1
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Niemyska W, Mukherjee S, Gren BA, Niewieczerzal S, Bujnicki JM, Sulkowska JI. Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology. J Mol Biol 2024; 436:168455. [PMID: 38272438 DOI: 10.1016/j.jmb.2024.168455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Knots are very common in polymers, including DNA and protein molecules. Yet, no genuine knot has been identified in natural RNA molecules to date. Upon re-examining experimentally determined RNA 3D structures, we discovered a trefoil knot 31, the most basic non-trivial knot, in the RydC RNA. This knotted RNA is a member of a small family of short bacterial RNAs, whose secondary structure is characterized by an H-type pseudoknot. Molecular dynamics simulations suggest a folding pathway of the RydC RNA that starts with a native twisted loop. Based on sequence analyses and computational RNA 3D structure predictions, we postulate that this trefoil knot is a conserved feature of all RydC-related RNAs. The first discovery of a knot in a natural RNA molecule introduces a novel perspective on RNA 3D structure formation and on fundamental research on the relationship between function and spatial structure of biopolymers.
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Affiliation(s)
- Wanda Niemyska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland.
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland
| | - Bartosz A Gren
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Szymon Niewieczerzal
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland.
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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2
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Sriramoju MK, Ko KT, Hsu STD. Tying a true topological protein knot by cyclization. Biochem Biophys Res Commun 2024; 696:149470. [PMID: 38244314 DOI: 10.1016/j.bbrc.2024.149470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024]
Abstract
Knotted proteins are fascinating to biophysicists because of their robust ability to fold into intricately defined three-dimensional structures with complex and topologically knotted arrangements. Exploring the biophysical properties of the knotted proteins is of significant interest, as they could offer enhanced chemical, thermal, and mechanostabilities. A true mathematical knot requires a closed path; in contrast, knotted protein structures have open N- and C-termini. To address the question of how a truly knotted protein differs from the naturally occurring counterpart, we enzymatically cyclized a 31 knotted YibK protein from Haemophilus influenza (HiYibK) to investigate the impact of path closure on its structure-function relationship and folding stability. Through the use of a multitude of structural and biophysical tools, including X-ray crystallography, NMR spectroscopy, small angle X-ray scattering, differential scanning calorimetry, and isothermal calorimetry, we showed that the path closure minimally perturbs the native structure and ligand binding of HiYibK. Nevertheless, the cyclization did alter the folding stability and mechanism according to chemical and thermal unfolding analysis. These molecular insights contribute to our fundamental understanding of protein folding and knotting that could have implications in the protein design with higher stabilities.
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Affiliation(s)
| | - Kuang-Ting Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, 106319, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (SKCM(2)), Hiroshima University, Higashihiroshima, 739-8527, Japan.
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3
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Zayats V, Sikora M, Perlinska AP, Stasiulewicz A, Gren BA, Sulkowska JI. Conservation of knotted and slipknotted topology in transmembrane transporters. Biophys J 2023; 122:4528-4541. [PMID: 37919904 PMCID: PMC10719070 DOI: 10.1016/j.bpj.2023.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023] Open
Abstract
The existence of nontrivial topology is well accepted in globular proteins but not in membrane proteins. Our comprehensive topological analysis of the Protein Data Bank structures reveals 18 families of transmembrane proteins with nontrivial topology, showing that they constitute a significant number of membrane proteins. Moreover, we found that they comprise one of the largest groups of secondary active transporters. We classified them based on their knotted fingerprint into four groups: three slipknotted and one knotted. Unexpectedly, we found that the same protein can possess two distinct slipknot motifs that correspond to its outward- and inward-open conformational state. Based on the analysis of structures and knotted fingerprints, we show that slipknot topology is directly involved in the conformational transition and substrate transfer. Therefore, entanglement can be used to classify proteins and to find their structure-function relationship. Furthermore, based on the topological analysis of the transmembrane protein structures predicted by AlphaFold, we identified new potentially slipknotted protein families.
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Affiliation(s)
- Vasilina Zayats
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maciej Sikora
- Centre of New Technologies, University of Warsaw, Warsaw, Poland; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | | | - Adam Stasiulewicz
- Centre of New Technologies, University of Warsaw, Warsaw, Poland; Department of Drug Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland
| | - Bartosz A Gren
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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4
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Hsu STD. Folding and functions of knotted proteins. Curr Opin Struct Biol 2023; 83:102709. [PMID: 37778185 DOI: 10.1016/j.sbi.2023.102709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
Abstract
Topologically knotted proteins have entangled structural elements within their native structures that cannot be disentangled simply by pulling from the N- and C-termini. Systematic surveys have identified different types of knotted protein structures, constituting as much as 1% of the total entries within the Protein Data Bank. Many knotted proteins rely on their knotted structural elements to carry out evolutionarily conserved biological functions. Being knotted may also provide mechanical stability to withstand unfolding-coupled proteolysis. Reconfiguring a knotted protein topology by circular permutation or cyclization provides insights into the importance of being knotted in the context of folding and functions. With the explosion of predicted protein structures by artificial intelligence, we are now entering a new era of exploring the entangled protein universe.
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Affiliation(s)
- Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
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5
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Jedrzejewski M, Belza B, Lewandowska I, Sadlej M, Perlinska AP, Augustyniak R, Christian T, Hou YM, Kalek M, Sulkowska JI. Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study. Comput Struct Biotechnol J 2023; 21:3999-4008. [PMID: 37649713 PMCID: PMC10462857 DOI: 10.1016/j.csbj.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/01/2023] Open
Abstract
The Nep1 protein is essential for the formation of eukaryotic and archaeal small ribosomal subunits, and it catalyzes the site-directed SAM-dependent methylation of pseudouridine (Ψ) during pre-rRNA processing. It possesses a non-trivial topology, namely, a 31 knot in the active site. Here, we address the issue of seemingly unfeasible deprotonation of Ψ in Nep1 active site by a distant aspartate residue (D101 in S. cerevisiae), using a combination of bioinformatics, computational, and experimental methods. We identified a conserved hydroxyl-containing amino acid (S233 in S. cerevisiae, T198 in A. fulgidus) that may act as a proton-transfer mediator. Molecular dynamics simulations, based on the crystal structure of S. cerevisiae, and on a complex generated by molecular docking in A. fulgidus, confirmed that this amino acid can shuttle protons, however, a water molecule in the active site may also serve this role. Quantum-chemical calculations based on density functional theory and the cluster approach showed that the water-mediated pathway is the most favorable for catalysis. Experimental kinetic and mutational studies reinforce the requirement for the aspartate D101, but not S233. These findings provide insight into the catalytic mechanisms underlying proton transfer over extended distances and comprehensively elucidate the mode of action of Nep1.
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Affiliation(s)
- Mateusz Jedrzejewski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Barbara Belza
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Iwona Lewandowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Marta Sadlej
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Agata P. Perlinska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Rafal Augustyniak
- Department of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 4201 Henry Ave, Philadelphia, PA 19144, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 4201 Henry Ave, Philadelphia, PA 19144, USA
| | - Marcin Kalek
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna I. Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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6
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Capała K, Szymczak P. Stochastic model of translocation of knotted proteins. Phys Rev E 2022; 106:054406. [PMID: 36559434 DOI: 10.1103/physreve.106.054406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022]
Abstract
Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model of this process with a time-periodic potential that mimics the action of a molecular motor. We calculate the translocation time as a function of the period of the pulling force, discuss the asymptotic limits and biological relevance of the results.
