1
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Frezza E, Laage D, Duboué-Dijon E. Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences. J Phys Chem Lett 2024; 15:4351-4358. [PMID: 38619551 DOI: 10.1021/acs.jpclett.4c00629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to OR, due to the different phosphate orientations in A-form double helical RNA.
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Affiliation(s)
- Elisa Frezza
- Université Paris Cité, CNRS, CiTCoM, Paris 75006, France
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure-PSL, Sorbonne Université, CNRS, Paris 75005, France
| | - Elise Duboué-Dijon
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, Paris 75005, France
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2
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Fantini J, Azzaz F, Chahinian H, Yahi N. Electrostatic Surface Potential as a Key Parameter in Virus Transmission and Evolution: How to Manage Future Virus Pandemics in the Post-COVID-19 Era. Viruses 2023; 15:v15020284. [PMID: 36851498 PMCID: PMC9964723 DOI: 10.3390/v15020284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
Virus-cell interactions involve fundamental parameters that need to be considered in strategies implemented to control viral outbreaks. Among these, the surface electrostatic potential can give valuable information to deal with new epidemics. In this article, we describe the role of this key parameter in the hemagglutination of red blood cells and in the co-evolution of synaptic receptors and neurotransmitters. We then establish the functional link between lipid rafts and the electrostatic potential of viruses, with special emphasis on gangliosides, which are sialic-acid-containing, electronegatively charged plasma membrane components. We describe the common features of ganglioside binding domains, which include a wide variety of structures with little sequence homology but that possess key amino acids controlling ganglioside recognition. We analyze the role of the electrostatic potential in the transmission and intra-individual evolution of HIV-1 infections, including gatekeeper and co-receptor switch mechanisms. We show how to organize the epidemic surveillance of influenza viruses by focusing on mutations affecting the hemagglutinin surface potential. We demonstrate that the electrostatic surface potential, by modulating spike-ganglioside interactions, controls the hemagglutination properties of coronaviruses (SARS-CoV-1, MERS-CoV, and SARS-CoV-2) as well as the structural dynamics of SARS-CoV-2 evolution. We relate the broad-spectrum antiviral activity of repositioned molecules to their ability to disrupt virus-raft interactions, challenging the old concept that an antibiotic or anti-parasitic cannot also be an antiviral. We propose a new concept based on the analysis of the electrostatic surface potential to develop, in real time, therapeutic and vaccine strategies adapted to each new viral epidemic.
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3
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Chawla M, Kalra K, Cao Z, Cavallo L, Oliva R. Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules. Nucleic Acids Res 2022; 50:11455-11469. [PMID: 36416268 PMCID: PMC9723503 DOI: 10.1093/nar/gkac1081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
We present a systematic structural and energetic characterization of phosphate(OP)-nucleobase anion…π stacking interactions in RNAs. We observed OP-nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol-1, for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP-uracil and OP-guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations.
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Affiliation(s)
- Mohit Chawla
- Correspondence may also be addressed to Mohit Chawla. ;
| | - Kanav Kalra
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad 121002, Haryana, India
| | - Zhen Cao
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Luigi Cavallo
- Correspondence may also be addressed to Luigi Cavallo. Tel: +966 02 8027566; Fax: +966 02 8021347;
| | - Romina Oliva
- To whom correspondence should be addressed. Tel: +39 081 5476541; Fax: +39 081 5476514;
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4
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Biedermannová L, Černý J, Malý M, Nekardová M, Schneider B. Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks. Acta Crystallogr D Struct Biol 2022; 78:1032-1045. [PMID: 35916227 PMCID: PMC9344474 DOI: 10.1107/s2059798322006234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022] Open
Abstract
Database-derived water probability densities around structurally and sequentially distinct DNA dinucleotide fragments reproduce the known hydration motifs, which thus can be used as building blocks to predict DNA hydration. Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 Å) and correctly reproduced the known features of DNA hydration, for example the ‘spine of hydration’ in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.
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Vasiliu T, Mocci F, Laaksonen A, Engelbrecht LDV, Perepelytsya S. Caging Polycations: Effect of Increasing Confinement on the Modes of Interaction of Spermidine3+ With DNA Double Helices. Front Chem 2022; 10:836994. [PMID: 35281557 PMCID: PMC8915389 DOI: 10.3389/fchem.2022.836994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/04/2022] [Indexed: 11/23/2022] Open
Abstract
Polyamines have important roles in the modulation of the cellular function and are ubiquitous in cells. The polyamines putrescine2+, spermidine3+, and spermine4+ represent the most abundant organic counterions of the negatively charged DNA in the cellular nucleus. These polyamines are known to stabilize the DNA structure and, depending on their concentration and additional salt composition, to induce DNA aggregation, which is often referred to as condensation. However, the modes of interactions of these elongated polycations with DNA and how they promote condensation are still not clear. In the present work, atomistic molecular dynamics (MD) computer simulations of two DNA fragments surrounded by spermidine3+ (Spd3+) cations were performed to study the structuring of Spd3+ “caged” between DNA molecules. Microsecond time scale simulations, in which the parallel DNA fragments were constrained at three different separations, but allowed to rotate axially and move naturally, provided information on the conformations and relative orientations of surrounding Spm3+ cations as a function of DNA-DNA separation. Novel geometric criteria allowed for the classification of DNA-Spd3+ interaction modes, with special attention given to Spd3+ conformational changes in the space between the two DNA molecules (caged Spd3+). This work shows how changes in the accessible space, or confinement, around DNA affect DNA-Spd3+ interactions, information fundamental to understanding the interactions between DNA and its counterions in environments where DNA is compacted, e.g. in the cellular nucleus.
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Affiliation(s)
- Tudor Vasiliu
- Centre of Advanced Research in Bionanoconjugates and Biopolymers “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
| | - Francesca Mocci
- Dipartimento di Scienze Chimiche e Geologiche, Cagliari University, Cagliari, Italy
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
| | - Aatto Laaksonen
- Centre of Advanced Research in Bionanoconjugates and Biopolymers “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
- Dipartimento di Scienze Chimiche e Geologiche, Cagliari University, Cagliari, Italy
- Division of Energy Science, Energy Engineering, Luleå University of Technology, Luleå, Sweden
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, China
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
| | | | - Sergiy Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the NAS of Ukraine, Kyiv, Ukraine
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
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6
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Gabas F, Conte R, Ceotto M. Quantum Vibrational Spectroscopy of Explicitly Solvated Thymidine in Semiclassical Approximation. J Phys Chem Lett 2022; 13:1350-1355. [PMID: 35109652 PMCID: PMC8842300 DOI: 10.1021/acs.jpclett.1c04087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
In this paper, we demonstrate the possibility to perform spectroscopy simulations of solvated biological species taking into consideration quantum effects and explicit solvation. We achieve this goal by interfacing our recently developed divide-and-conquer approach for semiclassical initial value representation molecular dynamics with the polarizable AMOEBABIO18 force field. The method is applied to the study of solvation of the thymidine nucleoside in two different polar solvents, water and N,N-dimethylformamide. Such systems are made of up to 2476 atoms. Experimental evidence concerning the different behavior of thymidine in the two solvents is well reproduced by our study, even though quantitative estimates are hampered by the limited accuracy of the classical force field employed. Overall, this study shows that semiclassically approximate quantum dynamical studies of explicitly solvated biological systems are both computationally affordable and insightful.
