1
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Jin K, Liao YC, Cheng TC, Li X, Lee WJ, Pi F, Jasinski D, Chen LC, Phelps MA, Ho YS, Guo P. In Vitro and In Vivo Evaluation of the Pathology and Safety Aspects of Three- and Four-Way Junction RNA Nanoparticles. Mol Pharm 2024; 21:718-728. [PMID: 38214504 PMCID: PMC10976369 DOI: 10.1021/acs.molpharmaceut.3c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
RNA therapeutics has advanced into the third milestone in pharmaceutical drug development, following chemical and protein therapeutics. RNA itself can serve as therapeutics, carriers, regulators, or substrates in drug development. Due to RNA's motile, dynamic, and deformable properties, RNA nanoparticles have demonstrated spontaneous targeting and accumulation in cancer vasculature and fast excretion through the kidney glomerulus to urine to prevent possible interactions with healthy organs. Furthermore, the negatively charged phosphate backbone of RNA results in general repulsion from negatively charged lipid cell membranes for further avoidance of vital organs. Thus, RNA nanoparticles can spontaneously enrich tumor vasculature and efficiently enter tumor cells via specific targeting, while those not entering the tumor tissue will clear from the body quickly. These favorable parameters have led to the expectation that RNA has low or little toxicity. RNA nanoparticles have been well characterized for their anticancer efficacy; however, little detail on RNA nanoparticle pathology and safety is known. Here, we report the in vitro and in vivo assessment of the pathology and safety aspects of different RNA nanoparticles including RNA three-way junction (3WJ) harboring 2'-F modified pyrimidine, folic acid, and Survivin siRNA, as well as the RNA four-way junction (4WJ) harboring 2'-F modified pyrimidine and 24 copies of SN38. Both animal models and patient serum were investigated. In vitro studies include hemolysis, platelet aggregation, complement activation, plasma coagulation, and interferon induction. In vivo studies include hematoxylin and eosin (H&E) staining, hematological and biochemical analysis as the serum profiling, and animal organ weight study. No significant toxicity, side effect, or immune responses were detected during the extensive safety evaluations of RNA nanoparticles. These results further complement previous cancer inhibition studies and demonstrate RNA nanoparticles as an effective and safe drug delivery vehicle for future clinical translations.
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Affiliation(s)
- Kai Jin
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - You-Cheng Liao
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
| | - Tzu-Chun Cheng
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung 406040, Taiwan
| | - Xin Li
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Fengmei Pi
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel Jasinski
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Li-Ching Chen
- Department of Biological Science and Technology, China Medical University, Taichung 406040, Taiwan
| | - Mitch A Phelps
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan-Soon Ho
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung 406040, Taiwan
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, United States
- James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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2
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Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions. Comput Struct Biotechnol J 2022; 20:6120-6137. [PMID: 36420155 PMCID: PMC9672130 DOI: 10.1016/j.csbj.2022.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) serves to further the development of a wide variety of functional nucleic acids and other related nanotechnology platforms. To aid in the dissemination of the most recent advancements, a biennial discussion focused on biomotors, viral assembly, and RNA nanobiotechnology has been established where international experts in interdisciplinary fields such as structural biology, biophysical chemistry, nanotechnology, cell and cancer biology, and pharmacology share their latest accomplishments and future perspectives. The results summarized here highlight advancements in our understanding of viral biology and the structure-function relationship of frame-shifting elements in genomic viral RNA, improvements in the predictions of SHAPE analysis of 3D RNA structures, and the understanding of dynamic RNA structures through a variety of experimental and computational means. Additionally, recent advances in the drug delivery, vaccine design, nanopore technologies, biomotor and biomachine development, DNA packaging, RNA nanotechnology, and drug delivery are included in this critical review. We emphasize some of the novel accomplishments, major discussion topics, and present current challenges and perspectives of these emerging fields.
