1
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Chowdhury AR, Sapkota D, Girodat D. Conformational changes of ribosomes during translation elongation resolved by molecular dynamics simulations. Curr Opin Struct Biol 2024; 86:102804. [PMID: 38569462 DOI: 10.1016/j.sbi.2024.102804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/06/2024] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Molecular dynamics simulations have emerged as a powerful set of tools to unravel the intricate dynamics of ribosomes during protein synthesis. Recent advancements in this field have enabled simulations to delve deep into the conformational rearrangements of ribosomes and associated factors, providing invaluable insights into the intricacies of translation. Emphasis on simulations has recently been on translation elongation, such as tRNA selection, translocation, and ribosomal head-swivel motions. These studies have offered crucial structural interpretations of how genetic information is faithfully translated into proteins. This review outlines recent discoveries concerning ribosome conformational changes occurring during translation elongation, as elucidated through molecular dynamics simulations.
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Affiliation(s)
- Anuradha Rai Chowdhury
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA. https://twitter.com/atomcellplankl
| | - Divya Sapkota
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Dylan Girodat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA.
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2
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Abu-Saleh AAAA, Sharma S, Yadav A, Poirier RA. Role of Asp190 in the Phosphorylation of the Antibiotic Kanamycin Catalyzed by the Aminoglycoside Phosphotransferase Enzyme: A Combined QM:QM and MD Study. J Phys Chem B 2020; 124:3494-3504. [DOI: 10.1021/acs.jpcb.0c01604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Abd Al-Aziz A. Abu-Saleh
- Chemistry Department, Memorial University, St. John’s, Newfoundland and Labrador A1B 3X7, Canada
| | - Sweta Sharma
- Department of Chemistry, University Institute of Engineering & Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur 208024, India
| | - Arpita Yadav
- Department of Chemistry, University Institute of Engineering & Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur 208024, India
| | - Raymond A. Poirier
- Chemistry Department, Memorial University, St. John’s, Newfoundland and Labrador A1B 3X7, Canada
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3
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Kulik M, Mori T, Sugita Y, Trylska J. Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides. Nucleic Acids Res 2019; 46:9960-9970. [PMID: 30239867 PMCID: PMC6212780 DOI: 10.1093/nar/gky833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/07/2018] [Indexed: 01/14/2023] Open
Abstract
A synthetic riboswitch N1, inserted into the 5'-untranslated mRNA region of yeast, regulates gene expression upon binding ribostamycin and neomycin. Interestingly, a similar aminoglycoside, paromomycin, differing from neomycin by only one substituent (amino versus hydroxyl), also binds to the N1 riboswitch, but without affecting gene expression, despite NMR evidence that the N1 riboswitch binds all aminoglycosides in a similar way. Here, to explore the details of structural dynamics of the aminoglycoside-N1 riboswitch complexes, we applied all-atom molecular dynamics (MD) and temperature replica-exchange MD simulations in explicit solvent. Indeed, we found that ribostamycin and neomycin affect riboswitch dynamics similarly but paromomycin allows for more flexibility because its complex lacks the contact between the distinctive 6' hydroxyl group and the G9 phosphate. Instead, a transient hydrogen bond of 6'-OH with A17 is formed, which partially diminishes interactions between the bulge and apical loop of the riboswitch, likely contributing to riboswitch inactivity. In many ways, the paromomycin complex mimics the conformations, interactions, and Na+ distribution of the free riboswitch. The MD-derived interaction network helps understand why riboswitch activity depends on aminoglycoside type, whereas for another aminoglycoside-binding site, aminoacyl-tRNA site in 16S rRNA, activity is not discriminatory.
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Affiliation(s)
- Marta Kulik
- RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | | | - Yuji Sugita
- RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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4
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Sanbonmatsu KY. Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR. Curr Opin Struct Biol 2019; 55:104-113. [PMID: 31125796 DOI: 10.1016/j.sbi.2019.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/11/2022]
Abstract
Recent advances in biotechnology such as Hi-C, CRISPR/Cas9 and ribosome display have placed nucleoprotein complexes at center stage. Understanding the structural dynamics of these complexes aids in optimizing protocols and interpreting data for these new technologies. The integration of simulation and experiment has helped advance mechanistic understanding of these systems. Coarse-grained simulations, reduced-description models, and explicit solvent molecular dynamics simulations yield useful complementary perspectives on nucleoprotein complex structural dynamics. When combined with Hi-C, cryo-EM, and single molecule measurements, these simulations integrate disparate forms of experimental data into a coherent mechanism.
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Leonarski F, Jasiński M, Trylska J. Thermodynamics of the fourU RNA thermal switch derived from molecular dynamics simulations and spectroscopic techniques. Biochimie 2018; 156:22-32. [PMID: 30244136 DOI: 10.1016/j.biochi.2018.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022]
Abstract
Bacterial 5' untranslated regions of mRNA, termed thermal switches or thermometers, change their structure in response to temperature change. This structural change provides for the regulation of gene expression. One of such thermal switches, called fourU, is present in the Salmonella species. Mutations of fourU were found to abrogate its regulatory properties. We investigated the thermodynamics of the fourU fragment responsible for its structural changes. All-atom molecular dynamics simulations at various temperatures and spectroscopic experiments in solution were performed for the wild-type fourU and its mutants. We found that the U11C and A8C mutations stabilize the fourU structure in comparison to the wild-type fourU, and the double-point G14A/C25U mutant has the most destabilizing effect on the fourU hairpin 2 responsible for temperature sensing. The G14A/C25U mutant is also the easiest to strand-invade by a complementary oligonucleotide as indicated by fluorescence spectroscopy experiments.
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Affiliation(s)
- Filip Leonarski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Maciej Jasiński
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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Jasiński M, Kulik M, Wojciechowska M, Stolarski R, Trylska J. Interactions of 2'-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site. PLoS One 2018; 13:e0191138. [PMID: 29351348 PMCID: PMC5774723 DOI: 10.1371/journal.pone.0191138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/28/2017] [Indexed: 12/15/2022] Open
Abstract
Synthetic oligonucleotides targeting functional regions of the prokaryotic rRNA could be promising antimicrobial agents. Indeed, such oligonucleotides were proven to inhibit bacterial growth. 2’-O-methylated (2’-O-Me) oligoribonucleotides with a sequence complementary to the decoding site in 16S rRNA were reported as inhibitors of bacterial translation. However, the binding mode and structures of the formed complexes, as well as the level of selectivity of the oligonucleotides between the prokaryotic and eukaryotic target, were not determined. We have analyzed three 2’-O-Me oligoribonucleotides designed to hybridize with the models of the prokaryotic rRNA containing two neighboring aminoglycoside binding pockets. One pocket is the paromomycin/kanamycin binding site corresponding to the decoding site in the small ribosomal subunit and the other one is the close-by hygromycin B binding site whose dynamics has not been previously reported. Molecular dynamics (MD) simulations, as well as isothermal titration calorimetry, gel electrophoresis and spectroscopic studies have shown that the eukaryotic rRNA model is less conformationally stable (in terms of hydrogen bonds and stacking interactions) than the corresponding prokaryotic one. In MD simulations of the eukaryotic construct, the nucleotide U1498, which plays an important role in correct positioning of mRNA during translation, is flexible and spontaneously flips out into the solvent. In solution studies, the 2’-O-Me oligoribonucleotides did not interact with the double stranded rRNA models but all formed stable complexes with the single-stranded prokaryotic target. 2’-O-Me oligoribonucleotides with one and two mismatches bound less tightly to the eukaryotic target. This shows that at least three mismatches between the 2’-O-Me oligoribonucleotide and eukaryotic rRNA are required to ensure target selectivity. The results also suggest that, in the ribosome environment, the strand invasion is the preferred binding mode of 2’-O-Me oligoribonucleotides targeting the aminoglycoside binding sites in 16S rRNA.
