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Rahaman MM, Zhang S. RNAMotifProfile: a graph-based approach to build RNA structural motif profiles. NAR Genom Bioinform 2024; 6:lqae128. [PMID: 39328267 PMCID: PMC11426329 DOI: 10.1093/nargab/lqae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/24/2024] [Accepted: 09/09/2024] [Indexed: 09/28/2024] Open
Abstract
RNA structural motifs are the recurrent segments in RNA three-dimensional structures that play a crucial role in the functional diversity of RNAs. Understanding the similarities and variations within these recurrent motif groups is essential for gaining insights into RNA structure and function. While recurrent structural motifs are generally assumed to be composed of the same isosteric base interactions, this consistent pattern is not observed across all examples of these motifs. Existing methods for analyzing and comparing RNA structural motifs may overlook variations in base interactions and associated nucleotides. RNAMotifProfile is a novel profile-to-profile alignment algorithm that generates a comprehensive profile from a group of structural motifs, incorporating all base interactions and associated nucleotides at each position. By structurally aligning input motif instances using a guide-tree-based approach, RNAMotifProfile captures the similarities and variations within recurrent motif groups. Additionally, RNAMotifProfile can function as a motif search tool, enabling the identification of instances of a specific motif family by searching with the corresponding profile. The ability to generate accurate and comprehensive profiles for RNA structural motif families, and to search for these motifs, facilitates a deeper understanding of RNA structure-function relationships and potential applications in RNA engineering and therapeutic design.
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Affiliation(s)
- Md Mahfuzur Rahaman
- Department of Computer Science, University of Central Florida, 4328 Scorpius Street, Orlando, FL 32816-2362, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, 4328 Scorpius Street, Orlando, FL 32816-2362, USA
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2
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Ormazábal A, Palma J, Pierdominici-Sottile G. Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods. Methods Mol Biol 2024; 2741:207-238. [PMID: 38217656 DOI: 10.1007/978-1-0716-3565-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Molecular dynamics simulations have proved extremely useful in investigating the functioning of proteins with atomic-scale resolution. Many applications to the study of RNA also exist, and their number increases by the day. However, implementing MD simulations for RNA molecules in solution faces challenges that the MD practitioner must be aware of for the appropriate use of this tool. In this chapter, we present the fundamentals of MD simulations, in general, and the peculiarities of RNA simulations, in particular. We discuss the strengths and limitations of the technique and provide examples of its application to elucidate small RNA's performance.
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Affiliation(s)
- Agustín Ormazábal
- Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Godoy Cruz, CABA, Argentina
| | - Juliana Palma
- Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Godoy Cruz, CABA, Argentina
| | - Gustavo Pierdominici-Sottile
- Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET, Godoy Cruz, CABA, Argentina.
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3
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Ali Z, Kukhta T, Jhunjhunwala A, Trant JF, Sharma P. Occurrence and classification of T-shaped interactions between nucleobases in RNA structures. RNA (NEW YORK, N.Y.) 2023; 29:1215-1229. [PMID: 37188492 PMCID: PMC10351890 DOI: 10.1261/rna.079486.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/25/2023] [Indexed: 05/17/2023]
Abstract
Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid-protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3261 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date data set of ≤3.5 Å resolution crystal structures deposited in the Protein Data Bank.
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Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Teagan Kukhta
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, Telangana, 500032, India
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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4
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Imamoto JM, Zauhar RJ, Bruist MF. Sarcin/Ricin Domain RNA Retains Its Structure Better Than A-RNA in Adaptively Biased Molecular Dynamics Simulations. J Phys Chem B 2022; 126:10018-10033. [PMID: 36417896 DOI: 10.1021/acs.jpcb.2c05859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Less than one in thirty of the RNA sequences transcribed in humans are translated into protein. The noncoding RNA (ncRNA) functions in catalysis, structure, regulation, and more. However, for the most part, these functions are poorly characterized. RNA is modular and described by motifs that include helical A-RNA with canonical Watson-Crick base-pairing as well as structures with only noncanonical base pairs. Understanding the structure and dynamics of motifs will aid in deciphering functions of specific ncRNAs. We present computational studies on a standard sarcin/ricin domain (SRD), citrus bark cracking viroid SRD, as well as A-RNA. We have applied enhanced molecular dynamics techniques that construct an inverse free-energy surface (iFES) determined by collective variables that monitor base-pairing and backbone conformation. Each SRD RNA is flanked on each side by A-RNA, allowing comparison of the behavior of these motifs in the same molecule. The RNA iFESs have single peaks, indicating that the combined motifs should denature as a single cohesive unit, rather than by regional melting. Local root-mean-square deviation (RMSD) analysis and communication propensity (CProp, variance in distances between residue pairs) reveal distinct motif properties. Our analysis indicates that the standard SRD is more stable than the viroid SRD, which is more stable than A-RNA. Base pairs at SRD to A-RNA transitions have limited flexibility. Application of CProp reveals extraordinary stiffness of the SRD, allowing residues on opposite sides of the motif to sense each other's motions.
