1
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Mahdizadeh SJ, Pålsson E, Carlesso A, Chevet E, Eriksson LA. QM/MM Well-Tempered Metadynamics Study of the Mechanism of XBP1 mRNA Cleavage by Inositol Requiring Enzyme 1α RNase. J Chem Inf Model 2022; 62:4247-4260. [PMID: 35960929 PMCID: PMC9472280 DOI: 10.1021/acs.jcim.2c00735] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A range of in silico methodologies were herein employed to study the unconventional XBP1 mRNA cleavage mechanism performed by the unfolded protein response (UPR) mediator Inositol Requiring Enzyme 1α (IRE1). Using Protein-RNA molecular docking along with a series of extensive restrained/unrestrained atomistic molecular dynamics (MD) simulations, the dynamical behavior of the system was evaluated and a reliable model of the IRE1/XBP1 mRNA complex was constructed. From a series of well-converged quantum mechanics molecular mechanics well-tempered metadynamics (QM/MM WT-MetaD) simulations using the Grimme dispersion interaction corrected semiempirical parametrization method 6 level of theory (PM6-D3) and the AMBER14SB-OL3 force field, the free energy profile of the cleavage mechanism was determined, along with intermediates and transition state structures. The results show two distinct reaction paths based on general acid-general base type mechanisms, with different activation energies that perfectly match observations from experimental mutagenesis data. The study brings unique atomistic insights into the cleavage mechanism of XBP1 mRNA by IRE1 and clarifies the roles of the catalytic residues H910 and Y892. Increased understanding of the details in UPR signaling can assist in the development of new therapeutic agents for its modulation.
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Affiliation(s)
- Sayyed Jalil Mahdizadeh
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Emil Pålsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Antonio Carlesso
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden.,Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera Italiana (USI),, Lugano 6904, Switzerland.,Department of Pharmacology, Sahlgrenska Academy, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Eric Chevet
- INSERM U1242, University of Rennes 1, 35000 Rennes, France.,Centre Eugène Marquis, 35000 Rennes, France
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
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2
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Shotgun scanning glycomutagenesis: A simple and efficient strategy for constructing and characterizing neoglycoproteins. Proc Natl Acad Sci U S A 2021; 118:2107440118. [PMID: 34551980 PMCID: PMC8488656 DOI: 10.1073/pnas.2107440118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2021] [Indexed: 11/18/2022] Open
Abstract
Asparagine-linked (N-linked) protein glycosylation—the covalent attachment of complex sugars to the nitrogen atom in asparagine side chains—is the most widespread posttranslational modification to proteins and also the most complex. N-glycosylation affects a significant number of cellular proteins and can have profound effects on their most important attributes such as biological activity, chemical solubility, folding and stability, immunogenicity, and serum half-life. Accordingly, the strategic installation of glycans at naïve sites has become an attractive means for endowing proteins with advantageous biological and/or biophysical properties. Here, we describe a glycoprotein engineering strategy that enables systematic investigation of the structural and functional consequences of glycan installation at every position along a protein backbone and provides a new route to bespoke glycoproteins. As a common protein modification, asparagine-linked (N-linked) glycosylation has the capacity to greatly influence the biological and biophysical properties of proteins. However, the routine use of glycosylation as a strategy for engineering proteins with advantageous properties is limited by our inability to construct and screen large collections of glycoproteins for cataloguing the consequences of glycan installation. To address this challenge, we describe a combinatorial strategy termed shotgun scanning glycomutagenesis in which DNA libraries encoding all possible glycosylation site variants of a given protein are constructed and subsequently expressed in glycosylation-competent bacteria, thereby enabling rapid determination of glycosylatable sites in the protein. The resulting neoglycoproteins can be readily subjected to available high-throughput assays, making it possible to systematically investigate the structural and functional consequences of glycan conjugation along a protein backbone. The utility of this approach was demonstrated with three different acceptor proteins, namely bacterial immunity protein Im7, bovine pancreatic ribonuclease A, and human anti-HER2 single-chain Fv antibody, all of which were found to tolerate N-glycan attachment at a large number of positions and with relatively high efficiency. The stability and activity of many glycovariants was measurably altered by N-linked glycans in a manner that critically depended on the precise location of the modification. Structural models suggested that affinity was improved by creating novel interfacial contacts with a glycan at the periphery of a protein–protein interface. Importantly, we anticipate that our glycomutagenesis workflow should provide access to unexplored regions of glycoprotein structural space and to custom-made neoglycoproteins with desirable properties.
