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Spangenberg J, Zu Siederdissen CH, Žarković M, Triebel S, Rose R, Christophersen CM, Paltzow L, Hegab MM, Wansorra A, Srivastava A, Krumbholz A, Marz M. Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533105. [PMID: 36993667 PMCID: PMC10055291 DOI: 10.1101/2023.03.17.533105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Oxford Nanopore Technologies (ONT) allows direct sequencing of ribonucleic acids (RNA) and, in addition, detection of possible RNA modifications due to deviations from the expected ONT signal. The software available so far for this purpose can only detect a small number of modifications. Alternatively, two samples can be compared for different RNA modifications. We present Magnipore, a novel tool to search for significant signal shifts between samples of Oxford Nanopore data from similar or related species. Magnipore classifies them into mutations and potential modifications. We use Magnipore to compare SARS-CoV-2 samples. Included were representatives of the early 2020s Pango lineages (n=6), samples from Pango lineages B.1.1.7 (n=2, Alpha), B.1.617.2 (n=1, Delta), and B.1.529 (n=7, Omicron). Magnipore utilizes position-wise Gaussian distribution models and a comprehensible significance threshold to find differential signals. In the case of Alpha and Delta, Magnipore identifies 55 detected mutations and 15 sites that hint at differential modifications. We predicted potential virus-variant and variant-group-specific differential modifications. Magnipore contributes to advancing RNA modification analysis in the context of viruses and virus variants.
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Affiliation(s)
- Jannes Spangenberg
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | | | - Milena Žarković
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - Sandra Triebel
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - Ruben Rose
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Brunswiker Straße 4, 24105 Kiel, Germany
| | | | - Lea Paltzow
- Labor Dr. Krause und Kollegen MVZ GmbH, Steenbeker Weg 23, 24106 Kiel, Germany
| | - Mohsen M Hegab
- Labor Dr. Krause und Kollegen MVZ GmbH, Steenbeker Weg 23, 24106 Kiel, Germany
| | - Anna Wansorra
- Labor Dr. Krause und Kollegen MVZ GmbH, Steenbeker Weg 23, 24106 Kiel, Germany
| | - Akash Srivastava
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Brunswiker Straße 4, 24105 Kiel, Germany
- Labor Dr. Krause und Kollegen MVZ GmbH, Steenbeker Weg 23, 24106 Kiel, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
- European Virus Bioinformatics Center 2, Leutragraben 1, 07743 Jena, Germany
- FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany
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Varikoti RA, Fonseka HYY, Kelly MS, Javidi A, Damre M, Mullen S, Nugent JL, Gonzales CM, Stan G, Dima RI. Exploring the Effect of Mechanical Anisotropy of Protein Structures in the Unfoldase Mechanism of AAA+ Molecular Machines. NANOMATERIALS 2022; 12:nano12111849. [PMID: 35683705 PMCID: PMC9182431 DOI: 10.3390/nano12111849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 02/06/2023]
Abstract
Essential cellular processes of microtubule disassembly and protein degradation, which span lengths from tens of μm to nm, are mediated by specialized molecular machines with similar hexameric structure and function. Our molecular simulations at atomistic and coarse-grained scales show that both the microtubule-severing protein spastin and the caseinolytic protease ClpY, accomplish spectacular unfolding of their diverse substrates, a microtubule lattice and dihydrofolate reductase (DHFR), by taking advantage of mechanical anisotropy in these proteins. Unfolding of wild-type DHFR requires disruption of mechanically strong β-sheet interfaces near each terminal, which yields branched pathways associated with unzipping along soft directions and shearing along strong directions. By contrast, unfolding of circular permutant DHFR variants involves single pathways due to softer mechanical interfaces near terminals, but translocation hindrance can arise from mechanical resistance of partially unfolded intermediates stabilized by β-sheets. For spastin, optimal severing action initiated by pulling on a tubulin subunit is achieved through specific orientation of the machine versus the substrate (microtubule lattice). Moreover, changes in the strength of the interactions between spastin and a microtubule filament, which can be driven by the tubulin code, lead to drastically different outcomes for the integrity of the hexameric structure of the machine.
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Affiliation(s)
- Rohith Anand Varikoti
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
| | - Hewafonsekage Yasan Y. Fonseka
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
| | - Maria S. Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
| | - Alex Javidi
- Data Sciences, Janssen Research and Development, Spring House, PA 19477, USA;
| | - Mangesh Damre
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
| | - Sarah Mullen
- Department of Chemistry, The College of Wooster, Wooster, OH 44691, USA;
| | - Jimmie L. Nugent
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
| | | | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
- Correspondence: (G.S.); (R.I.D.)
| | - Ruxandra I. Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (R.A.V.); (H.Y.Y.F.); (M.S.K.); (M.D.); (J.L.N.IV)
- Correspondence: (G.S.); (R.I.D.)
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Orlandini E, Micheletti C. Topological and physical links in soft matter systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:013002. [PMID: 34547745 DOI: 10.1088/1361-648x/ac28bf] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Linking, or multicomponent topological entanglement, is ubiquitous in soft matter systems, from mixtures of polymers and DNA filaments packedin vivoto interlocked line defects in liquid crystals and intertwined synthetic molecules. Yet, it is only relatively recently that theoretical and experimental advancements have made it possible to probe such entanglements and elucidate their impact on the physical properties of the systems. Here, we review the state-of-the-art of this rapidly expanding subject and organize it as follows. First, we present the main concepts and notions, from topological linking to physical linking and then consider the salient manifestations of molecular linking, from synthetic to biological ones. We next cover the main physical models addressing mutual entanglements in mixtures of polymers, both linear and circular. Finally, we consider liquid crystals, fluids and other non-filamentous systems where topological or physical entanglements are observed in defect or flux lines. We conclude with a perspective on open challenges.
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Affiliation(s)
- Enzo Orlandini
- Department of Physics and Astronomy, University of Padova and Sezione INFN, Via Marzolo 8, Padova, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, Trieste, Italy
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Fonseka HYY, Javidi A, Oliveira LFL, Micheletti C, Stan G. Unfolding and Translocation of Knotted Proteins by Clp Biological Nanomachines: Synergistic Contribution of Primary Sequence and Topology Revealed by Molecular Dynamics Simulations. J Phys Chem B 2021; 125:7335-7350. [PMID: 34110163 DOI: 10.1021/acs.jpcb.1c00898] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We use Langevin dynamics simulations to model, at an atomistic resolution, how various natively knotted proteins are unfolded in repeated allosteric translocating cycles of the ClpY ATPase. We consider proteins representative of different topologies, from the simplest knot (trefoil 31), to the three-twist 52 knot, to the most complex stevedore, 61, knot. We harness the atomistic detail of the simulations to address aspects that have so far remained largely unexplored, such as sequence-dependent effects on the ruggedness of the landscape traversed during knot sliding. Our simulations reveal the combined effect on translocation of the knotted protein structure, i.e., backbone topology and geometry, and primary sequence, i.e., side chain size and interactions, and show that the latter can dominate translocation hindrance. In addition, we observe that due to the interplay between the knotted topology and intramolecular contacts the transmission of tension along the polypeptide chain occurs very differently from that of homopolymers. Finally, by considering native and non-native interactions, we examine how the disruption or formation of such contacts can affect the translocation processivity and concomitantly create multiple unfolding pathways with very different activation barriers.
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Affiliation(s)
| | - Alex Javidi
- Data Sciences, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Luiz F L Oliveira
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Cristian Micheletti
- Molecular and Statistical Biophysics, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
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