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Affiliation(s)
- Jason M Imamoto
- Department of Chemistry and Biochemistry, St. Joseph's University, Philadelphia, Pennsylvania19131, United States
| | - Randy J Zauhar
- Department of Chemistry and Biochemistry, St. Joseph's University, Philadelphia, Pennsylvania19131, United States
| | - Michael F Bruist
- Department of Chemistry and Biochemistry, St. Joseph's University, Philadelphia, Pennsylvania19131, United States
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5
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Islam S, Rahaman MM, Zhang S. RNAMotifContrast: a method to discover and visualize RNA structural motif subfamilies. Nucleic Acids Res 2021; 49:e61. [PMID: 33693841 PMCID: PMC8216276 DOI: 10.1093/nar/gkab131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 01/17/2023] Open
Abstract
Understanding the 3D structural properties of RNAs will play a critical role in identifying their functional characteristics and designing new RNAs for RNA-based therapeutics and nanotechnology. While several existing computational methods can help in the analysis of RNA properties by recognizing structural motifs, they do not provide the means to compare and contrast those motifs extensively. We have developed a new method, RNAMotifContrast, which focuses on analyzing the similarities and variations of RNA structural motif characteristics. In this method, a graph is formed to represent the similarities among motifs, and a new traversal algorithm is applied to generate visualizations of their structural properties. Analyzing the structural features among motifs, we have recognized and generalized the concept of motif subfamilies. To asses its effectiveness, we have applied RNAMotifContrast on a dataset of known RNA structural motif families. From the results, we observed that the derived subfamilies possess unique structural variations while holding standard features of the families. Overall, the visualization approach of this method presents a new perspective to observe the relation among motifs more closely, and the discovered subfamilies provide opportunities to achieve valuable insights into RNA’s diverse roles.
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Affiliation(s)
- Shahidul Islam
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Md Mahfuzur Rahaman
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
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6
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Jhunjhunwala A, Ali Z, Bhattacharya S, Halder A, Mitra A, Sharma P. On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions. J Chem Inf Model 2021; 61:1470-1480. [PMID: 33570947 DOI: 10.1021/acs.jcim.0c01225] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The astonishing diversity in folding patterns of RNA three-dimensional (3D) structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. A systematic and comprehensive classification and annotation of these interactions is necessary for a molecular-level understanding of their roles. However, unlike in the case of base pairing, where a widely accepted nomenclature and classification scheme exists in the public domain, currently available classification schemes for base-base stacking need major enhancements to comprehensively capture the necessary features underlying the rich stacking diversity in RNA. Here, we extend the previous stacking classification based on nucleobase interacting faces by introducing a structurally intuitive geometry-cum topology-based scheme. Specifically, a stack is first classified in terms of the geometry described by the relative orientation of the glycosidic bonds, which generates eight basic stacking geometric families for heterodimeric stacks and six of those for homodimeric stacks. Further annotation in terms of the identity of the bases and the region of involvement of purines (five-membered, six-membered, or both rings) leads to the enumeration of 384 distinct RNA base stacks. Based on our classification scheme, we present an algorithm for automated identification of stacks in RNA crystal structures and analyze the stacking context in selected RNA structures. Overall, the work described here is expected to greatly facilitate the structure-based RNA research.
