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Luo Y, Pratihar S, Horste EH, Mitschka S, Mey ASJS, Al-Hashimi HM, Mayr C. mRNA interactions with disordered regions control protein activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.18.529068. [PMID: 36824771 PMCID: PMC9949118 DOI: 10.1101/2023.02.18.529068] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The cytoplasm is compartmentalized into different translation environments. mRNAs use their 3'UTRs to localize to distinct cytoplasmic compartments, including TIS granules (TGs). Many transcription factors, including MYC, are translated in TGs. It was shown that translation of proteins in TGs enables the formation of protein complexes that cannot be established when these proteins are translated in the cytosol, but the mechanism is poorly understood. Here we show that MYC protein complexes that involve binding to the intrinsically disordered region (IDR) of MYC are only formed when MYC is translated in TGs. TG-dependent protein complexes require TG-enriched mRNAs for assembly. These mRNAs bind to a new and widespread RNA-binding domain in neutral or negatively charged IDRs in several transcription factors, including MYC. RNA-IDR interaction changes the conformational ensemble of the IDR, enabling the formation of MYC protein complexes that act in the nucleus and control functions that cannot be accomplished by cytosolically-translated MYC. We propose that certain mRNAs have IDR chaperone activity as they control IDR conformations. In addition to post-translational modifications, we found a novel mode of protein activity regulation. Since RNA-IDR interactions are prevalent, we suggest that mRNA-dependent control of protein functional states is widespread.
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Affiliation(s)
- Yang Luo
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Supriya Pratihar
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ellen H. Horste
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
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2
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Abstract
RNA recognition frequently results in conformational changes that optimize intermolecular binding. As a consequence, the overall binding affinity of RNA to its binding partners depends not only on the intermolecular interactions formed in the bound state but also on the energy cost associated with changing the RNA conformational distribution. Measuring these "conformational penalties" is, however, challenging because bound RNA conformations tend to have equilibrium populations in the absence of the binding partner that fall outside detection by conventional biophysical methods. In this study we employ as a model system HIV-1 TAR RNA and its interaction with the ligand argininamide (ARG), a mimic of TAR's cognate protein binding partner, the transactivator Tat. We use NMR chemical shift perturbations and relaxation dispersion in combination with Bayesian inference to develop a detailed thermodynamic model of coupled conformational change and ligand binding. Starting from a comprehensive 12-state model of the equilibrium, we estimate the energies of six distinct detectable thermodynamic states that are not accessible by currently available methods. Our approach identifies a minimum of four RNA intermediates that differ in terms of the TAR conformation and ARG occupancy. The dominant bound TAR conformation features two bound ARG ligands and has an equilibrium population in the absence of ARG that is below detection limit. Consequently, even though ARG binds to TAR with an apparent overall weak affinity (Kdapp ≈ 0.2 mM), it binds the prefolded conformation with a Kd in the nM range. Our results show that conformational penalties can be major determinants of RNA-ligand binding affinity as well as a source of binding cooperativity, with important implications for a predictive understanding of how RNA is recognized and for RNA-targeted drug discovery.
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Affiliation(s)
- Nicole I. Orlovsky
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Terrence G. Oas
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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3
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An efficient tRNA cleaver without additional co-reactants at physiological condition. Biochem Biophys Res Commun 2019; 510:8-12. [PMID: 30661788 DOI: 10.1016/j.bbrc.2018.12.041] [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: 11/20/2018] [Accepted: 12/05/2018] [Indexed: 11/23/2022]
Abstract
A square-planar Cu(II) complex, [Cu(Me-Im)(gly-gly)]∙H2O 1 (Me-Im = 1-methyl-imidazole, gly-gly = glycylglycinato), has been prepared and structurally characterized by single crystal X-ray. The complex 1 was tested for its ability to the transfer RNA by UV-vis spectroscopy, cyclic voltammetry (CV), capillary electrophoresis (CE). Comparative spectroscopic analysis shows a maximum fluorescence-quenching ratio of 0.41 of 1 upon binding to RNA, which gives a binding constant (Kb) of 1.24 × 105 M-1. Cyclic voltammograms of complex 1 attached on the mercaptoethanol (-SH) linked Au electrodes in phosphate buffer solution give a well-defined and quasi-reversible redox couple, indicate complex 1 can efficiently degrade the high-order structure of RNA in physiological conditions (pH 7.0 phosphate buffer solution at 37 °C) without additional co-reactants, yielding a digestion coefficient more than 90% within 113 h. This study targeting the genetic biomacromolecule degradation based on the strong binding of chemical nucleases paves an important way to the novel materials in the decontamination of microorganisms (e.g., bacteria and viruses) at mild condition.
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4
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Ha L, Colquhoun J, Noinaj N, Das C, Dunman PM, Flaherty DP. Crystal structure of the ribonuclease-P-protein subunit from Staphylococcus aureus. Acta Crystallogr F Struct Biol Commun 2018; 74:632-637. [PMID: 30279314 PMCID: PMC6168776 DOI: 10.1107/s2053230x18011512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/14/2018] [Indexed: 02/03/2023] Open
Abstract
Staphylococcus aureus ribonuclease-P-protein subunit (RnpA) is a promising antimicrobial target that is a key protein component for two essential cellular processes, RNA degradation and transfer-RNA (tRNA) maturation. The first crystal structure of RnpA from the pathogenic bacterial species, S. aureus, is reported at 2.0 Å resolution. The structure presented maintains key similarities with previously reported RnpA structures from bacteria and archaea, including the highly conserved RNR-box region and aromatic residues in the precursor-tRNA 5'-leader-binding domain. This structure will be instrumental in the pursuit of structure-based designed inhibitors targeting RnpA-mediated RNA processing as a novel therapeutic approach for treating S. aureus infections.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Catalytic Domain
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Kinetics
- Models, Molecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribonuclease P/chemistry
- Ribonuclease P/genetics
- Ribonuclease P/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Staphylococcus aureus/chemistry
- Staphylococcus aureus/enzymology
- Substrate Specificity
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Affiliation(s)
- Lisha Ha
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
| | - Jennifer Colquhoun
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - Chittaranjan Das
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Paul M. Dunman
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Daniel P. Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
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5
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Lou X, Egli M, Yang X. Determining Functional Aptamer-Protein Interaction by Biolayer Interferometry. ACTA ACUST UNITED AC 2016; 67:7.25.1-7.25.15. [PMID: 27911494 DOI: 10.1002/cpnc.18] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Short single-stranded nucleic acids called aptamers are widely being explored as recognition molecules of high affinity and specificity for binding a wide range of target molecules, particularly protein targets. In biolayer interferometry (BLI), a simple Dip-and-Read approach in which the aptamer-coated biosensors are dipped into microplate wells is used to study the interactions between an aptamer and its target protein. Here we describe the protocol for the analysis of the interaction between a well-characterized anti-thrombin RNA aptamer with thrombin (Basic Protocol). We also report on the protocol for the affinity screening of a panel of anti-thrombin RNA aptamers with a single phosphorodithioate (PS2) modification, whereby the position of the modification along the RNA backbone is varied systematically (Support Protocol). The PS2 modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphodiester backbone linkage. The PS2-modified RNAs are nuclease resistant and several in vitro and in vivo assays have demonstrated their biological activity. For example, combining the PS2 with the 2'-OMe modification affords increased loading of modified small interfering RNA (siRNA) duplexes into the RNA-induced silencing complex (RISC) as well as enhanced gene-silencing antitumor activity. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