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7
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Xu Z, He Z, Quan X, Sun D, Miao Z, Yu H, Yang S, Chen Z, Zeng J, Zhou J. Molecular simulations of charged complex fluids: A review. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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8
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Kalra K, Gorle S, Cavallo L, Oliva R, Chawla M. Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs. Nucleic Acids Res 2020; 48:5825-5838. [PMID: 32392301 PMCID: PMC7293021 DOI: 10.1093/nar/gkaa345] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/21/2020] [Accepted: 05/07/2020] [Indexed: 01/15/2023] Open
Abstract
We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp-π) or the OH-π type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 Å for A, G and C, and approximately at 3.1-3.2 Å for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp-π interaction as compared to the OH-π one (3.0 versus 3.5 Å). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp-π or the OH-π type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the OW atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization of water-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.
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Affiliation(s)
- Kanav Kalra
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Suresh Gorle
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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9
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Kumar N, Marx D. Deciphering the Self-Cleavage Reaction Mechanism of Hairpin Ribozyme. J Phys Chem B 2020; 124:4906-4918. [PMID: 32453954 DOI: 10.1021/acs.jpcb.0c03768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hairpin ribozyme catalyzes the reversible self-cleavage of phosphodiester bonds which plays prominent roles in key biological processes involving RNAs. Despite impressive advances on ribozymatic self-cleavage, critical aspects of its molecular reaction mechanism remain controversially debated. Here, we generate and analyze the multidimensional free energy landscape that underlies the reaction using extensive QM/MM metadynamics simulations to investigate in detail the full self-cleavage mechanism. This allows us to answer several pertinent yet controversial questions concerning activation of the 2'-OH group, the mechanistic role of water molecules present in the active site, and the full reaction pathway including the structures of transition states and intermediates. Importantly, we find that a sufficiently unrestricted reaction subspace must be mapped using accelerated sampling methods in order to compute the underlying free energy landscape. It is shown that lower-dimensional sampling where the bond formation and cleavage steps are coupled does not allow the system to sufficiently explore the landscape. On the basis of a three-dimensional free energy surface spanned by flexible generalized coordinates, we find that 2'-OH is indirectly activated by adjacent G8 nucleobase in conjunction with stabilizing H-bonding involving water. This allows the proton of the 2'-OH group to directly migrate toward the 5'-leaving group via a nonbridging oxygen of the phosphodiester link. At variance with similar enzymatic processes where water wires connected to protonable side chains of the protein matrix act as transient proton shuttles, no such de/reprotonation events of water molecules are found to be involved in this ribozymatic transesterification. Overall, our results support an acid-catalyzed reaction mechanism where A38 nucleobase directly acts as an acid whereas G8, in stark contrast, participates only indirectly via stabilizing the nascent nucleophile for subsequent attack. Moreover, we conclude that self-cleavage of hairpin ribozyme follows an AN + DN two-step associative pathway where the rate-determining step is the cleavage of the phosphodiester bond. These results provide a major advancement in our understanding of the unique catalytic mechanism of hairpin ribozyme which will fruitfully impact on the design of synthetic ribozymes.
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Affiliation(s)
- Narendra Kumar
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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10
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Sung HL, Nesbitt DJ. DNA Hairpin Hybridization under Extreme Pressures: A Single-Molecule FRET Study. J Phys Chem B 2019; 124:110-120. [PMID: 31840514 DOI: 10.1021/acs.jpcb.9b10131] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Organisms have evolved to live in a variety of complex environments, which clearly has required cellular biology to accommodate to extreme conditions of hydraulic pressure and elevated temperature. In this work, we exploit single-molecule Forster resonance energy transfer (FRET) spectroscopy to probe structural changes in DNA hairpins as a function of pressure and temperature, which allows us to extract detailed thermodynamic information on changes in free energy (ΔG°), free volume (ΔV°), enthalpy (ΔH°), and entropy (ΔS°) associated with DNA loop formation and sequence-dependent stem hybridization. Specifically, time-correlated single-photon counting experiments on freely diffusing 40A DNA hairpin FRET constructs are performed in a 50 μm × 50 μm square quartz capillary cell pressurized from ambient pressure up to 3 kbar. By pressure-dependent van't Hoff analysis of the equilibrium constants, ΔV° for hybridization of the DNA hairpin can be determined as a function of stem length (nstem = 7-10) with single base-pair resolution, which further motivates a simple linear deconstruction into additive stem (ΔV°stem = ΔV°bp x nstem) and loop (ΔV°loop) contributions. We find that increasing pressure destabilizes the DNA hairpin stem region [ΔV°bp = +1.98(16) cm3/(mol bp)], with additional positive free volume changes [ΔV°loop = +7.0(14) cm3/mol] we ascribe to bending and base stacking disruption of the 40-dA loop. From a van't Hoff temperature-dependent analysis of the DNA 40A hairpin equilibria, the data support a similar additive loop/stem deconstruction of enthalpic (ΔH° = ΔH°loop + ΔH°stem) and entropic (ΔS° = ΔS°loop + ΔS°stem) contributions, which permits insightful comparison with predictions from nearest-neighbor thermodynamic models for DNA duplex formation. In particular, the stem thermodynamics is consistent with exothermically favored (ΔH°stem < 0) and entropically penalized (ΔS°stem < 0) hydrogen bonding but with additional enthalpic (ΔH°loop > 0) and entropic (ΔS°loop > 0) contributions due to loop bending effects consistent with distortion of dA base stacking in the 40-dA linker.