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3
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Eidelpes R, Hofer F, Röck M, Führer S, Kamenik AS, Liedl KR, Tollinger M. Structure and Zeatin Binding of the Peach Allergen Pru p 1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8120-8129. [PMID: 34260238 PMCID: PMC8323099 DOI: 10.1021/acs.jafc.1c01876] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/18/2021] [Accepted: 07/02/2021] [Indexed: 05/29/2023]
Abstract
Peach (Prunus persica) is among the fruits most frequently reported to cause food allergies. Allergic reactions commonly result from previous sensitization to the birch pollen allergen Bet v 1, followed by immunological cross-reactivity of IgE antibodies to structurally related proteins in peach. In this study, we present the three-dimensional NMR solution structure of the cross-reactive peach allergen Pru p 1 (isoform Pru p 1.0101). This 17.5 kDa protein adopts the canonical Bet v 1 fold, composed of a seven-stranded β-sheet and three α-helices enclosing an internal cavity. In Pru p 1, the inner surface of the cavity contains an array of hydroxyl-bearing amino acids surrounded by a hydrophobic patch, constituting a docking site for amphiphilic molecules. NMR-guided docking of the cytokinin molecule zeatin to the internal cavity of Pru p 1 provides a structure-based rationale for the effect that zeatin binding has on the protein's RNase activity.
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Affiliation(s)
- Reiner Eidelpes
- Institute
of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Florian Hofer
- Institute
of General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Manuel Röck
- Institute
of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Sebastian Führer
- Institute
of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Anna Sophia Kamenik
- Institute
of General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute
of General, Inorganic and Theoretical Chemistry, Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute
of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
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4
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Panova V, Gogoi M, Rodriguez-Rodriguez N, Sivasubramaniam M, Jolin HE, Heycock MWD, Walker JA, Rana BMJ, Drynan LF, Hodskinson M, Pannell R, King G, Wing M, Easton AJ, Oedekoven CA, Kent DG, Fallon PG, Barlow JL, McKenzie ANJ. Group-2 innate lymphoid cell-dependent regulation of tissue neutrophil migration by alternatively activated macrophage-secreted Ear11. Mucosal Immunol 2021; 14:26-37. [PMID: 32457448 PMCID: PMC7790759 DOI: 10.1038/s41385-020-0298-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/13/2020] [Accepted: 04/22/2020] [Indexed: 02/04/2023]
Abstract
Type-2 immunity is characterised by interleukin (IL)-4, IL-5 and IL-13, eosinophilia, mucus production, IgE, and alternatively activated macrophages (AAM). However, despite the lack of neutrophil chemoattractants such as CXCL1, neutrophils, a feature of type-1 immunity, are observed in type-2 responses. Consequently, alternative mechanisms must exist to ensure that neutrophils can contribute to type-2 immune reactions without escalation of deleterious inflammation. We now demonstrate that type-2 immune-associated neutrophil infiltration is regulated by the mouse RNase A homologue, eosinophil-associated ribonuclease 11 (Ear11), which is secreted by AAM downstream of IL-25-stimulated ILC2. Transgenic overexpression of Ear11 resulted in tissue neutrophilia, whereas Ear11-deficient mice have fewer resting tissue neutrophils, whilst other type-2 immune responses are not impaired. Notably, administration of recombinant mouse Ear11 increases neutrophil motility and recruitment. Thus, Ear11 helps maintain tissue neutrophils at homoeostasis and during type-2 reactions when chemokine-producing classically activated macrophages are infrequently elicited.
