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Pertermann R, Golbik RP, Tamilarasan S, Gursinsky T, Gago-Zachert S, Pantaleo V, Thondorf I, Behrens SE. RNA and Protein Determinants Mediate Differential Binding of miRNAs by a Viral Suppressor of RNA Silencing Thus Modulating Antiviral Immune Responses in Plants. Int J Mol Sci 2022; 23:4977. [PMID: 35563369 PMCID: PMC9103804 DOI: 10.3390/ijms23094977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023] Open
Abstract
Many plant viruses express suppressor proteins (VSRs) that can inhibit RNA silencing, a central component of antiviral plant immunity. The most common activity of VSRs is the high-affinity binding of virus-derived siRNAs and thus their sequestration from the silencing process. Since siRNAs share large homologies with miRNAs, VSRs like the Tombusvirus p19 may also bind miRNAs and in this way modulate cellular gene expression at the post-transcriptional level. Interestingly, the binding affinity of p19 varies considerably between different miRNAs, and the molecular determinants affecting this property have not yet been adequately characterized. Addressing this, we analyzed the binding of p19 to the miRNAs 162 and 168, which regulate the expression of the important RNA silencing constituents Dicer-like 1 (DCL1) and Argonaute 1 (AGO1), respectively. p19 binds miRNA162 with similar high affinity as siRNA, whereas the affinity for miRNA168 is significantly lower. We show that specific molecular features, such as mismatches and 'G-U wobbles' on the RNA side and defined amino acid residues on the VSR side, mediate this property. Our observations highlight the remarkable adaptation of VSR binding affinities to achieve differential effects on host miRNA activities. Moreover, they show that even minimal changes, i.e., a single base pair in a miRNA duplex, can have significant effects on the efficiency of the plant antiviral immune response.
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Affiliation(s)
- Robert Pertermann
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Saale, 06120 Halle, Germany; (R.P.); (R.P.G.); (S.T.); (T.G.); (S.G.-Z.); (I.T.)
| | - Ralph Peter Golbik
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Saale, 06120 Halle, Germany; (R.P.); (R.P.G.); (S.T.); (T.G.); (S.G.-Z.); (I.T.)
| | - Selvaraj Tamilarasan
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Saale, 06120 Halle, Germany; (R.P.); (R.P.G.); (S.T.); (T.G.); (S.G.-Z.); (I.T.)
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Saale, 06120 Halle, Germany; (R.P.); (R.P.G.); (S.T.); (T.G.); (S.G.-Z.); (I.T.)
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Saale, 06120 Halle, Germany; (R.P.); (R.P.G.); (S.T.); (T.G.); (S.G.-Z.); (I.T.)
| | - Vitantonio Pantaleo
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, Bari Unit, CNR, 70126 Bari, Italy;
| | - Iris Thondorf
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Saale, 06120 Halle, Germany; (R.P.); (R.P.G.); (S.T.); (T.G.); (S.G.-Z.); (I.T.)
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Saale, 06120 Halle, Germany; (R.P.); (R.P.G.); (S.T.); (T.G.); (S.G.-Z.); (I.T.)
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2
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Abstract
The therapeutic targeting of the nonstructural protein 5B (NS5B) RNA-dependent RNA polymerase (RdRp) of the Hepatitis C Virus (HCV) with nucleotide analogs led to a deep understanding of this enzymes structure, function and substrate specificity. Unlike previously studied DNA polymerases including the reverse transcriptase of Human Immunodeficiency Virus, development of biochemical assays for HCV RdRp proved challenging due to low solubility of the full-length protein and inefficient acceptance of exogenous primer/templates. Despite the poor apparent specific activity, HCV RdRp was found to support rapid and processive transcription once elongation is initiated in vitro consistent with its high level of viral replication in the livers of patients. Understanding of the substrate specificity of HCV RdRp led to the discovery of the active triphosphate of sofosbuvir as a nonobligate chain-terminator of viral RNA transcripts. The ternary crystal structure of HCV RdRp, primer/template, and incoming nucleotide showed the interaction between the nucleotide analog and the 2'-hydroxyl binding pocket and how an unfit mutation of serine 282 to threonine results in resistance by interacting with the uracil base and modified 2'-position of the analog. Host polymerases mediate off-target toxicity of nucleotide analogs and the active metabolite of sofosbuvir was found to not be efficiently incorporated by host polymerases including the mitochondrial RNA polymerase (POLRMT). Knowledge from studying inhibitors of HCV RdRp serves to advance antiviral drug discovery for other emerging RNA viruses including the discovery of remdesivir as an inhibitor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the virus that causes COVID-19.