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Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
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11
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Kumar N, Marx D. How do ribozymes accommodate additional water molecules upon hydrostatic compression deep into the kilobar pressure regime? Biophys Chem 2019; 252:106192. [DOI: 10.1016/j.bpc.2019.106192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 12/19/2022]
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12
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Bochicchio A, Krepl M, Yang F, Varani G, Sponer J, Carloni P. Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study. PLoS Comput Biol 2018; 14:e1006642. [PMID: 30521520 PMCID: PMC6307825 DOI: 10.1371/journal.pcbi.1006642] [Citation(s) in RCA: 9] [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: 07/11/2018] [Revised: 12/27/2018] [Accepted: 11/13/2018] [Indexed: 12/25/2022] Open
Abstract
The RNA recognition motif (RRM) is the most common RNA binding domain across eukaryotic proteins. It is therefore of great value to engineer its specificity to target RNAs of arbitrary sequence. This was recently achieved for the RRM in Rbfox protein, where four mutations R118D, E147R, N151S, and E152T were designed to target the precursor to the oncogenic miRNA 21. Here, we used a variety of molecular dynamics-based approaches to predict specific interactions at the binding interface. Overall, we have run approximately 50 microseconds of enhanced sampling and plain molecular dynamics simulations on the engineered complex as well as on the wild-type Rbfox·pre-miRNA 20b from which the mutated systems were designed. Comparison with the available NMR data on the wild type molecules (protein, RNA, and their complex) served to establish the accuracy of the calculations. Free energy calculations suggest that further improvements in affinity and selectivity are achieved by the S151T replacement. RNA is an outstanding target for oncological intervention. Engineering the most common RNA binding motif in human proteins (called RRM) so as to bind to a specific RNA has an enormous pharmacological potential. Yet, it is highly non trivial to design RRM-bearing protein variants with RNA selectivity and affinity sufficiently high for clinical applications. Here we present an extensive molecular simulation study which shed light on the exquisite molecular recognition of the empirically-engineered complex between the RRM-bearing protein Rbfox and its RNA target pre-miR21. The simulations allow predicting a variant, the S151T, which may lead to further enhancement of selectivity and affinity for pre-miR21.
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Affiliation(s)
- Anna Bochicchio
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- * E-mail: (MK); (PC)
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, Olomouc, Czech Republic
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
- JARA-HPC, Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, Germany
- * E-mail: (MK); (PC)
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13
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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: 327] [Impact Index Per Article: 54.5] [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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14
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Leidner F, Kurt Yilmaz N, Paulsen J, Muller YA, Schiffer CA. Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput 2018; 14:2784-2796. [PMID: 29570286 DOI: 10.1021/acs.jctc.8b00097] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Water is essential in many biological processes, and the hydration structure plays a critical role in facilitating protein folding, dynamics, and ligand binding. A variety of biophysical spectroscopic techniques have been used to probe the water solvating proteins, often complemented with molecular dynamics (MD) simulations to resolve the spatial and dynamic features of the hydration shell, but comparing relative water structure is challenging. In this study 1 μs MD simulations were performed to identify and characterize hydration sites around HIV-1 protease bound to an inhibitor, darunavir (DRV). The water density, hydration site occupancy, extent and anisotropy of fluctuations, coordinated water molecules, and hydrogen bonds were characterized and compared to the properties of bulk water. The water density of the principal hydration shell was found to be higher than bulk, dependent on the topology and physiochemical identity of the biomolecular surface. The dynamics of water molecules occupying principal hydration sites was highly dependent on the number of water-water interactions and inversely correlated with hydrogen bonds to the protein-inhibitor complex. While many waters were conserved following the symmetry of homodimeric HIV protease, the asymmetry induced by DRV resulted in asymmetric lower-occupancy hydration sites at the concave surface of the active site. Key interactions between water molecules and the protease, that stabilize the protein in the inhibited form, were altered in a drug resistant variant of the protease indicating that modulation of solvent-solute interactions might play a key role in conveying drug resistance. Our analysis provides insights into the interplay between an enzyme inhibitor complex and the hydration shell and has implications in elucidating water structure in a variety of biological processes and applications including ligand binding, inhibitor design, and resistance.
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Affiliation(s)
- Florian Leidner
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Janet Paulsen
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Yves A Muller
- Division of Biotechnology , Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen 91052 , Germany
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
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15
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Liu L, Kim BG, Feroze U, Macgregor RB, Chalikian TV. Probing the Ionic Atmosphere and Hydration of the c-MYC i-Motif. J Am Chem Soc 2018; 140:2229-2238. [DOI: 10.1021/jacs.7b11537] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Byul G. Kim
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Ujala Feroze
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B. Macgregor
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
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16
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Melvin RL, Gmeiner WH, Salsbury FR. All-atom MD indicates ion-dependent behavior of therapeutic DNA polymer. Phys Chem Chem Phys 2017; 19:22363-22374. [PMID: 28805211 PMCID: PMC5600158 DOI: 10.1039/c7cp03479b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Understanding the efficacy of and creating delivery mechanisms for therapeutic nucleic acids requires understanding structural and kinetic properties which allow these polymers to promote the death of cancerous cells. One molecule of interest is a 10 mer of FdUMP (5-fluoro-2'-deoxyuridine-5'-O-monophosphate) - also called F10. Here we investigate the structural and kinetic behavior of F10 in intracellular and extracellular solvent conditions along with non-biological conditions that may be efficacious in in vitro preparations of F10 delivery systems. From our all-atom molecular dynamics simulations totaling 80 microseconds, we predict that F10's phosphate groups form close-range interactions with calcium and zinc ions, with calcium having the highest affinity of the five ions investigated. We also predict that F10's interactions with magnesium, potassium and sodium are almost exclusively long-range interactions. In terms of intramolecular interactions, we find that F10 is least structured (in terms of hydrogen bonds among bases) in the 150 mM NaCl (extracellular-like solvent conditions) and most structured in 150 mM ZnCl2. Kinetically, we see that F10 is unstable in the presence of magnesium, sodium or potassium, finding stable kinetic traps in the presence of calcium or zinc.
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Affiliation(s)
- Ryan L Melvin
- Department of Physics, Wake Forest University, Winston Salem, NC, USA.