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Affiliation(s)
- Maciej Jasiński
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Marta Kulik
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Ryszard Stolarski
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- * E-mail:
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Abstract
Aminoglycoside antibiotics are protein synthesis inhibitors applied to treat infections caused mainly by aerobic Gram-negative bacteria. Due to their adverse side effects they are last resort antibiotics typically used to combat pathogens resistant to other drugs. Aminoglycosides target ribosomes. We describe the interactions of aminoglycoside antibiotics containing a 2-deoxystreptamine (2-DOS) ring with 16S rRNA. We review the computational studies, with a focus on molecular dynamics (MD) simulations performed on RNA models mimicking the 2-DOS aminoglycoside binding site in the small ribosomal subunit. We also briefly discuss thermodynamics of interactions of these aminoglycosides with their 16S RNA target.
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9
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Thoduka SG, Zaleski PA, Dąbrowska Z, Równicki M, Stróżecka J, Górska A, Olejniczak M, Trylska J. Analysis of ribosomal inter-subunit sites as targets for complementary oligonucleotides. Biopolymers 2017; 107. [PMID: 27858985 DOI: 10.1002/bip.23004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/06/2016] [Accepted: 11/10/2016] [Indexed: 01/15/2023]
Abstract
The bacterial ribosome has many functional ribosomal RNA (rRNA) sites. We have computationally analyzed the rRNA regions involved in the interactions between the 30S and 50S subunits. Various properties of rRNA such as solvent accessibility, opening energy, hydrogen bonding pattern, van der Waals energy, thermodynamic stability were determined. Based on these properties we selected rRNA targets for hybridization with complementary 2'-O-methyl oligoribonucleotides (2'-OMe RNAs). Further, the inhibition efficiencies of the designed ribosome-interfering 2'-OMe RNAs were tested using a β-galactosidase assay in a translation system based on the E. coli extract. Several of the oligonucleotides displayed IC50 values below 1 μM, which were in a similar range as those determined for known ribosome inhibitors, tetracycline and pactamycin. The calculated opening and van der Waals stacking energies of the rRNA targets correlated best with the inhibitory efficiencies of 2'-OMe RNAs. Moreover, the binding affinities of several oligonucleotides to both 70S ribosomes and isolated 30S and 50S subunits were measured using a double-filter retention assay. Further, we applied heat-shock chemical transformation to introduce 2'-OMe RNAs to E. coli cells and verify inhibition of bacterial growth. We observed high correlation between IC50 in the cell-free extract and bacterial growth inhibition. Overall, the results suggest that the computational analysis of potential rRNA targets within the conformationally dynamic regions of inter-subunit bridges can help design efficient antisense oligomers to probe the ribosome function.
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Affiliation(s)
- Sapna G Thoduka
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
| | - Paul A Zaleski
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, 61-614, Poland
| | - Zofia Dąbrowska
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
| | - Marcin Równicki
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, Warsaw, 02-097, Poland
| | - Joanna Stróżecka
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, 61-614, Poland
| | - Anna Górska
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
| | - Mikołaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, 61-614, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
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10
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Electrostatic interactions in aminoglycoside-RNA complexes. Biophys J 2015; 108:655-65. [PMID: 25650932 DOI: 10.1016/j.bpj.2014.12.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/20/2014] [Accepted: 12/10/2014] [Indexed: 11/21/2022] Open
Abstract
Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity.
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Panecka J, Šponer J, Trylska J. Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site. Biochimie 2015; 112:96-110. [PMID: 25748164 DOI: 10.1016/j.biochi.2015.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/23/2015] [Indexed: 01/12/2023]
Abstract
The aminoacyl-tRNA binding site (A-site) is located in helix 44 of small ribosomal subunit. The mobile adenines 1492 and 1493 (Escherichia coli numbering), forming the A-site bulge, act as a functional switch that ensures mRNA decoding accuracy. Structural data on the oligonucleotide models mimicking the ribosomal A-site with sequences corresponding to bacterial and human cytoplasmic sites confirm that this RNA motif forms also without the ribosome context. We performed all-atom molecular dynamics simulations of these crystallographic A-site models to compare their conformational properties. We found that the human A-site bulge is more internally flexible than the bacterial one and has different base pairing preferences, which result in the overall different shapes of these bulges and cation density distributions. Also, in the human A-site model we observed repetitive destacking of A1492, while A1493 was more stably paired than in the bacterial variant. Based on the dynamics of the A-sites we suggest why aminoglycoside antibiotics, which target the bacterial A-site, have lower binding affinities and anti-translational activities toward the human variant.
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Affiliation(s)
- Joanna Panecka
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Jiří Šponer
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic; Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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Panecka J, Mura C, Trylska J. Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study. PLoS One 2014; 9:e111811. [PMID: 25379961 PMCID: PMC4224418 DOI: 10.1371/journal.pone.0111811] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/07/2014] [Indexed: 12/28/2022] Open
Abstract
The conformational properties of the aminoacyl-tRNA binding site (A-site), and its surroundings in the Escherichia coli 30S ribosomal subunit, are of great relevance in designing antibacterial agents. The 30S subunit A-site is near ribosomal protein S12, which neighbors helices h27 and H69; this latter helix, of the 50S subunit, is a functionally important component of an intersubunit bridge. Experimental work has shown that specific point mutations in S12 (K42A, R53A) yield hyper-accurate ribosomes, which in turn confers resistance to the antibiotic 'paromomycin' (even when this aminoglycoside is bound to the A-site). Suspecting that these effects can be elucidated in terms of the local atomic interactions and detailed dynamics of this region of the bacterial ribosome, we have used molecular dynamics simulations to explore the motion of a fragment of the E. coli ribosome, including the A-site. We found that the ribosomal regions surrounding the A-site modify the conformational space of the flexible A-site adenines 1492/93. Specifically, we found that A-site mobility is affected by stacking interactions between adenines A1493 and A1913, and by contacts between A1492 and a flexible side-chain (K43) from the S12 protein. In addition, our simulations reveal possible indirect pathways by which the R53A and K42A mutations in S12 are coupled to the dynamical properties of the A-site. Our work extends what is known about the atomistic dynamics of the A-site, and suggests possible links between the biological effects of hyper-accurate mutations in the S12 protein and conformational properties of the ribosome; the implications for S12 dynamics help elucidate how the miscoding effects of paromomycin may be evaded in antibiotic-resistant mutants of the bacterial ribosome.