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Affiliation(s)
- Joy Y Feng
- Gilead Sciences, Inc., Foster City, CA, United States.
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3
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Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication. Int J Mol Sci 2020; 21:ijms21186955. [PMID: 32971876 PMCID: PMC7555993 DOI: 10.3390/ijms21186955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/26/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C virus (HCV) infects liver cells and often causes chronic infection, also leading to liver cirrhosis and cancer. In the cytoplasm, the viral structural and non-structural (NS) proteins are directly translated from the plus strand HCV RNA genome. The viral proteins NS3 to NS5B proteins constitute the replication complex that is required for RNA genome replication via a minus strand antigenome. The most C-terminal protein in the genome is the NS5B replicase, which needs to initiate antigenome RNA synthesis at the very 3′-end of the plus strand. Using ribosome profiling of cells replicating full-length infectious HCV genomes, we uncovered that ribosomes accumulate at the HCV stop codon and about 30 nucleotides upstream of it. This pausing is due to the presence of conserved rare, inefficient Wobble codons upstream of the termination site. Synonymous substitution of these inefficient codons to efficient codons has negative consequences for viral RNA replication but not for viral protein synthesis. This pausing may allow the enzymatically active replicase core to find its genuine RNA template in cis, while the protein is still held in place by being stuck with its C-terminus in the exit tunnel of the paused ribosome.
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Schmidt T, Friedrich S, Golbik RP, Behrens SE. NF90-NF45 is a selective RNA chaperone that rearranges viral and cellular riboswitches: biochemical analysis of a virus host factor activity. Nucleic Acids Res 2017; 45:12441-12454. [PMID: 29040738 PMCID: PMC5716087 DOI: 10.1093/nar/gkx931] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/10/2017] [Indexed: 01/28/2023] Open
Abstract
The heterodimer NF90-NF45 is an RNA-binding protein complex that modulates the expression of various cellular mRNAs on the post-transcriptional level. Furthermore, it acts as a host factor that supports the replication of several RNA viruses. The molecular mechanisms underlying these activities have yet to be elucidated. Recently, we showed that the RNA-binding capabilities and binding specificity of NF90 considerably improves when it forms a complex with NF45. Here, we demonstrate that NF90 has a substrate-selective RNA chaperone activity (RCA) involving RNA annealing and strand displacement activities. The mechanism of the NF90-catalyzed RNA annealing was elucidated to comprise a combination of 'matchmaking' and compensation of repulsive charges, which finally results in the population of dsRNA products. Heterodimer formation with NF45 enhances 'matchmaking' of complementary ssRNAs and substantially increases the efficiency of NF90's RCA. During investigations of the relevance of the NF90-NF45 RCA, the complex was shown to stimulate the first step in the RNA replication process of hepatitis C virus (HCV) in vitro and to stabilize a regulatory element within the mRNA of vascular endothelial growth factor (VEGF) by protein-guided changes of the RNAs' structures. Thus, our study reveals how the intrinsic properties of an RNA-binding protein determine its biological activities.
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Affiliation(s)
- Tobias Schmidt
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
- To whom correspondence should be addressed. Tel: +49 3455 5249 60; Fax: +49 3455 5273 87; . Correspondence may also be addressed to Tobias Schmidt.
| | - Susann Friedrich
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
| | - Ralph Peter Golbik
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI), Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
- To whom correspondence should be addressed. Tel: +49 3455 5249 60; Fax: +49 3455 5273 87; . Correspondence may also be addressed to Tobias Schmidt.
