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Morse M, Sefcikova J, McCauley MJ, Rouzina IF, Beuning PJ, Williams MC. Structure and function of SARS-CoV-2 nucleocapsid protein measured using optical tweezers, confocal fluorescence, and AFM. Biophys J 2023; 122:71a. [PMID: 36784974 PMCID: PMC9912768 DOI: 10.1016/j.bpj.2022.11.590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Michael Morse
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Jana Sefcikova
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | | | - Ioulia F. Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Penny J. Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
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2
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Morse M, Sefcikova J, Rouzina I, Beuning PJ, Williams M. Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates. Nucleic Acids Res 2022; 51:290-303. [PMID: 36533523 PMCID: PMC9841419 DOI: 10.1093/nar/gkac1179] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein performs several functions including binding, compacting, and packaging the ∼30 kb viral genome into the viral particle. N protein consists of two ordered domains, with the N terminal domain (NTD) primarily associated with RNA binding and the C terminal domain (CTD) primarily associated with dimerization/oligomerization, and three intrinsically disordered regions, an N-arm, a C-tail, and a linker that connects the NTD and CTD. We utilize an optical tweezers system to isolate a long single-stranded nucleic acid substrate to measure directly the binding and packaging function of N protein at a single molecule level in real time. We find that N protein binds the nucleic acid substrate with high affinity before oligomerizing and forming a highly compact structure. By comparing the activities of truncated protein variants missing the NTD, CTD, and/or linker, we attribute specific steps in this process to the structural domains of N protein, with the NTD driving initial binding to the substrate and ensuring high localized protein density that triggers interprotein interactions mediated by the CTD, which forms a compact and stable protein-nucleic acid complex suitable for packaging into the virion.
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Affiliation(s)
- Michael Morse
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Jana Sefcikova
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Mark C Williams
- To whom correspondence should be addressed. Tel: +1 617 373 5705;
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3
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Kankanamage RNT, Sefcikova J. Advancements of Xenobiotic Toxicity Screening for the Advancement of Human Health. Chem Res Toxicol 2021; 34:1699-1700. [PMID: 34110791 DOI: 10.1021/acs.chemrestox.0c00535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
"The TOXI Chemical Exposures and Impact on Health" session at the 2020 Fall ACS meeting presented analytical and biological approaches, advancing our understanding of legacy and emerging chemical pollutants and their impact on human health.
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Affiliation(s)
- Rumasha N T Kankanamage
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Jana Sefcikova
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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4
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Iyengar SM, Barnsley K, Yen Vu H, Dilworth R, Sefcikova J, Beuning P, Jo Ondrechen M. Prediction and Analysis of Multiple Sites and Inhibitors of SARS-CoV-2 Proteins. Biophys J 2021. [PMCID: PMC7879927 DOI: 10.1016/j.bpj.2020.11.1391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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5
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Abstract
RNA molecules are flexible yet foldable. Proteins must cope with this structural duality when forming biologically active complexes with RNA. Recent studies of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-mediated RNA immunity illustrate some remarkable mechanisms with which proteins interact with RNA. Currently known structures of CRISPR-Cas6 endoribonucleases bound with RNA suggest a conserved protein recognition mechanism mediated by RNA stem-loops. However, a survey of CRISPR RNA reveals that many repeats either lack a productive stem-loop (Relaxed) or possess stable but inhibitory structures (Tight), which raises the question of how the enzyme processes structurally diverse RNA. In reviewing recent literature, we propose a bivalent trapping and an unwinding mechanism for CRISPR-Cas6 to interact with the Relaxed and the Tight repeat RNA, respectively. Both mechanisms aim to create an identical RNA conformation at the cleavage site for accurate processing.