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Affiliation(s)
- Joanna Panecka
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States of America
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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Panecka J, Havrila M, Réblová K, Šponer J, Trylska J. Role of S-turn2 in the structure, dynamics, and function of mitochondrial ribosomal A-site. A bioinformatics and molecular dynamics simulation study. J Phys Chem B 2014; 118:6687-701. [PMID: 24845793 DOI: 10.1021/jp5030685] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The mRNA decoding site (A-site) in the small ribosomal subunit controls fidelity of the translation process. Here, using molecular dynamics simulations and bioinformatic analyses, we investigated the structural dynamics of the human mitochondrial A-site (native and A1490G mutant) and compared it with the dynamics of the bacterial A-site. We detected and characterized a specific RNA backbone configuration, S-turn2, which occurs in the human mitochondrial but not in the bacterial A-site. Mitochondrial and bacterial A-sites show different propensities to form S-turn2 that may be caused by different base-pairing patterns of the flanking nucleotides. Also, the S-turn2 structural stability observed in the simulations supports higher accuracy and lower speed of mRNA decoding in mitochondria in comparison with bacteria. In the mitochondrial A-site, we observed collective movement of stacked nucleotides A1408·C1409·C1410, which may explain the known differences in aminoglycoside antibiotic binding affinities toward the studied A-site variants.
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Affiliation(s)
- Joanna Panecka
- Department of Biophysics, Institute of Experimental Physics and ∥Centre of New Technologies, University of Warsaw , Żwirki i Wigury 93, 02-089 Warsaw, Poland
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Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. J Mol Biol 2014; 426:3201-3213. [PMID: 24813122 DOI: 10.1016/j.jmb.2014.04.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/13/2014] [Accepted: 04/14/2014] [Indexed: 11/22/2022]
Abstract
Ribosomes control the missense error rate of ~10(-4) during translation though quantitative contributions of individual mechanistic steps of the conformational changes yet to be fully determined. Biochemical and biophysical studies led to a qualitative tRNA selection model in which ribosomal A-site residues A1492 and A1493 (A1492/3) flip out in response to cognate tRNA binding, promoting the subsequent reactions, but not in the case of near-cognate or non-cognate tRNA. However, this model was recently questioned by X-ray structures revealing conformations of extrahelical A1492/3 and domain closure of the decoding center in both cognate and near-cognate tRNA bound ribosome complexes, suggesting that the non-specific flipping of A1492/3 has no active role in tRNA selection. We explore this question by carrying out molecular dynamics simulations, aided with fluorescence and NMR experiments, to probe the free energy cost of extrahelical flipping of 1492/3 and the strain energy associated with domain conformational change. Our rigorous calculations demonstrate that the A1492/3 flipping is indeed a specific response to the binding of cognate tRNA, contributing 3kcal/mol to the specificity of tRNA selection. Furthermore, the different A-minor interactions in cognate and near-cognate complexes propagate into the conformational strain and contribute another 4kcal/mol in domain closure. The recent structure of ribosome with features of extrahelical A1492/3 and closed domain in near-cognate complex is reconciled by possible tautomerization of the wobble base pair in mRNA-tRNA. These results quantitatively rationalize other independent experimental observations and explain the ribosomal discrimination mechanism of selecting cognate versus near-cognate tRNA.
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15
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Dudek M, Romanowska J, Wituła T, Trylska J. Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies. Biochimie 2014; 102:188-202. [PMID: 24769038 DOI: 10.1016/j.biochi.2014.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/20/2014] [Indexed: 10/25/2022]
Abstract
Amikacin is a 2-deoxystreptamine aminoglycoside antibiotic possessing a unique l-HABA (l-(-)-γ-amino-α-hydroxybutyric acid) group and applied in the treatment of hospital-acquired infections. Amikacin influences bacterial translation by binding to the decoding region of the small ribosomal subunit that overlaps with the binding site of aminoacylated-tRNA (A-site). Here, we have characterized thermodynamics of interactions of amikacin with a 27-mer RNA oligonucleotide mimicking the aminoglycoside binding site in the bacterial ribosome. We applied isothermal titration and differential scanning calorimetries, circular dichroism and thermal denaturation experiments, as well as computer simulations. Thermal denaturation studies have shown that amikacin affects only slightly the melting temperatures of the A-site mimicking RNA model suggesting a moderate stabilization of RNA by amikacin. Isothermal titration calorimetry gives the equilibrium dissociation constants for the binding reaction between amikacin and the A-site oligonucleotide in the micromolar range with a favorable enthalpic contribution. However, for amikacin we observe a positive entropic contribution to binding, contrary to other aminoglycosides, paromomycin and ribostamycin. Circular dichroism spectra suggest that the observed increase in entropy is not caused by structural changes of RNA because amikacin binding does not destabilize the helicity of the RNA model. To investigate the origins of this positive entropy change we performed all-atom molecular dynamics simulations in explicit solvent for the 27-mer RNA oligonucleotide mimicking one A-site and the crystal structure of an RNA duplex containing two A-sites. We observed that the diversity of the conformational states of the l-HABA group sampled in the simulations of the complex was larger than for the free amikacin in explicit water. Therefore, the larger flexibility of the l-HABA group in the bound form may contribute to an increase of entropy upon binding.
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Affiliation(s)
- Marta Dudek
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; First Faculty of Medicine, Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Al. Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Hoża 69, 00-681 Warsaw, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Tomasz Wituła
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland.
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16
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Hayashi Y, Sugiyama H, Suganami A, Higashi K, Kashiwagi K, Igarashi K, Kawauchi S, Tamura Y. Prediction of the interaction between spermidine and the G-G mismatch containing acceptor stem in tRNA(Ile): molecular modeling, density functional theory, and molecular dynamics study. Biochem Biophys Res Commun 2013; 441:999-1004. [PMID: 24239547 DOI: 10.1016/j.bbrc.2013.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 11/03/2013] [Indexed: 11/26/2022]
Abstract
Polyamines, putrescine, spermidine (SPD), and spermine are closely linked to cell growth, and highly regulate the levels of transcription, translation and protein turnover. We propose that SPD stimulates the formation of Ile-tRNA(Ile) by inducing a selective structural change of the G-G mismatch containing acceptor stem in tRNA(Ile). Here, we provide insight into how SPD recognizes and stabilizes the G-G mismatch containing acceptor stem in tRNA(Ile) with molecular modeling (MM), density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. The results of the MM and DFT calculations indicate that the negatively charged region of the G-G mismatch containing acceptor stem in tRNA(Ile) is preferentially recognized by positively charged SPD. In addition, MD simulations indicate that all of the positively charged amino groups of SPD under physiological conditions (N1(NH3(+)), N5(NH2(+)), and N10(NH3(+)) could form hydrogen bonds with tRNA(Ile) and trigger the SPD-induced stabilization and structural change of the G-G mismatch containing acceptor stem in tRNA(Ile). Thus, this approach should be useful for determining the preferential binding site and appropriate binding mode of polyamines on tRNA(Ile).