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17
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Krepl M, Blatter M, Cléry A, Damberger FF, Allain FH, Sponer J. Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition. Nucleic Acids Res 2017; 45:8046-8063. [PMID: 28505313 PMCID: PMC5737849 DOI: 10.1093/nar/gkx418] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/26/2017] [Accepted: 05/02/2017] [Indexed: 01/07/2023] Open
Abstract
The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Markus Blatter
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
- Present address: Global Discovery Chemistry, Novartis Institute for BioMedical Research, Basel CH-4002, Switzerland
| | - Antoine Cléry
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Fred F. Damberger
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Frédéric H.T. Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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18
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Dudek M, Trylska J. Molecular Dynamics Simulations of l-RNA Involving Homo- and Heterochiral Complexes. J Chem Theory Comput 2017; 13:1244-1253. [DOI: 10.1021/acs.jctc.6b01075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Marta Dudek
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Institute
of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego
5a, 02-106 Warsaw, Poland
- Department
of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Al. Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Joanna Trylska
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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19
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Atzori A, Liggi S, Laaksonen A, Porcu M, Lyubartsev AP, Saba G, Mocci F. Base sequence specificity of counterion binding to DNA: what can MD simulations tell us? CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0296] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleic acids are highly charged biopolymers whose secondary structure is strongly dependent on electrostatic interactions. Solvent molecules and ions are also believed to play an important role in mediating and directing both sequence recognition and interactions with other molecules, such as proteins and a variety of ligands. Therefore, to fully understand the biological functions of DNA, it is necessary to understand the interactions with the surrounding counterions. It is well known that monovalent counterions can bind to the minor groove of DNA with consecutive sequences of four, or more, adenine and thymine (A-tracts) with relatively long residence times. However, much less is known about their binding to the backbone and to the major groove. In this work, we used molecular dynamics simulations to both investigate the interactions between the backbone and major groove of DNA and one of its physiological counterions (Na+) and evaluate the relationship between these interactions and the nucleotide sequence. Three dodecamers, namely CGAAAATTTTCG, CGCTCTAGAGCG, and CGCGAATTCGCG, were simulated using the Toukan–Rahman flexible SPC water model and Smith and Dang parameters for Na+, revealing a significant sequence dependence on the ion binding to both backbone and major groove. In the absence of experimental data on the atomistic details of the studied interactions, the reliability of the results was evaluated performing the simulations with additional sets of potential parameters for ions and solvent, namely the Ȧqvist or the Joung and Cheatham ion parameters and the TIP3P water model. This allowed us to evaluate the results by verifying which features are preserved independently from the parameters adopted.
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Affiliation(s)
- Alessio Atzori
- Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Cittadella Universitaria di Monserrato, I-09042 Monserrato (CA), Italy
| | - Sonia Liggi
- Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Cittadella Universitaria di Monserrato, I-09042 Monserrato (CA), Italy
| | - Aatto Laaksonen
- Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Cittadella Universitaria di Monserrato, I-09042 Monserrato (CA), Italy
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
- Science for Life Laboratory, 171 21 Solna, Sweden
| | - Massimiliano Porcu
- Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Cittadella Universitaria di Monserrato, I-09042 Monserrato (CA), Italy
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
| | - Alexander P. Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
| | - Giuseppe Saba
- Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Cittadella Universitaria di Monserrato, I-09042 Monserrato (CA), Italy
| | - Francesca Mocci
- Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Cittadella Universitaria di Monserrato, I-09042 Monserrato (CA), Italy
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
- Science for Life Laboratory, 171 21 Solna, Sweden
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20
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Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. Biochim Biophys Acta Gen Subj 2016; 1860:1821-35. [PMID: 27241846 DOI: 10.1016/j.bbagen.2016.05.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics. SCOPE OF REVIEW This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties. MAJOR CONCLUSIONS In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration. GENERAL SIGNIFICANCE An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.
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21
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Kim HS, Martel A, Girard E, Moulin M, Härtlein M, Madern D, Blackledge M, Franzetti B, Gabel F. SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell. Biophys J 2016; 110:2185-94. [PMID: 27224484 PMCID: PMC4880798 DOI: 10.1016/j.bpj.2016.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/09/2016] [Accepted: 04/08/2016] [Indexed: 11/26/2022] Open
Abstract
Water molecules in the immediate vicinity of biomacromolecules, including proteins, constitute a hydration layer characterized by physicochemical properties different from those of bulk water and play a vital role in the activity and stability of these structures, as well as in intermolecular interactions. Previous studies using solution scattering, crystallography, and molecular dynamics simulations have provided valuable information about the properties of these hydration shells, including modifications in density and ionic concentration. Small-angle scattering of x-rays (SAXS) and neutrons (SANS) are particularly useful and complementary techniques to study biomacromolecular hydration shells due to their sensitivity to electronic and nuclear scattering-length density fluctuations, respectively. Although several sophisticated SAXS/SANS programs have been developed recently, the impact of physicochemical surface properties on the hydration layer remains controversial, and systematic experimental data from individual biomacromolecular systems are scarce. Here, we address the impact of physicochemical surface properties on the hydration shell by a systematic SAXS/SANS study using three mutants of a single protein, green fluorescent protein (GFP), with highly variable net charge (+36, -6, and -29). The combined analysis of our data shows that the hydration shell is locally denser in the vicinity of acidic surface residues, whereas basic and hydrophilic/hydrophobic residues only mildly modify its density. Moreover, the data demonstrate that the density modifications result from the combined effect of residue-specific recruitment of ions from the bulk in combination with water structural rearrangements in their vicinity. Finally, we find that the specific surface-charge distributions of the different GFP mutants modulate the conformational space of flexible parts of the protein.
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Affiliation(s)
- Henry S Kim
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | | | - Eric Girard
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | | | | | - Dominique Madern
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France
| | - Martin Blackledge
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France
| | - Bruno Franzetti
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France
| | - Frank Gabel
- University Grenoble Alpes, Grenoble, France; CNRS, Grenoble, France; CEA, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France.
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22
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Abstract
Metal ions are essential cofactors for the structure and functions of nucleic acids. Yet, the early discovery in the 70s of the crucial role of Mg(2+) in stabilizing tRNA structures has occulted for a long time the importance of monovalent cations. Renewed interest in these ions was brought in the late 90s by the discovery of specific potassium metal ions in the core of a group I intron. Their importance in nucleic acid folding and catalytic activity is now well established. However, detection of K(+) and Na(+) ions is notoriously problematic and the question about their specificity is recurrent. Here we review the different methods that can be used to detect K(+) and Na(+) ions in nucleic acid structures such as X-ray crystallography, nuclear magnetic resonance or molecular dynamics simulations. We also discuss specific versus non-specific binding to different structures through various examples.
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Affiliation(s)
- Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC, CNRS, 15 rue René Descartes, F-67084, Strasbourg, France.
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC, CNRS, 15 rue René Descartes, F-67084, Strasbourg, France.
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC, CNRS, 15 rue René Descartes, F-67084, Strasbourg, France.
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23
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Kührová P, Otyepka M, Šponer J, Banáš P. Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations. J Chem Theory Comput 2015; 10:401-11. [PMID: 26579919 DOI: 10.1021/ct400663s] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude and mechanism of the interplay between water molecules and the RNA structure are still poorly understood. In principle, such hydration effects can be studied by molecular dynamics (MD) simulations. In our recent MD studies, we observed that the choice of water model has a visible impact on the predicted structure and structural dynamics of RNA and, in particular, has a larger effect than type, parametrization, and concentration of the ions. Furthermore, the water model effect is sequence dependent and modulates the sequence dependence of A-RNA helical parameters. Clearly, the sensitivity of A-RNA structural dynamics to the water model parametrization is a rather spurious effect that complicates MD studies of RNA molecules. These results nevertheless suggest that the sequence dependence of the A-RNA structure, usually attributed to base stacking, might be driven by the structural dynamics of specific hydration. Here, we present a systematic MD study that aimed to (i) clarify the atomistic mechanism of the water model sensitivity and (ii) discover whether and to what extent specific hydration modulates the A-RNA structural variability. We carried out an extended set of MD simulations of canonical A-RNA duplexes with TIP3P, TIP4P/2005, TIP5P, and SPC/E explicit water models and found that different water models provided a different extent of water bridging between 2'-OH groups across the minor groove, which in turn influences their distance and consequently also inclination, roll, and slide parameters. Minor groove hydration is also responsible for the sequence dependence of these helical parameters. Our simulations suggest that TIP5P is not optimal for RNA simulations.