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3
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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4
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Li X, Bhullar AS, Binzel DW, Guo P. The dynamic, motile and deformative properties of RNA nanoparticles facilitate the third milestone of drug development. Adv Drug Deliv Rev 2022; 186:114316. [PMID: 35526663 DOI: 10.1016/j.addr.2022.114316] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/25/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022]
Abstract
Besides mRNA, rRNA, and tRNA, cells contain many other noncoding RNA that display critical roles in the regulation of cellular functions. Human genome sequencing revealed that the majority of non-protein-coding DNA actually codes for non-coding RNAs. The dynamic nature of RNA results in its motile and deformative behavior. These conformational transitions such as the change of base-pairing, breathing within complemented strands, and pseudoknot formation at the 2D level as well as the induced-fit and conformational capture at the 3D level are important for their biological functions including regulation, translation, and catalysis. The dynamic, motile and catalytic activity has led to a belief that RNA is the origin of life. We have recently reported that the deformative property of RNA nanoparticles enhances their penetration through the leaky blood vessel of cancers which leads to highly efficient tumor accumulation. This special deformative property also enables RNA nanoparticles to pass the glomerulus, overcoming the filtration size limit, resulting in fast renal excretion and rapid body clearance, thus low or no toxicity. The biodistribution of RNA nanoparticles can be further improved by the incorporation of ligands for cancer targeting. In addition to the favorable biodistribution profiles, RNA nanoparticles possess other properties including self-assembly, negative charge, programmability, and multivalency; making it a great material for pharmaceutical applications. The intrinsic negative charge of RNA nanoparticles decreases the toxicity of drugs by preventing nonspecific binding to the negative charged cell membrane and enhancing the solubility of hydrophobic drugs. The polyvalent property of RNA nanoparticles allows the multi-functionalization which can apply to overcome drug resistance. This review focuses on the summary of these unique properties of RNA nanoparticles, which describes the mechanism of RNA dynamic, motile and deformative properties, and elucidates and prepares to welcome the RNA therapeutics as the third milestone in pharmaceutical drug development.
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Affiliation(s)
- Xin Li
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Abhjeet S Bhullar
- Interdisciplinary Biophysics Graduate Program, College of Art and Science, The Ohio State University, Columbus, OH 43210, United States
| | - Daniel W Binzel
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
| | - Peixuan Guo
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, United States; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States; College of Medicine, The Ohio State University, Columbus, OH 43210, United States.
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5
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Mitroshin IV, Garber MB, Gabdulkhakov AG. Investigation of Structure of the Ribosomal L12/P Stalk. BIOCHEMISTRY (MOSCOW) 2017; 81:1589-1601. [PMID: 28260486 DOI: 10.1134/s0006297916130022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review contains recent data on the structure of the functionally important ribosomal domain, L12/P stalk, of the large ribosomal subunit. It is the most mobile site of the ribosome; it has been found in ribosomes of all living cells, and it is involved in the interaction between ribosomes and translation factors. The difference between the structures of the ribosomal proteins forming this protuberance (despite their general resemblance) determines the specificity of interaction between eukaryotic and prokaryotic ribosomes and the respective protein factors of translation. In this review, works on the structures of ribosomal proteins forming the L12/P-stalk in bacteria, archaea, and eukaryotes and data on structural aspects of interactions between these proteins and rRNA are described in detail.
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Affiliation(s)
- I V Mitroshin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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6
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Mitroshin I, Garber M, Gabdulkhakov A. Crystallographic analysis of archaeal ribosomal protein L11. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1083-7. [PMID: 26249704 DOI: 10.1107/s2053230x15011395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/12/2015] [Indexed: 11/10/2022]
Abstract
Ribosomal protein L11 is an important part of the GTPase-associated centre in ribosomes of all organisms. L11 is a highly conserved two-domain ribosomal protein. The C-terminal domain of L11 is an RNA-binding domain that binds to a fragment of 23S rRNA and stabilizes its structure. The complex between L11 and 23S rRNA is involved in the GTPase activity of the translation elongation and release factors. Bacterial and archaeal L11-rRNA complexes are targets for peptide antibiotics of the thiazole class. To date, there is no complete structure of archaeal L11 owing to the mobility of the N-terminal domain of the protein. Here, the crystallization and X-ray analysis of the ribosomal protein L11 from Methanococcus jannaschii are reported. Crystals of the native protein and its selenomethionine derivative belonged to the orthorhombic space group I222 and were suitable for structural studies. Native and single-wavelength anomalous dispersion data sets have been collected and determination of the structure is in progress.