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Affiliation(s)
- Karol Capała
- Personal Health Data Science Group, Sano - Centre for Computational Personalised Medicine, Czarnowiejska 36, 30-054 Kraków, Poland and Institute of Theoretical Physics, Department of Statistical Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
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7
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Strassler SE, Bowles IE, Dey D, Jackman JE, Conn GL. Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases. J Biol Chem 2022; 298:102393. [PMID: 35988649 PMCID: PMC9508554 DOI: 10.1016/j.jbc.2022.102393] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 10/25/2022] Open
Abstract
The SpoU-TrmD (SPOUT) methyltransferase superfamily was designated when structural similarity was identified between the transfer RNA-modifying enzymes TrmH (SpoU) and TrmD. SPOUT methyltransferases are found in all domains of life and predominantly modify transfer RNA or ribosomal RNA substrates, though one instance of an enzyme with a protein substrate has been reported. Modifications placed by SPOUT methyltransferases play diverse roles in regulating cellular processes such as ensuring translational fidelity, altering RNA stability, and conferring bacterial resistance to antibiotics. This large collection of S-adenosyl-L-methionine-dependent methyltransferases is defined by a unique α/β fold with a deep trefoil knot in their catalytic (SPOUT) domain. Herein, we describe current knowledge of SPOUT enzyme structure, domain architecture, and key elements of catalytic function, including S-adenosyl-L-methionine co-substrate binding, beginning with a new sequence alignment that divides the SPOUT methyltransferase superfamily into four major clades. Finally, a major focus of this review will be on our growing understanding of how these diverse enzymes accomplish the molecular feat of specific substrate recognition and modification, as highlighted by recent advances in our knowledge of protein-RNA complex structures and the discovery of the dependence of one SPOUT methyltransferase on metal ion binding for catalysis. Considering the broad biological roles of RNA modifications, developing a deeper understanding of the process of substrate recognition by the SPOUT enzymes will be critical for defining many facets of fundamental RNA biology with implications for human disease.
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Affiliation(s)
- Sarah E Strassler
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA
| | - Isobel E Bowles
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, Columbus, Ohio, USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, Columbus, Ohio, USA.
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA.
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8
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tRNA methylation resolves codon usage bias at the limit of cell viability. Cell Rep 2022; 41:111539. [PMID: 36288695 PMCID: PMC9643105 DOI: 10.1016/j.celrep.2022.111539] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/31/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
Codon usage of each genome is closely correlated with the abundance of tRNA isoacceptors. How codon usage bias is resolved by tRNA post-transcriptional modifications is largely unknown. Here we demonstrate that the N1-methylation of guanosine at position 37 (m1G37) on the 3′-side of the anticodon, while not directly responsible for reading of codons, is a neutralizer that resolves differential decoding of proline codons. A genome-wide suppressor screen of a non-viable Escherichia coli strain, lacking m1G37, identifies proS suppressor mutations, indicating a coupling of methylation with tRNA prolyl-aminoacylation that sets the limit of cell viability. Using these suppressors, where prolyl-aminoacylation is decoupled from tRNA methylation, we show that m1G37 neutralizes differential translation of proline codons by the major isoacceptor. Lack of m1G37 inactivates this neutralization and exposes the need for a minor isoacceptor for cell viability. This work has medical implications for bacterial species that exclusively use the major isoacceptor for survival. Masuda et al. show that loss of m1G37 from the 3′ side of the tRNA anticodon renders a modified wobble nucleotide of the anticodon insufficient to decode a set of rare codons, providing a functional underpinning for the “modification circuit” between position 37 and the wobble position of the tRNA anticodon.
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9
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Zhu H, Tian F, Sun L, Zhu Y, Qiu Q, Dai L. Computational Design of Extraordinarily Stable Peptide Structures through Side-Chain-Locked Knots. J Phys Chem Lett 2022; 13:7741-7748. [PMID: 35969173 DOI: 10.1021/acs.jpclett.2c02385] [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: 06/15/2023]
Abstract
Extraordinarily stable protein and peptide structures are critically demanded in many applications. Typical approaches to enhance protein and peptide stability are strengthening certain interactions. Here, we develop a very different approach: stabilizing peptide structures through side-chain-locked knots. More specifically, a peptide core consists of a knot, which is prevented from unknotting and unfolding by large side chains of amino acids at knot boundaries. These side chains impose free energy barriers for unknotting. The free energy barriers are quantified using all-atom and coarse-grained simulations. The barriers become infinitely high for large side chains and tight knot cores, resulting in stable peptide structures, which never unfold unless one chemical bond is broken. The extraordinary stability is essentially kinetic stability. Our new approach lifts the thermodynamic restriction in designing peptide structures, provides extra freedom in selecting sequence and structural motifs that are thermodynamically unstable, and should expand the functionality of peptides. This work also provides a bottom-up understanding of how knotting enhances protein stability.
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Affiliation(s)
- Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Yongjian Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Qiyuan Qiu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
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10
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Li F, Luo Y, Xi G, Fu J, Tu J. Single-Molecule Analysis of DNA structures using nanopore sensors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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Zhu Y, Zhu H, Tian F, Qiu Q, Dai L. Quantifying the effects of slit confinement on polymer knots using the tube model. Phys Rev E 2022; 105:024501. [PMID: 35291068 DOI: 10.1103/physreve.105.024501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Knots can spontaneously form in DNA, proteins, and other polymers and affect their properties. These knots often experience spatial confinement in biological systems and experiments. While confinement dramatically affects the knot behavior, the physical mechanisms underlying the confinement effects are not fully understood. In this work, we provide a simple physical picture of the polymer knots in slit confinement using the tube model. In the tube model, the polymer segments in the knot core are assumed to be confined in a virtual tube due to the topological restriction. We first perform Monte Carlo simulation of a flexible knotted chain confined in a slit. We find that with the decrease of the slit height from H=+∞ (the 3D case) to H=2a (the 2D case), the most probable knot size L_{knot}^{*} dramatically shrinks from (L_{knot}^{*})_{3D}≈140a to (L_{knot}^{*})_{2D}≈26a, where a is the monomer diameter of the flexible chain. Then we quantitatively explain the confinement-induced knot shrinking and knot deformation using the tube model. Our results for H=2a can be applied to a polymer knot on a surface, which resembles DNA knots measured by atomic force microscopy under the conditions that DNA molecules are weakly absorbed on the surface and reach equilibrium 2D conformations. This work demonstrates the effectiveness of the tube model in understanding polymer knots.
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Affiliation(s)
- Yongjian Zhu
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China and Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China and Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China and Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Qiyuan Qiu
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China and Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, 999077, China and Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
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12
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Wang J, Peng X. In silico method for identifying the key residues in a knotted protein: with MJ0366 as an example. Phys Chem Chem Phys 2022; 24:27495-27504. [DOI: 10.1039/d2cp03589h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A simple in silico method for predicting the key residues for knotting and unknotting a knotted protein is put forward, with the residues ranked by the relevance to knotting and unknotting in the annealing molecular dynamics simulations.