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Affiliation(s)
- Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17. Listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 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
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 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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24
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Anosova I, Kowal EA, Dunn MR, Chaput JC, Van Horn WD, Egli M. The structural diversity of artificial genetic polymers. Nucleic Acids Res 2015; 44:1007-21. [PMID: 26673703 PMCID: PMC4756832 DOI: 10.1093/nar/gkv1472] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/30/2015] [Indexed: 11/13/2022] Open
Abstract
Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson-Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space.
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Affiliation(s)
- Irina Anosova
- The Biodesign Institute, Virginia G. Piper Center for Personalized Diagnostics, School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Ewa A Kowal
- Department of Biochemistry, Center for Structural Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, School of Medicine, Nashville, TN 37232-0146, USA
| | - Matthew R Dunn
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, CA 92697, USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, CA 92697, USA
| | - Wade D Van Horn
- The Biodesign Institute, Virginia G. Piper Center for Personalized Diagnostics, School of Molecular Sciences, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Martin Egli
- Department of Biochemistry, Center for Structural Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, School of Medicine, Nashville, TN 37232-0146, USA
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25
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Gebala M, Giambasu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D. Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting. J Am Chem Soc 2015; 137:14705-15. [PMID: 26517731 PMCID: PMC4739826 DOI: 10.1021/jacs.5b08395] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ion atmosphere is a critical structural, dynamic, and energetic component of nucleic acids that profoundly affects their interactions with proteins and ligands. Experimental methods that "count" the number of ions thermodynamically associated with the ion atmosphere allow dissection of energetic properties of the ion atmosphere, and thus provide direct comparison to theoretical results. Previous experiments have focused primarily on the cations that are attracted to nucleic acid polyanions, but have also showed that anions are excluded from the ion atmosphere. Herein, we have systematically explored the properties of anion exclusion, testing the zeroth-order model that anions of different identity are equally excluded due to electrostatic repulsion. Using a series of monovalent salts, we find, surprisingly, that the extent of anion exclusion and cation inclusion significantly depends on salt identity. The differences are prominent at higher concentrations and mirror trends in mean activity coefficients of the electrolyte solutions. Salts with lower activity coefficients exhibit greater accumulation of both cations and anions within the ion atmosphere, strongly suggesting that cation-anion correlation effects are present in the ion atmosphere and need to be accounted for to understand electrostatic interactions of nucleic acids. To test whether the effects of cation-anion correlations extend to nucleic acid kinetics and thermodynamics, we followed the folding of P4-P6, a domain of the Tetrahymena group I ribozyme, via single-molecule fluorescence resonance energy transfer in solutions with different salts. Solutions of identical concentration but lower activity gave slower and less favorable folding. Our results reveal hitherto unknown properties of the ion atmosphere and suggest possible roles of oriented ion pairs or anion-bridged cations in the ion atmosphere for electrolyte solutions of salts with reduced activity. Consideration of these new results leads to a reevaluation of the strengths and limitations of Poisson-Boltzmann theory and highlights the need for next-generation atomic-level models of the ion atmosphere.
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Affiliation(s)
- Magdalena Gebala
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - George M. Giambasu
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig Maximilian University of Munich, 80799 Munich, Germany
| | - Namita Bisaria
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Steve Bonilla
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Guangchao Li
- School of Earth, Energy and Environment Sciences, Stanford University, Stanford, California 94305, United States
| | - Darrin M. York
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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26
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Gresh N, Sponer JE, Devereux M, Gkionis K, de Courcy B, Piquemal JP, Sponer J. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics. J Phys Chem B 2015; 119:9477-95. [DOI: 10.1021/acs.jpcb.5b01695] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Nohad Gresh
- Chemistry & Biology, Nucleo(s)tides & Immunology for Therapy (CBNIT), CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Judit E. Sponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
- CEITEC − Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Mike Devereux
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH 4056, Switzerland
| | - Konstantinos Gkionis
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
| | - Benoit de Courcy
- Chemistry & Biology, Nucleo(s)tides & Immunology for Therapy (CBNIT), CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Jiri Sponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
- CEITEC − Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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27
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Wagner D, Rinnenthal J, Narberhaus F, Schwalbe H. Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution. Nucleic Acids Res 2015; 43:5572-85. [PMID: 25940621 PMCID: PMC4477652 DOI: 10.1093/nar/gkv414] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/08/2015] [Indexed: 12/16/2022] Open
Abstract
The cyanobacterial hsp17 ribonucleicacid thermometer (RNAT) is one of the smallest naturally occurring RNAT. It forms a single hairpin with an internal 1×3-bulge separating the start codon in stem I from the ribosome binding site (RBS) in stem II. We investigated the temperature-dependent regulation of hsp17 by mapping individual base-pair stabilities from solvent exchange nuclear magnetic resonance (NMR) spectroscopy. The wild-type RNAT was found to be stabilized by two critical CG base pairs (C14-G27 and C13-G28). Replacing the internal 1×3 bulge by a stable CG base pair in hsp17rep significantly increased the global stability and unfolding cooperativity as evidenced by circular dichroism spectroscopy. From the NMR analysis, remote stabilization and non-nearest neighbour effects exist at the base-pair level, in particular for nucleotide G28 (five nucleotides apart from the side of mutation). Individual base-pair stabilities are coupled to the stability of the entire thermometer within both the natural and the stabilized RNATs by enthalpy–entropy compensation presumably mediated by the hydration shell. At the melting point the Gibbs energies of the individual nucleobases are equalized suggesting a consecutive zipper-type unfolding mechanism of the RBS leading to a dimmer-like function of hsp17 and switch-like regulation behaviour of hsp17rep. The data show how minor changes in the nucleotide sequence not only offset the melting temperature but also alter the mode of temperature sensing. The cyanobacterial thermosensor demonstrates the remarkable adjustment of natural RNATs to execute precise temperature control.