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6
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Abeydeera ND, Egli M, Cox N, Mercier K, Conde JN, Pallan PS, Mizurini DM, Sierant M, Hibti FE, Hassell T, Wang T, Liu FW, Liu HM, Martinez C, Sood AK, Lybrand TP, Frydman C, Monteiro RQ, Gomer RH, Nawrot B, Yang X. Evoking picomolar binding in RNA by a single phosphorodithioate linkage. Nucleic Acids Res 2016; 44:8052-64. [PMID: 27566147 PMCID: PMC5041495 DOI: 10.1093/nar/gkw725] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/02/2016] [Accepted: 08/06/2016] [Indexed: 11/12/2022] Open
Abstract
RNA aptamers are synthetic oligonucleotide-based affinity molecules that utilize unique three-dimensional structures for their affinity and specificity to a target such as a protein. They hold the promise of numerous advantages over biologically produced antibodies; however, the binding affinity and specificity of RNA aptamers are often insufficient for successful implementation in diagnostic assays or as therapeutic agents. Strong binding affinity is important to improve the downstream applications. We report here the use of the phosphorodithioate (PS2) substitution on a single nucleotide of RNA aptamers to dramatically improve target binding affinity by ∼1000-fold (from nanomolar to picomolar). An X-ray co-crystal structure of the α-thrombin:PS2-aptamer complex reveals a localized induced-fit rearrangement of the PS2-containing nucleotide which leads to enhanced target interaction. High-level quantum mechanical calculations for model systems that mimic the PS2 moiety and phenylalanine demonstrate that an edge-on interaction between sulfur and the aromatic ring is quite favorable, and also confirm that the sulfur analogs are much more polarizable than the corresponding phosphates. This favorable interaction involving the sulfur atom is likely even more significant in the full aptamer-protein complexes than in the model systems.
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Affiliation(s)
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Nehemiah Cox
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Karen Mercier
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Jonas Nascimento Conde
- Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Daniella M Mizurini
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Malgorzata Sierant
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland
| | - Fatima-Ezzahra Hibti
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Tom Hassell
- MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA
| | - Tianzhi Wang
- The Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Feng-Wu Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Carlos Martinez
- MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA
| | - Anil K Sood
- Departments of Gynecologic Oncology and Cancer Biology, and Center for RNAi and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Terry P Lybrand
- Departments of Chemistry and Pharmacology, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Chiraz Frydman
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Robson Q Monteiro
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Richard H Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland
| | - Xianbin Yang
- AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA
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7
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Shanker S, Bandyopadhyay P. How Mg 2+ ion and water network affect the stability and structure of non-Watson-Crick base pairs in E. coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study. J Biomol Struct Dyn 2016; 35:2103-2122. [PMID: 27426235 DOI: 10.1080/07391102.2016.1213186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The non-Watson-Crick (non-WC) base pairs of Escherichia coli loop E of 5S rRNA are stabilized by Mg2+ ions through water-mediated interaction. It is important to know the synergic role of Mg2+ and the water network surrounding Mg2+ in stabilizing the non-WC base pairs of RNA. For this purpose, free energy change of the system is calculated using molecular dynamics (MD) simulation as Mg2+ is pulled from RNA, which causes disturbance of the water network. It was found that Mg2+ remains hexahydrated unless it is close to or far from RNA. In the pentahydrated form, Mg2+ interacts directly with RNA. Water network has been identified by two complimentary methods; MD followed by a density-based clustering algorithm and three-dimensional-reference interaction site model. These two methods gave similar results. Identification of water network around Mg2+ and non-WC base pairs gives a clue to the strong effect of water network on the stability of this RNA. Based on sequence analysis of all Eubacteria 5s rRNA, we propose that hexahydrated Mg2+ is an integral part of this RNA and geometry of base pairs surrounding it adjust to accommodate the [Formula: see text]. Overall the findings from this work can help in understanding the basis of the complex structure and stability of RNA with non-WC base pairs.
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Affiliation(s)
- Sudhanshu Shanker
- a School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi 110067 , India
| | - Pradipta Bandyopadhyay
- a School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi 110067 , India
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8
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Blakeley BD, McNaughton BR. Synthetic RNA recognition motifs that selectively recognize HIV-1 trans-activation response element hairpin RNA. ACS Chem Biol 2014; 9:1320-9. [PMID: 24635165 DOI: 10.1021/cb500138h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A multitude of RNA hairpins are directly implicated in human disease. Many of these RNAs are potentially valuable targets for drug discovery and basic research. However, very little is known about the molecular requirements for achieving sequence-selective recognition of a particular RNA sequence and structure. Although a relatively modest number of synthetic small to medium-sized RNA-binding molecules have been reported, rapid identification of sequence-selective RNA-binding molecules remains a daunting challenge. RNA recognition motif (RRM) domains may represent unique privileged scaffolds for the generation of synthetic proteins that selectively recognize structured disease-relevant RNAs, including RNA hairpins. As a demonstration of this potential, we mutated putative RNA-binding regions within the U1A RRM and a variant thereof and screened these synthetic proteins for affinity to HIV-1 trans-activation response (TAR) element hairpin RNA. Some of these U1A-derived proteins bind TAR with single-digit micromolar dissociation constants, and they do so preferentially over the native protein's original target RNA (U1hpII) and a DNA TAR variant. Binding affinity is not appreciably diminished by addition of 10 molar equivalents of cellular tRNAs from Escherichia coli. Taken together, our findings represent the first synthetic RRMs that selectively bind a disease-relevant RNA hairpin and may represent a general approach for achieving sequence-selective recognition of RNA hairpins, which are the focus of therapeutic discovery and basic research.
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Affiliation(s)
- Brett D. Blakeley
- Department of Chemistry, and ‡Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Brian R. McNaughton
- Department of Chemistry, and ‡Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
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9
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Blakeley BD, Shattuck J, Coates MB, Tran E, Laird-Offringa IA, McNaughton BR. Analysis of protein-RNA complexes involving a RNA recognition motif engineered to bind hairpins with seven- and eight-nucleotide loops. Biochemistry 2013; 52:4745-7. [PMID: 23806102 DOI: 10.1021/bi400801q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
U1A binds U1hpII, a hairpin RNA with a 10-nucleotide loop. A U1A mutant (ΔK50ΔM51) binds U1hpII-derived hairpins with shorter loops, making it an interesting scaffold for engineering or evolving proteins that bind similarly sized disease-related hairpin RNAs. However, a more detailed understanding of complexes involving ΔK50ΔM51 is likely a prerequisite to generating such proteins. Toward this end, we measured mutational effects for complexes involving U1A ΔK50ΔM51 and U1hpII-derived hairpin RNAs with seven- or eight-nucleotide loops and identified contacts that are critical to the stabilization of these complexes. Our data provide valuable insight into sequence-selective recognition of seven- or eight-nucleotide loop hairpins by an engineered RNA binding protein.