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5
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Biophysical Mode-of-Action and Selectivity Analysis of Allosteric Inhibitors of Hepatitis C Virus (HCV) Polymerase. Viruses 2017. [PMID: 28621755 PMCID: PMC5490826 DOI: 10.3390/v9060151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Allosteric inhibitors of hepatitis C virus (HCV) non-structural protein 5B (NS5B) polymerase are effective for treatment of genotype 1, although their mode of action and potential to inhibit other isolates and genotypes are not well established. We have used biophysical techniques and a novel biosensor-based real-time polymerase assay to investigate the mode-of-action and selectivity of four inhibitors against enzyme from genotypes 1b (BK and Con1) and 3a. Two thumb inhibitors (lomibuvir and filibuvir) interacted with all three NS5B variants, although the affinities for the 3a enzyme were low. Of the two tested palm inhibitors (dasabuvir and nesbuvir), only dasabuvir interacted with the 1b variant, and nesbuvir interacted with NS5B 3a. Lomibuvir, filibuvir and dasabuvir stabilized the structure of the two 1b variants, but not the 3a enzyme. The thumb compounds interfered with the interaction between the enzyme and RNA and blocked the transition from initiation to elongation. The two allosteric inhibitor types have different inhibition mechanisms. Sequence and structure analysis revealed differences in the binding sites for 1b and 3a variants, explaining the poor effect against genotype 3a NS5B. The indirect mode-of-action needs to be considered when designing allosteric compounds. The current approach provides an efficient strategy for identifying and optimizing allosteric inhibitors targeting HCV genotype 3a.
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Dreßler L, Michel F, Thondorf I, Mansfeld J, Golbik R, Ulbrich-Hofmann R. Metal ions and phosphatidylinositol 4,5-bisphosphate as interacting effectors of α-type plant phospholipase D. PHYTOCHEMISTRY 2017; 138:57-64. [PMID: 28283189 DOI: 10.1016/j.phytochem.2017.02.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/02/2017] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
Plant phospholipases D (PLD) are typically characterized by a C2 domain with at least two Ca2+ binding sites. In vitro, the predominantly expressed α-type PLDs need 20-100 mM CaCl2 for optimum activity, whereas the essential activator of β- or γ-type PLDs, phosphatidylinositol 4,5-bisphosphate (PIP2), plays a secondary role. In the present paper, we have studied the interplay between PIP2 and metal ion activation of the well-known α-type PLD from cabbage (PLDα). With mixed micelles containing phosphatidyl-p-nitrophenol as substrate, PIP2-concentrations in the nanomolar range are able to activate the enzyme in addition to the essential Ca2+ activation. Mg2+ ions are able to replace Ca2+ ions but they do not activate PLDα. Rather, they abolish the activation of the enzyme by Ca2+ ions in the absence, but not in the presence, of PIP2. The presence of PIP2 causes a shift in the pH optimum of PLDα activity to the acidic range. Employing fluorescence measurements and replacing Ca2+ by Tb3+ ions, confirmed the presence of two metal ion-binding sites, in which the one of lower affinity proved crucial for PLD activation. Moreover, we have generated a homology model of the C2 domain of this enzyme, which was used for Molecular Dynamics (MD) simulations and docking studies. As is common for C2 domains, it shows two antiparallel β-sheets consisting of four β-strands each and loop regions that harbor two Ca2+ binding sites. Based on the findings of the MD simulation, one of the bound Ca2+ ions is coordinated by five amino acid residues. The second Ca2+ ion induces a loop movement upon its binding to three amino acid residues. Docking studies with PIP2 reveal, in addition to the previously postulated PIP2-binding site in the middle of the β-sheet structure, another PIP2-binding site near the two Ca2+ ions, which is in accordance with the experimental interplay of PIP2, Ca2+ and Mg2+ ions.
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Affiliation(s)
- Lars Dreßler
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
| | - Florian Michel
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
| | - Iris Thondorf
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
| | - Johanna Mansfeld
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
| | - Ralph Golbik
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
| | - Renate Ulbrich-Hofmann
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany.