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Affiliation(s)
- Dominic Wagner
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | - Jörg Rinnenthal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr University, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
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28
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Mlýnský V, Kührová P, Zgarbová M, Jurečka P, Walter NG, Otyepka M, Šponer J, Banáš P. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations. J Phys Chem B 2015; 119:4220-9. [DOI: 10.1021/jp512069n] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Vojtěch Mlýnský
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Marie Zgarbová
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Nils G. Walter
- Department
of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, 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
- CEITEC
− Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacky University, 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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29
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Ion-selective interactions of biologically relevant inorganic ions with alanine zwitterion: a 3D-RISM study. Amino Acids 2015; 47:1015-23. [DOI: 10.1007/s00726-015-1930-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/25/2015] [Indexed: 11/27/2022]
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30
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Pasi M, Maddocks JH, Lavery R. Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics. Nucleic Acids Res 2015; 43:2412-23. [PMID: 25662221 PMCID: PMC4344516 DOI: 10.1093/nar/gkv080] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact with the double helix. The oligomers studied contain all 136 distinct tetranucleotides and we are thus able to make a comprehensive analysis of base sequence effects. Using a recently developed curvilinear helicoidal coordinate method we are able to analyze the details of ion populations and densities within the major and minor grooves and in the space surrounding DNA. The results show higher ion populations than have typically been observed in earlier studies and sequence effects that go beyond the nature of individual base pairs or base pair steps. We also show that, in some special cases, ion distributions converge very slowly and, on a microsecond timescale, do not reflect the symmetry of the corresponding base sequence.
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Affiliation(s)
- Marco Pasi
- Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UM 5086/Université Lyon I, IBCP, 7 passage du Vercors, 69367 Lyon, France
| | - John H Maddocks
- Section de Mathématiques, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Richard Lavery
- Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UM 5086/Université Lyon I, IBCP, 7 passage du Vercors, 69367 Lyon, France
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31
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Pan F, Roland C, Sagui C. Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study. Nucleic Acids Res 2014; 42:13981-96. [PMID: 25428372 PMCID: PMC4267617 DOI: 10.1093/nar/gku1107] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 12/30/2022] Open
Abstract
The ion atmosphere around nucleic acids is an integral part of their solvated structure. However, detailed aspects of the ionic distribution are difficult to probe experimentally, and comparative studies for different structures of the same sequence are almost non-existent. Here, we have used large-scale molecular dynamics simulations to perform a comparative study of the ion distribution around (5'-CGCGCGCGCGCG-3')2 dodecamers in solution in B-DNA, A-RNA, Z-DNA and Z-RNA forms. The CG sequence is very sensitive to ionic strength and it allows the comparison with the rare but important left-handed forms. The ions investigated include Na(+), K(+) and Mg(2 +), with various concentrations of their chloride salts. Our results quantitatively describe the characteristics of the ionic distributions for different structures at varying ionic strengths, tracing these differences to nucleic acid structure and ion type. Several binding pockets with rather long ion residence times are described, both for the monovalent ions and for the hexahydrated Mg[(H2O)6](2+) ion. The conformations of these binding pockets include direct binding through desolvated ion bridges in the GpC steps in B-DNA and A-RNA; direct binding to backbone oxygens; binding of Mg[(H2O)6](2+) to distant phosphates, resulting in acute bending of A-RNA; tight 'ion traps' in Z-RNA between C-O2 and the C-O2' atoms in GpC steps; and others.
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Affiliation(s)
- Feng Pan
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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32
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Nakano M, Tateishi-Karimata H, Tanaka S, Sugimoto N. Affinity of Molecular Ions for DNA Structures Is Determined by Solvent-Accessible Surface Area. J Phys Chem B 2014; 118:9583-94. [DOI: 10.1021/jp505107g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | | | - Shigenori Tanaka
- Graduate
School of System Informatics, Department of Computational Science, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe 657-8501, Japan
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33
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Šponer J, Banáš P, Jurečka P, Zgarbová M, Kührová P, Havrila M, Krepl M, Stadlbauer P, Otyepka M. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. J Phys Chem Lett 2014; 5:1771-82. [PMID: 26270382 DOI: 10.1021/jz500557y] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.
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Affiliation(s)
- Jiří Šponer
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- ‡CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Marie Zgarbová
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Marek Havrila
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- ‡CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Krepl
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
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34
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Dračínský M, Šála M, Hodgkinson P. Dynamics of water molecules and sodium ions in solid hydrates of nucleotides. CrystEngComm 2014. [DOI: 10.1039/c4ce00727a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The dynamics of the co-ordinating water and metal cations in solid hydrates of nucleotide salts is explored with solid-state NMR spectroscopy and DFT calculations.
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Affiliation(s)
- Martin Dračínský
- Department of Chemistry
- Durham University
- Durham, UK
- Institute of Organic Chemistry and Biochemistry
- Prague, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry
- Prague, Czech Republic
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35
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Shek YL, Noudeh GD, Nazari M, Heerklotz H, Abu-Ghazalah RM, Dubins DN, Chalikian TV. Folding thermodynamics of the hybrid-1 type intramolecular human telomeric G-quadruplex. Biopolymers 2013; 101:216-27. [DOI: 10.1002/bip.22317] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Yuen Lai Shek
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Golamreza Dehghan Noudeh
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Mozhgan Nazari
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Heiko Heerklotz
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Rashid M. Abu-Ghazalah
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - David N. Dubins
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences; Leslie Dan Faculty of Pharmacy, University of Toronto; 144 College Street Toronto, Ontario Canada M5S 3M2
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36
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Bachmann SJ, Lin Z, Stafforst T, van Gunsteren WF, Dolenc J. On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters. J Chem Theory Comput 2013; 10:391-400. [DOI: 10.1021/ct400652w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Zhixiong Lin
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Thorsten Stafforst
- Laboratory
of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | | | - Jožica Dolenc
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Faculty
of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
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37
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Nolin F, Michel J, Wortham L, Tchelidze P, Balossier G, Banchet V, Bobichon H, Lalun N, Terryn C, Ploton D. Changes to cellular water and element content induced by nucleolar stress: investigation by a cryo-correlative nano-imaging approach. Cell Mol Life Sci 2013; 70:2383-94. [PMID: 23385351 PMCID: PMC11113571 DOI: 10.1007/s00018-013-1267-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 01/10/2013] [Accepted: 01/14/2013] [Indexed: 01/01/2023]
Abstract
The cell is a crowded volume, with estimated mean mass percentage of macromolecules and of water ranging from 7.5 to 45 and 55 to 92.5 %, respectively. However, the concentrations of macromolecules and water at the nanoscale within the various cell compartments are unknown. We recently developed a new approach, correlative cryo-analytical scanning transmission electron microscopy, for mapping the quantity of water within compartments previously shown to display GFP-tagged protein fluorescence on the same ultrathin cryosection. Using energy-dispersive X-ray spectrometry (EDXS), we then identified various elements (C, N, O, P, S, K, Cl, Mg) in these compartments and quantified them in mmol/l. Here, we used this new approach to quantify water and elements in the cytosol, mitochondria, condensed chromatin, nucleoplasm, and nucleolar components of control and stressed cancerous cells. The water content of the control cells was between 60 and 83 % (in the mitochondria and nucleolar fibrillar centers, respectively). Potassium was present at concentrations of 128-462 mmol/l in nucleolar fibrillar centers and condensed chromatin, respectively. The induction of nucleolar stress by treatment with a low dose of actinomycin-D to inhibit rRNA synthesis resulted in both an increase in water content and a decrease in the elements content in all cell compartments. We generated a nanoscale map of water and elements within the cell compartments, providing insight into their changes induced by nucleolar stress.