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Affiliation(s)
- Yoshihiro Hayashi
- Department of Organic and Polymeric Materials, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8522, Japan
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17
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Mukherjee S, Bhattacharyya D. Influence of divalent magnesium ion on DNA: molecular dynamics simulation studies. J Biomol Struct Dyn 2013; 31:896-912. [DOI: 10.1080/07391102.2012.713780] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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18
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Halder S, Bhattacharyya D. RNA structure and dynamics: a base pairing perspective. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:264-83. [PMID: 23891726 DOI: 10.1016/j.pbiomolbio.2013.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/25/2013] [Accepted: 07/16/2013] [Indexed: 12/12/2022]
Abstract
RNA is now known to possess various structural, regulatory and enzymatic functions for survival of cellular organisms. Functional RNA structures are generally created by three-dimensional organization of small structural motifs, formed by base pairing between self-complementary sequences from different parts of the RNA chain. In addition to the canonical Watson-Crick or wobble base pairs, several non-canonical base pairs are found to be crucial to the structural organization of RNA molecules. They appear within different structural motifs and are found to stabilize the molecule through long-range intra-molecular interactions between basic structural motifs like double helices and loops. These base pairs also impart functional variation to the minor groove of A-form RNA helices, thus forming anchoring site for metabolites and ligands. Non-canonical base pairs are formed by edge-to-edge hydrogen bonding interactions between the bases. A large number of theoretical studies have been done to detect and analyze these non-canonical base pairs within crystal or NMR derived structures of different functional RNA. Theoretical studies of these isolated base pairs using ab initio quantum chemical methods as well as molecular dynamics simulations of larger fragments have also established that many of these non-canonical base pairs are as stable as the canonical Watson-Crick base pairs. This review focuses on the various structural aspects of non-canonical base pairs in the organization of RNA molecules and the possible applications of these base pairs in predicting RNA structures with more accuracy.
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Affiliation(s)
- Sukanya Halder
- Biophysics division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India
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19
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Whitford PC, Blanchard SC, Cate JHD, Sanbonmatsu KY. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. PLoS Comput Biol 2013; 9:e1003003. [PMID: 23555233 PMCID: PMC3605090 DOI: 10.1371/journal.pcbi.1003003] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 02/04/2013] [Indexed: 12/27/2022] Open
Abstract
Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.
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Affiliation(s)
- Paul C Whitford
- Department of Physics, Northeastern University, Boston, Massachusetts, United States of America.
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20
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Abstract
The visualization of RNA conformational changes has provided fundamental insights into how regulatory RNAs carry out their biological functions. The RNA structural transitions that have been characterized to date involve long-lived species that can be captured by structure characterization techniques. Here, we report the Nuclear Magnetic Resonance visualization of RNA transitions towards invisible ‘excited states’ (ES), which exist in too little abundance (2–13%) and for too short periods of time (45–250 μs) to allow structural characterization by conventional techniques. Transitions towards ESs result in localized rearrangements in base-pairing that alter building block elements of RNA architecture, including helix-junction-helix motifs and apical loops. The ES can inhibit function by sequestering residues involved in recognition and signaling or promote ATP-independent strand exchange. Thus, RNAs do not adopt a single conformation, but rather exist in rapid equilibrium with alternative ESs, which can be stabilized by cellular cues to affect functional outcomes.
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21
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Romanowska J, Reuter N, Trylska J. Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes. Proteins 2012; 81:63-80. [PMID: 22907688 DOI: 10.1002/prot.24163] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 08/02/2012] [Accepted: 08/09/2012] [Indexed: 11/10/2022]
Abstract
Aminoglycoside antibiotics are used against severe bacterial infections. They bind to the bacterial ribosomal RNA and interfere with the translation process. However, bacteria produce aminoglycoside modifying enzymes (AME) to resist aminoglycoside actions. AMEs form a variable group and yet they specifically recognize and efficiently bind aminoglycosides, which are also diverse in terms of total net charge and the number of pseudo-sugar rings. Here, we present the results of 25 molecular dynamics simulations of three AME representatives and aminoglycoside ribosomal RNA binding site, unliganded and complexed with an aminoglycoside, kanamycin A. A comparison of the aminoglycoside binding sites in these different receptors revealed that the enzymes efficiently mimic the nucleic acid environment of the ribosomal RNA binding cleft. Although internal dynamics of AMEs and their interaction patterns with aminoglycosides differ, the energetical analysis showed that the most favorable sites are virtually the same in the enzymes and RNA. The most copied interactions were of electrostatic nature, but stacking was also replicated in one AME:kanamycin complex. In addition, we found that some water-mediated interactions were very stable in the simulations of the complexes. We show that our simulations reproduce well findings from NMR or X-ray structural studies, as well as results from directed mutagenesis. The outcomes of our analyses provide new insight into aminoglycoside resistance mechanism that is related to the enzymatic modification of these drugs.
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Affiliation(s)
- Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Hoża 69, 00-681 Warsaw, Poland.
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22
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Chen L, Calin GA, Zhang S. Novel insights of structure-based modeling for RNA-targeted drug discovery. J Chem Inf Model 2012; 52:2741-53. [PMID: 22947071 DOI: 10.1021/ci300320t] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Substantial progress in RNA biology highlights the importance of RNAs (e.g., microRNAs) in diseases and the potential of targeting RNAs for drug discovery. However, the lack of RNA-specific modeling techniques demands the development of new tools for RNA-targeted rational drug design. Herein, we implemented integrated approaches of accurate RNA modeling and virtual screening for RNA inhibitor discovery with the most comprehensive evaluation to date of five docking and 11 scoring methods. For the first time, statistical analysis was heavily employed to assess the significance of our predictions. We found that GOLD:GOLD Fitness and rDock:rDock_solv could accurately predict the RNA ligand poses, and ASP rescoring further improved the ranking of ligand binding poses. Due to the weak correlations (R(2) < 0.3) of existing scoring with experimental binding affinities, we implemented two new RNA-specific scoring functions, iMDLScore1 and iMDLScore2, and obtained better correlations with R(2) = 0.70 and 0.79, respectively. We also proposed a multistep virtual screening approach and demonstrated that rDock:rDock_solv together with iMDLScore2 rescoring obtained the best enrichment on the flexible RNA targets, whereas GOLD:GOLD Fitness combined with rDock_solv rescoring outperformed other methods for rigid RNAs. This study provided practical strategies for RNA modeling and offered new insights into RNA-small molecule interactions for drug discovery.