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Affiliation(s)
- Jianmei Wang
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
- Beijing Academy of Quantum Information Sciences, Beijing 100193, China
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13
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Clifton BE, Fariz MA, Uechi GI, Laurino P. Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation. Nucleic Acids Res 2021; 49:12467-12485. [PMID: 34761260 PMCID: PMC8643618 DOI: 10.1093/nar/gkab1067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
The tRNA modification m1G37, introduced by the tRNA methyltransferase TrmD, is thought to be essential for growth in bacteria because it suppresses translational frameshift errors at proline codons. However, because bacteria can tolerate high levels of mistranslation, it is unclear why loss of m1G37 is not tolerated. Here, we addressed this question through experimental evolution of trmD mutant strains of Escherichia coli. Surprisingly, trmD mutant strains were viable even if the m1G37 modification was completely abolished, and showed rapid recovery of growth rate, mainly via duplication or mutation of the proline-tRNA ligase gene proS. Growth assays and in vitro aminoacylation assays showed that G37-unmodified tRNAPro is aminoacylated less efficiently than m1G37-modified tRNAPro, and that growth of trmD mutant strains can be largely restored by single mutations in proS that restore aminoacylation of G37-unmodified tRNAPro. These results show that inefficient aminoacylation of tRNAPro is the main reason for growth defects observed in trmD mutant strains and that proS may act as a gatekeeper of translational accuracy, preventing the use of error-prone unmodified tRNAPro in translation. Our work shows the utility of experimental evolution for uncovering the hidden functions of essential genes and has implications for the development of antibiotics targeting TrmD.
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Affiliation(s)
- Ben E Clifton
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Muhammad A Fariz
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Gen-Ichiro Uechi
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
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14
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Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor. PLoS Comput Biol 2021; 17:e1009502. [PMID: 34648493 PMCID: PMC8562792 DOI: 10.1371/journal.pcbi.1009502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/02/2021] [Accepted: 09/28/2021] [Indexed: 11/20/2022] Open
Abstract
While the slipknot topology in proteins has been known for over a decade, its evolutionary origin is still a mystery. We have identified a previously overlooked slipknot motif in a family of two-domain membrane transporters. Moreover, we found that these proteins are homologous to several families of unknotted membrane proteins. This allows us to directly investigate the evolution of the slipknot motif. Based on our comprehensive analysis of 17 distantly related protein families, we have found that slipknotted and unknotted proteins share a common structural motif. Furthermore, this motif is conserved on the sequential level as well. Our results suggest that, regardless of topology, the proteins we studied evolved from a common unknotted ancestor single domain protein. Our phylogenetic analysis suggests the presence of at least seven parallel evolutionary scenarios that led to the current diversity of proteins in question. The tools we have developed in the process can now be used to investigate the evolution of other repeated-domain proteins. In proteins with the slipknot topology, the polypeptide chain forms a slipknot—a structure that is not necessarily manifest to a naked eye, but it can be detected using mathematical methods. Slipknots are conserved motifs often found at catalytic sites and are directly involved in molecular transport. Although the first proteins with slipknots were found in 2007, many questions remain unanswered, e.g. how these proteins appeared, or whether the slipknotted proteins evolved from unknotted ones or vice versa. Here we provide the first analysis of homologous slipknotted and unknotted transmembrane proteins in order to elucidate their evolutionary relationship. We show that two-domain slipknotted and unknotted membrane transporters share the same one-domain unknotted protein as an ancestor. The ancestor gene duplicated and underwent various diversification and fusion events during the evolution, which have led to the appearance of a large superfamily of secondary active transporters. The slipknot motif seems to have been created by chance after a fusion of two single domain genes. Therefore, we show here that the slipknotted transporter evolved from an unknotted one-domain protein and that there are at least seven different evolutionary scenarios that gave rise to this large superfamily of transporters.
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15
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Li R, Du T, Liu J, Aquino AJA, Zhang J. Theoretical Study of O-CH 3 Bond Dissociation Enthalpy in Anisole Systems. ACS OMEGA 2021; 6:21952-21959. [PMID: 34497890 PMCID: PMC8412933 DOI: 10.1021/acsomega.1c02310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Understanding ubiquitous methyl transfer reactions requires a systematic study of thermodynamical parameters that could reveal valuable information about the nature of the chemical bond and the feasibility of those processes. In the present study, the O-CH3 bond dissociation enthalpies (BDEs) of 67 compounds belonging to phenol/anisole systems were calculated employing the Gaussian-4 (G4) method. Those compounds contain different substituents including alkyl groups, electron-donating groups (EDGs), and electron-withdrawing groups (EWGs). The results show that the bigger branched alkyl groups and EDGs will destabilize the O-CH3 bond, while EWGs have the opposite effect. A combination of different effects including steric effects, hydrogen bonds, and substituents and their position can achieve around 20 kcal/mol difference compared to the basic phenyl frame. Also, the linear correlation between σp + and O-CH3 BDE can provide a reference for the O-CH3 BDE prediction. The present study represents a step forward to establish a comprehensive O-CH3 BDE database to understand the substituent effect and make its contribution to the rational design of inhibitors and drugs.
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Affiliation(s)
- Rui Li
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
| | - Tianshu Du
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
| | - Jingxing Liu
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
| | - Adelia J. A. Aquino
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
- Department
of Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
- Institute
for Soil Research, University of Natural
Resources and Life Sciences, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Jianyu Zhang
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
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16
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Masuda I, Hwang JY, Christian T, Maharjan S, Mohammad F, Gamper H, Buskirk AR, Hou YM. Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression. eLife 2021; 10:70619. [PMID: 34382933 PMCID: PMC8384417 DOI: 10.7554/elife.70619] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/09/2021] [Indexed: 01/20/2023] Open
Abstract
N1-methylation of G37 is required for a subset of tRNAs to maintain the translational reading-frame. While loss of m1G37 increases ribosomal +1 frameshifting, whether it incurs additional translational defects is unknown. Here, we address this question by applying ribosome profiling to gain a genome-wide view of the effects of m1G37 deficiency on protein synthesis. Using E coli as a model, we show that m1G37 deficiency induces ribosome stalling at codons that are normally translated by m1G37-containing tRNAs. Stalling occurs during decoding of affected codons at the ribosomal A site, indicating a distinct mechanism than that of +1 frameshifting, which occurs after the affected codons leave the A site. Enzyme- and cell-based assays show that m1G37 deficiency reduces tRNA aminoacylation and in some cases peptide-bond formation. We observe changes of gene expression in m1G37 deficiency similar to those in the stringent response that is typically induced by deficiency of amino acids. This work demonstrates a previously unrecognized function of m1G37 that emphasizes its role throughout the entire elongation cycle of protein synthesis, providing new insight into its essentiality for bacterial growth and survival.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Jae-Yeon Hwang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Sunita Maharjan
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Fuad Mohammad
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, United States
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17
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Sharma RK, Agrawal I, Dai L, Doyle P, Garaj S. DNA Knot Malleability in Single-Digit Nanopores. NANO LETTERS 2021; 21:3772-3779. [PMID: 33661654 DOI: 10.1021/acs.nanolett.0c05142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Knots in long DNA molecules are prevalent in biological systems and serve as a model system for investigating static and dynamic properties of biopolymers. We explore the dynamics of knots in double-stranded DNA in a new regime of nanometer-scale confinement, large forces, and short time scales, using solid-state nanopores. We show that DNA knots undergo isomorphic translocation through a nanopore, retaining their equilibrium morphology by swiftly compressing in a lateral direction to fit the constriction. We observe no evidence of knot tightening or jamming, even for single-digit nanopores. We explain the observations as the malleability of DNA, characterized by sharp buckling of the DNA in nanopores, driven by the transient disruption of base pairing. Our molecular dynamics simulations support the model. These results are relevant not only for the understanding of DNA packing and manipulation in living cells but also for the polymer physics of DNA and the development of nanopore-based sequencing technologies.
