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Special Issue "Entropy and RNA Structure, Folding and Mechanics"

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A special issue of Entropy (ISSN 1099-4300).

Deadline for manuscript submissions: closed (30 April 2015)

Special Issue Editor

Guest Editor
Dr. Wayne K. Dawson

Department of Biotechnology, Graduate School of Agriculture & Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
E-Mail
Interests: thermodynamics and RNA folding, RNA-RNA interactions, RNA-protein interactions, protein folding and protein-protein interactions; entropy driven mechanisms in biology; mathematical modeling; quantum mechanics; mechanics

Special Issue Information

Dear Colleagues,

Perhaps ironically, folding and structure in biopolymers is as much about entropy as it is about the binding free energy of the interacting residues. Entropy is the elastic memory of these systems: squish such polymers and they bounce back like a super ball, likewise, stretch them and they spring back like a rubber band. Entropy is utilized by biology to drive servo mechanical devices like ribosomal RNA and many riboswitches. Yet, because the binding interactions are weak and the entropy effects can spread over diverse parts of a molecule, it remains challenging to understand the structure and folding (let alone the mechanics) of biopolymers in general.
RNA folding offers an alternative window into protein folding. The folding times of RNA are on the order of ms to seconds compared to proteins that typically fold in approximately µs to ms. Trapping in non-native structures can also influence the rate of folding and the types of structures. RNA is also a heterogeneous polymer; however, RNA is not as heterogeneous in its diversity of side chains and modifications as proteins: making RNA more akin to traditional polymers. RNA can also be functional like proteins. Hence, studies on protein and RNA folding work hand in hand toward understanding folding processes and mechanisms in biopolymers.
Here, we welcome a diversity of views and methods centering around four themes: what common forms of entropy exist in RNA and other polymers in general; how to model entropy in RNA folding and structure, RNA-RNA interactions and RNA-protein interactions; how entropy plays a role in the mechanics of some functional RNA molecules; and the role of RNA folding entropy in evolution. Any experimental approaches that dig out further insights into measuring the entropy are also quite welcome.

Specific topics of interest include (but are not limited to):

  • RNA folding and thermodynamics
  • Statistical mechanics of RNA polymers
  • Entropy in RNA-RNA complexes
  • Entropy in RNA-protein interactions
  • Entropy mechanisms in RNA aptamers
  • Experimental studies in RNA folding
  • RNA folding and evolution

Dr. Wayne K Dawson
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Entropy is an international peer-reviewed Open Access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1400 CHF (Swiss Francs).


Published Papers (6 papers)

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Research

Open AccessArticle iDoRNA: An Interacting Domain-based Tool for Designing RNA-RNA Interaction Systems
Entropy 2016, 18(3), 83; doi:10.3390/e18030083
Received: 3 April 2015 / Revised: 26 February 2016 / Accepted: 26 February 2016 / Published: 7 March 2016
PDF Full-text (2402 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
RNA-RNA interactions play a crucial role in gene regulation in living organisms. They have gained increasing interest in the field of synthetic biology because of their potential applications in medicine and biotechnology. However, few novel regulators based on RNA-RNA interactions with desired structures
[...] Read more.
RNA-RNA interactions play a crucial role in gene regulation in living organisms. They have gained increasing interest in the field of synthetic biology because of their potential applications in medicine and biotechnology. However, few novel regulators based on RNA-RNA interactions with desired structures and functions have been developed due to the challenges of developing design tools. Recently, we proposed a novel tool, called iDoDe, for designing RNA-RNA interacting sequences by first decomposing RNA structures into interacting domains and then designing each domain using a stochastic algorithm. However, iDoDe did not provide an optimal solution because it still lacks a mechanism to optimize the design. In this work, we have further developed the tool by incorporating a genetic algorithm (GA) to find an RNA solution with maximized structural similarity and minimized hybridized RNA energy, and renamed the tool iDoRNA. A set of suitable parameters for the genetic algorithm were determined and found to be a weighting factor of 0.7, a crossover rate of 0.9, a mutation rate of 0.1, and the number of individuals per population set to 8. We demonstrated the performance of iDoRNA in comparison with iDoDe by using six RNA-RNA interaction models. It was found that iDoRNA could efficiently generate all models of interacting RNAs with far more accuracy and required far less computational time than iDoDe. Moreover, we compared the design performance of our tool against existing design tools using forty-four RNA-RNA interaction models. The results showed that the performance of iDoRNA is better than RiboMaker when considering the ensemble defect, the fitness score and computation time usage. However, it appears that iDoRNA is outperformed by NUPACK and RNAiFold 2.0 when considering the ensemble defect. Nevertheless, iDoRNA can still be an useful alternative tool for designing novel RNA-RNA interactions in synthetic biology research. The source code of iDoRNA can be downloaded from the site http://synbio.sbi.kmutt.ac.th. Full article
(This article belongs to the Special Issue Entropy and RNA Structure, Folding and Mechanics)
Figures