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Affiliation(s)
- Ivan Mitroshin
- Laboratory for Structural Studies of the Translation Apparatus, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Maria Garber
- Laboratory for Structural Studies of the Translation Apparatus, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Azat Gabdulkhakov
- Laboratory for Structural Studies of the Translation Apparatus, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
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7
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Jonker HRA, Baumann S, Wolf A, Schoof S, Hiller F, Schulte KW, Kirschner KN, Schwalbe H, Arndt HD. NMR structures of thiostrepton derivatives for characterization of the ribosomal binding site. Angew Chem Int Ed Engl 2011; 50:3308-12. [PMID: 21365717 DOI: 10.1002/anie.201003582] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 09/20/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Hendrik R A Jonker
- Johann Wolfgang Goethe-Universität, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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8
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Jonker HRA, Baumann S, Wolf A, Schoof S, Hiller F, Schulte KW, Kirschner KN, Schwalbe H, Arndt HD. NMR-Strukturen von Thiostrepton-Derivaten zur Charakterisierung der ribosomalen Bindetasche. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201003582] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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A Novel Unstructured Scaffold Based on 4EBP1 Enables the Functional Display of a Wide Range of Bioactive Peptides. J Mol Biol 2010; 404:819-31. [DOI: 10.1016/j.jmb.2010.09.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 09/22/2010] [Accepted: 09/29/2010] [Indexed: 01/11/2023]
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10
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Baumann S, Schoof S, Bolten M, Haering C, Takagi M, Shin-ya K, Arndt HD. Molecular Determinants of Microbial Resistance to Thiopeptide Antibiotics. J Am Chem Soc 2010; 132:6973-81. [DOI: 10.1021/ja909317n] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sascha Baumann
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Sebastian Schoof
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Marcel Bolten
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Claudia Haering
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Motoki Takagi
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kazuo Shin-ya
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hans-Dieter Arndt
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany, and Biomedicinal Information Research Center (BIRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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11
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Yesylevskyy SO, Kharkyanen VN. Fuzzy domains: new way of describing flexibility and interdependence of the protein domains. Proteins 2009; 74:980-95. [PMID: 18767167 DOI: 10.1002/prot.22208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We proposed the innovative method of domain identification based on the concept of the fuzzy domains. In this method each residue of the protein can belong to several domains simultaneously with certain weights, which reflect to what extent this residue shares the motion pattern of the given domain. Our method allows describing the fuzzy boundaries between the domains and the gradual changes of the motion pattern from one domain to the other. It provides the reasonable compromise between the continuous change of the protein dynamics from one residue to the other and the discrete description of the structure in terms of small number of domains. We suggested quantitative criterion, which shows the overall degree of domain flexibility in the protein. The concept of the fuzzy domains provides an innovative way of visualization of domain flexibility, which makes the gradual transitions between the domains clearly visible and comparable to available experimental and structural data. In the future, the concept of the fuzzy domains can be used in the coarse-grained simulations of the domain dynamics in order to account for internal protein flexibility.
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Affiliation(s)
- Semen O Yesylevskyy
- Department of Physics of Biological Systems, Institute of Physics, National Academy of Science of Ukraine, Prospect Nauki, 46, Kiev-03039, Ukraine.
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12
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Hall KB. RNA in motion. Curr Opin Chem Biol 2008; 12:612-8. [PMID: 18957331 DOI: 10.1016/j.cbpa.2008.09.033] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/05/2008] [Accepted: 09/20/2008] [Indexed: 10/21/2022]
Abstract
Although RNA duplex regions are highly structured and inflexible, other elements of an RNA molecule are capable of dynamic motions. These flexible regions are the sites of interactions with small molecules, proteins, and other RNAs, yet there are few descriptions of these regions that include the timescale and amplitude of their motions. No one technique is sufficient to accurately describe these motions, but the combination of in vitro methods, particularly NMR relaxation methods, and more robust in silico methods, is beginning to yield the type of data that can be used to understand RNA function. Very few RNAs have been described by both techniques, and here one such RNA and one RNA:protein complex are reviewed.
