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Hirano M, Yokoo H, Goto C, Oba M, Misawa T, Demizu Y. Magainin 2-derived stapled peptides derived with the ability to deliver pDNA, mRNA, and siRNA into cells. Chem Sci 2023; 14:10403-10410. [PMID: 37799999 PMCID: PMC10548513 DOI: 10.1039/d3sc04124g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 08/27/2023] [Indexed: 10/07/2023] Open
Abstract
We have developed cell-penetrating stapled peptides based on the amphipathic antimicrobial peptide magainin 2 for intracellular delivery of nucleic acids such as pDNA, mRNA, and siRNA. Various types of stapled peptides with a cross-linked structure were synthesised in the hydrophobic region of the amphipathic structure, and their efficacy in intracellular delivery of pDNA was evaluated. The results showed that the stapled peptide st7-5 could deliver pDNA into cells. To improve the deliverability of st7-5, we further designed st7-5_R, in which the Lys residues were replaced by Arg residues. The peptide st7-5_R formed compact and stable complexes with pDNA and was able to efficiently transfer pDNA into the cell. In addition to pDNA, st7-5_R was also able to deliver mRNA and siRNA into the cell. Thus, st7-5_R is a novel peptide that can achieve efficient intracellular delivery of three different nucleic acids.
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Affiliation(s)
- Motoharu Hirano
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26 Tonomachi Kawasaki Kanagawa 210-9501 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Yokohama Kanagawa 230-0045 Japan
| | - Hidetomo Yokoo
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26 Tonomachi Kawasaki Kanagawa 210-9501 Japan
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kyoto 606-0823 Japan
| | - Chihiro Goto
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26 Tonomachi Kawasaki Kanagawa 210-9501 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Yokohama Kanagawa 230-0045 Japan
| | - Makoto Oba
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kyoto 606-0823 Japan
| | - Takashi Misawa
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26 Tonomachi Kawasaki Kanagawa 210-9501 Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences 3-25-26 Tonomachi Kawasaki Kanagawa 210-9501 Japan
- Graduate School of Medical Life Science, Yokohama City University 1-7-29 Yokohama Kanagawa 230-0045 Japan
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Division of Pharmaceutical Science of Okayama University 1-1-1 Tsushimanaka Kita 700-8530 Japan
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2
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Egli M, Zhang S. Ned Seeman and the prediction of amino acid-basepair motifs mediating protein-nucleic acid recognition. Biophys J 2022; 121:4777-4787. [PMID: 35711143 PMCID: PMC9808504 DOI: 10.1016/j.bpj.2022.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 06/10/2022] [Indexed: 01/07/2023] Open
Abstract
Fifty years ago, the first atomic-resolution structure of a nucleic acid double helix, the mini-duplex (ApU)2, revealed details of basepair geometry, stacking, sugar conformation, and backbone torsion angles, thereby superseding earlier models based on x-ray fiber diffraction, including the original DNA double helix proposed by Watson and Crick. Just 3 years later, in 1976, Ned Seeman, John Rosenberg, and Alex Rich leapt from their structures of mini-duplexes and H-bonding motifs between bases in small-molecule structures and transfer RNA to predicting how proteins could sequence specifically recognize double helix nucleic acids. They proposed interactions between amino acid side chains and nucleobases mediated by two hydrogen bonds in the major or minor grooves. One of these, the arginine-guanine pair, emerged as the most favored amino acid-base interaction in experimental structures of protein-nucleic acid complexes determined since 1986. In this brief review we revisit the pioneering work by Seeman et al. and discuss the importance of the arginine-guanine pairing motif.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee.
| | - Shuguang Zhang
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts
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3
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Statistical potentials for RNA-protein interactions optimized by CMA-ES. J Mol Graph Model 2021; 110:108044. [PMID: 34736056 DOI: 10.1016/j.jmgm.2021.108044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/24/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022]
Abstract
Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.