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Affiliation(s)
- Brett D Blakeley
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, Colorado State University , Fort Collins, Colorado 80523, United States
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10
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Liu J, Tan LF, Jin LH, Luan F. Synthesis, Characterization, Nucleic Acid Binding, and Cytotoxic Activity of a Ru(II) Polypyridyl Complex. DNA Cell Biol 2012; 31:250-8. [DOI: 10.1089/dna.2011.1307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jin Liu
- Key Lab of Environment-Friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan, P.R. China
| | - Li-Feng Tan
- Key Lab of Environment-Friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan, P.R. China
- College of Chemistry, Xiangtan University, Xiangtan, P.R. China
| | - Lian-He Jin
- College of Chemistry, Xiangtan University, Xiangtan, P.R. China
| | - Fang Luan
- College of Chemistry, Xiangtan University, Xiangtan, P.R. China
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11
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Kormos BL, Pieniazek SN, Beveridge DL, Baranger AM. U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations. Biopolymers 2011; 95:591-606. [PMID: 21384338 DOI: 10.1002/bip.21616] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 01/01/2011] [Accepted: 02/07/2011] [Indexed: 01/02/2023]
Abstract
Molecular dynamics (MD) simulations were carried out to compare the free and bound structures of wild type U1A protein with several Phe56 mutant U1A proteins that bind the target stem loop 2 (SL2) RNA with a range of affinities. The simulations indicate the free U1A protein is more flexible than the U1A-RNA complex for both wild type and Phe56 mutant systems. A complete analysis of the hydrogen-bonding (HB) and non-bonded (VDW) interactions over the course of the MD simulations suggested that changes in the interactions in the free U1A protein caused by the Phe56Ala and Phe56Leu mutations may stabilize the helical character in loop 3, and contribute to the weak binding of these proteins to SL2 RNA. Compared with wild type, changes in HB and VDW interactions in Phe56 mutants of the free U1A protein are global, and include differences in β-sheet, loop 1 and loop 3 interactions. In the U1A-RNA complex, the Phe56Ala mutation leads to a series of differences in interactions that resonate through the complex, while the Phe56Leu and Phe56Trp mutations cause local differences around the site of mutation. The long-range networks of interactions identified in the simulations suggest that direct interactions and dynamic processes in both the free and bound forms contribute to complex stability.
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Affiliation(s)
- Bethany L Kormos
- Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
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12
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An L, Liu L, Wang S, Bazan G. An Optical Approach for Drug Screening Based on Light-Harvesting Conjugated Polyelectrolytes. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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An L, Liu L, Wang S, Bazan G. An Optical Approach for Drug Screening Based on Light-Harvesting Conjugated Polyelectrolytes. Angew Chem Int Ed Engl 2009; 48:4372-5. [DOI: 10.1002/anie.200900758] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Dutt A, Dutta A, Kar S, Koley P, Drew MG, Pramanik A. Stabilization of two smallest possible diastereomeric β-hairpins in a water soluble tetrapeptide containing non-coded α-amino isobutyric acid (Aib) and m-amino benzoic acid. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.03.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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16
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Varedian M, Erdélyi M, Persson Å, Gogoll A. Interplaying factors for the formation of photoswitchable β-hairpins: the advantage of a flexible switch. J Pept Sci 2008; 15:107-13. [DOI: 10.1002/psc.1103] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Wissler JH, Wissler JE, Logemann E. Extracellular functional noncoding nucleic acid bioaptamers and angiotropin RNP ribokines in vascularization and self-tolerance. Ann N Y Acad Sci 2008; 1137:316-42. [PMID: 18837966 DOI: 10.1196/annals.1448.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Endogenous extracellular and circulating functional small noncoding nucleic acids (ncNAs; <200 nucleotides) and complexes with proteins (ribonucleoproteins; RNPs) make up varying biolibraries of molecular imprints of cellular histories. They are nascently formed upon cellular activation by extrinsic (environmental) factors, including mitogens, cell-mediated immune memory reactions (Landsteiner-Chase-Lawrence transfer factors), and metabolic (hypoxia) and (physical) shear stress forces. Those factors are conventional models for epigenetic (non-Mendelian) vascular remodeling variations directed rather to proteinaceous gene expression and regulation than genomic DNA sequence changes. Structurally defined ncNAs are described as small hairpin nc-shRNA bioaptamers in interaction with proteins forming functional (Cu,Ca,Na,K)-metalloregulated complexes (CuRNP; angiotropins). As nonmitogenic angiomorphogen cytokines (ribokines), they may reprogram confluent quiescent (contact-inhibited) endothelial cell types to migratory, phagokinetically active phenotypes in the morphogenesis of tolerated neovascular patterns. Their functions in organized and mess-chaotic vascular patterns were investigated with regard to master gene, information, epigenetic, vascular, and tumor factors. Some ncNAs feature three-dimensional codes (3D episcripts) for distinct protein conformer phases. They are suggested as being specific recognition types, the estimated repertoires of which are superior in diversity and specificity to conventional immune (glyco-)proteins. For episcription of phenotype variations, they may address and integrate information flow on molecular shapes to protein-mediated nucleic acid processing and [post-]translational modification mechanisms in ncNA-, redox, and metalloregulated conformation phase pathway-locked loops (CPLL). Several vascular and cancer epigenetic regulator proteins are shown to be entangled by sharing helix-nucleating structural (proteomic) domains for interaction with functional nc-shRNA, termed K/RxxxH (K/R3H, -xK/RxxxHx(7-9)h/xx(7-9)h/xx(5-20)K/Rx-). This would suggest a tolerated mess-chaotic tumor vascularization as a bioaptamer disorder in ncNA-switched proteinaceous genetic and epigenetic processes.
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Affiliation(s)
- Josef H Wissler
- ARCONS Institute for Applied Research & Didactics, Bad Nauheim, Germany.
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18
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Eckert-Maksić M, Glasovac Z, Trošelj P, Kütt A, Rodima T, Koppel I, Koppel IA. Basicity of Guanidines with Heteroalkyl Side Chains in Acetonitrile. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800673] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Katritzky AR, Meher G, Narindoshvili T. Efficient Synthesis of Peptides by Extension at the N- and C-Terminii of Arginine. J Org Chem 2008; 73:7153-8. [DOI: 10.1021/jo800805w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alan R. Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Geeta Meher
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Tamari Narindoshvili
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
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20
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Abstract
This overview unit provides a thorough overview of biophysical methods used for structure analysis, including X-ray diffraction, nuclear magnetic resonance, optical spectroscopy, theoretical and computational methods, and single-molecule methods. Advantages and disadvantages of the methods are compared.