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Affiliation(s)
- Lu Chen
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, 1901 East Road, Houston Texas 77054, USA
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23
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Halder S, Bhattacharyya D. Structural Variations of Single and Tandem Mismatches in RNA Duplexes: A Joint MD Simulation and Crystal Structure Database Analysis. J Phys Chem B 2012; 116:11845-56. [PMID: 22953716 DOI: 10.1021/jp305628v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sukanya Halder
- Biophysics
Division and ‡Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, 700 064, India
| | - Dhananjay Bhattacharyya
- Biophysics
Division and ‡Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, 700 064, India
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24
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Romanowska J, Nowiński KS, Trylska J. Determining Geometrically Stable Domains in Molecular Conformation Sets. J Chem Theory Comput 2012; 8:2588-99. [DOI: 10.1021/ct300206j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Julia Romanowska
- Department of Biophysics,
Faculty of Physics, University of Warsaw, Hoża 69, 00-681 Warsaw, Poland
- Interdisciplinary
Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Pawińskiego
5a, 02-106 Warsaw, Poland
| | - Krzysztof S. Nowiński
- Interdisciplinary
Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Pawińskiego
5a, 02-106 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies
(CeNT), University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland
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25
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Burton B, Zimmermann MT, Jernigan RL, Wang Y. A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly. PLoS Comput Biol 2012; 8:e1002530. [PMID: 22654657 PMCID: PMC3359968 DOI: 10.1371/journal.pcbi.1002530] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 04/10/2012] [Indexed: 11/19/2022] Open
Abstract
Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. However, to date, no studies have attempted to elucidate these conformational changes. The present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of the ribosome. Ribosomal proteins are known to be positively charged and we find the percentage of positive residues in r-proteins to be about twice that of the average protein: Lys+Arg is 18.7% for E. coli and 21.2% for T. thermophilus. Also, positive residues constitute a large proportion of RNA contacting residues: 39% for E. coli and 46% for T. thermophilus. This affirms the known importance of charge-charge interactions in the assembly of the ribosome. We studied the dynamics of three primary proteins from E. coli and T. thermophilus 30S subunits that bind early in the assembly (S15, S17, and S20) with atomic molecular dynamic simulations, followed by a study of all r-proteins using elastic network models. Molecular dynamics simulations show that solvent-exposed proteins (S15 and S17) tend to adopt more stable solution conformations than an RNA-embedded protein (S20). We also find protein residues that contact the 16S rRNA are generally more mobile in comparison with the other residues. This is because there is a larger proportion of contacting residues located in flexible loop regions. By the use of elastic network models, which are computationally more efficient, we show that this trend holds for most of the 30S r-proteins. Ribosomes are complex cellular machines that synthesize new proteins in the cell. The accurate and efficient assembly of ribosomal proteins (r-proteins) and ribosomal RNA (rRNA) to form a functional ribosome is important for cell growth, metabolic reactions, and other cellular processes. Additionally, some antibacterial drugs are believed to target the bacterial ribosome during its construction. Hence, ribosomal assembly has been an active research topic for many years because understanding the assembly mechanisms can provide insight into protein/RNA recognitions important in many other cellular processes, as well as optimize the development of antibacterial therapeutics. Experimental studies thus far have provided still limited understanding about the assembly process. To further understand the assembly process, we have computationally studied the dynamic properties that r-proteins exhibit during assembly and the relationship between dynamics, physical properties, and binding propensity. We observe significant charged interactions between r-proteins and rRNA. We also detect a strong correlation between contact residues and their dynamic mobilities. Protein residues contacting with rRNA are observed to be more mobile in comparison with other residues. We also relate the location of the r-protein in the fully assembled ribosome to its susceptibility for large conformational changes prior to binding.
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Affiliation(s)
- Brittany Burton
- Department of Chemistry, The University of Memphis, Memphis, Tennessee, United States of America
| | - Michael T. Zimmermann
- Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Biochemistry, Biophysics and Molecular Biology, Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, Iowa, United States of America
| | - Robert L. Jernigan
- Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Biochemistry, Biophysics and Molecular Biology, Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, Iowa, United States of America
- * E-mail: (RLJ); (YW)
| | - Yongmei Wang
- Department of Chemistry, The University of Memphis, Memphis, Tennessee, United States of America
- * E-mail: (RLJ); (YW)
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26
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Sanbonmatsu KY. Computational studies of molecular machines: the ribosome. Curr Opin Struct Biol 2012; 22:168-74. [PMID: 22336622 DOI: 10.1016/j.sbi.2012.01.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/19/2012] [Accepted: 01/19/2012] [Indexed: 01/22/2023]
Abstract
The past decade has produced an avalanche of experimental data on the structure and dynamics of the ribosome. Groundbreaking studies in structural biology and kinetics have placed important constraints on ribosome structural dynamics. However, a gulf remains between static structures and time dependent data. In particular, X-ray crystallography and cryo-EM studies produce static models of the ribosome in various states, but lack dynamic information. Single molecule studies produce information on the rates of transitions between these states but do not have high-resolution spatial information. Computational studies have aided in bridging this gap by providing atomic resolution simulations of structural fluctuations and transitions between configurations.
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27
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28
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Wanunu M, Bhattacharya S, Xie Y, Tor Y, Aksimentiev A, Drndic M. Nanopore analysis of individual RNA/antibiotic complexes. ACS NANO 2011; 5:9345-53. [PMID: 22067050 PMCID: PMC3253136 DOI: 10.1021/nn203764j] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Nanopores in thin solid-state membranes are used to rapidly analyze individual RNA/drug complexes. The interactions of a truncated A-site RNA model of the prokaryotic ribosome with aminoglycoside antibiotics are characterized by passing individual molecules through a 3-3.5 nm diameter pore fabricated in a 8-10 nm thick silicon nitride membrane. Complexes of the A-site RNA with aminoglycosides can be distinguished from unbound A-site based on the ion current signatures produced as they pass through the nanopores. Counting the fraction of free and drug-bound molecules affords label-free drug-RNA binding isotherms consistent with literature reports and with data generated using independent fluorescence-based assays. Our measurements are supported by molecular dynamics simulations, which illustrate the relationship between the ionic current and complexation of the A-site RNA with paramomycin, a prototypical aminoglycoside antibiotic.
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Affiliation(s)
- Meni Wanunu
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University
- Corresponding authors: ; ;
| | | | - Yun Xie
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, Urbana, IL
- Corresponding authors: ; ;
| | - Marija Drndic
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University
- Corresponding authors: ; ;
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29
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Allnér O, Nilsson L. Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome. RNA (NEW YORK, N.Y.) 2011; 17:2177-2188. [PMID: 22028366 PMCID: PMC3222130 DOI: 10.1261/rna.029231.111] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 09/14/2011] [Indexed: 05/31/2023]
Abstract
We have carried out molecular dynamics simulations of the tRNA anticodon and mRNA codon, inside the ribosome, to study the effect of the common tRNA modifications cmo(5)U34 and m(6)A37. In tRNA(Val), these modifications allow all four nucleotides to be successfully read at the wobble position in a codon. Previous data suggest that entropic effects are mainly responsible for the extended reading capabilities, but detailed mechanisms have remained unknown. We have performed a wide range of simulations to elucidate the details of these mechanisms at the atomic level and quantify their effects: extensive free energy perturbation coupled with umbrella sampling, entropy calculations of tRNA (free and bound to the ribosome), and thorough structural analysis of the ribosomal decoding center. No prestructuring effect on the tRNA anticodon stem-loop from the two modifications could be observed, but we identified two mechanisms that may contribute to the expanded decoding capability by the modifications: The further reach of the cmo(5)U34 allows an alternative outer conformation to be formed for the noncognate base pairs, and the modification results in increased contacts between tRNA, mRNA, and the ribosome.