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Affiliation(s)
- Rajesh Kumar Sharma
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, Singapore 117546, Singapore
| | - Ishita Agrawal
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, P. R. China
| | - Patrick Doyle
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Slaven Garaj
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, Singapore 117546, Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
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18
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Zhu H, Tian F, Sun L, Wang S, Dai L. Revisiting the Non-monotonic Dependence of Polymer Knotting Probability on the Bending Stiffness. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P. R. China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P. R. China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P. R. China
| | - Simin Wang
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P. R. China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P. R. China
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19
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Abstract
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here, we investigate the relation between knotoids differing only by small perturbations of the direction of projection. Since such knotoids are connected by at most a single forbidden move, we characterize forbidden moves in terms of equivariant band attachment between strongly invertible knots and of strand passages between
θ
-curves. This allows for the determination of the optimal sample size needed to produce a well-approximated knotoid distribution. Based on that and on topological properties of the distribution, we probe the depth of knotted proteins with the trefoil as the predominant knot type without using subchain analysis.
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Affiliation(s)
- Agnese barbensi
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
| | - Dimos Goundaroulis
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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20
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Lu L, Zhu H, Yuyuan Lu, An L, Dai L. Application of the Tube Model to Explain the Unexpected Decrease in Polymer Bending Energy Induced by Knot Formation. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luwei Lu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P.R. China
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Chinese Academy of Sciences, Hefei 230026, P.R. China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P.R. China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Yuyuan Lu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Science and Technology of China, Chinese Academy of Sciences, Hefei 230026, P.R. China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, P.R. China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
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21
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Thomas SE, Whitehouse AJ, Brown K, Burbaud S, Belardinelli J, Sangen J, Lahiri R, Libardo M, Gupta P, Malhotra S, Boshoff HIM, Jackson M, Abell C, Coyne A, Blundell TL, Floto RA, Mendes V. Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification. Nucleic Acids Res 2020; 48:8099-8112. [PMID: 32602532 PMCID: PMC7641325 DOI: 10.1093/nar/gkaa539] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022] Open
Abstract
Translational frameshift errors are often deleterious to the synthesis of functional proteins and could therefore be promoted therapeutically to kill bacteria. TrmD (tRNA-(N(1)G37) methyltransferase) is an essential tRNA modification enzyme in bacteria that prevents +1 errors in the reading frame during protein translation and represents an attractive potential target for the development of new antibiotics. Here, we describe the application of a structure-guided fragment-based drug discovery approach to the design of a new class of inhibitors against TrmD in Mycobacterium abscessus. Fragment library screening, followed by structure-guided chemical elaboration of hits, led to the rapid development of drug-like molecules with potent in vitro TrmD inhibitory activity. Several of these compounds exhibit activity against planktonic M. abscessus and M. tuberculosis as well as against intracellular M. abscessus and M. leprae, indicating their potential as the basis for a novel class of broad-spectrum mycobacterial drugs.
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Affiliation(s)
- Sherine E Thomas
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Andrew J Whitehouse
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Karen Brown
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB2 0AY, UK
| | - Sophie Burbaud
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Juan M Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jasper Sangen
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ramanuj Lahiri
- National Hansen's Disease Program, Healthcare Systems Bureau, Health Resources and Services Administration, Department of Health and Human Services, Baton Rouge, LA, USA
| | - Mark Daben J Libardo
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Pooja Gupta
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Sony Malhotra
- Birkbeck College, University of London, Malet Street WC1E7HX, UK
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Rodrigo Andres Floto
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB2 0AY, UK
| | - Vítor Mendes
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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22
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Perlinska AP, Kalek M, Christian T, Hou YM, Sulkowska JI. Mg 2+-Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study. ACS Catal 2020; 10:8058-8068. [PMID: 32904895 PMCID: PMC7462349 DOI: 10.1021/acscatal.0c00059] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 06/18/2020] [Indexed: 11/27/2022]
Abstract
![]()
Mg2+ is required for the catalytic activity of TrmD,
a bacteria-specific methyltransferase that is made up of a protein
topological knot-fold, to synthesize methylated m1G37-tRNA
to support life. However, neither the location of Mg2+ in
the structure of TrmD nor its role in the catalytic mechanism is known.
Using molecular dynamics (MD) simulations, we identify a plausible
Mg2+ binding pocket within the active site of the enzyme,
wherein the ion is coordinated by two aspartates and a glutamate.
In this position, Mg2+ additionally interacts with the
carboxylate of a methyl donor cofactor S-adenosylmethionine (SAM).
The computational results are validated by experimental mutation studies,
which demonstrate the importance of the Mg2+-binding residues
for the catalytic activity. The presence of Mg2+ in the
binding pocket induces SAM to adopt a unique bent shape required for
the methyl transfer activity and causes a structural reorganization
of the active site. Quantum mechanical calculations show that the
methyl transfer is energetically feasible only when Mg2+ is bound in the position revealed by the MD simulations, demonstrating
that its function is to align the active site residues within the
topological knot-fold in a geometry optimal for catalysis. The obtained
insights provide the opportunity for developing a strategy of antibacterial
drug discovery based on targeting of Mg2+-binding to TrmD.
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Affiliation(s)
- Agata P. Perlinska
- Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw 02-097, Poland
| | - Marcin Kalek
- Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - Joanna I. Sulkowska
- Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw 02-097, Poland
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23
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A Supersymmetry and Quantum Cryptosystem with Path Integral Approach in Biology. Symmetry (Basel) 2020. [DOI: 10.3390/sym12081214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The source of cancerous mutations and the relationship to telomeres is explained in an alternative way. We define the smallest subunit in the genetic code as a loop braid group element. The loop braid group is suitable to be defined as a configuration space in the process of converting the information written in the DNA into the structure of a folded protein. This smallest subunit, or a flying ring in our definition, is a representation of 8-spinor field in the supermanifold of the genetic code. The image of spectral analysis from the tensor correlation of mutation genes as our biological system is produced. We apply the loop braid group for biology and authentication in quantum cryptography to understand the cell cocycle and division mechanism of telomerase aging. A quantum biological cryptosystem is used to detect cancer signatures in 36 genotypes of the bone ALX1 cancer gene. The loop braid group with the RSA algorithm is applied for the calculation of public and private keys as cancer signatures in genes. The key role of this approach is the use of the Chern–Simons current and then the fiber bundle representation of the genetic code that allows a quantization procedure.