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7
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The properties of the RNA-binding protein NF90 are considerably modulated by complex formation with NF45. Biochem J 2016; 474:259-280. [PMID: 28062840 DOI: 10.1042/bcj20160790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/07/2016] [Accepted: 11/11/2016] [Indexed: 12/31/2022]
Abstract
Nuclear factor 90 (NF90) is an RNA-binding protein (RBP) that regulates post-transcriptionally the expression of various mRNAs. NF90 was recently shown to be capable of discriminating between different RNA substrates. This is mediated by an adaptive and co-operative interplay between three RNA-binding motifs (RBMs) in the protein's C-terminus. In many cell types, NF90 exists predominantly in a complex with NF45. Here, we compared the RNA-binding properties of the purified NF90 monomer and the NF90-NF45 heterodimer by biophysical and biochemical means, and demonstrate that the interaction with NF45 considerably affects the characteristics of NF90. Along with a thermodynamic stabilization, complex formation substantially improves the RNA-binding capacity of NF90 by modulating its binding mode and by enhancing its affinity for single- and double-stranded RNA substrates. Our data suggest that features of both the N- and C-termini of NF90 participate in the heterodimerization with NF45 and that the formation of NF90-NF45 changes the conformation of NF90's RBMs to a status in which the co-operative interplay of the RBMs is optimal. NF45 is considered to act as a conformational scaffold for NF90's RBMs, which alters the RNA-binding specificity of NF90. Accordingly, the monomeric NF90 and the NF90-NF45 heterodimer may exert different functions in the cell.
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8
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Sesmero E, Brown JA, Thorpe IF. Molecular simulations to delineate functional conformational transitions in the HCV polymerase. J Comput Chem 2016; 38:1125-1137. [PMID: 27859387 DOI: 10.1002/jcc.24662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/29/2016] [Accepted: 10/18/2016] [Indexed: 01/08/2023]
Abstract
Hepatitis C virus (HCV) is a global health concern for which there is no vaccine available. The HCV polymerase is responsible for the critical function of replicating the RNA genome of the virus. Transitions between at least two conformations (open and closed) are necessary to allow the enzyme to replicate RNA. In this study, molecular dynamic simulations were initiated from multiple crystal structures to understand the free energy landscape (FEL) explored by the enzyme as it interconverts between these conformations. Our studies reveal the location of distinct states within the FEL as well as the molecular interactions associated with these states. Specific hydrogen bonds appear to play a key role in modulating conformational transitions. This knowledge is essential to elucidate the role of these conformations in replication and may also be valuable in understanding the basis by which this enzyme is inhibited by small molecules. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ester Sesmero
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland, 21250
| | - Jodian A Brown
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland, 21250
| | - Ian F Thorpe
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland, 21250
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9
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Schmidt T, Knick P, Lilie H, Friedrich S, Golbik RP, Behrens SE. Coordinated Action of Two Double-Stranded RNA Binding Motifs and an RGG Motif Enables Nuclear Factor 90 To Flexibly Target Different RNA Substrates. Biochemistry 2016; 55:948-59. [PMID: 26795062 DOI: 10.1021/acs.biochem.5b01072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanisms of how RNA binding proteins (RBP) bind to and distinguish different RNA molecules are yet uncertain. Here, we performed a comprehensive analysis of the RNA binding properties of multidomain RBP nuclear factor 90 (NF90) by investigating specifically the functional activities of two double-stranded RNA binding motifs (dsRBM) and an RGG motif in the protein's unstructured C-terminus. By comparison of the RNA binding affinities of several NF90 variants and their modes of binding to a set of defined RNA molecules, the activities of the motifs turned out to be very different. While dsRBM1 contributes little to RNA binding, dsRBM2 is essential for effective binding of double-stranded RNA. The protein's immediate C-terminus, including the RGG motif, is indispensable for interactions of the protein with single-stranded RNA, and the RGG motif decisively contributes to NF90's overall RNA binding properties. Conformational studies, which compared wild-type NF90 with a variant that contains a pseudophosphorylated residue in the RGG motif, suggest that the NF90 C-terminus is involved in conformational changes in the protein after RNA binding, with the RGG motif acting as a central regulatory element. In summary, our data propose a concerted action of all RNA binding motifs within the frame of the full-length protein, which may be controlled by regulation of the activity of the RGG motif, e.g., by phosphorylation. This multidomain interplay enables the RBP NF90 to discriminate RNA features by dynamic and adaptable interactions.