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Affiliation(s)
- Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA.
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13
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Yesylevskyy SO, Kharkyanen VN, Demchenko AP. The blind search for the closed states of hinge-bending proteins. Proteins 2007; 71:831-43. [DOI: 10.1002/prot.21743] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Methylation is one of the most common protein modifications. Many different prokaryotic and eukaryotic proteins are methylated, including proteins involved in translation, including ribosomal proteins (RPs) and translation factors (TFs). Positions of the methylated residues in six Escherichia coli RPs and two Saccharomyces cerevisiae RPs have been determined. At least two RPs, L3 and L12, are methylated in both organisms. Both prokaryotic and eukaryotic elongation TFs (EF1A) are methylated at lysine residues, while both release factors are methylated at glutamine residues. The enzymes catalysing methylation reactions, protein methyltransferases (MTases), generally use S-adenosylmethionine as the methyl donor to add one to three methyl groups that, in case of arginine, can be asymetrically positioned. The biological significance of RP and TF methylation is poorly understood, and deletions of the MTase genes usually do not cause major phenotypes. Apparently methylation modulates intra- or intermolecular interactions of the target proteins or affects their affinity for RNA, and, thus, influences various cell processes, including transcriptional regulation, RNA processing, ribosome assembly, translation accuracy, protein nuclear trafficking and metabolism, and cellular signalling. Differential methylation of specific RPs and TFs in a number of organisms at different physiological states indicates that this modification may play a regulatory role.
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Affiliation(s)
- Bogdan Polevoda
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA.
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15
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Kavran JM, Steitz TA. Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements. J Mol Biol 2007; 371:1047-59. [PMID: 17599351 DOI: 10.1016/j.jmb.2007.05.091] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 05/24/2007] [Accepted: 05/30/2007] [Indexed: 11/16/2022]
Abstract
Initiation factors, elongation factors, and release factors all interact with the L7/L12 stalk of the large ribosomal subunit during their respective GTP-dependent cycles on the ribosome. Electron density corresponding to the stalk is not present in previous crystal structures of either 50 S subunits or 70 S ribosomes. We have now discovered conditions that result in a more ordered factor-binding center in the Haloarcula marismortui (H.ma) large ribosomal subunit crystals and consequently allows the visualization of the full-length L11, the N-terminal domain (NTD) of L10 and helices 43 and 44 of 23 S rRNA. The resulting model is currently the most complete reported structure of a L7/L12 stalk in the context of a ribosome. This region contains a series of intermolecular interfaces that are smaller than those typically seen in other ribonucleoprotein interactions within the 50 S subunit. Comparisons of the L11 NTD position between the current structure, which is has an NTD splayed out with respect to previous structures, and other structures of ribosomes in different functional states demonstrates a dynamic range of L11 NTD movements. We propose that the L11 NTD moves through three different relative positions during the translational cycle: apo-ribosome, factor-bound pre-GTP hydrolysis and post-GTP hydrolysis. These positions outline a pathway for L11 NTD movements that are dependent on the specific nucleotide state of the bound ligand. These three states are represented by the orientations of the L11 NTD relative to the ribosome and suggest that L11 may play a more specialized role in the factor binding cycle than previously appreciated.
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Affiliation(s)
- Jennifer M Kavran
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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16
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Demirci H, Gregory ST, Dahlberg AE, Jogl G. Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA. EMBO J 2007; 26:567-77. [PMID: 17215866 PMCID: PMC1783454 DOI: 10.1038/sj.emboj.7601508] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Accepted: 11/27/2006] [Indexed: 11/09/2022] Open
Abstract
Bacterial ribosomal protein L11 is post-translationally trimethylated at multiple residues by a single methyltransferase, PrmA. Here, we describe four structures of PrmA from the extreme thermophile Thermus thermophilus. Two apo-PrmA structures at 1.59 and 2.3 A resolution and a third with bound cofactor S-adenosyl-L-methionine at 1.75 A each exhibit distinct relative positions of the substrate recognition and catalytic domains, revealing how PrmA can position the L11 substrate for multiple, consecutive side-chain methylation reactions. The fourth structure, the PrmA-L11 enzyme-substrate complex at 2.4 A resolution, illustrates the highly specific interaction of the N-terminal domain with its substrate and places Lys39 in the PrmA active site. The presence of a unique flexible loop in the cofactor-binding site suggests how exchange of AdoMet with the reaction product S-adenosyl-L-homocysteine can occur without necessitating the dissociation of PrmA from L11. Finally, the mode of interaction of PrmA with L11 explains its observed preference for L11 as substrate before its assembly into the 50S ribosomal subunit.