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24
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Piejko M, Niewieczerzal S, Sulkowska JI. The Folding of Knotted Proteins: Distinguishing the Distinct Behavior of Shallow and Deep Knots. Isr J Chem 2020. [DOI: 10.1002/ijch.202000036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maciej Piejko
- Faculty of ChemistryUniversity of Warsaw Pasteura 1 Warsaw 02-093 Poland
- Centre of New TechnologiesUniversity of Warsaw Banacha 2c Warsaw 02-097 Poland
| | | | - Joanna I. Sulkowska
- Faculty of ChemistryUniversity of Warsaw Pasteura 1 Warsaw 02-093 Poland
- Centre of New TechnologiesUniversity of Warsaw Banacha 2c Warsaw 02-097 Poland
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25
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Hou YM, Masuda I, Foster LJ. tRNA methylation: An unexpected link to bacterial resistance and persistence to antibiotics and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1609. [PMID: 32533808 DOI: 10.1002/wrna.1609] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 02/02/2023]
Abstract
A major threat to public health is the resistance and persistence of Gram-negative bacteria to multiple drugs during antibiotic treatment. The resistance is due to the ability of these bacteria to block antibiotics from permeating into and accumulating inside the cell, while the persistence is due to the ability of these bacteria to enter into a nonreplicating state that shuts down major metabolic pathways but remains active in drug efflux. Resistance and persistence are permitted by the unique cell envelope structure of Gram-negative bacteria, which consists of both an outer and an inner membrane (OM and IM, respectively) that lay above and below the cell wall. Unexpectedly, recent work reveals that m1 G37 methylation of tRNA, at the N1 of guanosine at position 37 on the 3'-side of the tRNA anticodon, controls biosynthesis of both membranes and determines the integrity of cell envelope structure, thus providing a novel link to the development of bacterial resistance and persistence to antibiotics. The impact of m1 G37-tRNA methylation on Gram-negative bacteria can reach further, by determining the ability of these bacteria to exit from the persistence state when the antibiotic treatment is removed. These conceptual advances raise the possibility that successful targeting of m1 G37-tRNA methylation can provide new approaches for treating acute and chronic infections caused by Gram-negative bacteria. This article is categorized under: Translation > Translation Regulation RNA Processing > RNA Editing and Modification RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Leonard J Foster
- Department of Biochemistry & Molecular Biology, and Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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26
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Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites. PLoS Comput Biol 2020; 16:e1007904. [PMID: 32453784 PMCID: PMC7319350 DOI: 10.1371/journal.pcbi.1007904] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 06/26/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023] Open
Abstract
S-adenosylmethionine (SAM) is one of the most important enzyme substrates. It is vital for the function of various proteins, including large group of methyltransferases (MTs). Intriguingly, some bacterial and eukaryotic MTs, while catalysing the same reaction, possess significantly different topologies, with the former being a knotted one. Here, we conducted a comprehensive analysis of SAM conformational space and factors that affect its vastness. We investigated SAM in two forms: free in water (via NMR studies and explicit solvent simulations) and bound to proteins (based on all data available in the PDB and on all-atom molecular dynamics simulations in water). We identified structural descriptors—angles which show the major differences in SAM conformation between unknotted and knotted methyltransferases. Moreover, we report that this is caused mainly by a characteristic for knotted MTs compact binding site formed by the knot and the presence of adenine-binding loop. Additionally, we elucidate conformational restrictions imposed on SAM molecules by other protein groups in comparison to conformational space in water. The topology of a folded polypeptide chain has great impact on the resulting protein function and its interaction with ligands. Interestingly, topological constraints appear to affect binding of one of the most ubiquitous substrates in the cell, S-adenosylmethionine (SAM), to its target proteins. Here, we demonstrate how binding sites of specific proteins restrict SAM conformational freedom in comparison to its unbound state, with a special interest in proteins with non-trivial topology, including an exciting group of knotted methyltransferases. Using a vast array of computational methods combined with NMR experiments, we identify key structural features of knotted methyltransferases that impose unorthodox SAM conformations. We compare them with the characteristics of standard, unknotted SAM binding proteins. These results are significant for understanding differences between analogous, yet topologically different enzymes, as well as for future rational drug design.
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27
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Capraro DT, Burban DJ, Jennings PA. Unraveling Allostery in a Knotted Minimal Methyltransferase by NMR Spectroscopy. J Mol Biol 2020; 432:3018-3032. [PMID: 32135193 DOI: 10.1016/j.jmb.2020.02.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 11/17/2022]
Abstract
The methyltransferases that belong to the SpoU-TrmD family contain trefoil knots in their backbone fold. Recent structural dynamic and binding analyses of both free and bound homologs indicate that the knot within the polypeptide backbone plays a significant role in the biological activity of the molecule. The knot loops form the S-adenosyl-methionine (SAM)-binding pocket as well as participate in SAM binding and catalysis. Knots contain both at once a stable core as well as moving parts that modulate long-range motions. Here, we sought to understand allosteric effects modulated by the knotted topology. Uncovering the residues that contribute to these changes and the functional aspects of these protein motions are essential to understanding the interplay between the knot, activation of the methyltransferase, and the implications in RNA interactions. The question we sought to address is as follows: How does the knot, which constricts the backbone as well as forms the SAM-binding pocket with its three distinctive loops, affect the binding mechanism? Using a minimally tied trefoil protein as the framework for understanding the structure-function roles, we offer an unprecedented view of the conformational mechanics of the knot and its relationship to the activation of the ligand molecule. Focusing on the biophysical characterization of the knot region by NMR spectroscopy, we identify the SAM-binding region and observe changes in the dynamics of the loops that form the knot. Importantly, we also observe long-range allosteric changes in flanking helices consistent with winding/unwinding in helical propensity as the knot tightens to secure the SAM cofactor.
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Affiliation(s)
- Dominique T Capraro
- University of California, San Diego, 9500 Gilman Drive, Natural Science Building #3110, La Jolla, CA 92093, USA
| | - David J Burban
- University of California, San Diego, 9500 Gilman Drive, Natural Science Building #3110, La Jolla, CA 92093, USA
| | - Patricia A Jennings
- University of California, San Diego, 9500 Gilman Drive, Natural Science Building #3110, La Jolla, CA 92093, USA.
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28
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Vandans O, Yang K, Wu Z, Dai L. Identifying knot types of polymer conformations by machine learning. Phys Rev E 2020; 101:022502. [PMID: 32168694 DOI: 10.1103/physreve.101.022502] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/14/2020] [Indexed: 02/04/2023]
Abstract
We investigate the use of artificial neural networks (NNs) as an alternative tool to current analytical methods for recognizing knots in a given polymer conformation. The motivation is twofold. First, it is of interest to examine whether NNs are effective at learning the global and sequential properties that uniquely define a knot. Second, knot classification is an important and unsolved problem in mathematical and physical sciences, and NNs may provide insights into this problem. Motivated by these points, we generate millions of polymer conformations for five knot types: 0, 3_{1}, 4_{1}, 5_{1}, and 5_{2}, and we design various NN models for classification. Our best model achieves a five-class classification accuracy of above 99% on a polymer of 100 monomers. We find that the sequential modeling ability of recurrent NNs is crucial for this result, as it outperforms feed-forward NNs and successfully generalizes to differently sized conformations as well. We present our methods and suggest that deep learning may be used in specific applications of knot detection where some error is permissible. Hopefully, with further development, NNs can offer an alternative computational method for knot identification and facilitate knot research in mathematical and physical sciences.
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Affiliation(s)
- Olafs Vandans
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Kaiyuan Yang
- Department of Computer Science, School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Zhongtao Wu
- Department of Mathematics, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China.,Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
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29
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Sulkowska JI. On folding of entangled proteins: knots, lassos, links and θ-curves. Curr Opin Struct Biol 2020; 60:131-141. [PMID: 32062143 DOI: 10.1016/j.sbi.2020.01.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/02/2020] [Accepted: 01/12/2020] [Indexed: 12/15/2022]
Abstract
Around 6% of protein structures deposited in the PDB are entangled, forming knots, slipknots, lassos, links, and θ-curves. In each of these cases, the protein backbone weaves through itself in a complex way, and at some point passes through a closed loop, formed by other regions of the protein structure. Such a passing can be interpreted as crossing a topological barrier. How proteins overcome such barriers, and therefore different degrees of frustration, challenged scientists and has shed new light on the field of protein folding. In this review, we summarize the current knowledge about the free energy landscape of proteins with non-trivial topology. We describe identified mechanisms which lead proteins to self-tying. We discuss the influence of excluded volume, such as crowding and chaperones, on tying, based on available data. We briefly discuss the diversity of topological complexity of proteins and their evolution. We also list available tools to investigate non-trivial topology. Finally, we formulate intriguing and challenging questions at the boundary of biophysics, bioinformatics, biology, and mathematics, which arise from the discovery of entangled proteins.