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Affiliation(s)
- Veera Panova
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK ,grid.451388.30000 0004 1795 1830Present Address: The Francis Crick Institute, London, NW1 1AT UK
| | - Mayuri Gogoi
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Noe Rodriguez-Rodriguez
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Meera Sivasubramaniam
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Helen E. Jolin
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Morgan W. D. Heycock
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Jennifer A. Walker
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Batika M. J. Rana
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Lesley F. Drynan
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Michael Hodskinson
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Richard Pannell
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Gareth King
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Mark Wing
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
| | - Andrew J. Easton
- grid.7372.10000 0000 8809 1613School of Life Sciences, University of Warwick, Coventry, CV4 7AL UK
| | | | - David G. Kent
- Stem Cell Institute, Clifford-Allbutt Building, Hills Road, Cambridge, CB2 0AH UK ,grid.5685.e0000 0004 1936 9668Present Address: Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
| | - Padraic G. Fallon
- grid.8217.c0000 0004 1936 9705Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Jillian L. Barlow
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK ,grid.5685.e0000 0004 1936 9668Present Address: Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
| | - Andrew N. J. McKenzie
- grid.42475.300000 0004 0605 769XMedical Research Council, Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH UK
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5
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Pillon MC, Goslen KH, Gordon J, Wells ML, Williams JG, Stanley RE. It takes two (Las1 HEPN endoribonuclease domains) to cut RNA correctly. J Biol Chem 2020; 295:5857-5870. [PMID: 32220933 DOI: 10.1074/jbc.ra119.011193] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 03/23/2020] [Indexed: 12/26/2022] Open
Abstract
The ribosome biogenesis factor Las1 is an essential endoribonuclease that is well-conserved across eukaryotes and a newly established member of the higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain-containing nuclease family. HEPN nucleases participate in diverse RNA cleavage pathways and share a short HEPN nuclease motif (RφXXXH) important for RNA cleavage. Most HEPN nucleases participate in stress-activated RNA cleavage pathways; Las1 plays a fundamental role in processing pre-rRNA. Underscoring the significance of Las1 function in the cell, mutations in the human LAS1L (LAS1-like) gene have been associated with neurological dysfunction. Two juxtaposed HEPN nuclease motifs create Las1's composite nuclease active site, but the roles of the individual HEPN motif residues are poorly defined. Here using a combination of in vivo experiments in Saccharomyces cerevisiae and in vitro assays, we show that both HEPN nuclease motifs are required for Las1 nuclease activity and fidelity. Through in-depth sequence analysis and systematic mutagenesis, we determined the consensus HEPN motif in the Las1 subfamily and uncovered its canonical and specialized elements. Using reconstituted Las1 HEPN-HEPN' chimeras, we defined the molecular requirements for RNA cleavage. Intriguingly, both copies of the Las1 HEPN motif were important for nuclease function, revealing that both HEPN motifs participate in coordinating the RNA within the Las1 active site. We also established that conformational flexibility of the two HEPN domains is important for proper nuclease function. The results of our work reveal critical information about how dual HEPN domains come together to drive Las1-mediated RNA cleavage.
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Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Kevin H Goslen
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Jacob Gordon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Melissa L Wells
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Jason G Williams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709.