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Affiliation(s)
- I Tinoco
- University of California, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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21
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Petzold K, Duchardt E, Flodell S, Larsson G, Kidd-Ljunggren K, Wijmenga S, Schleucher J. Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns. Nucleic Acids Res 2007; 35:6854-61. [PMID: 17933777 PMCID: PMC2175316 DOI: 10.1093/nar/gkm774] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The number of regulatory RNAs with identified non-canonical structures is increasing, and structural transitions often play a role in their biological function. This stimulates interest in internal motions of RNA, which can underlie structural transitions. Heteronuclear NMR relaxation measurements, which are commonly used to study internal motion, only report on local motions of few sites within the molecule. Here we have studied a 27-nt segment of the human hepatitis B virus (HBV) pregenomic RNA, which is essential for viral replication. We combined heteronuclear relaxation with the new off-resonance ROESY technique, which reports on internal motions of H,H contacts. Using off-resonance ROESY, we could for the first time detect motion of through-space H,H contacts, such as in intra-residue base-ribose contacts or inter-nucleotide contacts, both essential for NMR structure determination. Motions in non-canonical structure elements were found primarily on the sub-nanosecond timescale. Different patterns of mobility were observed among several mobile nucleotides. The most mobile nucleotides are highly conserved among different HBV strains, suggesting that their mobility patterns may be necessary for the RNA’s biological function.
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Affiliation(s)
- Katja Petzold
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
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22
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WISSLER JOSEFH. Redox- and Metalloregulated RNA Bioaptamer Targets of Proteins Associated with Parkinson's and Other Neurodegenerative Diseases. Ann N Y Acad Sci 2006. [DOI: 10.1111/j.1749-6632.2003.tb07499.x] [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]
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23
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Erdélyi M, Karlén A, Gogoll A. A New Tool in Peptide Engineering: A Photoswitchable Stilbene-type β-Hairpin Mimetic. Chemistry 2006; 12:403-12. [PMID: 16187380 DOI: 10.1002/chem.200500648] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Peptide secondary structure mimetics are important tools in medicinal chemistry, as they provide analogues of endogenous peptides with new physicochemical and pharmacological properties. The development, synthesis, photochemical investigation, and conformational analysis of a stilbene-type beta-hairpin mimetic capable of light-triggered conformational changes have been achieved. In addition to standard spectroscopic techniques (nuclear Overhauser effects, amide temperature coefficients, circular dichroism spectroscopy), the applicability of self-diffusion measurements (longitudinal eddy current delay pulsed-field gradient spin echo (LED-PGSE) NMR technique) in conformational studies of oligopeptides is demonstrated. The title compound shows photoisomerization of the stilbene chromophore, resulting in a change in solution conformation between an unfolded structure and a folded beta-hairpin.
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Affiliation(s)
- Máté Erdélyi
- Department of Chemistry, Organic Chemistry, Uppsala University, Box 599, 751 24 Uppsala, Sweden
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24
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Kirchner B, Reiher M. Understanding the Template Preorganization Step of an Artificial Arginine Receptor§. J Am Chem Soc 2005; 127:8748-56. [PMID: 15954781 DOI: 10.1021/ja050614+] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A biomimetic complex which mimics the arginine-phosphonate diester interaction of the arginine fork is investigated with respect to structure and energetics of stable configurations. Within this work, we provide knowledge on local minima of the isolated system obtained from first-principles calculations. Non-negligible solvation effects are studied in a microsolvation approach. The interactions which govern the structural patterns of molecular recognition in this tweezer-guest complex can be significantly modulated by the action of hydrogen bond accepting and donating solvent molecules, such as dimethyl sulfoxide or water, which were present in experimental investigations on this system. Different tweezer-guest structures are evaluated with respect to their temperature-dependent thermodynamical properties as products of the first association reaction step of the bisphosphonate tweezer template and the guanidinium moiety.
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Affiliation(s)
- Barbara Kirchner
- Theoretische Chemie, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, D-53115 Bonn, Germany.
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25
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Johnson NP, Baase WA, von Hippel PH. Investigating local conformations of double-stranded DNA by low-energy circular dichroism of pyrrolo-cytosine. Proc Natl Acad Sci U S A 2005; 102:7169-73. [PMID: 15883388 PMCID: PMC1129127 DOI: 10.1073/pnas.0502359102] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Local base stacking and conformational mobility play a major role in the structure and function of nucleic acids. We have recently shown that the low-energy CD spectrum of 2-aminopurine (2-AP), i.e., the CD spectral region above 300 nm, can be used to monitor conformational changes in polynucleotides at or near mono- and dinucleotide 2-AP residues that replace adenine residues in DNA and RNA. Here, we extend this technique to pyrrolo-cytosine (PC), a fluorescent analogue of cytosine. The low-energy CD spectrum of a PC dinucleotide in dsDNA exhibits an exciton couplet with two bands of opposite sign centered at 350 nm. This signal is characteristic of base stacking between adjacent PC residues in a right helical conformation. Isolated PC nucleotide residues inserted into polynucleotide chains also display chirality that reflects the asymmetric environment of their sequence context. Thus, we show that the low-energy CD spectra of C(PC)A and A(PC)C sequences in dsDNA have opposite signs. It appears that the measurement of the low-energy CD spectra of PC residues will usefully complement 2-AP measurements by serving to characterize the local conformations and dynamics of nucleic acids near C residues and G-C base pairs.
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Affiliation(s)
- Neil P Johnson
- Institut de Pharmacologie et de Biologie Structurale, Unité Mixte de Recherche 5089, Centre National de la Recherche Scientifique, 205 route de Narbonne, 31077 Toulouse, France.
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26
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Tian B, Bevilacqua PC, Diegelman-Parente A, Mathews MB. The double-stranded-RNA-binding motif: interference and much more. Nat Rev Mol Cell Biol 2005; 5:1013-23. [PMID: 15573138 DOI: 10.1038/nrm1528] [Citation(s) in RCA: 188] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA duplexes have been catapulted into the spotlight by the discovery of RNA interference and related phenomena. But double-stranded and highly structured RNAs have long been recognized as key players in cell processes ranging from RNA maturation and localization to the antiviral response in higher organisms. Penetrating insights into the metabolism and functions of such RNAs have come from the identification and study of proteins that contain the double-stranded-RNA-binding motif.