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Affiliation(s)
- Joanna Ida Sulkowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland; Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
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30
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Abstract
The origin of protein backbone threading through a topological knot remains elusive. To understand the evolutionary origin of protein knots, in this issue of StructureKo et al. (2019) used circular permutation to untie a knotted protein. They showed that a domain-swapped dimer releases the knot and the associated high-energy state for substrate binding.
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31
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Sriramoju MK, Chen Y, Hsu STD. Protein knots provide mechano-resilience to an AAA+ protease-mediated proteolysis with profound ATP energy expenses. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140330. [PMID: 31756432 DOI: 10.1016/j.bbapap.2019.140330] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/23/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022]
Abstract
Knotted proteins are some of the most fascinating examples of how linear polypeptide chains can achieve intricate topological arrangements efficiently and spontaneously. The entanglements of polypeptide chains could potentially enhance their folding stabilities. We recently reported the unprecedented mechanostability of the Gordian (52) knotted family of human ubiquitin C-terminal hydrolases (UCHs) in the context of withstanding the mechanical unfolding of the bacterial AAA+ proteasome, ClpXP; a green fluorescence protein (GFP) was fused to the N-terminus of various UCHs as a reporter of the unfolding and degradation of these topologically knotted substrates, but it also limited the ability to examine the effect of untying the knotted topology via N-terminal truncation. In this study, we directly monitored the ClpXP-mediated degradation of UCH variants by electrophoresis and quantitative imaging analyses. We demonstrated that untying of the 52 knot in UCHL1 via N-terminal truncation (UCHL1Δ11) significantly reduces its mechanostability. We further quantified the ATP expenditures of degrading different UCH variants by ClpXP. The unknotted UCHL1Δ11 underwent accelerated ClpXP-dependent proteolysis, with a 30-fold reduction in ATP consumption compared to the knotted wild type. Unlike all other known ClpXP substrates, UCHL5, which is the most resilient substrate known to date, significantly slowed down the ATP turnover rate by ClpXP. Furthermore, UCHL5 required 1000-fold more ATP to be fully degraded by ClpXP compared to GFP. Our results underscored how the complex, knotted folding topology in UCHs may interfere with the mechano-unfolding processes of the AAA+ unfoldase, ClpX.
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Affiliation(s)
| | - Yen Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.
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Jaroensuk J, Wong YH, Zhong W, Liew CW, Maenpuen S, Sahili AE, Atichartpongkul S, Chionh YH, Nah Q, Thongdee N, McBee ME, Prestwich EG, DeMott MS, Chaiyen P, Mongkolsuk S, Dedon PC, Lescar J, Fuangthong M. Crystal structure and catalytic mechanism of the essential m 1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa. RNA (NEW YORK, N.Y.) 2019; 25:1481-1496. [PMID: 31399541 PMCID: PMC6795141 DOI: 10.1261/rna.066746.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 07/28/2019] [Indexed: 06/10/2023]
Abstract
The tRNA (m1G37) methyltransferase TrmD catalyzes m1G formation at position 37 in many tRNA isoacceptors and is essential in most bacteria, which positions it as a target for antibiotic development. In spite of its crucial role, little is known about TrmD in Pseudomonas aeruginosa (PaTrmD), an important human pathogen. Here we present detailed structural, substrate, and kinetic properties of PaTrmD. The mass spectrometric analysis confirmed the G36G37-containing tRNAs Leu(GAG), Leu(CAG), Leu(UAG), Pro(GGG), Pro(UGG), Pro(CGG), and His(GUG) as PaTrmD substrates. Analysis of steady-state kinetics with S-adenosyl-l-methionine (SAM) and tRNALeu(GAG) showed that PaTrmD catalyzes the two-substrate reaction by way of a ternary complex, while isothermal titration calorimetry revealed that SAM and tRNALeu(GAG) bind to PaTrmD independently, each with a dissociation constant of 14 ± 3 µM. Inhibition by the SAM analog sinefungin was competitive with respect to SAM (Ki = 0.41 ± 0.07 µM) and uncompetitive for tRNA (Ki = 6.4 ± 0.8 µM). A set of crystal structures of the homodimeric PaTrmD protein bound to SAM and sinefungin provide the molecular basis for enzyme competitive inhibition and identify the location of the bound divalent ion. These results provide insights into PaTrmD as a potential target for the development of antibiotics.
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Affiliation(s)
- Juthamas Jaroensuk
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Wenhe Zhong
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Chong Wai Liew
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Abbas E Sahili
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | | | - Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Qianhui Nah
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Narumon Thongdee
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
- Department of Biotechnology, Faculty of Sciences, Mahidol University, Bangkok 10400, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok 10400, Thailand
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Mayuree Fuangthong
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok 10400, Thailand
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Kumar Sharma R, Agrawal I, Dai L, Doyle PS, Garaj S. Complex DNA knots detected with a nanopore sensor. Nat Commun 2019; 10:4473. [PMID: 31578328 PMCID: PMC6775256 DOI: 10.1038/s41467-019-12358-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/27/2019] [Indexed: 01/15/2023] Open
Abstract
Equilibrium knots are common in biological polymers-their prevalence, size distribution, structure, and dynamics have been extensively studied, with implications to fundamental biological processes and DNA sequencing technologies. Nanopore microscopy is a high-throughput single-molecule technique capable of detecting the shape of biopolymers, including DNA knots. Here we demonstrate nanopore sensors that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding. We show the occurrence of both tight and loose knots, reconciling previous contradictory results from different experimental techniques. We evidence the occurrence of two quantitatively different modes of knot translocation through the nanopores, involving very different tension forces. With large statistics, we explore the complex knots and, for the first time, reveal the existence of rare composite knots. We use parametrized complexity, in concert with simulations, to test the theoretical assumptions of the models, further asserting the relevance of nanopores in future investigation of knots.
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Affiliation(s)
- Rajesh Kumar Sharma
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
- Singapore-MIT Alliance for Research and Technology Centre, 1 CREATE Way, Singapore, 138602, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore
| | - Ishita Agrawal
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
| | - Liang Dai
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Patrick S Doyle
- Singapore-MIT Alliance for Research and Technology Centre, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
| | - Slaven Garaj
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore.
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore.
- Department of Physics, National University of Singapore, Singapore, Science Drive 3, Singapore, 117551, Singapore.
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Affiliation(s)
- Liang Dai
- Department of Physics, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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35
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Niewieczerzal S, Niemyska W, Sulkowska JI. Defining and detecting links in chromosomes. Sci Rep 2019; 9:11753. [PMID: 31409805 PMCID: PMC6692345 DOI: 10.1038/s41598-019-47999-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 07/03/2019] [Indexed: 11/09/2022] Open
Abstract
Sophisticated methods for mapping chromatin contacts enable to generate data of the genome structure that provide deep insights into the formation of chromatin interactions within cell nuclei. Due to the recent progress in this field, three-dimensional genomic structures of individual haploid mouse embryonic stem cells have been determined. Here, we analyze these data (8 cells) and determine comprehensive landscape of entanglements between interphase chromosomes. We find a significant number of stable links formed by chromosome pairs. Some links are even conserved between cells. Moreover, examples of stable multiple links, with at least three chromosomes engaged, are also identified. Types of links and their location along chromosomes are determined based on computations of HOMFLY-PT polynomials and Gauss Linking Numbers. Furthermore, stability of links is studied between different models, cells, and based on relaxation simulations of the genomic structure in a simplified structure-based representation. Identified links suggest that small fraction of chromosomes are entangled not only locally. How topoisomerases engineer such configurations remains an open question. Furthermore, presented methods can be used as a quantitative assessment - descriptor - to distinguish the quality of modeled data.