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Affiliation(s)
- Tobias Schmidt
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Paul Knick
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Susann Friedrich
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Ralph Peter Golbik
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
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Gupta G, Song J. C-Terminal Auto-Regulatory Motif of Hepatitis C Virus NS5B Interacts with Human VAPB-MSP to Form a Dynamic Replication Complex. PLoS One 2016; 11:e0147278. [PMID: 26784321 PMCID: PMC4718513 DOI: 10.1371/journal.pone.0147278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 01/02/2016] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) is a pathogen of global importance and nearly 200 million people are chronically infected with HCV. HCV is an enveloped single-stranded RNA virus, which is characteristic of the formation of the host membrane associated replication complex. Previous functional studies have already established that the human ER-anchored VAPB protein acts as a host factor to form a complex with HCV NS5A and NS5B, which may be established as a drug target. However, there is lacking of biophysical characterization of the structures and interfaces of the complex, partly due to the dynamic nature of the complex formation and dissociation, which is extensively involved in intrinsically-disordered domains. Here by an integrated use of domain dissection and NMR spectroscopy, for the first time we have successfully deciphered that the HCV NS5B utilizes its auto-regulatory C-linker to bind the VAPB-MSP domain to form a dynamic complex. This finding implies that the NS5B C-linker is capable of playing dual roles by a switch between the folded and disordered states. Interestingly, our previous and present studies together reveal that both HCV NS5A and NS5B bind to the MSP domains of the dimeric VAP with significantly overlapped interfaces and similar affinities. The identification that EphA2 and EphA5 bind to the MSP domain with higher affinity than EphA4 provides a biophysical basis for further exploring whether other than inducing ALS-like syndrome, the HCV infection might also trigger pathogenesis associated with signalling pathways mediated by EphA2 and EphA5.
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Affiliation(s)
- Garvita Gupta
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- * E-mail:
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11
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Reich S, Kovermann M, Lilie H, Knick P, Geissler R, Golbik RP, Balbach J, Behrens SE. Initiation of RNA synthesis by the hepatitis C virus RNA-dependent RNA polymerase is affected by the structure of the RNA template. Biochemistry 2014; 53:7002-12. [PMID: 25310724 PMCID: PMC4230328 DOI: 10.1021/bi5006656] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The
hepatitis C virus (HCV) RNA-dependent RNA polymerase NS5B is
a central enzyme of the intracellular replication of the viral (+)RNA
genome. Here, we studied the individual steps of NS5B-catalyzed RNA
synthesis by a combination of biophysical methods, including real-time
1D 1H NMR spectroscopy. NS5B was found to bind to a nonstructured
and a structured RNA template in different modes. Following NTP binding
and conversion to the catalysis-competent ternary complex, the polymerase
revealed an improved affinity for the template. By monitoring the
folding/unfolding of 3′(−)SL by 1H NMR, the
base pair at the stem’s edge was identified as the most stable
component of the structure. 1H NMR real-time analysis of
NS5B-catalyzed RNA synthesis on 3′(−)SL showed that
a pronounced lag phase preceded the processive polymerization reaction.
The presence of the double-stranded stem with the edge base pair acting
as the main energy barrier impaired RNA synthesis catalyzed by NS5B.
Our observations suggest a crucial role of RNA-modulating factors
in the HCV replication process.