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Affiliation(s)
- Frédérique Nolin
- Laboratoire de Recherche en Nanosciences, Université de Reims Champagne Ardenne, Reims, France
| | - Jean Michel
- Laboratoire de Recherche en Nanosciences, Université de Reims Champagne Ardenne, Reims, France
| | - Laurence Wortham
- Laboratoire de Recherche en Nanosciences, Université de Reims Champagne Ardenne, Reims, France
| | - Pavel Tchelidze
- CNRS FRE 3481, Université de Reims Champagne Ardenne, Reims, France
| | - Gérard Balossier
- Laboratoire de Recherche en Nanosciences, Université de Reims Champagne Ardenne, Reims, France
| | - Vincent Banchet
- Laboratoire de Recherche en Nanosciences, Université de Reims Champagne Ardenne, Reims, France
| | - Hélène Bobichon
- CNRS FRE 3481, Université de Reims Champagne Ardenne, Reims, France
| | - Nathalie Lalun
- CNRS FRE 3481, Université de Reims Champagne Ardenne, Reims, France
| | - Christine Terryn
- Plate-forme IBISA, SFR CAP-SANTE, Université de Reims Champagne Ardenne, Reims, France
| | - Dominique Ploton
- CNRS FRE 3481, Université de Reims Champagne Ardenne, Reims, France
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38
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Kim M, Kim HR, Chae SY, Larson RG, Lee H, Park JC. Effect of Arginine-Rich Peptide Length on the Structure and Binding Strength of siRNA–Peptide Complexes. J Phys Chem B 2013; 117:6917-26. [DOI: 10.1021/jp402868g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Minwoo Kim
- Bio Research Center, Samsung
Advanced Institute of Technology (SAIT), Samsung Electronics Co., Ltd., Yongin, 446-712, South Korea
| | - Hyun Ryoung Kim
- Bio Research Center, Samsung
Advanced Institute of Technology (SAIT), Samsung Electronics Co., Ltd., Yongin, 446-712, South Korea
| | - Su Young Chae
- Bio Research Center, Samsung
Advanced Institute of Technology (SAIT), Samsung Electronics Co., Ltd., Yongin, 446-712, South Korea
| | - Ronald G. Larson
- Department of Chemical Engineering,
Biomedical Engineering, Mechanical Engineering, and Macromolecular
Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin, 448-701, South Korea
| | - Jae Chan Park
- Bio Research Center, Samsung
Advanced Institute of Technology (SAIT), Samsung Electronics Co., Ltd., Yongin, 446-712, South Korea
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39
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Do TN, Carloni P, Varani G, Bussi G. RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations. J Chem Theory Comput 2013; 9:1720-30. [PMID: 26587630 DOI: 10.1021/ct3009914] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking methods are insufficient. We here present a computational method which allows studying the binding of RNA molecules and charged peptides with atomistic, explicit-solvent molecular dynamics. In our method, a suitable estimate of the electrostatic interaction is used as an order parameter (collective variable) which is then accelerated using bidirectional pulling simulations. Since the electrostatic interaction is only used to enhance the sampling, the approximations used to compute it do not affect the final accuracy. The method is employed to characterize the binding of TAR RNA from HIV-1 and a small cyclic peptide. Our simulation protocol allows blindly predicting the binding pocket and pose as well as the binding affinity. The method is general and could be applied to study other electrostatics-driven binding events.
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Affiliation(s)
- Trang N Do
- SISSA/ISAS - International School for Advanced Studies, Trieste 34136, Italy
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany and Institute for Advanced Simulation IAS-5, Computational Biomedicine, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gabriele Varani
- Department of Chemistry and Department of Biochemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Giovanni Bussi
- SISSA/ISAS - International School for Advanced Studies, Trieste 34136, Italy
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40
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Allolio C, Sajadi M, Ernsting NP, Sebastiani D. An Ab Initio Microscope: Molecular Contributions to the Femtosecond Time-Dependent Fluorescence Shift of a Reichardt-Type Dye. Angew Chem Int Ed Engl 2013; 52:1813-6. [DOI: 10.1002/anie.201204532] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 09/30/2012] [Indexed: 11/08/2022]
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41
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Unter dem Ab-initio-Mikroskop: molekulare Beiträge in der Femtosekunden-Stokes-Verschiebung eines Reichardt-Farbstoffs. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Cao Y, Xie J, Liu B, Han L, Che S. Synthesis and characterization of multi-helical DNA–silica fibers. Chem Commun (Camb) 2013; 49:1097-9. [DOI: 10.1039/c2cc37470f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Lee TS, Wong KY, Giambasu GM, York DM. Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 120:25-91. [PMID: 24156941 PMCID: PMC4747252 DOI: 10.1016/b978-0-12-381286-5.00002-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Herein we summarize our progress toward the understanding of hammerhead ribozyme (HHR) catalysis through a multiscale simulation strategy. Simulation results collectively paint a picture of HHR catalysis: HHR first folds to form an electronegative active site pocket to recruit a threshold occupation of cationic charges, either a Mg(2+) ion or multiple monovalent cations. Catalytically active conformations that have good in-line fitness are supported by specific metal ion coordination patterns that involve either a bridging Mg(2+) ion or multiple Na(+) ions, one of which is also in a bridging coordination pattern. In the case of a single Mg(2+) ion bound in the active site, the Mg(2+) ion undergoes a migration that is coupled with deprotonation of the nucleophile (C17:O2'). As the reaction proceeds, the Mg(2+) ion stabilizes the accumulating charge of the leaving group and significantly increases the general acid ability of G8:O2'. Further computational mutagenesis simulations suggest that the disruptions due to mutations may severely impact HHR catalysis at different stages of the reaction. Catalytic mechanisms supported by the simulation results are consistent with available structural and biochemical experiments, and together they advance our understanding of HHR catalysis.