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6
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Bafna K, Narayanan C, Chennubhotla SC, Doucet N, Agarwal PK. Nucleotide substrate binding characterization in human pancreatic-type ribonucleases. PLoS One 2019; 14:e0220037. [PMID: 31393891 PMCID: PMC6687278 DOI: 10.1371/journal.pone.0220037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/07/2019] [Indexed: 12/15/2022] Open
Abstract
Human genome contains a group of more than a dozen similar genes with diverse biological functions including antiviral, antibacterial and angiogenesis activities. The characterized gene products of this group show significant sequence similarity and a common structural fold associated with binding and cleavage of ribonucleic acid (RNA) substrates. Therefore, these proteins have been categorized as members of human pancreatic-type ribonucleases (hRNases). hRNases differ in cell/tissue localization and display distinct substrate binding preferences and a wide range of ribonucleolytic catalytic efficiencies. Limited information is available about structural and dynamical properties that influence this diversity among these homologous RNases. Here, we use computer simulations to characterize substrate interactions, electrostatics and dynamical properties of hRNases 1-7 associated with binding to two nucleotide substrates (ACAC and AUAU). Results indicate that even with complete conservation of active-site catalytic triad associated with ribonucleolytic activity, these enzymes show significant differences in substrate interactions. Detailed characterization suggests that in addition to binding site electrostatic and van der Waals interactions, dynamics of distal regions may also play a role in binding. Another key insight is that a small difference in temperature of 300 K (used in experimental studies) and 310 K (physiological temperature) shows significant changes in enzyme-substrate interactions.
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Affiliation(s)
- Khushboo Bafna
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - S. Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Québec, Quebec, Canada
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
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7
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Tomić A, Abramić M, Spoljarić J, Agić D, Smith DM, Tomić S. Human dipeptidyl peptidase III: insights into ligand binding from a combined experimental and computational approach. J Mol Recognit 2012; 24:804-14. [PMID: 21812054 DOI: 10.1002/jmr.1115] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human dipeptidyl peptidase III (DPP III) is a zinc-exopeptidase with implied roles in protein catabolism, pain modulation, and defense against oxidative stress. To understand the mode of ligand binding into its active site, we performed molecular modeling, site-directed mutagenesis, and biochemical analyses. Using the recently determined crystal structure of the human DPP III we built complexes between both, the wild-type (WT) protein and its mutant H568N with the preferred substrate Arg-Arg-2-naphthylamide (RRNA) and a competitive inhibitor Tyr-Phe-hydroxamate (Tyr-Phe-NHOH). The mutation of the conserved His568, structurally equivalent to catalytically important His231 in thermolysin, to Asn, resulted in a 1300-fold decrease of k(cat) for RRNA hydrolysis and in significantly lowered affinity for the inhibitor. Molecular dynamics simulations revealed the key protein-ligand interactions as well as the ligand-induced reorganization of the binding site and its partial closure. Simultaneously, the non-catalytic domain was observed to stretch and the opening at the wide side of the inter-domain cleft became enhanced. The driving force for these changes was the formation of the hydrogen bond between Asp372 and the bound ligand. The structural and dynamical differences, found for the ligand binding to the WT enzyme and the H568N mutant, and the calculated binding free energies, agree well with the measured affinities. On the basis of the obtained results we suggest a possible reaction mechanism. In addition, this work provides a foundation for further site-directed mutagenesis experiments, as well as for modeling the reaction itself.