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Affiliation(s)
- Stefan Reich
- Institute of Biochemistry and Biotechnology, Section of Microbial Biotechnology, ‡Institute of Physics, Section of Biophysics, §Institute of Biochemistry and Biotechnology, Section of Technical Biochemistry, Martin Luther University Halle-Wittenberg , D-06120 Halle/Saale, Germany
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AUF1 p45 promotes West Nile virus replication by an RNA chaperone activity that supports cyclization of the viral genome. J Virol 2014; 88:11586-99. [PMID: 25078689 DOI: 10.1128/jvi.01283-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
UNLABELLED A central aspect of current virology is to define the function of cellular proteins (host factors) that support the viral multiplication process. This study aimed at characterizing cellular proteins that assist the RNA replication process of the prevalent human pathogen West Nile virus (WNV). Using in vitro and cell-based approaches, we defined the p45 isoform of AU-rich element RNA-binding protein 1 (AUF1) as a host factor that enables efficient WNV replication. It was demonstrated that AUF1 p45 has an RNA chaperone activity, which aids the structural rearrangement and cyclization of the WNV RNA that is required by the viral replicase to initiate RNA replication. The obtained data suggest the RNA chaperone activity of AUF1 p45 is an important determinant of the WNV life cycle. IMPORTANCE In this study, we identified a cellular protein, AUF1 (also known as heterogeneous ribonucleoprotein D [hnRNPD]), acting as a helper (host factor) of the multiplication process of the important human pathogen West Nile virus. Several different variants of AUF1 exist in the cell, and one variant, AUF1 p45, was shown to support viral replication most significantly. Interestingly, we obtained a set of experimental data indicating that a main function of AUF1 p45 is to modify and thus prepare the West Nile virus genome in such a way that the viral enzyme that generates progeny genomes is empowered to do this considerably more efficiently than in the absence of the host factor. The capability of AUF1 p45 to rearrange the West Nile virus genome was thus identified to be an important aspect of a West Nile virus infection.
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Boyce SE, Tirunagari N, Niedziela-Majka A, Perry J, Wong M, Kan E, Lagpacan L, Barauskas O, Hung M, Fenaux M, Appleby T, Watkins WJ, Schmitz U, Sakowicz R. Structural and regulatory elements of HCV NS5B polymerase--β-loop and C-terminal tail--are required for activity of allosteric thumb site II inhibitors. PLoS One 2014; 9:e84808. [PMID: 24416288 PMCID: PMC3886995 DOI: 10.1371/journal.pone.0084808] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/19/2013] [Indexed: 01/01/2023] Open
Abstract
Elucidation of the mechanism of action of the HCV NS5B polymerase thumb site II inhibitors has presented a challenge. Current opinion holds that these allosteric inhibitors stabilize the closed, inactive enzyme conformation, but how this inhibition is accomplished mechanistically is not well understood. Here, using a panel of NS5B proteins with mutations in key regulatory motifs of NS5B – the C-terminal tail and β-loop – in conjunction with a diverse set of NS5B allosteric inhibitors, we show that thumb site II inhibitors possess a distinct mechanism of action. A combination of enzyme activity studies and direct binding assays reveals that these inhibitors require both regulatory elements to maintain the polymerase inhibitory activity. Removal of either element has little impact on the binding affinity of thumb site II inhibitors, but significantly reduces their potency. NS5B in complex with a thumb site II inhibitor displays a characteristic melting profile that suggests stabilization not only of the thumb domain but also the whole polymerase. Successive truncations of the C-terminal tail and/or removal of the β-loop lead to progressive destabilization of the protein. Furthermore, the thermal unfolding transitions characteristic for thumb site II inhibitor – NS5B complex are absent in the inhibitor – bound constructs in which interactions between C-terminal tail and β-loop are abolished, pointing to the pivotal role of both regulatory elements in communication between domains. Taken together, a comprehensive picture of inhibition by compounds binding to thumb site II emerges: inhibitor binding provides stabilization of the entire polymerase in an inactive, closed conformation, propagated via coupled interactions between the C-terminal tail and β-loop.
