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Sikorska J, Hou Y, Chiurazzi P, Siu T, Baltus GA, Sheth P, McLaren D, Truong Q, Parish C, Wyss D. Characterization of RNA driven structural changes in full length RIG-I leading to its agonism or antagonism. Nucleic Acids Res 2023; 51:9356-9368. [PMID: 37486777 PMCID: PMC10516622 DOI: 10.1093/nar/gkad606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 06/30/2023] [Accepted: 07/20/2023] [Indexed: 07/26/2023] Open
Abstract
RIG-I (retinoic acid inducible gene-I) can sense subtle differences between endogenous and viral RNA in the cytoplasm, triggering an anti-viral immune response through induction of type I interferons (IFN) and other inflammatory mediators. Multiple crystal and cryo-EM structures of RIG-I suggested a mechanism in which the C-terminal domain (CTD) is responsible for the recognition of viral RNA with a 5'-triphoshate modification, while the CARD domains serve as a trigger for downstream signaling, leading to the induction of type I IFN. However, to date contradicting conclusions have been reached around the role of ATP in the mechanism of the CARD domains ejection from RIG-I's autoinhibited state. Here we present an application of NMR spectroscopy to investigate changes induced by the binding of 5'-triphosphate and 5'-OH dsRNA, both in the presence and absence of nucleotides, to full length RIG-I with all its methionine residues selectively labeled (Met-[ϵ-13CH3]). With this approach we were able to identify residues on the CTD, helicase domain, and CARDs that served as probes to sense RNA-induced conformational changes in those respective regions. Our results were analyzed in the context of either agonistic or antagonistic RNAs, by and large supporting a mechanism proposed by the Pyle Lab in which CARD release is primarily dependent on the RNA binding event.
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Affiliation(s)
| | - Yan Hou
- Merck & Co., Inc., Rahway, NJ, USA
| | | | - Tony Siu
- Merck & Co., Inc., Rahway, NJ, USA
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Pal S, Kumar A, Vashisth H. Role of Dynamics and Mutations in Interactions of a Zinc Finger Antiviral Protein with CG-rich Viral RNA. J Chem Inf Model 2023; 63:1002-1011. [PMID: 36707411 PMCID: PMC10129844 DOI: 10.1021/acs.jcim.2c01487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Zinc finger antiviral protein (ZAP) is a host antiviral factor that selectively inhibits the replication of a variety of viruses. ZAP recognizes the CG-enriched RNA sequences and activates the viral RNA degradation machinery. In this work, we investigated the dynamics of a ZAP/RNA complex and computed the energetics of mutations in ZAP that affect its binding to the viral RNA. The crystal structure of a mouse-ZAP/RNA complex showed that RNA interacts with the zinc finger 2 (ZF2) and ZF3 domains. However, we found that due to the dynamic behavior of the single-stranded RNA, the terminal nucleotides C1 and G2 of RNA change their positions from the ZF3 to the ZF1 domain. Moreover, the electrostatic interactions between the zinc ions and the viral RNA provide further stability to the ZAP/RNA complex. We also provide structural and thermodynamic evidence for seven residue pairs (C1-Arg74, C1-Arg179, G2-Arg74, U3-Lys76, C4-Lys76, G5-Arg95, and U6-Glu204) that show favorable ZAP/RNA interactions, although these interactions were not observed in the ZAP/RNA crystal structure. Consistent with the observations from the mouse-ZAP/RNA crystal structure, we found that four residue pairs (C4-Lys89, C4-Leu90, C4-Tyr108, and G5-Lys107) maintained stable interactions in MD simulations. Based on experimental mutagenesis studies and our residue-level interaction analysis, we chose seven residues (Arg74, Lys76, Lys89, Arg95, Lys107, Tyr108, and Arg179) for individual alanine mutations. In addition, we studied mutations in those residues that are only observed in the crystal structures as interacting with RNA (Tyr98, Glu148, and Arg170). Out of these 10 mutations, we found that the Ala mutation in each of the five residues Arg74, Lys76, Lys89, Lys107, and Glu148 significantly reduced the binding affinity of ZAP to RNA.