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Affiliation(s)
- Jana Sefcikova
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA
| | - Mitchell Roth
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Ge Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
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6
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Han GW, Ko J, Farr CL, Deller MC, Xu Q, Chiu HJ, Miller MD, Sefcikova J, Somarowthu S, Beuning PJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, Ondrechen MJ. Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity. Proteins 2011; 79:2146-60. [PMID: 21538547 DOI: 10.1002/prot.23035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 03/07/2011] [Accepted: 03/15/2011] [Indexed: 11/09/2022]
Abstract
The crystal structures of an unliganded and adenosine 5'-monophosphate (AMP) bound, metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis are reported at 2.4 and 1.94 Å, respectively. Functional characterization of this enzyme was guided by computational analysis and then confirmed by experiment. The structure consists of a polymerase and histidinol phosphatase (PHP, Pfam: PF02811) domain with a second domain (residues 105-178) inserted in the middle of the PHP sequence. The insert domain functions in binding AMP, but the precise function and substrate specificity of this domain are unknown. Initial bioinformatics analyses yielded multiple potential functional leads, with most of them suggesting DNA polymerase or DNA replication activity. Phylogenetic analysis indicated a potential DNA polymerase function that was somewhat supported by global structural comparisons identifying the closest structural match to the alpha subunit of DNA polymerase III. However, several other functional predictions, including phosphoesterase, could not be excluded. Theoretical microscopic anomalous titration curve shapes, a computational method for the prediction of active sites from protein 3D structures, identified potential reactive residues in YP_910028.1. Further analysis of the predicted active site and local comparison with its closest structure matches strongly suggested phosphoesterase activity, which was confirmed experimentally. Primer extension assays on both normal and mismatched DNA show neither extension nor degradation and provide evidence that YP_910028.1 has neither DNA polymerase activity nor DNA-proofreading activity. These results suggest that many of the sequence neighbors previously annotated as having DNA polymerase activity may actually be misannotated.
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Affiliation(s)
- Gye Won Han
- Joint Center for Structural Genomics, Scripps Research Institute, La Jolla, California 92037, USA
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7
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Parasuram R, Sharma R, Sefcikova J, Beuning PJ, Ondrechen MJ. Identification of critical residues in DNA polymerase III alpha through protein engineering. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.880.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Rajal Sharma
- Chemistry & Chemical BiologyNortheastern UniversityBostonMA
| | - Jana Sefcikova
- Chemistry & Chemical BiologyNortheastern UniversityBostonMA
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8
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Beuning PJ, Sefcikova J, Fang J, Engen JR, Silva MC. The DNA damage inducible protein UmuD inhibits replication. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.492.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - John R Engen
- Chemistry and Chemical Biology
- Barnett InstituteNortheastern UniversityBostonMA
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9
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Beuning PJ, Fang J, Sefcikova J, Silva MC, Engen JR. The Dynamic DNA Damage Inducible Protein UmuD Inhibits Replication. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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10
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Beuning PJ, Sefcikova J, Fang JS, Engen JR. Regulation of DNA damage responses by the polymerase manager proteins UmuD and UmuD′. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.837.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Penny J Beuning
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - Jana Sefcikova
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - Jing Susan Fang
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - John R Engen
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
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11
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Sefcikova J, Malcho J, Foley K, Beuning P. Quantitative Characterization of Interactions of the Escherichia Coli SOS DNA Damage Response Proteins UmuD and UmuD' with the Replicative DNA Polymerase. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.1714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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12
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McCauley MJ, Shokri L, Sefcikova J, Venclovas Č, Beuning PJ, Williams MC. Distinct double- and single-stranded DNA binding of E. coli replicative DNA polymerase III alpha subunit. ACS Chem Biol 2008; 3:577-87. [PMID: 18652472 PMCID: PMC2665888 DOI: 10.1021/cb8001107] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The α subunit of the replicative DNA polymerase III of Escherichia coli is the active polymerase of the 10-subunit bacterial replicase. The C-terminal region of the α subunit is predicted to contain an oligonucleotide binding (OB-fold) domain. In a series of optical tweezers experiments, the α subunit is shown to have an affinity for both double- and single-stranded DNA, in distinct subdomains of the protein. The portion of the protein that binds to double-stranded DNA stabilizes the DNA helix, because protein binding must be at least partially disrupted with increasing force to melt DNA. Upon relaxation, the DNA fails to fully reanneal, because bound protein interferes with the reformation of the double helix. In addition, the single-stranded DNA binding component appears to be passive, as the protein does not facilitate melting but instead binds to single-stranded regions already separated by force. From DNA stretching measurements we determine equilibrium association constants for the binding of α and several fragments to dsDNA and ssDNA. The results demonstrate that ssDNA binding is localized to the C-terminal region that contains the OB-fold domain, while a tandem helix-hairpin-helix (HhH)2 motif contributes significantly to dsDNA binding.