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Affiliation(s)
- Sarah E. Boyce
- Gilead Sciences Inc., Foster City, California, United States of America
| | - Neeraj Tirunagari
- Gilead Sciences Inc., Foster City, California, United States of America
| | | | - Jason Perry
- Gilead Sciences Inc., Foster City, California, United States of America
| | - Melanie Wong
- Gilead Sciences Inc., Foster City, California, United States of America
| | - Elaine Kan
- Gilead Sciences Inc., Foster City, California, United States of America
| | - Leanna Lagpacan
- Gilead Sciences Inc., Foster City, California, United States of America
| | - Ona Barauskas
- Gilead Sciences Inc., Foster City, California, United States of America
| | - Magdeleine Hung
- Gilead Sciences Inc., Foster City, California, United States of America
| | - Martijn Fenaux
- Gilead Sciences Inc., Foster City, California, United States of America
| | - Todd Appleby
- Gilead Sciences Inc., Foster City, California, United States of America
| | | | - Uli Schmitz
- Gilead Sciences Inc., Foster City, California, United States of America
| | - Roman Sakowicz
- Gilead Sciences Inc., Foster City, California, United States of America
- * E-mail:
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14
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Maynard A, Crosby RM, Ellis B, Hamatake R, Hong Z, Johns BA, Kahler KM, Koble C, Leivers A, Leivers MR, Mathis A, Peat AJ, Pouliot JJ, Roberts CD, Samano V, Schmidt RM, Smith GK, Spaltenstein A, Stewart EL, Thommes P, Turner EM, Voitenleitner C, Walker JT, Waitt G, Weatherhead J, Weaver K, Williams S, Wright L, Xiong ZZ, Haigh D, Shotwell JB. Discovery of a Potent Boronic Acid Derived Inhibitor of the HCV RNA-Dependent RNA Polymerase. J Med Chem 2013; 57:1902-13. [DOI: 10.1021/jm400317w] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Andrew Maynard
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Renae M. Crosby
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Byron Ellis
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Robert Hamatake
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Zhi Hong
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Brian A. Johns
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Kirsten M. Kahler
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Cecilia Koble
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Anna Leivers
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Martin R. Leivers
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Amanda Mathis
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Andrew J. Peat
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Jeffrey J. Pouliot
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Christopher D. Roberts
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Vicente Samano
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Rachel M. Schmidt
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Gary K. Smith
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Andrew Spaltenstein
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Eugene L. Stewart
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Pia Thommes
- GlaxoSmithKline, Infectious Diseases Centre
for Excellence for Drug Discovery, Gunnels Wood Road, Stevenage, Hertfordshire
SG1 1NY, U.K
| | - Elizabeth M. Turner
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Christian Voitenleitner
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Jill T. Walker
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Greg Waitt
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Jason Weatherhead
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Kurt Weaver
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Shawn Williams
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Lois Wright
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Zhiping Z. Xiong
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - David Haigh
- GlaxoSmithKline, Infectious Diseases Centre
for Excellence for Drug Discovery, Gunnels Wood Road, Stevenage, Hertfordshire
SG1 1NY, U.K
| | - J. Brad Shotwell
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
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15
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Salvatierra K, Fareleski S, Forcada A, López-Labrador FX. Hepatitis C virus resistance to new specifically-targeted antiviral therapy: A public health perspective. World J Virol 2013; 2:6-15. [PMID: 24175225 PMCID: PMC3785043 DOI: 10.5501/wjv.v2.i1.6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Revised: 12/30/2012] [Accepted: 01/17/2013] [Indexed: 02/05/2023] Open
Abstract
Until very recently, treatment for chronic hepatitis C virus (HCV) infection has been based on the combination of two non-viral specific drugs: pegylated interferon-α and ribavirin, which is effective in, overall, about 40%-50% of cases. To improve the response to treatment, novel drugs have been designed to specifically block viral proteins. Multiple compounds are under development, and the approval for clinical use of the first of such direct-acting antivirals in 2011 (Telaprevir and Boceprevir), represents a milestone in HCV treatment. HCV therapeutics is entering a new expanding era, and a highly-effective cure is envisioned for the first time since the discovery of the virus in 1989. However, any antiviral treatment may be limited by the capacity of the virus to overcome the selective pressure of new drugs, generating antiviral resistance. Here, we try to provide a basic overview of new treatments, HCV resistance to new antivirals and some considerations derived from a Public Health perspective, using HCV resistance to protease and polymerase inhibitors as examples.