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Affiliation(s)
- Antonija Tomić
- Division of Physical Chemistry, Rudjer Bošković Institute Bijenička 54,10002 Zagreb, Croatia
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8
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Korennykh AV, Korostelev AA, Egea PF, Finer-Moore J, Stroud RM, Zhang C, Shokat KM, Walter P. Structural and functional basis for RNA cleavage by Ire1. BMC Biol 2011; 9:47. [PMID: 21729333 PMCID: PMC3149027 DOI: 10.1186/1741-7007-9-47] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 07/06/2011] [Indexed: 11/12/2022] Open
Abstract
Background The unfolded protein response (UPR) controls the protein folding capacity of the endoplasmic reticulum (ER). Central to this signaling pathway is the ER-resident bifunctional transmembrane kinase/endoribonuclease Ire1. The endoribonuclease (RNase) domain of Ire1 initiates a non-conventional mRNA splicing reaction, leading to the production of a transcription factor that controls UPR target genes. The mRNA splicing reaction is an obligatory step of Ire1 signaling, yet its mechanism has remained poorly understood due to the absence of substrate-bound crystal structures of Ire1, the lack of structural similarity between Ire1 and other RNases, and a scarcity of quantitative enzymological data. Here, we experimentally define the active site of Ire1 RNase and quantitatively evaluate the contribution of the key active site residues to catalysis. Results This analysis and two new crystal structures suggest that Ire1 RNase uses histidine H1061 and tyrosine Y1043 as the general acid-general base pair contributing ≥ 7.6 kcal/mol and 1.4 kcal/mol to transition state stabilization, respectively, and asparagine N1057 and arginine R1056 for coordination of the scissile phosphate. Investigation of the stem-loop recognition revealed that additionally to the stem-loops derived from the classic Ire1 substrates HAC1 and Xbp1 mRNA, Ire1 can site-specifically and rapidly cleave anticodon stem-loop (ASL) of unmodified tRNAPhe, extending known substrate specificity of Ire1 RNase. Conclusions Our data define the catalytic center of Ire1 RNase and suggest a mechanism of RNA cleavage: each RNase monomer apparently contains a separate catalytic apparatus for RNA cleavage, whereas two RNase subunits contribute to RNA stem-loop docking. Conservation of the key residues among Ire1 homologues suggests that the mechanism elucidated here for yeast Ire1 applies to Ire1 in metazoan cells, and to the only known Ire1 homologue RNase L.
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Affiliation(s)
- Alexei V Korennykh
- Howard Hughes Medical Institute, University Of California, San Francisco, Genentech Hall, 600-16th Street, San Francisco, CA 94158, USA.
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9
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Formoso E, Matxain JM, Lopez X, York DM. Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes. J Phys Chem B 2010; 114:7371-82. [PMID: 20455590 PMCID: PMC2892782 DOI: 10.1021/jp909004y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.
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Affiliation(s)
- Elena Formoso
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain.
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10
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Cassano AG, Anderson VE, Harris ME. Understanding the transition states of phosphodiester bond cleavage: insights from heavy atom isotope effects. Biopolymers 2004; 73:110-29. [PMID: 14691944 DOI: 10.1002/bip.10517] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nucleotides of DNA and RNA are joined by phosphodiester linkages whose synthesis and hydrolysis are catalyzed by numerous essential enzymes. Two prominent mechanisms have been proposed for RNA and protein enzyme catalyzed cleavage of phosphodiester bonds in RNA: (a) intramolecular nucleophilic attack by the 2'-hydroxyl group adjacent to the reactive phosphate; and (b) intermolecular nucleophilic attack by hydroxide, or other oxyanion. The general features of these two mechanisms have been established by physical organic chemical analyses; however, a more detailed understanding of the transition states of these reactions is emerging from recent kinetic isotope effect (KIE) studies. The recent data show interesting differences between the chemical mechanisms and transition state structures of the inter- and intramolecular reactions, as well as provide information on the impact of metal ion, acid, and base catalysis on these mechanisms. Importantly, recent nonenzymatic model studies show that interactions with divalent metal ions, an important feature of many phosphodiesterase active sites, can influence both the mechanism and transition state structure of nonenzymatic phosphodiester cleavage. Such detailed investigations are important because they mimic catalytic strategies employed by both RNA and protein phosphodiesterases, and so set the stage for explorations of enzyme-catalyzed transition states. Application of KIE analyses for this class of enzymes is just beginning, and several important technical challenges remain to be overcome. Nonetheless, such studies hold great promise since they will provide novel insights into the role of metal ions and other active site interactions.