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4
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Matsuoka T, Nagae T, Ode H, Awazu H, Kurosawa T, Hamano A, Matsuoka K, Hachiya A, Imahashi M, Yokomaku Y, Watanabe N, Iwatani Y. Structural basis of chimpanzee APOBEC3H dimerization stabilized by double-stranded RNA. Nucleic Acids Res 2019; 46:10368-10379. [PMID: 30060196 PMCID: PMC6212771 DOI: 10.1093/nar/gky676] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/17/2018] [Indexed: 12/22/2022] Open
Abstract
APOBEC3H (A3H) is a mammal-specific cytidine deaminase that potently restricts the replication of retroviruses. Primate A3Hs are known to exert key selective pressures against the cross-species transmission of primate immunodeficiency viruses from chimpanzees to humans. Despite recent advances, the molecular structures underlying the functional mechanisms of primate A3Hs have not been fully understood. Here, we reveal the 2.20-Å crystal structure of the chimpanzee A3H (cpzA3H) dimer bound to a short double-stranded RNA (dsRNA), which appears to be similar to two recently reported structures of pig-tailed macaque A3H and human A3H. In the structure, the dsRNA-binding interface forms a specialized architecture with unique features. The analysis of the dsRNA nucleotides in the cpzA3H complex revealed the GC-rich palindrome-like sequence preference for dsRNA interaction, which is largely determined by arginine residues in loop 1. In cells, alterations of the cpzA3H residues critical for the dsRNA interaction severely reduce intracellular protein stability due to proteasomal degradation. This suggests that cpzA3H stability is regulated by the dsRNA-mediated dimerization as well as by unknown cellular machinery through proteasomal degradation in cells. Taken together, these findings highlight unique structural features of primate A3Hs that are important to further understand their cellular functions and regulation.
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Affiliation(s)
- Tatsuya Matsuoka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan.,Department of Biotechnology, Nagoya University Graduate School of Engineering, Nagoya, Aichi 464-8603, Japan
| | - Takayuki Nagae
- Synchrotron Radiation Research Center, Nagoya University, Nagoya, Aichi 464-8603, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Hiroaki Awazu
- Department of Biotechnology, Nagoya University Graduate School of Engineering, Nagoya, Aichi 464-8603, Japan
| | - Teppei Kurosawa
- Department of Biotechnology, Nagoya University Graduate School of Engineering, Nagoya, Aichi 464-8603, Japan
| | - Akiko Hamano
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Kazuhiro Matsuoka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Atsuko Hachiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Mayumi Imahashi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Nobuhisa Watanabe
- Department of Biotechnology, Nagoya University Graduate School of Engineering, Nagoya, Aichi 464-8603, Japan.,Synchrotron Radiation Research Center, Nagoya University, Nagoya, Aichi 464-8603, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan.,Program in Integrated Molecular Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
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5
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Arginine homopeptides for plasmid DNA purification using monolithic supports. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1087-1088:149-157. [DOI: 10.1016/j.jchromb.2018.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/11/2018] [Accepted: 04/15/2018] [Indexed: 12/15/2022]
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6
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Reiss CW, Xiong Y, Strobel SA. Structural Basis for Ligand Binding to the Guanidine-I Riboswitch. Structure 2016; 25:195-202. [PMID: 28017522 DOI: 10.1016/j.str.2016.11.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/11/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022]
Abstract
The guanidine-I riboswitch is a conserved RNA element with approximately 2,000 known examples across four phyla of bacteria. It exists upstream of nitrogen metabolism and multidrug resistance transporter genes and alters expression through the specific recognition of a free guanidinium cation. Here we report the structure of a guanidine riboswitch aptamer from Sulfobacillus acidophilus at 2.7 Å resolution. Helices P1, P1a, P1b, and P2 form a coaxial stack that acts as a scaffold for ligand binding. A previously unidentified P3 helix docks into P1a to form the guanidinium binding pocket, which is completely enclosed. Every functional group of the ligand is recognized through hydrogen bonding to guanine bases and phosphate oxygens. Guanidinium binding is further stabilized through cation-π interactions with guanine bases. This allows the riboswitch to recognize guanidinium while excluding other bacterial metabolites with a guanidino group, including the amino acid arginine.
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Affiliation(s)
- Caroline W Reiss
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yong Xiong
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Scott A Strobel
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.