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Affiliation(s)
- Saikat Pal
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire03824, United States
| | - Amit Kumar
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire03824, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire03824, United States
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Kumar A, Satpati P. Structure-based thermodynamics of ion selectivity (Mg 2+versus Ca 2+ and K +versus Na +) in the active site of the eukaryotic lariat group II intron from algae Pylaiella littoralis. Phys Chem Chem Phys 2022; 24:24192-24202. [PMID: 36168989 DOI: 10.1039/d2cp03472g] [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: 11/21/2022]
Abstract
Group II introns are metalloenzymes that can catalyze self-splicing. Recently, the crystal structures of the eukaryotic group IIB lariat intron from the brown algae Pylaiella littoralis have been reported for two intermediate states (pre-hydrolytic (2s) and post-hydrolytic) along the self-splicing pathway. Three characteristic metal-ion binding sites (M1 and M2 sites for catalytic Mg2+ ions, and K1 site for K+) in the catalytic pocket of the lariat intron have been identified and proposed to be crucial for self-splicing. Using the X-ray structures as a template, we quantitatively estimated the energetics of divalent (Mg2+versus Ca2+) and monovalent (K+versus Na+) ion selectivity and established a direct link between the energetics and structures of this lariat intron (bound to cognate and near-cognate metal ions). Molecular dynamics (MD) free energy simulations showed that the lariat intron was strongly selective between divalent metal ions. The strength of divalent metal-ion selectivity was noticeably high in the post-hydrolytic state (ΔΔG ≈ 20 kcal mol-1) relative to its pre-hydrolytic (2s) state (ΔΔG ≈ 13 kcal mol-1). Quantum chemical calculations ensured that the sign of the estimated divalent metal-ion selectivity was correct. The M1-binding pocket was less solvent-exposed in the case of the post-hydrolytic state relative to the pre-hydrolytic (2s) state, which boosted the metal-ion selectivity of the former. Surprisingly, in contrast to the bacterial linear group II intron, the lariat intron was found to be non-selective between monovalent ions (K+versus Na+). The interaction network in the first coordination shell of Ca2+ in the M1-binding pocket was different relative to Mg2+. Mg2+ substitution by Ca2+ resulted in the substitution of a single M1-RNA interaction by the M1-water interaction. In the pre-hydrolytic (2s) state, Ca2+ substitution completely disrupted the M1⋯5'-exon interaction; thus, the nature of the divalent metal ion is critical for catalysis. The interaction network in the M2 site was independent of the nature of the divalent metal ions (Mg2+ or Ca2+). The monovalent ion was loosely bound in the wet binding pocket (K1 site) of the lariat intron; thus, the substitution of K+ by Na+ could not significantly alter the free energy of the complex. The metal ion selectivity was dependent on the solvent accessibility of the metal-ion-binding-pocket, dry pocket enhanced the selectivity.