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Affiliation(s)
- Szymon Niewieczerzal
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Wanda Niemyska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.,Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, 02-097, Warsaw, Poland
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland. .,Departament of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
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36
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Ko KT, Hu IC, Huang KF, Lyu PC, Hsu STD. Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer. Structure 2019; 27:1224-1233.e4. [DOI: 10.1016/j.str.2019.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/01/2019] [Accepted: 04/05/2019] [Indexed: 11/28/2022]
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Masuda I, Takase R, Matsubara R, Paulines MJ, Gamper H, Limbach PA, Hou YM. Selective terminal methylation of a tRNA wobble base. Nucleic Acids Res 2019; 46:e37. [PMID: 29361055 PMCID: PMC5909439 DOI: 10.1093/nar/gky013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/09/2018] [Indexed: 12/14/2022] Open
Abstract
Active tRNAs are extensively post-transcriptionally modified, particularly at the wobble position 34 and the position 37 on the 3′-side of the anticodon. The 5-carboxy-methoxy modification of U34 (cmo5U34) is present in Gram-negative tRNAs for six amino acids (Ala, Ser, Pro, Thr, Leu and Val), four of which (Ala, Ser, Pro and Thr) have a terminal methyl group to form 5-methoxy-carbonyl-methoxy-uridine (mcmo5U34) for higher reading-frame accuracy. The molecular basis for the selective terminal methylation is not understood. Many cmo5U34-tRNAs are essential for growth and cannot be substituted for mutational analysis. We show here that, with a novel genetic approach, we have created and isolated mutants of Escherichia coli tRNAPro and tRNAVal for analysis of the selective terminal methylation. We show that substitution of G35 in the anticodon of tRNAPro inactivates the terminal methylation, whereas introduction of G35 to tRNAVal confers it, indicating that G35 is a major determinant for the selectivity. We also show that, in tRNAPro, the terminal methylation at U34 is dependent on the primary m1G methylation at position 37 but not vice versa, indicating a hierarchical ranking of modifications between positions 34 and 37. We suggest that this hierarchy provides a mechanism to ensure top performance of a tRNA inside of cells.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ryuichi Takase
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ryuma Matsubara
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Mellie June Paulines
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Perego C, Potestio R. Searching the Optimal Folding Routes of a Complex Lasso Protein. Biophys J 2019; 117:214-228. [PMID: 31235180 PMCID: PMC6700606 DOI: 10.1016/j.bpj.2019.05.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/29/2019] [Accepted: 05/30/2019] [Indexed: 10/27/2022] Open
Abstract
Understanding how polypeptides can efficiently and reproducibly attain a self-entangled conformation is a compelling biophysical challenge that might shed new light on our general knowledge of protein folding. Complex lassos, namely self-entangled protein structures characterized by a covalent loop sealed by a cysteine bridge, represent an ideal test system in the framework of entangled folding. Indeed, because cysteine bridges form in oxidizing conditions, they can be used as on/off switches of the structure topology to investigate the role played by the backbone entanglement in the process. In this work, we have used molecular dynamics to simulate the folding of a complex lasso glycoprotein, granulocyte-macrophage colony-stimulating factor, modeling both reducing and oxidizing conditions. Together with a well-established Gō-like description, we have employed the elastic folder model, a coarse-grained, minimalistic representation of the polypeptide chain driven by a structure-based angular potential. The purpose of this study is to assess the kinetically optimal pathways in relation to the formation of the native topology. To this end, we have implemented an evolutionary strategy that tunes the elastic folder model potentials to maximize the folding probability within the early stages of the dynamics. The resulting protein model is capable of folding with high success rate, avoiding the kinetic traps that hamper the efficient folding in the other tested models. Employing specifically designed topological descriptors, we could observe that the selected folding routes avoid the topological bottleneck by locking the cysteine bridge after the topology is formed. These results provide valuable insights on the selection of mechanisms in self-entangled protein folding while, at the same time, the proposed methodology can complement the usage of established minimalistic models and draw useful guidelines for more detailed simulations.
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Affiliation(s)
- Claudio Perego
- Polymer Theory Department, Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Raffaello Potestio
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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Masuda I, Matsubara R, Christian T, Rojas ER, Yadavalli SS, Zhang L, Goulian M, Foster LJ, Huang KC, Hou YM. tRNA Methylation Is a Global Determinant of Bacterial Multi-drug Resistance. Cell Syst 2019; 8:302-314.e8. [PMID: 30981730 DOI: 10.1016/j.cels.2019.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 12/19/2018] [Accepted: 03/15/2019] [Indexed: 10/27/2022]
Abstract
Gram-negative bacteria are intrinsically resistant to drugs because of their double-membrane envelope structure that acts as a permeability barrier and as an anchor for efflux pumps. Antibiotics are blocked and expelled from cells and cannot reach high-enough intracellular concentrations to exert a therapeutic effect. Efforts to target one membrane protein at a time have been ineffective. Here, we show that m1G37-tRNA methylation determines the synthesis of a multitude of membrane proteins via its control of translation at proline codons near the start of open reading frames. Decreases in m1G37 levels in Escherichia coli and Salmonella impair membrane structure and sensitize these bacteria to multiple classes of antibiotics, rendering them incapable of developing resistance or persistence. Codon engineering of membrane-associated genes reduces their translational dependence on m1G37 and confers resistance. These findings highlight the potential of tRNA methylation in codon-specific translation to control the development of multi-drug resistance in Gram-negative bacteria.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ryuma Matsubara
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Enrique R Rojas
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Srujana S Yadavalli
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
| | - Lisheng Zhang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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40
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Hou YM, Masuda I, Gamper H. Codon-Specific Translation by m 1G37 Methylation of tRNA. Front Genet 2019; 9:713. [PMID: 30687389 PMCID: PMC6335274 DOI: 10.3389/fgene.2018.00713] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 12/20/2018] [Indexed: 12/31/2022] Open
Abstract
Although the genetic code is degenerate, synonymous codons for the same amino acid are not translated equally. Codon-specific translation is important for controlling gene expression and determining the proteome of a cell. At the molecular level, codon-specific translation is regulated by post-transcriptional epigenetic modifications of tRNA primarily at the wobble position 34 and at position 37 on the 3'-side of the anticodon. Modifications at these positions determine the quality of codon-anticodon pairing and the speed of translation on the ribosome. Different modifications operate in distinct mechanisms of codon-specific translation, generating a diversity of regulation that is previously unanticipated. Here we summarize recent work that demonstrates codon-specific translation mediated by the m1G37 methylation of tRNA at CCC and CCU codons for proline, an amino acid that has unique features in translation.
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Affiliation(s)
- Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, United States
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41
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Dabrowski-Tumanski P, Rubach P, Goundaroulis D, Dorier J, Sułkowski P, Millett KC, Rawdon EJ, Stasiak A, Sulkowska JI. KnotProt 2.0: a database of proteins with knots and other entangled structures. Nucleic Acids Res 2019; 47:D367-D375. [PMID: 30508159 PMCID: PMC6323932 DOI: 10.1093/nar/gky1140] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/24/2018] [Accepted: 11/30/2018] [Indexed: 01/08/2023] Open
Abstract
The KnotProt 2.0 database (the updated version of the KnotProt database) collects information about proteins which form knots and other entangled structures. New features in KnotProt 2.0 include the characterization of both probabilistic and deterministic entanglements which can be formed by disulfide bonds and interactions via ions, a refined characterization of entanglement in terms of knotoids, the identification of the so-called cysteine knots, the possibility to analyze all or a non-redundant set of proteins, and various technical updates. The KnotProt 2.0 database classifies all entangled proteins, represents their complexity in the form of a knotting fingerprint, and presents many biological and geometrical statistics based on these results. Currently the database contains >2000 entangled structures, and it regularly self-updates based on proteins deposited in the Protein Data Bank (PDB).