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7
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Jakubec D, Laskowski RA, Vondrasek J. Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis. PLoS One 2016; 11:e0158704. [PMID: 27384774 PMCID: PMC4934765 DOI: 10.1371/journal.pone.0158704] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/21/2016] [Indexed: 12/24/2022] Open
Abstract
Decades of intensive experimental studies of the recognition of DNA sequences by proteins have provided us with a view of a diverse and complicated world in which few to no features are shared between individual DNA-binding protein families. The originally conceived direct readout of DNA residue sequences by amino acid side chains offers very limited capacity for sequence recognition, while the effects of the dynamic properties of the interacting partners remain difficult to quantify and almost impossible to generalise. In this work we investigated the energetic characteristics of all DNA residue—amino acid side chain combinations in the conformations found at the interaction interface in a very large set of protein—DNA complexes by the means of empirical potential-based calculations. General specificity-defining criteria were derived and utilised to look beyond the binding motifs considered in previous studies. Linking energetic favourability to the observed geometrical preferences, our approach reveals several additional amino acid motifs which can distinguish between individual DNA bases. Our results remained valid in environments with various dielectric properties.
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Affiliation(s)
- David Jakubec
- Institute of Organic Chemistry and Biochemistry, Prague 6, Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Roman A. Laskowski
- EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jiri Vondrasek
- Institute of Organic Chemistry and Biochemistry, Prague 6, Czech Republic
- * E-mail:
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8
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Hossain ST, Malhotra A, Deutscher MP. How RNase R Degrades Structured RNA: ROLE OF THE HELICASE ACTIVITY AND THE S1 DOMAIN. J Biol Chem 2016; 291:7877-87. [PMID: 26872969 DOI: 10.1074/jbc.m116.717991] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Indexed: 11/06/2022] Open
Abstract
RNase R, a ubiquitous 3' exoribonuclease, plays an important role in many aspects of RNA metabolism. In contrast to other exoribonucleases, RNase R can efficiently degrade highly structured RNAs, but the mechanism by which this is accomplished has remained elusive. It is known that RNase R contains an unusual, intrinsic RNA helicase activity that facilitates degradation of duplex RNA, but how it stimulates the nuclease activity has also been unclear. Here, we have made use of specifically designed substrates to compare the nuclease and helicase activities of RNase R. We have also identified and mutated several residues in the S1 RNA-binding domain that are important for interacting with duplex RNA and have measured intrinsic tryptophan fluorescence to analyze the conformational changes that occur upon binding of structured RNA. Using these approaches, we have determined the relation of the RNA helicase, ATP binding, and nuclease activities of RNase R. This information has been combined with a structural analysis of RNase R, based on its homology to RNase II, whose structure has been determined, to develop a detailed model that explains how RNase R digests structured RNA and how this differs from its action on single-stranded RNA.
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Affiliation(s)
- Sk Tofajjen Hossain
- From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101
| | - Arun Malhotra
- From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101
| | - Murray P Deutscher
- From the Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33101
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9
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Moutiez M, Seguin J, Fonvielle M, Belin P, Jacques IB, Favry E, Arthur M, Gondry M. Specificity determinants for the two tRNA substrates of the cyclodipeptide synthase AlbC from Streptomyces noursei. Nucleic Acids Res 2014; 42:7247-58. [PMID: 24782519 PMCID: PMC4066775 DOI: 10.1093/nar/gku348] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNA substrates in a sequential ping-pong mechanism to form a cyclodipeptide. The crystal structures of three CDPSs have been determined and all show a Rossmann-fold domain similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs). Structural features and mutational analyses however suggest that CDPSs and aaRSs interact differently with their tRNA substrates. We used AlbC from Streptomyces noursei that mainly produces cyclo(l-Phe-l-Leu) to investigate the interaction of a CDPS with its substrates. We demonstrate that Phe-tRNAPhe is the first substrate accommodated by AlbC. Its binding to AlbC is dependent on basic residues located in the helix α4 that form a basic patch at the surface of the protein. AlbC does not use all of the Leu-tRNALeu isoacceptors as a second substrate. We show that the G1-C72 pair of the acceptor stem is essential for the recognition of the second substrate. Substitution of D163 located in the loop α6–α7 or D205 located in the loop β6–α8 affected Leu-tRNALeu isoacceptors specificity, suggesting the involvement of these residues in the binding of the second substrate. This is the first demonstration that the two substrates of CDPSs are accommodated in different binding sites.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Binding Sites