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Affiliation(s)
- Hasan Demirci
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Steven T Gregory
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Albert E Dahlberg
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Box G-E129, Providence, RI 2912, USA. Tel.: +1 401 863 6123; Fax: +1 401 863 6114; E-mail:
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17
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Lee D, Walsh JD, Yu P, Markus MA, Choli-Papadopoulou T, Schwieters CD, Krueger S, Draper DE, Wang YX. The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes. J Mol Biol 2007; 367:1007-22. [PMID: 17292917 PMCID: PMC2045704 DOI: 10.1016/j.jmb.2007.01.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 11/21/2006] [Accepted: 01/04/2007] [Indexed: 11/22/2022]
Abstract
The L11 binding site is one of the most important functional sites in the ribosome. The N-terminal domain of L11 has been implicated as a "reversible switch" in facilitating the coordinated movements associated with EF-G-driven GTP hydrolysis. The reversible switch mechanism has been hypothesized to require conformational flexibility involving re-orientation and re-positioning of the two L11 domains, and warrants a close examination of the structure and dynamics of L11. Here we report the solution structure of free L11, and relaxation studies of free L11, L11 complexed to its 58 nt RNA recognition site, and L11 in a ternary complex with the RNA and thiostrepton antibiotic. The binding site of thiostrepton on L11 was also defined by analysis of structural and dynamics data and chemical shift mapping. The conclusions of this work are as follows: first, the binding of L11 to RNA leads to sizable conformation changes in the regions flanking the linker and in the hinge area that links a beta-sheet and a 3(10)-helix-turn-helix element in the N terminus. Concurrently, the change in the relative orientation may lead to re-positioning of the N terminus, as implied by a decrease of radius of gyration from 18.5 A to 16.2 A. Second, the regions, which undergo large conformation changes, exhibit motions on milliseconds-microseconds or nanoseconds-picoseconds time scales. Third, binding of thiostrepton results in more rigid conformations near the linker (Thr71) and near its putative binding site (Leu12). Lastly, conformational changes in the putative thiostrepton binding site are implicated by the re-emergence of cross-correlation peaks in the spectrum of the ternary complex, which were missing in that of the binary complex. Our combined analysis of both the chemical shift perturbation and dynamics data clearly indicates that thiostrepton binds to a pocket involving residues in the 3(10)-helix in L11.
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Affiliation(s)
- Donghan Lee
- Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, NIH, Frederick, MD 21702, U.S.A
- Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, U.S.A
| | - Joseph D. Walsh
- Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, NIH, Frederick, MD 21702, U.S.A
| | - Ping Yu
- Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, NIH, Frederick, MD 21702, U.S.A
- Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, U.S.A
| | - Michelle A. Markus
- Structural Biology and Computational Chemistry, Wyeth Research, 87 CambridgePark Drive Cambridge, MA 02140
| | - Theodora Choli-Papadopoulou
- Laboratory of Biochemistry, School of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54006, Greece
| | - Charles D. Schwieters
- Computational Bioscience and Engineering Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624
| | - Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8562, Bldg. 235/Room E151, Gaithersburg, MD 20899-8562, U.S.A
| | - David E. Draper
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21210, U.S.A
| | - Yun-Xing Wang
- Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, NIH, Frederick, MD 21702, U.S.A
- *To whom correspondence should be addressed: (e-mail) , (Phone) 301-846-5985, (Fax) 301-846-6231
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18
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Conners SB, Mongodin EF, Johnson MR, Montero CI, Nelson KE, Kelly RM. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species. FEMS Microbiol Rev 2006; 30:872-905. [PMID: 17064285 DOI: 10.1111/j.1574-6976.2006.00039.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
High-throughput sequencing of microbial genomes has allowed the application of functional genomics methods to species lacking well-developed genetic systems. For the model hyperthermophile Thermotoga maritima, microarrays have been used in comparative genomic hybridization studies to investigate diversity among Thermotoga species. Transcriptional data have assisted in prediction of pathways for carbohydrate utilization, iron-sulfur cluster synthesis and repair, expolysaccharide formation, and quorum sensing. Structural genomics efforts aimed at the T. maritima proteome have yielded hundreds of high-resolution datasets and predicted functions for uncharacterized proteins. The information gained from genomics studies will be particularly useful for developing new biotechnology applications for T. maritima enzymes.