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Affiliation(s)
- Olof Allnér
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet, SE-141 83 Huddinge, Sweden
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30
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Réblová K, Šponer JE, Špačková N, Beššeová I, Šponer J. A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis. J Phys Chem B 2011; 115:13897-910. [PMID: 21999672 DOI: 10.1021/jp2065584] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The RNA kink-turn is an important recurrent RNA motif, an internal loop with characteristic consensus sequence forming highly conserved three-dimensional structure. Functional arrangement of RNA kink-turns shows a sharp bend in the phosphodiester backbone. Among other signature interactions, kink-turns form A-minor interaction between their two stems. Most kink-turns possess extended A-minor I (A-I) interaction where adenine of the second A•G base pair of the NC-stem interacts with the first canonical pair of the C-stem (i.e., the receptor pair) via trans-sugar-edge/sugar-edge (tSS) and cis-sugar-edge/sugar-edge (cSS) interactions. The remaining kink-turns have less compact A-minor 0 (A-0) interaction with just one tSS contact. We show that kink-turns with A-I in ribosomal X-ray structures keep G═C receptor base pair during evolution while the inverted pair (C═G) is not realized. In contrast, kink-turns with A-0 in the observed structures alternate G═C and C═G base pairs in sequences. We carried out an extended set (~5 μs) of explicit-solvent molecular dynamics simulations of kink-turns to rationalize this structural/evolutionary pattern. The simulations were done using a net-neutral Na(+) cation atmosphere (with ~0.25 M cation concentration) supplemented by simulations with either excess salt KCl atmosphere or inclusion of Mg(2+). The results do not seem to depend on the treatment of ions. The simulations started with X-ray structures of several kink-turns while we tested the response of the simulated system to base substitutions, modest structural perturbations and constraints. The trends seen in the simulations reveal that the A-I/G═C arrangement is preferred over all three other structures. The A-I/C═G triple appears structurally entirely unstable, consistent with the covariation patterns seen during the evolution. The A-0 arrangements tend to shift toward the A-I pattern in simulations, which suggests that formation of the A-0 interaction is likely supported by the surrounding protein and RNA molecules. A-0 may also be stabilized by additional kink-turn nucleotides not belonging to the kink-turn consensus, as shown for the kink-turn from ribosomal Helix 15. Quantum-chemical calculations on all four A-minor triples suggest that there is a different balance of electrostatic and dispersion stabilization in the A-I/G═C and A-I/C═G triples, which may explain different behavior of these otherwise isosteric triples in the context of kink-turns.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.
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31
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Sklenovský P, Florová P, Banáš P, Réblová K, Lankaš F, Otyepka M, Šponer J. Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs. J Chem Theory Comput 2011; 7:2963-80. [PMID: 26605485 DOI: 10.1021/ct200204t] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Reverse kink-turn is a recurrent elbow-like RNA building block occurring in the ribosome and in the group I intron. Its sequence signature almost matches that of the conventional kink-turn. However, the reverse and conventional kink-turns have opposite directions of bending. The reverse kink-turn lacks basically any tertiary interaction between its stems. We report unrestrained, explicit solvent molecular dynamics simulations of ribosomal and intron reverse kink-turns (54 simulations with 7.4 μs of data in total) with different variants (ff94, ff99, ff99bsc0, ff99χOL, and ff99bsc0χOL) of the Cornell et al. force field. We test several ion conditions and two water models. The simulations characterize the directional intrinsic flexibility of reverse kink-turns pertinent to their folded functional geometries. The reverse kink-turns are the most flexible RNA motifs studied so far by explicit solvent simulations which are capable at the present simulation time scale to spontaneously and reversibly sample a wide range of geometries from tightly kinked ones through flexible intermediates up to extended, unkinked structures. A possible biochemical role of the flexibility is discussed. Among the tested force fields, the latest χOL variant is essential to obtaining stable trajectories while all force field versions lacking the χ correction are prone to a swift degradation toward senseless ladder-like structures of stems, characterized by high-anti glycosidic torsions. The type of explicit water model affects the simulations considerably more than concentration and the type of ions.
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Affiliation(s)
- Petr Sklenovský
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Florová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Filip Lankaš
- Centre for Complex Molecular Systems and Biomolecules, Institute of Organic Chemistry and Biochemistry , Flemingovo nam. 2, 166 10 Praha 6, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
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32
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Romanowska J, McCammon JA, Trylska J. Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site. PLoS Comput Biol 2011; 7:e1002099. [PMID: 21814503 PMCID: PMC3140962 DOI: 10.1371/journal.pcbi.1002099] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 05/08/2011] [Indexed: 01/15/2023] Open
Abstract
Paromomycin is an aminoglycosidic antibiotic that targets the RNA of the bacterial small ribosomal subunit. It binds in the A-site, which is one of the three tRNA binding sites, and affects translational fidelity by stabilizing two adenines (A1492 and A1493) in the flipped-out state. Experiments have shown that various mutations in the A-site result in bacterial resistance to aminoglycosides. In this study, we performed multiple molecular dynamics simulations of the mutated A-site RNA fragment in explicit solvent to analyze changes in the physicochemical features of the A-site that were introduced by substitutions of specific bases. The simulations were conducted for free RNA and in complex with paromomycin. We found that the specific mutations affect the shape and dynamics of the binding cleft as well as significantly alter its electrostatic properties. The most pronounced changes were observed in the U1406C∶U1495A mutant, where important hydrogen bonds between the RNA and paromomycin were disrupted. The present study aims to clarify the underlying physicochemical mechanisms of bacterial resistance to aminoglycosides due to target mutations.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Bacteria/drug effects
- Bacteria/genetics
- Bacteria/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding Sites
- Drug Resistance, Bacterial/drug effects
- Drug Resistance, Bacterial/genetics
- Hydrogen Bonding
- Molecular Dynamics Simulation
- Mutation
- Paromomycin/pharmacology
- Protein Binding
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Ribosome Subunits, Small, Bacterial/genetics
- Ribosome Subunits, Small, Bacterial/metabolism
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Affiliation(s)
- Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw Poland.
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33
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Panecka J, Mura C, Trylska J. Molecular dynamics of potential rRNA binders: single-stranded nucleic acids and some analogues. J Phys Chem B 2010; 115:532-46. [PMID: 21192664 DOI: 10.1021/jp106404u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
By hindering or "silencing" protein translation in vivo, antisense nucleic acid analogues that hybridize to bacterial rRNA could serve as a promising class of antibacterial compounds. Thus, we performed a comparative analysis of the dynamical properties of modified oligonucleotides based upon a sequence (5')r(UGUUACGACU)(3') that is complementary to bacterial ribosomal A-site RNA. In particular, 25 ns explicit solvent molecular dynamics simulations were computed for the following six single-stranded decamers: (1) the above RNA in unmodified form; (2) the 2'-O-methyl-modified RNA; (3) peptide nucleic acid (PNA) analogues of the above sequence, containing either (a) T or (b) U; and (4) two serine-substituted PNAs. Our results show that 2'-O-methylation attenuates RNA backbone dynamics, thereby preventing interconversion between stacked and unstacked conformations. The PNA analogue is rendered less flexible by replacing uracil with thymine; in addition, we found that derivatizing the PNA backbone with serine leads to enhanced base-stacking interactions. Consistent with known solubility properties of these classes of molecules, both RNAs exhibited greater localization of water molecules than did PNA. In terms of counterions, the initially helical conformation of the 2'-O-methyl RNA exhibits the highest Na(+) density among all the simulated decamers, while Na(+) build-up was most negligible for the neutral PNA systems. Further studies of the conformational and physicochemical properties of such modified single-stranded oligomers may facilitate better design of nucleic acid analogues, particularly those capable of serving as specific, high-affinity ribosomal A-site binders.