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Affiliation(s)
- Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Sohini Bhattacharya
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
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Freidhoff P, Bruist MF. In silico survey of the central conserved regions in viroids of the Pospiviroidae family for conserved asymmetric loop structures. RNA (NEW YORK, N.Y.) 2019; 25:985-1003. [PMID: 31123078 PMCID: PMC6633198 DOI: 10.1261/rna.070409.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/14/2019] [Indexed: 06/01/2023]
Abstract
Viroids are the smallest replicative pathogens, consisting of RNA circles (∼300 nucleotides) that require host machinery to replicate. Structural RNA elements recruit these host factors. Currently, many of these structural elements and the nature of their interactions are unknown. All Pospiviroidae have homology in the central conserved region (CCR). The CCR of potato spindle tuber viroid (PSTVd) contains a sarcin/ricin domain (SRD), the only viroid structural element with an unequivocal replication role. We assumed that every member of this family uses this region to recruit host factors, and that each CCR has an SRD-like asymmetric loop within it. Potential SRD or SRD-like motifs were sought in the CCR of each Pospiviroidae member as follows. Motif location in each CCR was predicted with MUSCLE alignment and Vienna RNAfold. Viroid-specific models of SRD-like motifs were built by superimposing noncanonical base pairs and nucleotides on a model of an SRD. The RNA geometry search engine FR3D was then used to find nucleotide groups close to the geometry suggested by this superimposition. Atomic resolution structures were assembled using the molecular visualization program Chimera, and the stability of each motif was assessed with molecular dynamics (MD). Some models required a protonated cytosine. To be stable within a cell, the pKa of that cytosine must be shifted up. Constant pH-replica exchange MD analysis showed such a shift in the proposed structures. These data show that every Pospiviroidae member could form a motif that resembles an SRD in its CCR, and imply there could be undiscovered mimics of other RNA domains.
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Affiliation(s)
- Paul Freidhoff
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, USA
| | - Michael F Bruist
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, USA
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8
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Bhattacharya S, Jhunjhunwala A, Halder A, Bhattacharyya D, Mitra A. Going beyond base-pairs: topology-based characterization of base-multiplets in RNA. RNA (NEW YORK, N.Y.) 2019; 25:573-589. [PMID: 30792229 PMCID: PMC6467009 DOI: 10.1261/rna.068551.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/18/2019] [Indexed: 05/17/2023]
Abstract
Identification and characterization of base-multiplets, which are essentially mediated by base-pairing interactions, can provide insights into the diversity in the structure and dynamics of complex functional RNAs, and thus facilitate hypothesis driven biological research. The necessary nomenclature scheme, an extension of the geometric classification scheme for base-pairs by Leontis and Westhof, is however available only for base-triplets. In the absence of information on topology, this scheme is not applicable to quartets and higher order multiplets. Here we propose a topology-based classification scheme which, in conjunction with a graph-based algorithm, can be used for the automated identification and characterization of higher order base-multiplets in RNA structures. Here, the RNA structure is represented as a graph, where nodes represent nucleotides and edges represent base-pairing connectivity. Sets of connected components (of n nodes) within these graphs constitute subgraphs representing multiplets of "n" nucleotides. The different topological variants of the RNA multiplets thus correspond to different nonisomorphic forms of these subgraphs. To annotate RNA base-multiplets unambiguously, we propose a set of topology-based nomenclature rules for quartets, which are extendable to higher multiplets. We also demonstrate the utility of our approach toward the identification and annotation of higher order RNA multiplets, by investigating the occurrence contexts of selected examples in order to gain insights regarding their probable functional roles.