- Peptide Synthases/chemistry
- Peptide Synthases/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Leu/chemistry
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- Streptomyces/enzymology
- Substrate Specificity
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Affiliation(s)
- Mireille Moutiez
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Jérôme Seguin
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Matthieu Fonvielle
- INSERM, U1138, LRMA, Equipe 12 du Centre de Recherche des Cordeliers, Paris 75006, France Université Pierre et Marie Curie, UMR S 1138, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR S 1138, Paris, France
| | - Pascal Belin
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Isabelle Béatrice Jacques
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Emmanuel Favry
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Michel Arthur
- INSERM, U1138, LRMA, Equipe 12 du Centre de Recherche des Cordeliers, Paris 75006, France Université Pierre et Marie Curie, UMR S 1138, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR S 1138, Paris, France
| | - Muriel Gondry
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
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10
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Barik A, Mishra A, Bahadur RP. PRince: a web server for structural and physicochemical analysis of protein-RNA interface. Nucleic Acids Res 2012; 40:W440-4. [PMID: 22689640 PMCID: PMC3394290 DOI: 10.1093/nar/gks535] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein–RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in ‘.pdb’ format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein–RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein–RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein–RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.
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Affiliation(s)
- Amita Barik
- Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, India
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11
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Arenas NE, Salazar LM, Soto CY, Vizcaíno C, Patarroyo ME, Patarroyo MA, Gómez A. Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: possible misannotation of this tubercle bacilli-hemolysin. BMC STRUCTURAL BIOLOGY 2011; 11:16. [PMID: 21443791 PMCID: PMC3072309 DOI: 10.1186/1472-6807-11-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 03/28/2011] [Indexed: 11/24/2022]
Abstract
Background The TlyA protein has a controversial function as a virulence factor in Mycobacterium tuberculosis (M. tuberculosis). At present, its dual activity as hemolysin and RNA methyltransferase in M. tuberculosis has been indirectly proposed based on in vitro results. There is no evidence however for TlyA relevance in the survival of tubercle bacilli inside host cells or whether both activities are functionally linked. A thorough analysis of structure prediction for this mycobacterial protein in this study shows the need for reevaluating TlyA's function in virulence. Results Bioinformatics analysis of TlyA identified a ribosomal protein binding domain (S4 domain), located between residues 5 and 68 as well as an FtsJ-like methyltranferase domain encompassing residues 62 and 247, all of which have been previously described in translation machinery-associated proteins. Subcellular localization prediction showed that TlyA lacks a signal peptide and its hydrophobicity profile showed no evidence of transmembrane helices. These findings suggested that it may not be attached to the membrane, which is consistent with a cytoplasmic localization. Three-dimensional modeling of TlyA showed a consensus structure, having a common core formed by a six-stranded β-sheet between two α-helix layers, which is consistent with an RNA methyltransferase structure. Phylogenetic analyses showed high conservation of the tlyA gene among Mycobacterium species. Additionally, the nucleotide substitution rates suggested purifying selection during tlyA gene evolution and the absence of a common ancestor between TlyA proteins and bacterial pore-forming proteins. Conclusion Altogether, our manual in silico curation suggested that TlyA is involved in ribosomal biogenesis and that there is a functional annotation error regarding this protein family in several microbial and plant genomes, including the M. tuberculosis genome.