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Affiliation(s)
- Adam G Cassano
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
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11
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12
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Peeters A, Swerts B, Van Alsenoy C. Ab Initio and Molecular Dynamics Study of the Active Site of the Reaction between Ribonuclease A and Cytidyl-3‘,5‘-Adenosine. J Phys Chem B 2003. [DOI: 10.1021/jp027648d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anik Peeters
- Department of Chemistry, University of Antwerp (UIA), Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Ben Swerts
- Department of Chemistry, University of Antwerp (UIA), Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Christian Van Alsenoy
- Department of Chemistry, University of Antwerp (UIA), Universiteitsplein 1, B-2610 Wilrijk, Belgium
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13
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Replacement of His12 or His119 of bovine pancreatic ribonuclease A with acidic amino acid residues for the modification of activity and stability. J Biosci Bioeng 2002. [DOI: 10.1016/s1389-1723(02)80114-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Jardine AM, Leonidas DD, Jenkins JL, Park C, Raines RT, Acharya KR, Shapiro R. Cleavage of 3',5'-pyrophosphate-linked dinucleotides by ribonuclease A and angiogenin. Biochemistry 2001; 40:10262-72. [PMID: 11513604 DOI: 10.1021/bi010888j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, 3',5'-pyrophosphate-linked 2'-deoxyribodinucleotides were shown to be >100-fold more effective inhibitors of RNase A superfamily enzymes than were the corresponding monophosphate-linked (i.e., standard) dinucleotides. Here, we have investigated two ribo analogues of these compounds, cytidine 3'-pyrophosphate (P'-->5') adenosine (CppA) and uridine 3'-pyrophosphate (P'-->5') adenosine (UppA), as potential substrates for RNase A and angiogenin. CppA and UppA are cleaved efficiently by RNase A, yielding as products 5'-AMP and cytidine or uridine cyclic 2',3'-phosphate. The k(cat)/K(m) values are only 4-fold smaller than for the standard dinucleotides CpA and UpA, and the K(m) values (10-16 microM) are lower than those reported for any earlier small substrates (e.g., 500-700 microM for CpA and UpA). The k(cat)/K(m) value for CppA with angiogenin is also only severalfold smaller than for CpA, but the effect of lengthening the internucleotide linkage on K(m) is more modest. Ribonucleotide 3',5'-pyrophosphate linkages were proposed previously to exist in nature as chemically labile intermediates in the pathway for the generation of cyclic 2',3'-phosphate termini in various RNAs. We demonstrate that in fact they are relatively stable (t(1/2) > 15 days for uncatalyzed degradation of UppA at pH 6 and 25 degrees C) and that cleavage in vivo is most likely enzymatic. Replacements of the RNase A catalytic residues His12 and His119 by alanine reduce activity toward UppA by approximately 10(5)-and 10(3.3)-fold, respectively. Thus, both residues play important roles. His12 probably acts as a base catalyst in cleavage of UppA (as with RNA). However, the major function of His119 in RNA cleavage, protonation of the 5'-O leaving group, is not required for UppA cleavage because the pK(a) of the leaving group is much lower than that for RNA substrates. A crystal structure of the complex of RNase A with 2'-deoxyuridine 3'-pyrophosphate (P'-->5') adenosine (dUppA), determined at 1.7 A resolution, together with models of the UppA complex based on this structure suggest that His119 contributes to UppA cleavage through a hydrogen bond with a nonbridging oxygen atom in the pyrophosphate and through pi-pi stacking with the six-membered ring of adenine.
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Affiliation(s)
- A M Jardine
- Center for Biochemical and Biophysical Sciences and Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
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Chatani E, Hayashi R. Functional and structural roles of constituent amino acid residues of bovine pancreatic ribonuclease A. J Biosci Bioeng 2001. [DOI: 10.1016/s1389-1723(01)80208-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Konevetz DA, Beck IE, Beloglazova NG, Sulimenkov IV, Sil'nikov VN, Zenkova MA, Shishkin GV, Vlassov VV. Artificial ribonucleases: synthesis and RNA cleaving properties of cationic conjugates bearing imidazole residues. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(98)01048-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Affiliation(s)
- Ronald T. Raines
- Departments of Biochemistry and Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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