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Affiliation(s)
- Sohini Bhattacharya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF, Bidhannagar, Kolkata 700064, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India
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9
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How Ricin Damages the Ribosome. Toxins (Basel) 2019; 11:toxins11050241. [PMID: 31035546 PMCID: PMC6562825 DOI: 10.3390/toxins11050241] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022] Open
Abstract
Ricin belongs to the group of ribosome-inactivating proteins (RIPs), i.e., toxins that have evolved to provide particular species with an advantage over other competitors in nature. Ricin possesses RNA N-glycosidase activity enabling the toxin to eliminate a single adenine base from the sarcin-ricin RNA loop (SRL), which is a highly conserved structure present on the large ribosomal subunit in all species from the three domains of life. The SRL belongs to the GTPase associated center (GAC), i.e., a ribosomal element involved in conferring unidirectional trajectory for the translational apparatus at the expense of GTP hydrolysis by translational GTPases (trGTPases). The SRL represents a critical element in the GAC, being the main triggering factor of GTP hydrolysis by trGTPases. Enzymatic removal of a single adenine base at the tip of SRL by ricin blocks GTP hydrolysis and, at the same time, impedes functioning of the translational machinery. Here, we discuss the consequences of SRL depurination by ricin for ribosomal performance, with emphasis on the mechanistic model overview of the SRL modus operandi.
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10
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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: 357] [Impact Index Per Article: 59.5] [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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11
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New tRNA contacts facilitate ligand binding in a Mycobacterium smegmatis T box riboswitch. Proc Natl Acad Sci U S A 2018; 115:3894-3899. [PMID: 29581302 DOI: 10.1073/pnas.1721254115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
T box riboswitches are RNA regulatory elements widely used by organisms in the phyla Firmicutes and Actinobacteria to regulate expression of amino acid-related genes. Expression of T box family genes is down-regulated by transcription attenuation or inhibition of translation initiation in response to increased charging of the cognate tRNA. Three direct contacts with tRNA have been described; however, one of these contacts is absent in a subclass of T box RNAs and the roles of several structural domains conserved in most T box RNAs are unknown. In this study, structural elements of a Mycobacterium smegmatis ileS T box riboswitch variant with an Ultrashort (US) Stem I were sequentially deleted, which resulted in a progressive decrease in binding affinity for the tRNAIle ligand. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) revealed structural changes in conserved riboswitch domains upon interaction with the tRNA ligand. Cross-linking and mutational analyses identified two interaction sites, one between the S-turn element in Stem II and the T arm of tRNAIle and the other between the Stem IIA/B pseudoknot and the D loop of tRNAIle These newly identified RNA contacts add information about tRNA recognition by the T box riboswitch and demonstrate a role for the S-turn and pseudoknot elements, which resemble structural elements that are common in many cellular RNAs.
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12
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Zgarbová M, Jurečka P, Banáš P, Havrila M, Šponer J, Otyepka M. Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field. J Phys Chem B 2017; 121:2420-2433. [PMID: 28290207 DOI: 10.1021/acs.jpcb.7b00262] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The sugar-phosphate backbone of RNA can exist in diverse rotameric substates, giving RNA molecules enormous conformational variability. The most frequent noncanonical backbone conformation in RNA is α/γ = t/t, which is derived from the canonical backbone by a crankshaft motion and largely preserves the standard geometry of the RNA duplex. A similar conformation also exists in DNA, where it has been extensively studied and shown to be involved in DNA-protein interactions. However, the function of the α/γ = t/t conformation in RNA is poorly understood. Here, we present molecular dynamics simulations of several prototypical RNA structures obtained from X-ray and NMR experiments, including canonical and mismatched RNA duplexes, UUCG and GAGA tetraloops, Loop E, the sarcin-ricin loop, a parallel guanine quadruplex, and a viral pseudoknot. The stability of various noncanonical α/γ backbone conformations was analyzed with two AMBER force fields, ff99bsc0χOL3 and ff99bsc0χOL3 with the recent εζOL1 and βOL1 corrections for DNA. Although some α/γ substates were stable with seemingly well-described equilibria, many were unstable in our simulations. Notably, the most frequent noncanonical conformer α/γ = t/t was unstable in both tested force fields. Possible reasons for this instability are discussed. Our work reveals a potentially important artifact in RNA force fields and highlights a need for further force field refinement.