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Affiliation(s)
- Nelson E Arenas
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 45 No. 26-85 Bogotá, DC. Colombia
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12
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Lee WR, Jang JY, Kim JS, Kwon MH, Kim YS. Gene silencing by cell-penetrating, sequence-selective and nucleic-acid hydrolyzing antibodies. Nucleic Acids Res 2009; 38:1596-609. [PMID: 20007602 PMCID: PMC2836572 DOI: 10.1093/nar/gkp1145] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Targeting particular mRNAs for degradation is a fascinating approach to achieve gene silencing. Here we describe a new gene silencing tool exploiting a cell-penetrating, nucleic-acid hydrolyzing, single-domain antibody of the light-chain variable domain, 3D8 VL. We generated a synthetic library of 3D8 VL on the yeast surface by randomizing residues located in one of two β-sheets. Using 18-bp single-stranded nucleic acids as target substrates, including the human Her2/neu-targeting sequence, we selected 3D8 VL variants that had ∼100–1000-fold higher affinity and ∼2–5-fold greater selective hydrolyzing activity for target substrates than for off targets. 3D8 VL variants efficiently penetrated into living cells to be accumulated in the cytosol and selectively decreased the amount of target sequence-carrying mRNAs as well as the proteins encoded by these mRNAs with minimal effects on off-target genes. In particular, one 3D8 VL variant targeting the Her2 sequence showed more efficient downregulation of Her2 expression than a small-interfering RNA targeting the same Her2 sequence, resulting in apoptotic cell death of Her2-overexpressing breast cancer cells. Our results demonstrate that cell-penetrating 3D8 VL variants with sequence-selective, nucleic-acid-hydrolyzing activity can selectively degrade target mRNAs in the cytosol, providing a new gene silencing tool mediated by antibody.
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Affiliation(s)
- Woo-Ram Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
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13
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Rodríguez-Casado A, Molina M, Carmona P. Core protein-nucleic acid interactions in hepatitis C virus as revealed by Raman and circular dichroism spectroscopy. APPLIED SPECTROSCOPY 2007; 61:1219-1224. [PMID: 18028701 DOI: 10.1366/000370207782597139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Molecular interactions required for hepatitis C virus (HCV) assembly are not well known and are poorly understood. The 5' untranslated region (5'UTR) of the RNA genome is highly conserved and has extensive secondary structure, and the highly basic core protein is rich in arginine residues. Using Raman and circular dichroism (CD) spectroscopies, specific interactions have been demonstrated here between the 5'UTR sequence and the core protein that may be important for the specific encapsidation of the viral genome during HCV replication. These interactions can be described as follows: (1) hydrogen bonding of arginine with unpaired guanine and/or with wobble GU base pairs, and arginine-phosphate electrostatic contacts; (2) although the percentage of base pairs in the A-form is maintained in 5'UTR, the HCVc-120 protein is beta-sheet and beta-helix enriched upon formation of protein-5'UTR macromolecular assemblies; (3) protein-5'UTR interactions resulting in protein alpha-helix formation involve guanine bases in duplex segments. The mentioned interactions may represent novel targets for antiviral strategies against this important virus.
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14
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Terribilini M, Lee JH, Yan C, Jernigan RL, Honavar V, Dobbs D. Prediction of RNA binding sites in proteins from amino acid sequence. RNA (NEW YORK, N.Y.) 2006; 12:1450-62. [PMID: 16790841 PMCID: PMC1524891 DOI: 10.1261/rna.2197306] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Accepted: 05/13/2006] [Indexed: 05/10/2023]
Abstract
RNA-protein interactions are vitally important in a wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses. We have developed a computational tool for predicting which amino acids of an RNA binding protein participate in RNA-protein interactions, using only the protein sequence as input. RNABindR was developed using machine learning on a validated nonredundant data set of interfaces from known RNA-protein complexes in the Protein Data Bank. It generates a classifier that captures primary sequence signals sufficient for predicting which amino acids in a given protein are located in the RNA-protein interface. In leave-one-out cross-validation experiments, RNABindR identifies interface residues with >85% overall accuracy. It can be calibrated by the user to obtain either high specificity or high sensitivity for interface residues. RNABindR, implementing a Naive Bayes classifier, performs as well as a more complex neural network classifier (to our knowledge, the only previously published sequence-based method for RNA binding site prediction) and offers the advantages of speed, simplicity and interpretability of results. RNABindR predictions on the human telomerase protein hTERT are in good agreement with experimental data. The availability of computational tools for predicting which residues in an RNA binding protein are likely to contact RNA should facilitate design of experiments to directly test RNA binding function and contribute to our understanding of the diversity, mechanisms, and regulation of RNA-protein complexes in biological systems. (RNABindR is available as a Web tool from http://bindr.gdcb.iastate.edu.).