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Affiliation(s)
- Tai-Sung Lee
- Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA,Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Kin-Yiu Wong
- Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA,Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - George M. Giambasu
- Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA,Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Darrin M. York
- Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA,Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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44
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Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys 2012; 45:427-91. [PMID: 23217364 PMCID: PMC3533255 DOI: 10.1017/s003358351200011x] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.
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Affiliation(s)
- Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin
| | | | | | | | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio
| | - Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Nathan A. Baker
- To whom correspondence should be addressed. Pacific Northwest National Laboratory, PO Box 999, MSID K7-29, Richland, WA 99352. Phone: +1-509-375-3997,
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45
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Pascal TA, Goddard WA, Maiti PK, Vaidehi N. Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures. J Phys Chem B 2012; 116:12159-67. [DOI: 10.1021/jp306473u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Tod A. Pascal
- Materials
and Process Simulation
Center, California Institute of Technology, Pasadena, California 91125, United States
| | - William A. Goddard
- Materials
and Process Simulation
Center, California Institute of Technology, Pasadena, California 91125, United States
- World Class University (WCU)
Professor, Graduate School of EEWS, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Prabal K. Maiti
- Center for Condensed Matter Theory,
Department of Physics, Indian Institute of Science, Bangalore, India 560012
| | - Nagarajan Vaidehi
- Division of Immunology, Beckman Research Institute of the City of Hope, Duarte,
California 91010, United States
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46
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Kumar P, Lehmann J, Libchaber A. Kinetics of bulge bases in small RNAs and the effect of pressure on it. PLoS One 2012; 7:e42052. [PMID: 22916118 PMCID: PMC3423399 DOI: 10.1371/journal.pone.0042052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 07/02/2012] [Indexed: 11/19/2022] Open
Abstract
Due to their self-catalytic properties, small RNAs with bulge bases are hypothesized to be primordial molecules which could form elementary translation systems. Using molecular dynamics simulations, we study the binding propensity of small RNAs by calculating the free energy barrier corresponding to the looped out conformations of bulge bases, which presumably act as the binding sites for ligands in these small RNAs. We find that base flipping kinetics can proceed at atmospheric pressure but with a very small propensity. Furthermore, the free energy barrier associated with base flipping depends on the stacking with neighboring bases. Next, we studied the base flipping kinetics with pressure. We find that the free energy associated with base looping out increases monotonically as the pressure is increased. Furthermore, we calculate the mean first-passage time of conformational looping out of the bulge base using the diffusion of reaction coordinate associated with the base flipping on the underlying free energy surface. We find that the mean first-passage time associated with bulge looping out increases slowly upon increasing pressures up to atm but changes dramatically for atm. Finally, we discuss our results in the light of the role of hydration shell of water around RNA. Our results are relevant for the RNA world hypothesis.
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Affiliation(s)
- Pradeep Kumar
- Center for Studies in Physics and Biology, Rockefeller University, New York, New York, USA.
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47
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Giel-Pietraszuk M, Barciszewski J. Hydrostatic and osmotic pressure study of the RNA hydration. Mol Biol Rep 2012; 39:6309-18. [PMID: 22314910 PMCID: PMC3310992 DOI: 10.1007/s11033-012-1452-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 01/23/2012] [Indexed: 11/17/2022]
Abstract
The tertiary structure of nucleic acids results from an equilibrium between electrostatic interactions of phosphates, stacking interactions of bases, hydrogen bonds between polar atoms and water molecules. Water interactions with ribonucleic acid play a key role in its structure formation, stabilization and dynamics. We used high hydrostatic pressure and osmotic pressure to analyze changes in RNA hydration. We analyzed the lead catalyzed hydrolysis of tRNAPhe from S. cerevisiae as well as hydrolytic activity of leadzyme. Pb(II) induced hydrolysis of the single phosphodiester bond in tRNAPhe is accompanied by release of 98 water molecules, while other molecule, leadzyme releases 86.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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48
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šponer J, Cang X, Cheatham TE. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods 2012; 57:25-39. [PMID: 22525788 PMCID: PMC3775459 DOI: 10.1016/j.ymeth.2012.04.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 11/29/2022] Open
Abstract
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.
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Affiliation(s)
- Jiří šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Xiaohui Cang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, 2000 East 30 South, University of Utah, Salt Lake City, UT 84112, United States
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49
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Sim AYL, Minary P, Levitt M. Modeling nucleic acids. Curr Opin Struct Biol 2012; 22:273-8. [PMID: 22538125 DOI: 10.1016/j.sbi.2012.03.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 03/25/2012] [Indexed: 01/24/2023]
Abstract
Nucleic acids are an important class of biological macromolecules that carry out a variety of cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold into precise three-dimensional structures. Due to their self-assembling characteristics, nucleic acids have also been widely studied in the field of nanotechnology, and a diverse range of intricate three-dimensional nanostructures have been designed and synthesized. Different physical terms such as base-pairing and stacking interactions, tertiary contacts, electrostatic interactions and entropy all affect nucleic acid folding and structure. Here we review general computational approaches developed to model nucleic acid systems. We focus on four key areas of nucleic acid modeling: molecular representation, potential energy function, degrees of freedom and sampling algorithm. Appropriate choices in each of these key areas in nucleic acid modeling can effectively combine to aid interpretation of experimental data and facilitate prediction of nucleic acid structure.
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Affiliation(s)
- Adelene Y L Sim
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
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50
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Parisien M, Major F. Determining RNA three-dimensional structures using low-resolution data. J Struct Biol 2012; 179:252-60. [PMID: 22387042 DOI: 10.1016/j.jsb.2011.12.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 11/29/2011] [Accepted: 12/06/2011] [Indexed: 11/25/2022]
Abstract
Knowing the 3-D structure of an RNA is fundamental to understand its biological function. Nowadays X-ray crystallography and NMR spectroscopy are systematically applied to newly discovered RNAs. However, the application of these high-resolution techniques is not always possible, and thus scientists must turn to lower resolution alternatives. Here, we introduce a pipeline to systematically generate atomic resolution 3-D structures that are consistent with low-resolution data sets. We compare and evaluate the discriminative power of a number of low-resolution experimental techniques to reproduce the structure of the Escherichia coli tRNA(VAL) and P4-P6 domain of the Tetrahymena thermophila group I intron. We test single and combinations of the most accessible low-resolution techniques, i.e. hydroxyl radical footprinting (OH), methidiumpropyl-EDTA (MPE), multiplexed hydroxyl radical cleavage (MOHCA), and small-angle X-ray scattering (SAXS). We show that OH-derived constraints are accurate to discriminate structures at the atomic level, whereas EDTA-based constraints apply to global shape determination. We provide a guide for choosing which experimental techniques or combination of thereof is best in which context. The pipeline represents an important step towards high-throughput low-resolution RNA structure determination.
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Affiliation(s)
- Marc Parisien
- Biochemistry Department, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
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