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Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Marek Havrila
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic.,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, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
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13
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Šponer J, Krepl M, Banáš P, Kührová P, Zgarbová M, Jurečka P, Havrila M, Otyepka M. How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes? WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27863061 DOI: 10.1002/wrna.1405] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/13/2016] [Accepted: 10/10/2016] [Indexed: 01/01/2023]
Abstract
We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems. Fundamental limitations are the short physical time-scale of simulations, which can be partially alleviated by enhanced-sampling techniques, and the highly approximate atomistic force fields describing the simulated molecules. The applicability and present limitations of MD are demonstrated on studies of tetranucleotides, tetraloops, ribozymes, riboswitches and protein/RNA complexes. Wisely applied simulations respecting the approximations of the model can successfully complement structural and biochemical experiments. WIREs RNA 2017, 8:e1405. doi: 10.1002/wrna.1405 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Marek Havrila
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
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14
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Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. J Phys Chem B 2015; 119:15176-90. [DOI: 10.1021/acs.jpcb.5b08876] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marek Havrila
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, 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
| | - 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
| | - 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
| | - Miroslav Krepl
- 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
| | - 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
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15
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Bhattacharya S, Mittal S, Panigrahi S, Sharma P, S P P, Paul R, Halder S, Halder A, Bhattacharyya D, Mitra A. RNABP COGEST: a resource for investigating functional RNAs. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav011. [PMID: 25776022 PMCID: PMC4360618 DOI: 10.1093/database/bav011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structural bioinformatics of RNA has evolved mainly in response to the rapidly accumulating evidence that non-(protein)-coding RNAs (ncRNAs) play critical roles in gene regulation and development. The structures and functions of most ncRNAs are however still unknown. Most of the available RNA structural databases rely heavily on known 3D structures, and contextually correlate base pairing geometry with actual 3D RNA structures. None of the databases provide any direct information about stabilization energies. However, the intrinsic interaction energies of constituent base pairs can provide significant insights into their roles in the overall dynamics of RNA motifs and structures. Quantum mechanical (QM) computations provide the only approach toward their accurate quantification and characterization. ‘RNA Base Pair Count, Geometry and Stability’ (http://bioinf.iiit.ac.in/RNABPCOGEST) brings together information, extracted from literature data, regarding occurrence frequency, experimental and quantum chemically optimized geometries, and computed interaction energies, for non-canonical base pairs observed in a non-redundant dataset of functional RNA structures. The database is designed to enable the QM community, on the one hand, to identify appropriate biologically relevant model systems and also enable the biology community to easily sift through diverse computational results to gain theoretical insights which could promote hypothesis driven biological research. Database URL:http://bioinf.iiit.ac.in/RNABPCOGEST
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Affiliation(s)
- Sohini Bhattacharya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Shriyaa Mittal
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Swati Panigrahi
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Purshotam Sharma
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Preethi S P
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Rahul Paul
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Sukanya Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Dhananjay Bhattacharyya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, and Computational Science Division, Saha Institute of Nuclear Physics (SINP), 1/AF Bidhannagar, Kolkata 700064, India
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16
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Kruse H, Šponer J. Towards biochemically relevant QM computations on nucleic acids: controlled electronic structure geometry optimization of nucleic acid structural motifs using penalty restraint functions. Phys Chem Chem Phys 2014; 17:1399-410. [PMID: 25427983 DOI: 10.1039/c4cp04680c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Recent developments in dispersion-corrected density functional theory methods allow for the first time the description of large fragments of nucleic acids (hundreds of atoms) with an accuracy clearly surpassing the accuracy of common biomolecular force fields. Such calculations can significantly improve the description of the potential energy surface of nucleic acid molecules, which may be useful for studies of molecular interactions and conformational preferences of nucleic acids, as well as verification and parameterization of other methods. The first of such studies, however, demonstrated that successful applications of accurate QM calculations to larger nucleic acid building blocks are hampered by difficulties in obtaining geometries that are biochemically relevant and are not biased by non-native structural features. We present an approach that can greatly facilitate large-scale QM studies on nucleic acids, namely electronic structure geometry optimization of nucleic acid fragments utilizing a penalty function to restrain key internal coordinates with a specific focus on the torsional backbone angles. This work explores the viability of these restraint optimizations for DFT-D3, PM6-D3H and HF-3c optimizations on a set of examples (a UpA dinucleotide, a DNA G-quadruplex and a B-DNA fragment). Evaluation of different penalty function strengths reveals only a minor system-dependency and reasonable restraint values range from 0.01 to 0.05 Eh rad(-2) for the backbone torsions. Restraints are crucial to perform the QM calculations on biochemically relevant conformations in implicit solvation and gas phase geometry optimizations. The reasons for using restrained instead of constrained or unconstrained optimizations are explained and an open-source external optimizer is provided.