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Affiliation(s)
- Michael Terribilini
- Bioinformatics and Computationa Biology, Graduate Program, Iowa State University, Ames, Iowa 50010, USA.
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15
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Fodor E, Mingay LJ, Crow M, Deng T, Brownlee GG. A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase promotes the generation of defective interfering RNAs. J Virol 2003; 77:5017-20. [PMID: 12663810 PMCID: PMC152145 DOI: 10.1128/jvi.77.8.5017-5020.2003] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An R638A mutation of the polymerase acidic protein (PA) subunit of the RNA polymerase of influenza A/WSN/33 virus results in severe attenuation of viral growth in cell culture by promoting the synthesis of defective interfering RNAs. We propose that R638A is an "elongation" mutant that destabilizes PA-RNA template interactions during elongation. A C453R mutation in PA can compensate for this defect, suggesting that amino acids C453 and R638 form part of the same domain.
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Affiliation(s)
- Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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16
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Hsieh M, Collins ED, Blomquist T, Lustig B. Flexibility of BIV TAR-Tat: models of peptide binding. J Biomol Struct Dyn 2002; 20:243-51. [PMID: 12354076 DOI: 10.1080/07391102.2002.10506840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A new approach in determining local residue flexibility from base-amino acid contact frequencies is applied to the twelve million lattice chains modeling BIV Tat peptide binding to TAR RNA fragment. Many of the resulting key features in flexibility correspond to RMSD calculations derived from a set of five NMR derived structures (X. Ye, R. A. Kumar, and D. J. Patel, Protein Data Bank: Database of three-dimensional structures determined from NMR (1996)) and binding studies of mutants (L. Chen and A. D. Frankel, Proc. Natl. Acad. Sci. USA 92, 5077-5081 (1995)). The lattice and RMSD calculations facilitate the identification of peptide hinge regions that can best utilize the introduction of Gly or other flexible residues. This approach for identifying potential sites amenable to substitution of more flexible residues to enhance peptide binding to RNA targets could be a useful design tool.
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Affiliation(s)
- Mark Hsieh
- Department of Chemistry, San Jose State University, CA 95192-0101, USA
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17
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Vitagliano L, Adinolfi S, Sica F, Merlino A, Zagari A, Mazzarella L. A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease. J Mol Biol 1999; 293:569-77. [PMID: 10543951 DOI: 10.1006/jmbi.1999.3158] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bovine seminal ribonuclease (BS-RNase) is a peculiar member of the pancreatic-like ribonuclease superfamily endowed with unique biological functions. It has been shown that native BS-RNase is a mixture of two distinct dimeric forms. The most abundant form is characterised by the swapping of the N-terminal helix. Kinetic studies have shown that this dimer is allosterically regulated, whereas the minor component, in which no swapping occurs, exhibits typical Michaelian kinetics. In order to correlate the catalytic properties with the structural features of BS-RNase, we have determined the crystal structure of the BS-RNase swapping dimer complexed with uridylyl(2'-5')guanosine. The structure of the complex was refined to an R value of 0.189 at 1.9 A resolution. Surprisingly, the enzyme binds four dinucleotide molecules, all in a non-productive way. In the two active sites, the guanine base is located in the subsite that is specific for pyrimidines. This unusual binding has been observed also in complexes of RNase A with guanine-containing nucleotides (retro-binding). One of the two additional dinucleotide molecules bound to the enzyme is located on the surface of the protein in a pocket generated by crystal packing; the second was found in a cavity at the interface between the two subunits of the swapping dimer. There are indications that the interface site plays a role in the allosteric regulation exhibited by BS-RNase. This finding suggests that domain swapping may not merely be a mechanism that proteins adopt for the transition from a monomeric to oligomeric state but can be used to achieve modulations in catalytic function.