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Affiliation(s)
- Abhishek Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Kumar A, Satpati P. Divalent-Metal-Ion Selectivity of the CRISPR-Cas System-Associated Cas1 Protein: Insights from Classical Molecular Dynamics Simulations and Electronic Structure Calculations. J Phys Chem B 2021; 125:11943-11954. [PMID: 34694813 DOI: 10.1021/acs.jpcb.1c07744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-associated protein 1 (Cas1) is a universally conserved essential metalloenzyme of the clustered regularly interspaced short palindromic repeat (CRISPR) immune system of prokaryotes (bacteria, archaea) that can cut and integrate a part of viral DNA to its host genome with the help of other proteins. The integrated DNA acts as a memory of viral infection, which can be transcribed to RNA and stop future infection by recognition (based on the RNA/DNA complementarity principle) followed by protein-mediated degradation of the viral DNA. It has been proposed that the presence of a single manganese (Mn2+) ion in a conserved divalent-metal-ion binding pocket (key residues: E190, H254, D265, D268) of Cas1 is crucial for its function. Cas1-mediated DNA degradation was proposed to be hindered by metal substitution, metal chelation, or mutation of the binding pocket residues. Cas1 is active toward dsDNA degradation with both Mn2+ and Mg2+. X-ray structures of Cas1 revealed an intricate atomic interaction network of the divalent-metal-ion binding pocket and opened up the possibility of modeling related metal ions (viz., Mg2+, Ca2+) in the binding pocket of wild-type (WT) and mutated Cas1 proteins for computational analysis, which includes (1) quantitative estimation of the energetics of the divalent-metal-ion preference and (2) exploring the structural and dynamical aspects of the protein in response to divalent-metal-ion substitution or amino acid mutation. Using the X-ray structure of the Cas1 protein from Pseudomonas aeruginosa as a template (PDB 3GOD), we performed (∼2.23 μs) classical molecular dynamics (MD) simulations to compare structural and dynamical differences between Mg2+- and Ca2+-bound binding pockets of wild-type (WT) and mutant (E190A, H254A, D265A, D268A) Cas1. Furthermore, reduced binding pocket models were generated from X-ray and molecular dynamics (MD) trajectories, and the resulting structures were subjected to quantum chemical calculations. Results suggest that Cas1 prefers Mg2+ binding relative to Ca2+ and the preference is the strongest for WT and the weakest for the D268A mutant. Quantum chemical calculations indicate that Mn2+ is the most preferred relative to both Mg2+ and Ca2+ in the wild-type and mutant Cas1. Substitution of Mg2+ by Ca2+ does not alter the interaction network between Cas1 and the divalent metal ion but increases the wetness of the binding pocket by introducing a single water molecule in the first coordination shell of the latter. The strength of metal-ion preference (Mg2+ versus Ca2+) seems to be dependent on the solvent accessibility of the divalent-metal-ion binding pocket, strongest for wild-type Cas1 (in which the metal-ion binding pocket is dry, which includes two water molecules) and the weakest for the D268A mutant (in which the metal-ion binding pocket is wet, which includes four water molecules).
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Affiliation(s)
- Abhishek Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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Kumar A, Satpati P. Why double-stranded RNA with 5'-monophosphate is a poor binder to retinoic acid-inducible gene-I with respect to 5'-hydroxyl analogue? J Biomol Struct Dyn 2020; 38:4048-4055. [PMID: 31543002 DOI: 10.1080/07391102.2019.1671225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbbreviationsAActiveABNRAdopted basis Newton-RaphsonCARDsCaspase activation and recruitment domainsCTDC-terminal domaindsRNADouble-stranded RNAHEL1Helicase1HEL2Helicase2HEL2iHelicase2 insertionMDMolecular dynamicsNAInactivePPincerPDBprotein data bankPMEParticle mesh EwaldRIG-IRetinoic acid-inducible gene-IRMSDRoot mean square deviationRMSFRoot mean square fluctuationSDSteepest descentTIThermodynamic IntegrationCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amit Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Ren X, Linehan MM, Iwasaki A, Pyle AM. RIG-I Selectively Discriminates against 5'-Monophosphate RNA. Cell Rep 2020; 26:2019-2027.e4. [PMID: 30784585 DOI: 10.1016/j.celrep.2019.01.107] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/31/2018] [Accepted: 01/29/2019] [Indexed: 12/25/2022] Open
Abstract
The innate immune sensor RIG-I must sensitively detect and respond to viral RNAs that enter the cytoplasm, while remaining unresponsive to the abundance of structurally similar RNAs that are the products of host metabolism. In the case of RIG-I, these viral and host targets differ by only a few atoms, and a molecular mechanism for such selective differentiation has remained elusive. Using a combination of quantitative biophysical and immunological studies, we show that RIG-I, which is normally activated by duplex RNAs containing a 5'-tri- or diphosphate (5'-ppp or 5'-pp RNAs), is actively antagonized by RNAs containing 5'-monophosphates (5'-p RNAs). This is accomplished by a gating mechanism in which an alternative RIG-I conformation blocks the C-terminal domain (CTD) upon 5'-p RNA binding, thereby short circuiting the activation of signaling.