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Affiliation(s)
- Micah J. McCauley
- Department of Physics, Northeastern University, Boston, Massachusetts, 02115
| | - Leila Shokri
- Department of Physics, Northeastern University, Boston, Massachusetts, 02115
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
| | - Jana Sefcikova
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
| | - Česlovas Venclovas
- Laboratory of Bioinformatics, Institute of Biotechnology, Vilnius LT-02241, Lithuania
| | - Penny J. Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
- Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, Massachusetts, 02115
- Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
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13
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Beuning PJ, Shurtleff BW, Sefcikova J, Walker GC. Steric Gate Variants in a Y family DNA Polymerase Confer UV‐Hypersensitivity. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.990.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Penny J Beuning
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | | | - Jana Sefcikova
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
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14
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Koleva BN, Ordazzo MJ, Fung A, Sefcikova J, Wales TE, Engen JR, Beuning PJ. Dynamics of the polymerase manager protein UmuD: DNA damage tolerance in
E. coli. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.591.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Amy Fung
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - Jana Sefcikova
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - Thomas E. Wales
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - John R. Engen
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
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15
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Sefcikova J, Krasovska MV, Spacková N, Sponer J, Walter NG. Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme. Biopolymers 2007; 85:392-406. [PMID: 17253610 DOI: 10.1002/bip.20693] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The self-cleaving hepatitis delta virus (HDV) ribozyme is essential for the replication of HDV, a liver disease causing pathogen in humans. The catalytically critical nucleotide C75 of the ribozyme is buttressed by a trefoil turn pivoting around an extruded G76. In all available crystal structures, the conformation of G76 is restricted by stacking with G76 of a neighboring molecule. To test whether this crystal contact introduces a structural perturbation into the catalytic core, we have analyzed approximately 200 ns of molecular dynamics (MD) simulations. In the absence of crystal packing, the simulated G76 fluctuates between several conformations, including one wherein G76 establishes a perpendicular base quadruplet in the major groove of the adjacent P1 stem. Second-site mutagenesis experiments suggest that the identity of the nucleotide in position 76 (N76) indeed contributes to the catalytic activity of a trans-acting HDV ribozyme through its capacity for hydrogen bonding with P1. By contrast, in the cis-cleaving genomic ribozyme the functional relevance of N76 is less pronounced and not correlated with the P1 sequence. Terbium(III) footprinting and additional MD show that the activity differences between N76 mutants of this ribozyme are related instead to changes in average conformation and modified cross-correlations in the trefoil turn.
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Affiliation(s)
- Jana Sefcikova
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA
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16
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Sefcikova J, Krasovska MV, Šponer J, Walter NG. The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis. Nucleic Acids Res 2007; 35:1933-46. [PMID: 17337436 PMCID: PMC1874588 DOI: 10.1093/nar/gkl1104] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The genome of the human hepatitis delta virus (HDV) harbors a self-cleaving catalytic RNA motif, the genomic HDV ribozyme, whose crystal structure shows the dangling nucleotides 5′ of the cleavage site projecting away from the catalytic core. This 5′-sequence contains a clinically conserved U − 1 that we find to be essential for fast cleavage, as the order of activity follows U − 1 > C − 1 > A − 1 > G − 1, with a >25-fold activity loss from U − 1 to G − 1. Terbium(III) footprinting detects conformations for the P1.1 stem, the cleavage site wobble pair and the A-minor motif of the catalytic trefoil turn that depend on the identity of the N − 1 base. The most tightly folded catalytic core, resembling that of the reaction product, is found in the U − 1 wild-type precursor. Molecular dynamics simulations demonstrate that a U − 1 forms the most robust kink around the scissile phosphate, exposing it to the catalytic C75 in a previously unnoticed U-turn motif found also, for example, in the hammerhead ribozyme and tRNAs. Strikingly, we find that the common structural U-turn motif serves distinct functions in the HDV and hammerhead ribozymes.
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Affiliation(s)
- Jana Sefcikova
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Maryna V. Krasovska
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055, USA and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- *To whom correspondence should be addressed. +1-(734) 615-2060+1-(734) 647-4865
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Krasovska MV, Sefcikova J, Réblová K, Schneider B, Walter NG, Sponer J. Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. Biophys J 2006; 91:626-38. [PMID: 16617077 PMCID: PMC1483112 DOI: 10.1529/biophysj.105.079368] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or artificial placement of this Mg2+ into the product structure result in its swift expulsion from the active site. These findings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg2+ act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.