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Affiliation(s)
- Karina Salvatierra
- Karina Salvatierra, Sabrina Fareleski, F Xavier López-Labrador, Joint Unit in Genomics and Health, Centre for Public Health Research, Public Health Department, Generalitat Valenciana/Institut Cavanilles, University of Valencia, 46020 Valencia, Spain
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16
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Structural biology of dengue virus enzymes: towards rational design of therapeutics. Antiviral Res 2012; 96:115-26. [PMID: 22995600 DOI: 10.1016/j.antiviral.2012.09.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/03/2012] [Accepted: 09/07/2012] [Indexed: 02/07/2023]
Abstract
Development of anti-dengue therapy represents an urgent un-met medical need. Towards antiviral therapy, recent advances in crystal structures of DENV enzymes have led to the possibility of structure-based rational design of inhibitors for anti-dengue therapy. These include (i) the structure of the 'active' form of the DENV protease in complex with a peptide substrate; (ii) the structure of DENV methyltransferase bound to an inhibitor that selectively suppresses viral methyltransferase, but not human methyltransferases; (iii) the structure of DENV RNA-dependent RNA polymerase in complex with a small-molecule compound. This review summarizes the structural biology of these three key enzymes (protease, methyltransferase, and polymerase) that are essential for DENV replication. The new structural information has provided new avenues for development of anti-dengue therapy.
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17
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Geissler R, Golbik RP, Behrens SE. The DEAD-box helicase DDX3 supports the assembly of functional 80S ribosomes. Nucleic Acids Res 2012; 40:4998-5011. [PMID: 22323517 PMCID: PMC3367175 DOI: 10.1093/nar/gks070] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The DEAD-box helicase DDX3 has suggested functions in innate immunity, mRNA translocation and translation, and it participates in the propagation of assorted viruses. Exploring initially the role of DDX3 in the life cycle of hepatitis C virus, we observed the protein to be involved in translation directed by different viral internal ribosomal entry sites. Extension of these studies revealed a general supportive role of DDX3 in translation initiation. DDX3 was found to interact in an RNA-independent manner with defined components of the translational pre-initiation complex and to specifically associate with newly assembling 80S ribosomes. DDX3 knock down and in vitro reconstitution experiments revealed a significant function of the protein in the formation of 80S translation initiation complexes. Our study implies that DDX3 assists the 60S subunit joining process to assemble functional 80S ribosomes.
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Affiliation(s)
- Rene Geissler
- Institute of Biochemistry and Biotechnology, Faculty of Life Sciences (NFI), Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle/Saale, Germany
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18
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Campagnola G, Gong P, Peersen OB. High-throughput screening identification of poliovirus RNA-dependent RNA polymerase inhibitors. Antiviral Res 2011; 91:241-51. [PMID: 21722674 PMCID: PMC3159743 DOI: 10.1016/j.antiviral.2011.06.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 05/11/2011] [Accepted: 06/14/2011] [Indexed: 11/26/2022]
Abstract
Viral RNA-dependent RNA polymerase (RdRP) enzymes are essential for the replication of positive-strand RNA viruses and established targets for the development of selective antiviral therapeutics. In this work we have carried out a high-throughput screen of 154,267 compounds to identify poliovirus polymerase inhibitors using a fluorescence based RNA elongation assay. Screening and subsequent validation experiments using kinetic methods and RNA product analysis resulted in the identification of seven inhibitors that affect the RNA binding, initiation, or elongation activity of the polymerase. X-ray crystallography data show clear density for five of the compounds in the active site of the poliovirus polymerase elongation complex. The inhibitors occupy the NTP binding site by stacking on the priming nucleotide and interacting with the templating base, yet competition studies show fairly weak IC50 values in the low μM range. A comparison with nucleotide bound structures suggests that weak binding is likely due to the lack of a triphosphate group on the inhibitors. Consequently, the inhibitors are primarily effective at blocking polymerase initiation and do not effectively compete with NTP binding during processive elongation. These findings are discussed in the context of the polymerase elongation complex structure and allosteric control of the viral RdRP catalytic cycle.
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Affiliation(s)
- Grace Campagnola
- Department of Biochemistry & Molecular Biology 1870 Campus Delivery Colorado State University Fort Collins, CO 80523-1870
| | - Peng Gong
- Department of Biochemistry & Molecular Biology 1870 Campus Delivery Colorado State University Fort Collins, CO 80523-1870
| | - Olve B. Peersen
- Department of Biochemistry & Molecular Biology 1870 Campus Delivery Colorado State University Fort Collins, CO 80523-1870
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