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Affiliation(s)
- Holger Kruse
- CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic.
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17
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Osborn MF, White JD, Haley MM, DeRose VJ. Platinum-RNA modifications following drug treatment in S. cerevisiae identified by click chemistry and enzymatic mapping. ACS Chem Biol 2014; 9:2404-11. [PMID: 25055168 PMCID: PMC4201330 DOI: 10.1021/cb500395z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
With
the importance of RNA-based regulatory pathways, the potential
for targeting noncoding and coding RNAs by small molecule therapeutics
is of great interest. Platinum(II) complexes including cisplatin (cis-diamminedichloroplatinum(II)) are widely prescribed
anticancer compounds that form stable adducts on nucleic acids. In
tumors, DNA damage from Pt(II) initiates apoptotic signaling, but
this activity is not necessary for cytotoxicity (e.g., Yu et al., 2008), suggesting accumulation and consequences
of Pt(II) lesions on non-DNA targets. We previously reported an azide-functionalized
compound, picazoplatin, designed for post-treatment click labeling
that enables detection of Pt complexes (White et al., 2013). Here, we report in-gel fluorescent detection of Pt-bound
rRNA and tRNA extracted from picazoplatin-treated S. cerevisiae and labeled using Cu-free click chemistry. These data provide the
first evidence that cellular tRNA is a platinum drug substrate. We
assess Pt(II) binding sites within rRNA from cisplatin-treated S. cerevisiae, in regions where damage is linked to significant
downstream consequences including the sarcin-ricin loop (SRL) Helix
95. Pt-RNA adducts occur on the nucleotide substrates of ribosome-inactivating
proteins, as well as on the bulged-G motif critical for elongation
factor recognition of the loop. At therapeutically relevant concentrations,
Pt(II) also binds robustly within conserved cation-binding pockets
in Domains V and VI rRNA at the peptidyl transferase center. Taken
together, these results demonstrate a convenient click chemistry methodology
that can be applied to identify other metal or covalent modification-based
drug targets and suggest a ribotoxic mechanism for cisplatin cytotoxicity.
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Affiliation(s)
- Maire F. Osborn
- Department of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Jonathan D. White
- Department of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Michael M. Haley
- Department of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Victoria J. DeRose
- Department of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
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18
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Panecka J, Havrila M, Réblová K, Šponer J, Trylska J. Role of S-turn2 in the structure, dynamics, and function of mitochondrial ribosomal A-site. A bioinformatics and molecular dynamics simulation study. J Phys Chem B 2014; 118:6687-701. [PMID: 24845793 DOI: 10.1021/jp5030685] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The mRNA decoding site (A-site) in the small ribosomal subunit controls fidelity of the translation process. Here, using molecular dynamics simulations and bioinformatic analyses, we investigated the structural dynamics of the human mitochondrial A-site (native and A1490G mutant) and compared it with the dynamics of the bacterial A-site. We detected and characterized a specific RNA backbone configuration, S-turn2, which occurs in the human mitochondrial but not in the bacterial A-site. Mitochondrial and bacterial A-sites show different propensities to form S-turn2 that may be caused by different base-pairing patterns of the flanking nucleotides. Also, the S-turn2 structural stability observed in the simulations supports higher accuracy and lower speed of mRNA decoding in mitochondria in comparison with bacteria. In the mitochondrial A-site, we observed collective movement of stacked nucleotides A1408·C1409·C1410, which may explain the known differences in aminoglycoside antibiotic binding affinities toward the studied A-site variants.
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Affiliation(s)
- Joanna Panecka
- Department of Biophysics, Institute of Experimental Physics and ∥Centre of New Technologies, University of Warsaw , Żwirki i Wigury 93, 02-089 Warsaw, Poland
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19
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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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20
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Kruse H, Havrila M, Šponer J. QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin–Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches. J Chem Theory Comput 2014; 10:2615-29. [DOI: 10.1021/ct500183w] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Holger Kruse
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
| | - Marek Havrila
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Jiřı́ Šponer
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
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