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Affiliation(s)
- Bin Tian
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, 185 South Orange Avenue, PO Box 1709, Newark, New Jersey 07101-1709, USA
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27
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Süleymanoĝlu E. Molecular phylogenetics and functional evolution of major RNA recognition domains of recently cloned and characterized autoimmune RNA-binding particle. GENOMICS PROTEOMICS & BIOINFORMATICS 2005; 1:310-20. [PMID: 15629060 PMCID: PMC5172410 DOI: 10.1016/s1672-0229(03)01037-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are spliceosomal macromolecular assemblages and thus actively participate in pre-mRNA metabolism. They are composed of evolutionarily conserved and tandemly repeated motifs, where both RNA-binding and protein-protein recognition occur to achieve cellular activities. By yet unknown mechanisms, these ribonucleoprotein (RNP) particles are targeted by autoantibodies and hence play significant role in a variety of human systemic autoimmune diseases. This feature makes them important prognostic markers in terms of molecular epidemiology and pathogenesis of autoimmunity. Since RNP domain is one of the most conserved and widespread scaffolds, evolutionary analyses of these RNA-binding domains can provide further clues on disease-specific epitope formation. The study presented herein represents a sequence comparison of RNA-recognition regions of recently cloned and characterized human hnRNP A3 with those of other relevant hnRNP A/B-type proteins. Their implications in human autoimmunity are particularly emphasized.
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Affiliation(s)
- Erhan Süleymanoĝlu
- Medical Faculty, Vienna Biocenter, Institute of Biochemistry, University of Vienna, Vienna, Austria.
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28
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Sanford AR, Yuan L, Feng W, Yamato K, Flowers RA, Gong B. Cyclic aromatic oligoamides as highly selective receptors for the guanidinium ion. Chem Commun (Camb) 2005:4720-2. [PMID: 16175304 DOI: 10.1039/b504411a] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A class of six-residue, shape-persistent aromatic oligoamide macrocycles bind the guanidinium ion with very high selectivity.
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Affiliation(s)
- Adam R Sanford
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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29
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Detering C, Varani G. Validation of automated docking programs for docking and database screening against RNA drug targets. J Med Chem 2004; 47:4188-201. [PMID: 15293991 DOI: 10.1021/jm030650o] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The increasing awareness of the essential role of RNA in controlling viral replication and in bacterial protein synthesis emphasizes the potential of ribonucleoproteins as targets for developing new antibacterial and antiviral drugs. RNA forms well defined three-dimensional structures with clefts and binding pockets reminiscent of the active sites of proteins. Furthermore, it precedes proteins in the translation pathway; inhibiting the function of a single RNA molecule would result in inhibition of multiple proteins. Thus, small molecules that bind RNA specifically would combine the advantages of antisense and RNAi strategies with the much more favorable medicinal chemistry of small-molecule therapeutics. The discovery of small-molecule inhibitors of RNA with attractive pharmacological potential would be facilitated if we had available effective computational tools of structure-based drug design. Here, we systematically test automated docking tools developed for proteins using existing three-dimensional structures of RNA-small molecule complexes. The results show that the native structures can generally be reproduced to within 2.5 angstroms more than 50-60% of the time. For more than half of the test complexes, the native ligand ranked among the top 10% compounds in a database-scoring test. Through this work, we provide parameters for the validated application of automated docking tools to the discovery of new inhibitors of RNA function.
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Affiliation(s)
- Carsten Detering
- Departments of Chemistry and Biochemistry, University of Washington, Seattle, Washington 98195-1700, USA
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30
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Wissler JH. Extracellular and circulating redox- and metalloregulated eRNA and eRNP: copper ion-structured RNA cytokines (angiotropin ribokines) and bioaptamer targets imparting RNA chaperone and novel biofunctions to S100-EF-hand and disease-associated proteins. Ann N Y Acad Sci 2004; 1022:163-84. [PMID: 15251957 DOI: 10.1196/annals.1318.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Bioassays for cellular differentiation and tissue morphogenesis were used to design methods for isolation of bioactive redox- and metalloregulated nucleic acids and copper ion complexes with proteins from extracellular, circulating, wound, and supernatant fluids of cultured cells. In extracellular biospheres, diversities of nucleic acids were found to be secreted by cells upon activation. They may reflect nucleic acid biolibraries with molecular imprints of cellular history. After removal of protein components, eRNA prototypes exuded by activated cells were sequenced. They are small, endogenous, highly modified and edited, redox- and metalloregulated 5'-end phosphorylated extracellular eRNA (approximately 2-200 bases) with cellular, enzymic, and bioaptamer functions. Fenton-type OH* radical redox reactions may form modified nucleotides in RNA as wobbles eRNA per se, or as copper ion-complex with protein (e.g., S100A12-EF-hand protein, angiotropin-related protein, calgranulin-C, hippocampal neurite differentiation factor) are shown to be bioactive in vivo and in vitro as cytokines (ribokines) and as nonmitogenic angiomorphogens for endothelial cell differentiation in the formation of organoid supracellular capillary structures. As bioaptamers, copper ion-structured eRNA imparts novel biofunctions to proteins that they do not have on their own. The origin of extracellular RNA and intermediate precursors (up to 500 bases) was traced to intracellular parent nucleic acids. Intermediate precursors with and without partial homology were found. This suggests that bioaptamers are not directly retranslatable gene products. Metalloregulated eRNA bioaptamer function was investigated by domains (e.g. 5'...CUG...3' hairpin loop) for folding, bioactivity, and binding of protein with copper, calcium, and alkali metal ion affinity. Vice versa, metalloregulated nucleic acid-binding domains (K3H, R3H) in proteins were identified. Interaction of protein and eRNA docking potentials were visualized by 3D-rapid prototyping of accurate molecular image models based on crystallographic or NMR data. For S100A12-homologous proteins, receptor- and metalloregulated RNA chaperone-shaped protein assemblies were investigated. They suggest insight into signaling cascades as to how eRNA transmits its cytokine (ribokine) bioinformation from the extracellular RNA biosphere into cells. Proteomics of the extracellular RNA biosphere demonstrate the presence of nucleic acid-binding domain homologies in defense-, aging-, and disease-associated neuronal and other proteins as targets for RNA orphans. By structural relationships found to transmissible processes, proteinaceous transfer ("infectivity") and feedback of bioinformation beyond the central dogma of molecular biology are considered in terms of metalloregulated RNA bioaptamer function, nucleic acid-binding domains, and protein conformation.
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Affiliation(s)
- Josef H Wissler
- ARCONS Institute for Applied Research & Didactics, D-61231 Bad Nauheim, Germany.
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31
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Tassew N, Thompson M. Kinetic characterization of TAR RNA-Tat peptide and neomycin interactions by acoustic wave biosensor. Biophys Chem 2004; 106:241-52. [PMID: 14556896 DOI: 10.1016/s0301-4622(03)00155-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The kinetics of binding of short Tat peptides and an aminoglycoside molecule to the human immunodeficiency virus-type 1(HIV-1) TAR RNA and to a bulge mutant analogue (MTAR) is studied in a biosensor format by monitoring the time course of the response in a series resonance frequency, using an acoustic wave biosensor. Association and dissociation rate constants are evaluated by fitting the experimental data to a simple 1:1 (Langmuir) model. Kinetic rate and equilibrium dissociation constants show that MTAR-peptide complexes are subject to a higher dissociation rate and are less stable compared to the corresponding TAR-peptide complexes. In addition, longer peptides display enhanced discrimination ability than a shorter peptide according to the equilibrium dissociation constants evaluated using this technique. K(D) values for TAR-Tat vs. MTAR-Tat complexes are 2.6 vs. 3.8 microM for Tat-12, 0.87 vs. 4.3 microM for Tat-18 and 0.93 vs. 1.6 microM for Tat-20. The equilibrium dissociation constant for TAR-neomycin complex is 12.4 microM and it is comparable to the values obtained from non-biosensor type assays. These findings are in parallel with those cited in the literature and the results from this study underline the potential of the acoustic wave sensor for detailed biophysical analysis of nucleic acid-ligand binding.