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Affiliation(s)
- Joanna Panecka
- Department of Biophysics, Institute of Experimental Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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34
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Whitford PC, Onuchic JN, Sanbonmatsu KY. Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome. J Am Chem Soc 2010; 132:13170-1. [PMID: 20806913 DOI: 10.1021/ja1061399] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using explicit-solvent simulations of the 70S ribosome, the barrier-crossing attempt frequency was calculated for aminoacyl-tRNA elbow-accommodation. In seven individual trajectories (200-300 ns, each, for an aggregate time of 2.1 μs), the relaxation time of tRNA structural fluctuations was determined to be ∼10 ns, and the barrier-crossing attempt frequency of tRNA accommodation is ∼1-10 μs(-1). These calculations provide a quantitative relationship between the free-energy barrier and experimentally measured rates of accommodation, which demonstrate that the free-energy barrier of elbow-accommodation is less than 15 k(B)T, in vitro and in vivo.
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Affiliation(s)
- Paul C Whitford
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, MS K710, Los Alamos, New Mexico 87545, USA.
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35
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Spacková N, Réblová K, Sponer J. Structural dynamics of the box C/D RNA kink-turn and its complex with proteins: the role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations. J Phys Chem B 2010; 114:10581-93. [PMID: 20701388 DOI: 10.1021/jp102572k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Kink-turns (K-turns) are recurrent elbow-like RNA motifs that participate in protein-assisted RNA folding and contribute to RNA dynamics. We carried out a set of molecular dynamics (MD) simulations using parm99 and parmbsc0 force fields to investigate structural dynamics of the box C/D RNA and its complexes with two proteins: native archaeal L7ae protein and human 15.5 kDa protein, originally bound to very similar structure of U4 snRNA. The box C/D RNA forms K-turn with A-minor 0 tertiary interaction between its canonical (C) and noncanonical (NC) stems. The local K-turn architecture is thus different from the previously studied ribosomal K-turns 38 and 42 having A-minor I interaction. The simulations reveal visible structural dynamics of this tertiary interaction involving altogether six substates which substantially contribute to the elbow-like flexibility of the K-turn. The interaction can even temporarily shift to the A-minor I type pattern; however, this is associated with distortion of the G/A base pair in the NC-stem of the K-turn. The simulations show reduction of the K-turn flexibility upon protein binding. The protein interacts with the apex of the K-turn and with the NC-stem. The protein-RNA interface includes long-residency hydration sites. We have also found long-residency hydration sites and major ion-binding sites associated with the K-turn itself. The overall topology of the K-turn remains stable in all simulations. However, in simulations of free K-turn, we observed instability of the key C16(O2')-A7(N1) H-bond, which is a signature interaction of K-turns and which was visibly more stable in simulations of K-turns possessing A-minor I interaction. It may reflect either some imbalance of the force field or it may be a correct indication of early stages of unfolding since this K-turn requires protein binding for its stabilization. Interestingly, the 16(O2')-7(N1) H- bond is usually not fully lost since it is replaced by a water bridge with a tightly bound water, which is adenine-specific similarly as the original interaction. The 16(O2')-7(N1) H-bond is stabilized by protein binding. The stabilizing effect is more visible with the human 15.5 kDa protein, which is attributed to valine to arginine substitution in the binding site. The behavior of the A-minor interaction is force-field-dependent because the parmbsc0 force field attenuates the A-minor fluctuations compared to parm99 simulations. Behavior of other regions of the box C/D RNA is not sensitive to the force field choice. Simulation with net-neutralizing Na(+) and 0.2 M excess salt conditions appear in all aspects equivalent. The simulations show loss of a hairpin tetraloop, which is not part of the K-turn. This was attributed to force field limitations.
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Affiliation(s)
- Nad'a Spacková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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36
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Halder S, Bhattacharyya D. Structural Stability of Tandemly Occurring Noncanonical Basepairs within Double Helical Fragments: Molecular Dynamics Studies of Functional RNA. J Phys Chem B 2010; 114:14028-40. [DOI: 10.1021/jp102835t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Sukanya Halder
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata—700 064, India
| | - Dhananjay Bhattacharyya
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata—700 064, India
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37
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Abstract
Computational modeling studies that investigate activity of the bacterial ribosome were reviewed. Computational approaches became possible with the availability of three-dimensional atomic resolution structures of the ribosomal subunits. However, due to the enormous size of the system, theoretical efforts to study the ribosome are few and challenging. For example, to extend the simulation timescales to biologically relevant ones, often, reduced models that require tedious parameterizations need to be applied. To that end, modeling of the ribosome focused on its internal dynamics, electrostatic properties, inhibition by antibiotics, polypeptide folding in the ribosome tunnel and assembly mechanisms driving the formation of the small ribosomal subunit.
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Mlýnský V, Banáš P, Hollas D, Réblová K, Walter NG, Šponer J, Otyepka M. Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J Phys Chem B 2010; 114:6642-52. [PMID: 20420375 PMCID: PMC2872159 DOI: 10.1021/jp1001258] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The hairpin ribozyme is a prominent member of the group of small catalytic RNAs (RNA enzymes or ribozymes) because it does not require metal ions to achieve catalysis. Biochemical and structural data have implicated guanine 8 (G8) and adenine 38 (A38) as catalytic participants in cleavage and ligation catalyzed by the hairpin ribozyme, yet their exact role in catalysis remains disputed. To gain insight into dynamics in the active site of a minimal self-cleaving hairpin ribozyme, we have performed extensive classical, explicit-solvent molecular dynamics (MD) simulations on time scales of 50-150 ns. Starting from the available X-ray crystal structures, we investigated the structural impact of the protonation states of G8 and A38, and the inactivating A-1(2'-methoxy) substitution employed in crystallography. Our simulations reveal that a canonical G8 agrees well with the crystal structures while a deprotonated G8 profoundly distorts the active site. Thus MD simulations do not support a straightforward participation of the deprotonated G8 in catalysis. By comparison, the G8 enol tautomer is structurally well tolerated, causing only local rearrangements in the active site. Furthermore, a protonated A38H(+) is more consistent with the crystallography data than a canonical A38. The simulations thus support the notion that A38H(+) is the dominant form in the crystals, grown at pH 6. In most simulations, the canonical A38 departs from the scissile phosphate and substantially perturbs the structures of the active site and S-turn. Yet, we occasionally also observe formation of a stable A-1(2'-OH)...A38(N1) hydrogen bond, which documents the ability of the ribozyme to form this hydrogen bond, consistent with a potential role of A38 as general base catalyst. The presence of this hydrogen bond is, however, incompatible with the expected in-line attack angle necessary for self-cleavage, requiring a rapid transition of the deprotonated 2'-oxyanion to a position more favorable for in-line attack after proton transfer from A-1(2'-OH) to A38(N1). The simulations revealed a potential force field artifact, occasional but irreversible formation of "ladder-like", underwound A-RNA structure in one of the external helices. Although it does not affect the catalytic center of the hairpin ribozyme, further studies are under way to better assess possible influence of such force field behavior on long RNA simulations.