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Affiliation(s)
- L Vitagliano
- Centro di Studio di Biocristallografia, CNR, and Dipartimento di Chimica, Universita' degli Studi di Napoli "Federico II", Via Mezzocannone 4, Napoli, I-80134, Italy
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18
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Pichierri F, Aida M, Gromiha MM, Sarai A. Free-Energy Maps of Base−Amino Acid Interactions for DNA−Protein Recognition. J Am Chem Soc 1999. [DOI: 10.1021/ja984124b] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fabio Pichierri
- Contribution from the Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba 305-0074, Japan, and National Cancer Center Research Institute, Tsukiji, Tokyo 104-0045, Japan
| | - Misako Aida
- Contribution from the Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba 305-0074, Japan, and National Cancer Center Research Institute, Tsukiji, Tokyo 104-0045, Japan
| | - M. Michael Gromiha
- Contribution from the Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba 305-0074, Japan, and National Cancer Center Research Institute, Tsukiji, Tokyo 104-0045, Japan
| | - Akinori Sarai
- Contribution from the Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba 305-0074, Japan, and National Cancer Center Research Institute, Tsukiji, Tokyo 104-0045, Japan
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19
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van Lieshout E, Hemminga MA. NMR study on the binding of d(GGAAATTTCC)2 with a positively charged pentacosapeptide. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1442:137-47. [PMID: 9804928 DOI: 10.1016/s0167-4781(98)00157-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
To obtain a better understanding of the electrostatic nature of protein-nucleic acid interactions, we have investigated the interaction of a double-stranded decamer d(GGAAATTTCC)2 with a synthetic arginine and lysine-rich pentacosapeptide (Pep25), using NMR and optical spectroscopy. The chemical shift data of the decamer under various experimental conditions show that the binding of Pep25 changes the conformation of the decamer in a different way, as compared to the conformational changes induced by a variation in temperature or ionic strength. The chemical shift results are interpreted in terms of ring current effects that emerge into a model for the conformational change, in which the double-stranded helix of the decamer undergoes a decrease of twist and rise to accommodate Pep25. The binding results indicate that the positively charged arginine and lysine side chains of Pep25 not only have a stabilising electrostatic interaction with the negatively charged backbone phosphates of d(GGAAATTTCC)2, but also that a stabilisation of the base pairs of d(GGAAATTTCC)2 by Pep25 takes place.
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Affiliation(s)
- E van Lieshout
- Department of Molecular Physics, Wageningen Agricultural University, Dreijenlaan 3, 6703 HA Wageningen, Netherlands
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20
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Erard M, Barker DG, Amalric F, Jeang KT, Gatignol A. An Arg/Lys-rich core peptide mimics TRBP binding to the HIV-1 TAR RNA upper-stem/loop. J Mol Biol 1998; 279:1085-99. [PMID: 9642086 DOI: 10.1006/jmbi.1998.1831] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
TRBP is a cellular protein that binds to the HIV-1 leader RNA, TAR. Circular dichroism experiments have shown that a 24 amino acid peptide (TR1), located within a dsRNA binding domain (dsRBD) of TRBP, binds TAR with a 3:1 stoichiometry, eliciting a conformational change involving base unstacking. The binding characteristics of synthetic structural variants of TAR indicate that guanine residues play a key role in the TR1-RNA interaction and that binding sites exist in the upper-stem/loop and lower stem region of TAR. Deletion analysis of TR1 has led to the identification of a 15 amino acid subpeptide (TR13) which is necessary and sufficient to bind to the high affinity upper-stem/loop binding site of TAR. Alanine scanning of TR13 has revealed that mutations in either Lys or Arg residues result in altered TAR-binding, and molecular modelling/docking experiments have shown that the two Arg residues of TR13 can interact with two appropriately spaced guanine residues in the upper-stem/loop of TAR. The TR13 lysine residues appear to be essential for maintaining structural integrity and the correct positioning of the Arg side-chains. We propose that TRBP binds TAR by means of a "2-G hook" motif and that the binding specificity of this particular member of the family of double-stranded RNA-binding proteins lies within the highly conserved dsRBD core motif. Finally, our results also suggest that TRBP may function in vivo by modifying the tertiary structure of TAR RNA.
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Affiliation(s)
- M Erard
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS, 118 route de Narbonne, Toulouse Cedex, 31062, France.
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