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Affiliation(s)
- Nardos Tassew
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6
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32
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Kim H, Jeong E, Lee SW, Han K. Computational analysis of hydrogen bonds in protein-RNA complexes for interaction patterns. FEBS Lett 2003; 552:231-9. [PMID: 14527692 DOI: 10.1016/s0014-5793(03)00930-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Structural analysis of protein-RNA complexes is labor-intensive, yet provides insight into the interaction patterns between a protein and RNA. As the number of protein-RNA complex structures reported has increased substantially in the last few years, a systematic method is required for automatically identifying interaction patterns. This paper presents a computational analysis of the hydrogen bonds in the most representative set of protein-RNA complexes. The analysis revealed several interesting interaction patterns. (1) While residues in the beta-sheets favored unpaired nucleotides, residues in the helices showed no preference and residues in turns favored paired nucleotides. (2) The backbone hydrogen bonds were more dominant than the base hydrogen bonds in the paired nucleotides, but the reverse was observed in the unpaired nucleotides. (3) The protein-RNA complexes contained more paired nucleotides than unpaired nucleotides, but the unpaired nucleotides were observed more frequently interacting with the proteins. And (4) Arg-U, Thr-A, Lys-A, and Asn-U were the most frequently observed pairs. The interaction patterns discovered from the analysis will provide us with useful information in predicting the structure of the RNA binding protein and the structure of the protein binding RNA.
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Affiliation(s)
- Hyunwoo Kim
- School of Computer Science and Engineering, Inha University, 402-751 Inchon, South Korea
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33
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Leitner A, Lindner W. Probing of arginine residues in peptides and proteins using selective tagging and electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:891-899. [PMID: 12938110 DOI: 10.1002/jms.477] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A general labelling method is presented which allows the determination of the number of guanidine groups (related to arginine and homoarginine in peptides and proteins) by means of mass spectrometry. It implies a guanidine-selective derivatization step with 2,3-butanedione and an arylboronic acid under aqueous, alkaline conditions (pH 8-10). The reaction mixture is then directly analysed by electrospray ionization mass spectrometry without further sample pretreatment. Other amino acids are not affected by this reaction although it is demonstrated that lysine side-chains may be unambiguously identified when they are converted to homoarginine prior to derivatization. Guanidine functionalities, as e.g. in the amino acid arginine, are easily identified by the characteristic mass shift between underivatized and derivatized analyte. The tagging procedure is straightforward and selective for guanidine groups. The influence of several experimental parameters, especially the pH of the solution and the choice of reagents, is examined and the method is applied to various arginine-containing peptides and to lysozyme as a representative protein. Possible applications of this technique and its limitations are discussed.
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Affiliation(s)
- Alexander Leitner
- Christian Doppler Laboratory for Molecular Recognition Materials, Institute of Analytical Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
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34
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Volpon L, Lievre C, Osborne MJ, Gandhi S, Iannuzzi P, Larocque R, Cygler M, Gehring K, Ekiel I. The solution structure of YbcJ from Escherichia coli reveals a recently discovered alphaL motif involved in RNA binding. J Bacteriol 2003; 185:4204-10. [PMID: 12837795 PMCID: PMC164884 DOI: 10.1128/jb.185.14.4204-4210.2003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structure of the recombinant Escherichia coli protein YbcJ, a representative of a conserved family of bacterial proteins (COG2501), was determined by nuclear magnetic resonance. The fold of YbcJ identified it as a member of the larger family of S4-like RNA binding domains. These domains bind to structured RNA, such as that found in tRNA, rRNA, and a pseudoknot of mRNA. The structure of YbcJ revealed a highly conserved patch of basic residues, comprising amino acids K26, K38, R55, K56, and K59, which likely participate in RNA binding.
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Affiliation(s)
- Laurent Volpon
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada
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35
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Castrignanò T, Chillemi G, Varani G, Desideri A. Molecular dynamics simulation of the RNA complex of a double-stranded RNA-binding domain reveals dynamic features of the intermolecular interface and its hydration. Biophys J 2002; 83:3542-52. [PMID: 12496121 PMCID: PMC1302429 DOI: 10.1016/s0006-3495(02)75354-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The interaction between double-stranded RNA (dsRNA) and the third double-stranded domain (dsRBD) from Drosophila Staufen protein represents a paradigm to understand how the dsRBD protein family, one of the most common RNA-binding protein units, binds dsRNA. The nuclear magnetic resonance (NMR) structure of this complex and the x-ray structure of another family member revealed the stereochemical basis for recognition, but also raised new questions. Although the crystallographic studies revealed a highly ordered interface containing numerous water-mediated contacts, NMR suggested extensive residual motion at the interface. To address how interfacial motion contributes to molecular recognition in the dsRBD-dsRNA system, we conducted a 2-ns molecular dynamics simulation of the complex derived from Staufen protein and of the separate protein and RNA components. The results support the observation that a high degree of conformational flexibility is retained upon complex formation and that this involves interfacial residues that are critical for dsRBD-dsRNA binding. The structural origin of this residual flexibility is revealed by the analysis of the trajectory of motion. Individual basic side chains switch continuously from one RNA polar group to another with a residence time seldom exceeding 100 ps, while retaining favorable interaction with RNA throughout much of the simulation. Short-lived water molecules mediate some of these interactions for a large fraction of the trajectory studied here. This result indicates that water molecules are not statically associated with the interface, but continuously exchange with the bulk solvent on a 1-10-ps time scale. This work provides new insight into dsRBD-dsRNA recognition and builds upon a growing body of evidence, suggesting that short-lived dynamic interactions play important roles in protein-nucleic acid interactions.
