methyl groups exclusively present in the protein. These dynamics drive heteronuclear cross relaxation and thus allow specific hyperpolarization transfer across the biomolecular complex's interface. For the example of the L7Ae protein in complex with a 26mer guide RNA minimal construct from the box C/D complex in archaea, we demonstrate that a single methyl-nucleotide contact is responsible for most of the polarization transfer to the RNA, and that this specific transfer can be used to boost both NMR spectral sensitivity and specificity by DNP.
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Affiliation(s)
- Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Str. 27, 18059, Rostock, Germany
- Department Life, Light & Matter, University of Rostock, Albert-Einstein-Str. 25, 18059, Rostock, Germany
| | - Arun K Sreemantula
- Institute for Organic Chemistry and, Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Str. 27, 18059, Rostock, Germany
- Department Life, Light & Matter, University of Rostock, Albert-Einstein-Str. 25, 18059, Rostock, Germany
| | - Alexander Marchanka
- Institute for Organic Chemistry and, Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Str. 27, 18059, Rostock, Germany
- Department Life, Light & Matter, University of Rostock, Albert-Einstein-Str. 25, 18059, Rostock, Germany
- Leibniz Institute for Catalysis, Albert-Einstein-Str. 29, 18059, Rostock, Germany
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Aguion PI, Kirkpatrick J, Carlomagno T, Marchanka A. Identifizierung von RNA‐Basenpaaren und vollständige Zuordnung von Nukleobasen‐Resonanzen durch Protonen‐detektierte Festkörper‐NMR‐Spektroskopie bei MAS Geschwindigkeiten von 100 kHz. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Philipp Innig Aguion
- Institut für organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Deutschland
| | - John Kirkpatrick
- Institut für organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Deutschland
- NMR-basierte strukturelle Chemie Helmholtz-Zentrum für Infektionsforschung Inhoffenstrasse 7 38124 Braunschweig Deutschland
| | - Teresa Carlomagno
- Institut für organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Deutschland
- NMR-basierte strukturelle Chemie Helmholtz-Zentrum für Infektionsforschung Inhoffenstrasse 7 38124 Braunschweig Deutschland
| | - Alexander Marchanka
- Institut für organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Deutschland
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Carlomagno T, Aguion P, Kirkpatrick J, Marchanka A. Identification of RNA base pairs and complete assignment of nucleobase resonances by 1H-detected solid-state NMR spectroscopy at 100 kHz MAS. Angew Chem Int Ed Engl 2021; 60:23903-23910. [PMID: 34379871 PMCID: PMC8597087 DOI: 10.1002/anie.202107263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Indexed: 12/02/2022]
Abstract
Knowledge of RNA structure, either in isolation or in complex, is fundamental to understand the mechanism of cellular processes. Solid‐state NMR (ssNMR) is applicable to high molecular‐weight complexes and does not require crystallization; thus, it is well‐suited to study RNA as part of large multicomponent assemblies. Recently, we solved the first structures of both RNA and an RNA‐protein complex by ssNMR using conventional 13C‐ and 15N‐detection. This approach is limited by the severe overlap of the RNA peaks together with the low sensitivity of multidimensional experiments. Here, we overcome the limitations in sensitivity and resolution by using 1H‐detection at fast MAS rates. We develop experiments that allow the identification of complete nucleobase spin‐systems together with their site‐specific base pair pattern using sub‐milligram quantities of one uniformly labelled RNA sample. These experiments provide rapid access to RNA secondary structure by ssNMR in protein‐RNA complexes of any size.
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Affiliation(s)
- Teresa Carlomagno
- Leibniz Universität Hannover, BMWZ Institute of Organic Chemistry, Schneiderberg 38, 30167, Hannover, GERMANY
| | - Philipp Aguion
- Leibniz Universität Hannover: Leibniz Universitat Hannover, Institute of Organic Chemistry, Hannover, GERMANY
| | - John Kirkpatrick
- Leibniz Universität Hannover: Leibniz Universitat Hannover, Institute of Organic Chemistry, GERMANY
| | - Alexander Marchanka
- Leibniz Universität Hannover: Leibniz Universitat Hannover, Institute of Organic Chemistry, GERMANY
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Zehnder J, Cadalbert R, Terradot L, Ernst M, Böckmann A, Güntert P, Meier BH, Wiegand T. Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase. Chemistry 2021; 27:7745-7755. [PMID: 33822417 PMCID: PMC8252064 DOI: 10.1002/chem.202100462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg2+ cofactor with Mn2+ or Co2+ . Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF4 - and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn2+ and Co2+ in localizing the ATP cofactor in large oligomeric protein assemblies. 31 P PCSs induced in the Co2+ -containing sample are then used to localize the DNA phosphate groups on the Co2+ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.
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Affiliation(s)
- Johannes Zehnder
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Riccardo Cadalbert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Matthias Ernst
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Peter Güntert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
- Institute of Biophysical ChemistryCenter for Biomolecular Magnetic ResonanceGoethe University Frankfurt am Main60438Frankfurt am MainGermany
- Department of ChemistryTokyo Metropolitan UniversityHachiojiTokyo1920397Japan
| | - Beat H. Meier
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Thomas Wiegand
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
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