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Affiliation(s)
- Shannon B Conners
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
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19
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Jonker HRA, Ilin S, Grimm SK, Wöhnert J, Schwalbe H. L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy. Nucleic Acids Res 2006; 35:441-54. [PMID: 17169991 PMCID: PMC1802607 DOI: 10.1093/nar/gkl1066] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Ribosomal proteins are assumed to stabilize specific RNA structures and promote compact folding of the large rRNA. The conformational dynamics of the protein between the bound and unbound state play an important role in the binding process. We have studied those dynamical changes in detail for the highly conserved complex between the ribosomal protein L11 and the GTPase region of 23S rRNA. The RNA domain is compactly folded into a well defined tertiary structure, which is further stabilized by the association with the C-terminal domain of the L11 protein (L11ctd). In addition, the N-terminal domain of L11 (L11ntd) is implicated in the binding of the natural thiazole antibiotic thiostrepton, which disrupts the elongation factor function. We have studied the conformation of the ribosomal protein and its dynamics by NMR in the unbound state, the RNA bound state and in the ternary complex with the RNA and thiostrepton. Our data reveal a rearrangement of the L11ntd, placing it closer to the RNA after binding of thiostrepton, which may prevent binding of elongation factors. We propose a model for the ternary L11–RNA–thiostrepton complex that is additionally based on interaction data and conformational information of the L11 protein. The model is consistent with earlier findings and provides an explanation for the role of L11ntd in elongation factor binding.
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Affiliation(s)
- Hendrik R. A. Jonker
- Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic ResonanceMax-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Serge Ilin
- Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic ResonanceMax-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - S. Kaspar Grimm
- Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic ResonanceMax-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
- University of Texas Health Science Center SA, Department of Biochemistry7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Jens Wöhnert
- Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic ResonanceMax-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
- University of Texas Health Science Center SA, Department of Biochemistry7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Harald Schwalbe
- Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic ResonanceMax-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
- To whom correspondence should be addressed. Tel: +69 7982 9737; Fax: +69 7982 9515;
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20
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Yesylevskyy SO, Kharkyanen VN, Demchenko AP. The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon? Biophys J 2006; 91:3002-13. [PMID: 16877502 PMCID: PMC1578460 DOI: 10.1529/biophysj.106.087866] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of changes in the dynamics of protein domains on ligand binding is important in several aspects: for the understanding of the hierarchical nature of protein folding and dynamics at equilibrium; for analysis of signal transduction mechanisms triggered by ligand binding, including allostery; for drug design; and for construction of biosensors reporting on the presence of target ligand in studied media. In this work we use the recently developed HCCP computational technique for the analysis of stabilities of dynamic domains in proteins, their intrinsic motions and of their changes on ligand binding. The work is based on comparative studies of 157 ligand binding proteins, for which several crystal structures (in ligand-free and ligand-bound forms) are available. We demonstrate that the domains of the proteins presented in the Protein DataBank are far more robust than it was thought before: in the majority of the studied proteins (152 out of 157), the ligand binding does not lead to significant change of domain stability. The exceptions from this rule are only four bacterial periplasmic transport proteins and calmodulin. Thus, as a rule, the pattern of correlated motions in dynamic domains, which determines their stability, is insensitive to ligand binding. This rule may be the general feature for a vast majority of proteins.
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Affiliation(s)
- Semen O Yesylevskyy
- Department of Physics of Biological Systems, Institute of Physics, National Academy of Science of Ukraine, Kiev, Ukraine.
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