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Affiliation(s)
- Tiziana Castrignanò
- Consorzio interuniversitario per le Applicazioni di Supercalculo per Università e Ricerca, University of Rome La Sapienza, 00185 Rome, Italy
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36
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Bell TW, Khasanov AB, Drew MGB. Role of pyridine hydrogen-bonding sites in recognition of basic amino acid side chains. J Am Chem Soc 2002; 124:14092-103. [PMID: 12440908 DOI: 10.1021/ja0273694] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of three, new artificial receptors for guanidinium and ammonium guests has been synthesized. All three receptors have highly preorganized clefts bearing two carboxylate groups. They differ in the number of nitrogen atoms contained in their clefts, as follows: four N atoms in receptor 3, three N atoms in 4, and two nitrogens in 5. Crystallographic studies have produced the solid-state structures of the following guanidinium complexes of each receptor: 3.2CH(3)CH(2)NHC(NH(2))(2)(+), 4.2CH(3)NHC(NH(2))(2)(+), and 5.2C(NH(2))(3)(+). The conformations of the receptor molecules in all three complexes are very similar. N-Alkylguanidinium guests are bound in the clefts of 3 and 4 in similar manners, despite the loss of one hydrogen-bond acceptor nitrogen in 4 and the possible hindrance of the cavity by a CH group. In the guanidinium complex of 5, neither guest enters the cavity containing two CH groups. Complexation studies were conducted in methanol by (1)H NMR titration for several guanidinium and ammonium guests, including derivatives of the amino acids arginine and lysine. Receptor 5 binds all such guests weakly (K(s) < 4000), while 3 binds most guests very strongly (K(s) > 100 000). Receptor 3 is selective for arginine versus lysine, while 4 binds lysine better than does 3. The results generally underscore the importance of receptor preorganization and hydrogen-bonding complementarity in the design of receptors that can serve as probes for biomolecules.
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Affiliation(s)
- Thomas W Bell
- Department of Chemistry/216, University of Nevada, Reno, NV 89557-0020, USA.
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Abstract
The RNA recognition motif (RRM) is one of the most common RNA binding domains. There have been few investigations of small molecule inhibitors of RRM-RNA complexes, although these inhibitors could be valuable tools for probing biological processes involving RRM-RNA complexes and would have the potential to be effective drugs. In this paper, the inhibition by small molecules of the complex formed between the N-terminal RRM of the U1A protein and stem loop 2 of U1 snRNA has been investigated. An aminoacridine derivative has been found to promote dissociation of the U1A-stem loop 2 RNA complex with an IC(50) value of 1 microM. Fluorescence experiments indicate that two aminoacridine ligands bind to each RNA target site. RNase A footprinting suggests that one binding site may be near the base pair that closes the loop and the other may be in a more flexible region of the loop. The addition of the aminoacridine derivative to stem loop 2 RNA increases the susceptibility of other portions of the loop to digestion by RNase A, which implies that binding of the ligand changes the conformation or dynamics of the stem loop target site. Either direct binding to the RNA or indirect alteration of the structure or dynamics of the loop would be likely to inhibit binding of the U1A protein to this RNA.
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Affiliation(s)
- Alicia Y Gayle
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
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Abstract
NOESY and ROESY cross-peak intensities depend on internuclear distances and internal motion. Internal motion is usually ignored, and NOESY cross-peak intensities are interpreted in terms of internuclear distances only. Off-resonance ROESY experiments measure a weighted average of NOE and ROE. The weight can be described and experimentally set by an angle theta;. For large enough molecules, NOE and ROE have opposite signs. Therefore, each cross-peak intensity becomes zero for an angle theta;(0). For any sample, the maximum angle theta;(0) is determined by the overall motion of the molecule. Smaller theta;(0) values reflect the angular component of internal motions. Because individual cross-peaks are analyzed, the method evaluates internal motions of individual H,H vectors. The reduction of theta;(0) is largest for internal motions on a time scale of 100-300 ps. The sensitivity of theta;(0) for internal motions decreases with increasing molecular weight. We estimate that detecting internal motions will be practicable for molecules up to about 15 kDa. We describe a protocol to measure theta;(0) from a series of off-resonance ROESY spectra. For such a series, we describe the choice of experimental parameters, a procedure to extract theta;(0) from the raw data, and the interpretation of theta;(0) in terms of internal motions. In the small protein BPTI, we analyzed 75 cross-peaks. The precision of theta;(0) was 0.25 degrees, as compared to typical reductions of theta;(0) of 3 degrees. We found a well-defined maximum theta;(0) for cross-peaks in rigid parts of the molecule, which reflects the overall motion of the molecule. For BPTI, also many structurally important long-range cross-peaks appear rigid. The lower theta;(0) values of long-range contacts involving methyl groups are consistent with methyl rotation on the 25-ps time scale. The lower theta;(0) values of the flexible C-terminus and of flexible side chains translate into upper limits for the angular order parameter of 0.4 and 0.5-0.8, respectively. Off-resonance ROESY can monitor internal motions of H,H contacts that are used in a structure calculation. Because no isotope labeling is needed, off-resonance ROESY can be used to detect internal motions in a wide range of natural products.
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Affiliation(s)
- Jürgen Schleucher
- Department of Medical Biochemistry and Biophysics, and Department of Organic Chemistry, Umeå University, S-90187 Umeå, Sweden.
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39
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Wang W, Donini O, Reyes CM, Kollman PA. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 30:211-43. [PMID: 11340059 DOI: 10.1146/annurev.biophys.30.1.211] [Citation(s) in RCA: 389] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Computer modeling has been developed and widely applied in studying molecules of biological interest. The force field is the cornerstone of computer simulations, and many force fields have been developed and successfully applied in these simulations. Two interesting areas are (a) studying enzyme catalytic mechanisms using a combination of quantum mechanics and molecular mechanics, and (b) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE) calculation methods. Enzyme catalysis involves forming and breaking of covalent bonds and requires the use of quantum mechanics. Noncovalent interactions appear ubiquitously in biology, but here we confine ourselves to review only noncovalent interactions between protein and protein, protein and ligand, and protein and nucleic acids.
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Affiliation(s)
- W Wang
- Graduate Group in Biophysics, University of California San Francisco, California 94143, USA.
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40
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Karan C, Miller BL. RNA-selective coordination complexes identified via dynamic combinatorial chemistry. J Am Chem Soc 2001; 123:7455-6. [PMID: 11472190 DOI: 10.1021/ja010325v] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C Karan
- Department of Chemistry University of Rochester Rochester, New York 14627, USA
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41
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Abstract
The past few years have witnessed remarkable progress in knowledge of the structure and function of RNA-binding proteins and their RNA complexes. X-ray crystallography and NMR spectroscopy have provided structures for all major classes of RNA-binding proteins, both alone and complexed with RNA. New computational and experimental tools have provided unprecedented insight into the molecular basis of RNA recognition.