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Affiliation(s)
- Maryna V Krasovska
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
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18
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Krasovska MV, Sefcikova J, Spacková N, Sponer J, Walter NG. Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. J Mol Biol 2005; 351:731-48. [PMID: 16045932 DOI: 10.1016/j.jmb.2005.06.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 05/31/2005] [Accepted: 06/07/2005] [Indexed: 11/22/2022]
Abstract
The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme involved in the replication of a human pathogen, the hepatitis delta virus. Recent crystal structures of the precursor and product of self-cleavage, together with detailed kinetic analyses, have led to hypotheses on the catalytic strategies employed by the HDV ribozyme. We report molecular dynamics (MD) simulations (approximately 120 ns total simulation time) to test the plausibility that specific conformational rearrangements are involved in catalysis. Site-specific self-cleavage requires cytidine in position 75 (C75). A precursor simulation with unprotonated C75 reveals a rather weak dynamic binding of C75 in the catalytic pocket with spontaneous, transient formation of a H-bond between U-1(O2') and C75(N3). This H-bond would be required for C75 to act as the general base. Upon protonation in the precursor, C75H+ has a tendency to move towards its product location and establish a firm H-bonding network within the catalytic pocket. However, a C75H+(N3)-G1(O5') H-bond, which would be expected if C75 acted as a general acid catalyst, is not observed on the present simulation timescale. The adjacent loop L3 is relatively dynamic and may serve as a flexible structural element, possibly gated by the closing U20.G25 base-pair, to facilitate a conformational switch induced by a protonated C75H+. L3 also controls the electrostatic environment of the catalytic core, which in turn may modulate C75 base strength and metal ion binding. We find that a distant RNA tertiary interaction involving a protonated cytidine (C41) becomes unstable when left unprotonated, leading to disruptive conformational rearrangements adjacent to the catalytic core. A Na ion temporarily compensates for the loss of the protonated hydrogen bond, which is strikingly consistent with the experimentally observed synergy between low pH and high Na+ concentrations in mediating residual self-cleavage of the HDV ribozyme in the absence of divalents.
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Affiliation(s)
- Maryna V Krasovska
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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Jeong S, Sefcikova J, Tinsley RA, Rueda D, Walter NG. Trans-acting hepatitis delta virus ribozyme: catalytic core and global structure are dependent on the 5' substrate sequence. Biochemistry 2003; 42:7727-40. [PMID: 12820882 DOI: 10.1021/bi034627g] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hepatitis delta virus (HDV), an infectious human pathogen affecting millions of people worldwide, leads to intensified disease symptoms, including progression to liver cirrhosis upon coinfection with its helper virus, HBV. Both the circular RNA genome of HDV and its complementary antigenome contain a common cis-cleaving catalytic RNA motif, the HDV ribozyme, which plays a crucial role in viral replication. Previously, the crystal structure of the product form of the cis-acting genomic HDV ribozyme has been determined, and the precursor form has been suggested to be structurally similar. In contrast, solution studies by fluorescence resonance energy transfer (FRET) on a trans-cleaving form of the ribozyme have shown significant global conformational changes upon catalysis, while 2-aminopurine (AP) fluorescence assays have detected concomitant local conformational changes in the catalytic core. Here, we augment these studies by using terbium(III) to probe the structure of the trans-acting HDV ribozyme at nucleotide resolution. We observe significant structural differences between the precursor and product forms, especially in the P1.1 helix and the trefoil turn in the single-stranded region connecting P4 and P2 (termed J4/2) of the catalytic core. We show, using terbium(III) footprinting and sensitized luminescence spectroscopy as well as steady-state, time-resolved, and gel-mobility FRET assays on a systematic set of substrates, that the substrate sequence immediately 5' to the cleavage site significantly modulates these local as well as resultant global structural differences. Our results suggest a structural basis for the previously observed impact of the 5' substrate sequence on catalytic activity.
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Affiliation(s)
- Sohee Jeong
- Department of Chemistry, The University of Michigan, 930 North University, Ann Arbor, Michigan 48109-1055, USA
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