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Affiliation(s)
- Xiaoming Ren
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Melissa M Linehan
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Akiko Iwasaki
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Immunobiology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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Kumar A, Åqvist J, Satpati P. Principles of tRNA Ala Selection by Alanyl-tRNA Synthetase Based on the Critical G3·U70 Base Pair. ACS OMEGA 2019; 4:15539-15548. [PMID: 31572855 PMCID: PMC6761608 DOI: 10.1021/acsomega.9b01827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Throughout evolution, the presence of a single G3·U70 mismatch in the acceptor stem of tRNAAla is the major determinant for aminoacylation with alanine by alanyl-tRNA synthetase (AlaRS). Recently reported crystal structures of the complexes AlaRS-tRNAAla/G3·U70 and AlaRS-tRNAAla/A3·U70 suggest two very different conformations, representing a reactive and a nonreactive state, respectively. On the basis of these structures, it has been proposed that the G3·U70 base pair guides the -CCA end of the tRNA acceptor stem into the active site of AlaRS, thereby enabling aminoacylation. The crystal structures open up the possibility of directly computing the energetics of tRNA specificity by AlaRS. We have carried out molecular dynamics free-energy simulations to quantitatively estimate tRNA discrimination by AlaRS, focusing on the mutations of the single critical base pair G3·U70 to uncover the energetics underlying the accuracy of tRNA selection. The calculations show that the reactive complex is highly selective in favor of the cognate tRNAAla/G3·U70 over its noncognate analogues (A3·U70/G3·C70/A3·C70). In contrast, the nonreactive complex is predicted to be unselective between tRNAAla/G3·U70 and tRNAAla/A3·U70. Utilizing our calculated relative binding free energies, we show how a simple three-step kinetic scheme for aminoacylation, involving both an initial nonspecific binding step and a subsequent transition to a selective reactive complex, accounts for the observed kinetics of the process.
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Affiliation(s)
- Amit Kumar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Johan Åqvist
- Department
of Cell and Molecular Biology, Uppsala University,
Biomedical Center, Box 596, Uppsala SE-751 24, Sweden
| | - Priyadarshi Satpati
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, Assam, India
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Brisse M, Ly H. Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5. Front Immunol 2019; 10:1586. [PMID: 31379819 PMCID: PMC6652118 DOI: 10.3389/fimmu.2019.01586] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. While RIG-I and MDA5 share many genetic, structural and functional similarities, there is increasing evidence that they can have significantly different strategies to recognize different pathogens, PAMPs, and in different host species. This review article discusses the similarities and differences between RIG-I and MDA5 from multiple perspectives, including their structures, evolution and functional relationships with other cellular proteins, their differential mechanisms of distinguishing between host and viral dsRNAs and interactions with host and viral protein factors, and their immunogenic signaling. A comprehensive comparative analysis can help inform future studies of RIG-I and MDA5 in order to fully understand their functions in order to optimize potential therapeutic approaches targeting them.
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Affiliation(s)
- Morgan Brisse
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Twin Cities, St. Paul, MN, United States
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States
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Sarkar S, Maity A, Sarma Phukon A, Ghosh S, Chakrabarti R. Salt Induced Structural Collapse, Swelling, and Signature of Aggregation of Two ssDNA Strands: Insights from Molecular Dynamics Simulation. J Phys Chem B 2018; 123:47-56. [DOI: 10.1021/acs.jpcb.8b09098] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Soham Sarkar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Atanu Maity
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Aditya Sarma Phukon
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Soumadwip Ghosh
- Beckman Research Institute of the City of Hope National Medical Center, 1500 East Duarte Road, Duarte, California 91010, United States
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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