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42
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Tok JB, Des Jean RC, Fenker J. Binding of a cyclic BIV beta-Tat peptide with its TAR RNA construct. Bioorg Med Chem Lett 2001; 11:43-6. [PMID: 11140729 DOI: 10.1016/s0960-894x(00)00591-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability of RNA structures to adopt diverse yet complex tertiary structures has resulted in numerous fascinating RNA-protein recognition events. It was recently reported that a close relative of the HIV Rev peptide, namely a 17 residue Tat peptide from bovine immuno-deficiency virus (BIV), is able to bind to the 28 nucleotide BIV TAR RNA construct. Here we report that by simply converting the 17 residue beta-ribbon peptide structure to a 19 residue cyclopeptide, the binding affinity (Kd) of the resulting cyclopeptide to the TAR RNA target, observed by fluorescence binding study, was enhanced approximately 5-fold.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cattle
- Fluorescein
- Fluorescence
- Gene Products, tat/chemistry
- Gene Products, tat/metabolism
- HIV Long Terminal Repeat/genetics
- Immunodeficiency Virus, Bovine/genetics
- Immunodeficiency Virus, Bovine/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Peptide Fragments/chemistry
- Peptide Fragments/metabolism
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/metabolism
- Protein Binding
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- Thermodynamics
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Affiliation(s)
- J B Tok
- Department of Chemistry, Indiana University-Purdue University, Fort Wayne, 46805, USA.
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43
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Belen’kii L, Kruchkovskaya N, Gramenitskaya V. The Literature of Heterocyclic Chemistry, Part VII: 1997–1999. ADVANCES IN HETEROCYCLIC CHEMISTRY 2001. [DOI: 10.1016/s0065-2725(01)79024-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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44
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Abstract
This review focuses on a very important but little understood type of molecular recognition--the recognition between highly flexible molecular structures. The formation of a specific complex in this case is a dynamic process that can occur through sequential steps of mutual conformational adaptation. This allows modulation of specificity and affinity of interaction in extremely broad ranges. The interacting partners can interact together to form a complex with entirely new properties and produce conformational signal transduction at substantial distance. We show that this type of recognition is frequent in formation of different protein-protein and protein-nucleic acid complexes. It is also characteristic for self-assembly of protein molecules from their unfolded fragments as well as for interaction of molecular chaperones with their substrates and it can be the origin of 'protein misfolding' diseases. Thermodynamic and kinetic features of this type of dynamic recognition and the principles underlying their modeling and analysis are discussed.
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Affiliation(s)
- A P Demchenko
- The Palladin Institute of Biochemistry of the Academy of Sciences of Ukraine, Kiev 252030, Ukraine.
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45
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Clavier G, Ilhan F, Rotello VM. Photochemical Control of the Macroconformation of Polystyrene Using Azobenzene Side Chains. Macromolecules 2000. [DOI: 10.1021/ma0011901] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gilles Clavier
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Faysal Ilhan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
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46
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Bayer P, Varani L, Varani G. Nuclear magnetic resonance methods to study RNA-protein complexes. Methods Enzymol 2000; 317:198-220. [PMID: 10829282 DOI: 10.1016/s0076-6879(00)17016-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- P Bayer
- MRC Laboratory of Molecular Biology, Cambridge, England
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47
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Luchansky SJ, Nolan SJ, Baranger AM. Contribution of RNA Conformation to the Stability of a High-Affinity RNA−Protein Complex. J Am Chem Soc 2000. [DOI: 10.1021/ja000837u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah J. Luchansky
- Department of Chemistry, Wesleyan University Middletown, Connecticut 06459
| | - Scott J. Nolan
- Department of Chemistry, Wesleyan University Middletown, Connecticut 06459
| | - Anne M. Baranger
- Department of Chemistry, Wesleyan University Middletown, Connecticut 06459
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48
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Ramos A, Grünert S, Adams J, Micklem DR, Proctor MR, Freund S, Bycroft M, St Johnston D, Varani G. RNA recognition by a Staufen double-stranded RNA-binding domain. EMBO J 2000; 19:997-1009. [PMID: 10698941 PMCID: PMC305639 DOI: 10.1093/emboj/19.5.997] [Citation(s) in RCA: 290] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/1999] [Revised: 12/21/1999] [Accepted: 01/12/2000] [Indexed: 11/14/2022] Open
Abstract
The double-stranded RNA-binding domain (dsRBD) is a common RNA-binding motif found in many proteins involved in RNA maturation and localization. To determine how this domain recognizes RNA, we have studied the third dsRBD from Drosophila Staufen. The domain binds optimally to RNA stem-loops containing 12 uninterrupted base pairs, and we have identified the amino acids required for this interaction. By mutating these residues in a staufen transgene, we show that the RNA-binding activity of dsRBD3 is required in vivo for Staufen-dependent localization of bicoid and oskar mRNAs. Using high-resolution NMR, we have determined the structure of the complex between dsRBD3 and an RNA stem-loop. The dsRBD recognizes the shape of A-form dsRNA through interactions between conserved residues within loop 2 and the minor groove, and between loop 4 and the phosphodiester backbone across the adjacent major groove. In addition, helix alpha1 interacts with the single-stranded loop that caps the RNA helix. Interactions between helix alpha1 and single-stranded RNA may be important determinants of the specificity of dsRBD proteins.
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Affiliation(s)
- A Ramos
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH
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49
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Abstract
We have solved the crystal structure of the heat shock protein Hsp15, a newly isolated and very highly inducible heat shock protein that binds the ribosome. Comparison of its structure with those of two RNA-binding proteins, ribosomal protein S4 and threonyl-tRNA synthetase, reveals a novel RNA-binding motif. This newly recognized motif is remarkably common, present in at least eight different protein families that bind RNA. The motif's surface is populated by conserved, charged residues that define a likely RNA-binding site. An intriguing pattern emerges: stress proteins, ribosomal proteins and tRNA synthetases repeatedly share a conserved motif. This may imply a hitherto unrecognized functional similarity between these three protein classes.
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Affiliation(s)
- B L Staker
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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50
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Spitzfaden C, Nicholson N, Jones JJ, Guth S, Lehr R, Prescott CD, Hegg LA, Eggleston DS. The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA. J Mol Biol 2000; 295:105-15. [PMID: 10623511 DOI: 10.1006/jmbi.1999.3341] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ribonuclease P (RNaseP) catalyses the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5' terminus. The prokaryotic RNaseP holoenzyme consists of a catalytic RNA component and a protein subunit (RNaseP protein), which plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. We determined the three-dimensional high-resolution structure of the RNaseP protein from Staphylococcus aureus (117 amino acid residues) by nuclear magnetic resonance (NMR) spectroscopy in solution. The protein has an alphabeta-fold, similar to the ribonucleoprotein domain. We used small nucleic acid molecules as a model for the 5'-leader sequence to probe the propensity for generic single-stranded RNA binding on the protein surface. The NMR results reveal a contiguous interaction site, which is identical with the previously identified leader sequence binding site in RNaseP holoenzyme. The conserved arginine-rich motif does not bind single-stranded RNA. It is likely that this peptide segment binds selectively to double-stranded sections of P RNA, which are conformationally more rigid. Given the essentiality of RNaseP for the viability of the organism, knowledge of the S. aureus protein structure and insight into its interaction with RNA will help us to develop RNaseP and RNaseP protein as targets for novel antibiotics against this pathogen.
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Affiliation(s)
- C Spitzfaden
- Computational and Structural Sciences, SmithKline Beecham Pharmaceuticals, Harlow, CM19 5AW, UK.
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