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland
| | - Pawel Rubach
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland
- Warsaw School of Economics, Al. Niepodlegosci 162, Warsaw, Poland
| | - Dimos Goundaroulis
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Julien Dorier
- Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Piotr Sułkowski
- Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, Poland
- Walter Burke Institute for Theoretical Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kenneth C Millett
- Department of Mathematics, University of California, Santa Barbara, CA 93106, USA
| | - Eric J Rawdon
- Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Joanna I Sulkowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland
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42
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Krishnamohan A, Jackman JE. A Family Divided: Distinct Structural and Mechanistic Features of the SpoU-TrmD (SPOUT) Methyltransferase Superfamily. Biochemistry 2018; 58:336-345. [PMID: 30457841 DOI: 10.1021/acs.biochem.8b01047] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The SPOUT family of enzymes makes up the second largest of seven structurally distinct groups of methyltransferases and is named after two evolutionarily related RNA methyltransferases, SpoU and TrmD. A deep trefoil knotted domain in the tertiary structures of member enzymes defines the SPOUT family. For many years, formation of a homodimeric quaternary structure was thought to be a strict requirement for all SPOUT enzymes, critical for substrate binding and formation of the active site. However, recent structural characterization of two SPOUT members, Trm10 and Sfm1, revealed that they function as monomers without the requirement of this critical dimerization. This unusual monomeric form implies that these enzymes must exhibit a nontraditional substrate binding mode and active site architecture and may represent a new division in the SPOUT family with distinct properties removed from the dimeric enzymes. Here we discuss the mechanistic features of SPOUT enzymes with an emphasis on the monomeric members and implications of this "novel" monomeric structure on cofactor and substrate binding.
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Affiliation(s)
- Aiswarya Krishnamohan
- The Ohio State Biochemistry Program, Center for RNA Biology, and Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Jane E Jackman
- The Ohio State Biochemistry Program, Center for RNA Biology, and Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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Dabrowski-Tumanski P, Sulkowska JI. The APS-bracket – A topological tool to classify lasso proteins, RNAs and other tadpole-like structures. REACT FUNCT POLYM 2018. [DOI: 10.1016/j.reactfunctpolym.2018.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Jarmolinska AI, Perlinska AP, Runkel R, Trefz B, Ginn HM, Virnau P, Sulkowska JI. Proteins' Knotty Problems. J Mol Biol 2018; 431:244-257. [PMID: 30391297 DOI: 10.1016/j.jmb.2018.10.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022]
Abstract
Knots in proteins are increasingly being recognized as an important structural concept, and the folding of these peculiar structures still poses considerable challenges. From a functional point of view, most protein knots discovered so far are either enzymes or DNA-binding proteins. Our comprehensive topological analysis of the Protein Data Bank reveals several novel structures including knotted mitochondrial proteins and the most deeply embedded protein knot discovered so far. For the latter, we propose a novel folding pathway based on the idea that a loose knot forms at a terminus and slides to its native position. For the mitochondrial proteins, we discuss the folding problem from the perspective of transport and suggest that they fold inside the mitochondria. We also discuss the evolutionary origin of a novel class of knotted membrane proteins and argue that a novel knotted DNA-binding protein constitutes a new fold. Finally, we have also discovered a knot in an artificially designed protein structure.
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Affiliation(s)
- Aleksandra I Jarmolinska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Banacha 2c, 02-097 Warsaw, Poland
| | - Agata P Perlinska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Banacha 2c, 02-097 Warsaw, Poland
| | - Robert Runkel
- Department of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Benjamin Trefz
- Department of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany; Graduate School Material Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Helen M Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Virnau
- Department of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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Dabrowski-Tumanski P, Piejko M, Niewieczerzal S, Stasiak A, Sulkowska JI. Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting from the Ribosome Exit Channel. J Phys Chem B 2018; 122:11616-11625. [PMID: 30198720 DOI: 10.1021/acs.jpcb.8b07634] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The mechanism of folding of deeply knotted proteins into their native structure is still not understood. Current thinking about protein folding is dominated by the Anfinsen dogma, stating that the structure of the folded proteins is uniquely dictated by the amino acid sequence of a given protein and that the folding is driven uniquely by the energy gained from interactions between amino acids that contact each other in the native structure of the protein. The role of ribosomes in protein folding was only seen as permitting the folding to progress from the N-terminal part of nascent protein chains. We propose here that ribosomes can participate actively in the folding of knotted proteins by actively threading nascent chains emerging from the ribosome exit channels through loops formed by a synthesized earlier portion of the same protein. Our simulations of folding of deeply knotted protein Tp0624 positively verify the proposed ribosome-driven active threading mechanism leading to the formation of deeply knotted proteins.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 , Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Maciej Piejko
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 , Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Szymon Niewieczerzal
- Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Andrzej Stasiak
- Center for Integrative Genomics , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Joanna I Sulkowska
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 , Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
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Comparative folding analyses of unknotted versus trefoil-knotted ornithine transcarbamylases suggest stabilizing effects of protein knots. Biochem Biophys Res Commun 2018; 503:822-829. [DOI: 10.1016/j.bbrc.2018.06.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/16/2022]
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48
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Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore 117543
| | - Patrick S. Doyle
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore 117543
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
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49
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Sriramoju MK, Chen Y, Lee YTC, Hsu STD. Topologically knotted deubiquitinases exhibit unprecedented mechanostability to withstand the proteolysis by an AAA+ protease. Sci Rep 2018; 8:7076. [PMID: 29728659 PMCID: PMC5935755 DOI: 10.1038/s41598-018-25470-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/23/2018] [Indexed: 01/03/2023] Open
Abstract
More than one thousand knotted protein structures have been identified so far, but the functional roles of these knots remain elusive. It has been postulated that backbone entanglement may provide additional mechanostability. Here, we employed a bacterial proteasome, ClpXP, to mechanically unfold 52-knotted human ubiquitin C-terminal hydrolase (UCH) paralogs from their C-termini, followed by processive translocation into the proteolytic chamber for degradation. Our results revealed unprecedentedly slow kinetics of ClpXP-mediated proteolysis for the proteasome-associated UCHL5: ten thousand times slower than that of a green fluorescence protein (GFP), which has a comparable size to the UCH domain but much higher chemical and thermal stabilities. The ClpXP-dependent mechanostability positively correlates with the intrinsic unfolding rates of the substrates, spanning over several orders of magnitude for the UCHs. The broad range of mechanostability within the same protein family may be associated with the functional requirements for their differential malleabilities.
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Affiliation(s)
| | - Yen Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun-Tzai Cloud Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
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Jarmolinska AI, Kadlof M, Dabrowski-Tumanski P, Sulkowska JI. GapRepairer: a server to model a structural gap and validate it using topological analysis. Bioinformatics 2018; 34:3300-3307. [DOI: 10.1093/bioinformatics/bty334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 04/27/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Aleksandra I Jarmolinska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Warsaw, Poland
| | - Michal Kadlof
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Pawel Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
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