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Affiliation(s)
- Vojtěch Mlýnský
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Daniel Hollas
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109-1055, USA
| | - Jiří Šponer
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
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39
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Réblová K, Střelcová Z, Kulhánek P, Beššeová I, Mathews DH, Van Nostrand K, Yildirim I, Turner DH, Šponer J. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5′-UAA/5′-GAN Internal Loops Studied by Molecular Dynamics Methods. J Chem Theory Comput 2010; 6:910-29. [DOI: 10.1021/ct900440t] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Zora Střelcová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Petr Kulhánek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Ivana Beššeová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - David H. Mathews
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Keith Van Nostrand
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Ilyas Yildirim
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Douglas H. Turner
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
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40
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Réblová K, Střelcová Z, Kulhánek P, Beššeová I, Mathews DH, Nostrand KV, Yildirim I, Turner DH, Šponer J. An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods. J Chem Theory Comput 2010; 2010:910-929. [PMID: 21132104 PMCID: PMC2994019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Functional RNA molecules such as ribosomal RNAs frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt distinctive structure inconsistent with secondary structure predictions. The structure has a narrow major groove and forms a trans Hoogsteen/Sugar edge (tHS) A/G base pair followed by an unpaired stacked adenine, a trans Watson-Crick/Hoogsteen (tWH) U/A base pair and finally by a bulged nucleotide (N). The structure is further stabilized by a three-adenine stack and base-phosphate interaction. In the ribosome, the UAA/GAN internal loops are involved in extensive tertiary contacts, mainly as donors of A-minor interactions. Further, this sequence can adopt an alternative 2D/3D pattern stabilized by a four-adenine stack involved in a smaller number of tertiary interactions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (cWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 µs of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by MM-PBSA free energy calculations, locally enhanced sampling (LES) runs, targeted MD (TMD) and nudged elastic band (NEB) analysis. We compared parm99 and parmbsc0 force fields and net-neutralizing Na(+) vs. excess salt KCl ion environments. Both force fields provide a similar description of the simulated structures, with the parmbsc0 leading to modest narrowing of the major groove. The excess salt simulations also cause a similar effect. While the NMR structure is entirely stable in simulations, the simulated X-ray structure shows considerable widening of the major groove, loss of base-phosphate interaction and other instabilities. The alternative X-ray geometry even undergoes conformational transition towards the solution 2D structure. Free energy calculations confirm that the X-ray arrangement is less stable than the solution structure. LES, TMD and NEB provide a rather consistent pathway for interconversion between the X-ray and NMR structures. In simulations, the incomplete cWS A/U base pair of the NMR structure is water mediated and alternates with the canonical A-U base pair, which is not indicated by the NMR data. Completion of full cWS A/U base pair is prevented by the overall internal loop arrangement. In summary, the simulations confirm that the UAA/GAN internal loop is a molecular switch RNA module that adopts its functional geometry upon specific tertiary contexts.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Zora Střelcová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Petr Kulhánek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Ivana Beššeová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - David H. Mathews
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642
| | - Keith Van Nostrand
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642
| | - Ilyas Yildirim
- Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
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41
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Chen SY, Lin TH. A molecular dynamics study on binding recognition between several 4,5 and 4,6-linked aminoglycosides with A-site RNA. J Mol Recognit 2009; 23:423-34. [DOI: 10.1002/jmr.1008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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42
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Réblová K, Rázga F, Li W, Gao H, Frank J, Sponer J. Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Nucleic Acids Res 2009; 38:1325-40. [PMID: 19952067 PMCID: PMC2831300 DOI: 10.1093/nar/gkp1057] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Helix 38 (H38) of the large ribosomal subunit, with a length of 110 A, reaches the small subunit through intersubunit bridge B1a. Previous cryo-EM studies revealed that the tip of H38 moves by more than 10 A from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible H38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. We investigate a region including the elbow-shaped kink-turn (Kt-38) in the Haloarcula marismortui archaeal ribosome, and equivalently positioned elbows in three eubacterial species, located at the H38 base. We performed explicit solvent molecular dynamics simulations on the H38 elbows in all four species. They are formed by at first sight unrelated sequences resulting in diverse base interactions but built with the same overall topology, as shown by X-ray crystallography. The elbows display similar fluctuations and intrinsic flexibilities in simulations indicating that the eubacterial H38 elbows are structural and dynamical analogs of archaeal Kt-38. We suggest that this structural element plays a pivotal role in the large motions of H38 and may act as fulcrum for the abovementioned tip motion. The directional flexibility inferred from simulations correlates well with the cryo-EM results.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolská 135, 61265 Brno, Czech Republic
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43
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Setny P, Trylska J. Search for novel aminoglycosides by combining fragment-based virtual screening and 3D-QSAR scoring. J Chem Inf Model 2009; 49:390-400. [PMID: 19434840 DOI: 10.1021/ci800361a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aminoglycosides are antibiotics targeting the 16S RNA A site of the bacterial ribosome. There have been many efforts directed toward design of their synthetic derivatives, however with only few successes. As RNA binders, aminoglycosides are also a difficult target for computational drug design, since most of the existing methods were developed for protein ligands. Here, we present an approach that allows for evading the problems related to still poorly developed RNA docking and scoring algorithms. It is aimed at identification of new molecular scaffolds potentially binding to the A site. The considered molecules are based on the neamine core, which is common for all aminoglycosides and provides specificity toward the binding site, linked with diverse molecular fragments via its O5 or O6 oxygen atom. Suitable fragments are selected with the use of 3D searches of molecular fragments library against two distinct pharmacophores designed on the basis of available structural data for aminoglycoside-RNA complexes. The compounds resulting from fragments assembly with neamine are then scored with a 3D-QSAR model developed using the biological data for known aminoglycoside derivatives. Twenty-one new potential ligands are obtained, four of which have predicted activities comparable to less potent aminoglycoside antibiotics.
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Affiliation(s)
- Piotr Setny
- Interdisciplinary Centre for Mathematical and Computational Modelling and Faculty of Physics, University of Warsaw, Warsaw 02-089, Poland.
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44
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Beššeová I, Otyepka M, Réblová K, Šponer J. Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys Chem Chem Phys 2009; 11:10701-11. [DOI: 10.1039/b911169g] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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