Open AccessArticle Theoretical Search for RNA Folding Nuclei
Entropy 2015, 17(11), 7827-7847; doi:10.3390/e17117827
Received: 30 April 2015 / Revised: 5 November 2015 / Accepted: 17 November 2015 / Published: 23 November 2015
PDF Full-text (2639 KB) | HTML Full-text | XML Full-text
Abstract
The functions of RNA molecules are defined by their spatial structure, whose folding is regulated by numerous factors making RNA very similar to proteins. Prediction of RNA folding nuclei gives the possibility to take a fresh look at the problems of the multiple
[...] Read more.
The functions of RNA molecules are defined by their spatial structure, whose folding is regulated by numerous factors making RNA very similar to proteins. Prediction of RNA folding nuclei gives the possibility to take a fresh look at the problems of the multiple folding pathways of RNA molecules and RNA stability. The algorithm previously developed for prediction of protein folding nuclei has been successfully applied to ~150 various RNA structures: hairpins, tRNAs, structures with pseudoknots, and the large structured P4-P6 domain of the Tetrahymena group I intron RNA. The calculated Φ-values for tRNA structures agree with the experimental data obtained earlier. According to the experiment the nucleotides of the D and T hairpin loops are the last to be involved in the tRNA tertiary structure. Such agreement allowed us to do a prediction for an example of large structured RNA, the P4-P6 RNA domain. One of the advantages of our method is that it allows us to make predictions about the folding nucleus for nontrivial RNA motifs: pseudoknots and tRNA. Full article
(This article belongs to the Special Issue Entropy and RNA Structure, Folding and Mechanics)
Open AccessArticle Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins
Entropy 2015, 17(3), 1477-1507; doi:10.3390/e17031477
Received: 4 September 2014 / Revised: 11 March 2015 / Accepted: 17 March 2015 / Published: 23 March 2015
Cited by 4 | PDF Full-text (1576 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The fuzzy oil drop model, a tool which can be used to study the structure of the hydrophobic core in proteins, has been applied in the analysis of proteins belonging to the jumonji group—JARID2, JARID1A, JARID1B and JARID1D—proteins that share the property of
[...] Read more.
The fuzzy oil drop model, a tool which can be used to study the structure of the hydrophobic core in proteins, has been applied in the analysis of proteins belonging to the jumonji group—JARID2, JARID1A, JARID1B and JARID1D—proteins that share the property of being able to interact with DNA. Their ARID and PHD domains, when analyzed in the context of the fuzzy oil drop model, are found to exhibit structural variability regarding the status of their secondary folds, including the β-hairpin which determines their biological function. Additionally, the structure of disordered fragments which are present in jumonji proteins (as confirmed by the DisProt database) is explained on the grounds of the hydrophobic core model, suggesting that such fragments contribute to tertiary structural stabilization. This conclusion is supported by divergence entropy measurements, expressing the degree of ordering in each protein’s hydrophobic core. Full article
(This article belongs to the Special Issue Entropy and RNA Structure, Folding and Mechanics)
Figures

Open AccessArticle Describing the Structural Diversity within an RNA’s Ensemble
Entropy 2014, 16(3), 1331-1348; doi:10.3390/e16031331
Received: 6 August 2013 / Revised: 15 January 2014 / Accepted: 21 February 2014 / Published: 3 March 2014
Cited by 1 | PDF Full-text (3639 KB) | HTML Full-text | XML Full-text
Abstract
RNA is usually classified as either structured or unstructured; however, neither category is adequate in describing the diversity of secondary structures expected in biological systems We describe this diversity within the ensemble of structures by using two different metrics: the average Shannon entropy
[...] Read more.
RNA is usually classified as either structured or unstructured; however, neither category is adequate in describing the diversity of secondary structures expected in biological systems We describe this diversity within the ensemble of structures by using two different metrics: the average Shannon entropy and the ensemble defect. The average Shannon entropy is a measure of the structural diversity calculated from the base pair probability matrix. The ensemble defect, a tool in identifying optimal sequences for a given structure, is a measure of the average number of structural differences between a target structure and all the structures that make up the ensemble, scaled to the length of the sequence. In this paper, we show examples and discuss various uses of these metrics in both structured and unstructured RNA. By exploring how these two metrics describe RNA as an ensemble of different structures, as would be found in biological systems, it will push the field beyond the standard “structured” and “unstructured” categorization. Full article
(This article belongs to the Special Issue Entropy and RNA Structure, Folding and Mechanics)
Open AccessArticle Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP
Entropy 2013, 15(12), 5362-5383; doi:10.3390/e15125362
Received: 13 September 2013 / Revised: 19 November 2013 / Accepted: 22 November 2013 / Published: 3 December 2013
Cited by 8 | PDF Full-text (1704 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
3′,5′-Cyclic GMP spontaneously nonenzymatically polymerizes in a base-catalyzed reaction affording G oligonucleotides. When reacted with fully or partially sequence-complementary RNA (oligo C), the abiotically generated oligo G RNA displays a typical ribozyme activity consisting of terminal ligation accompanied by cleavage of an internal
[...] Read more.
3′,5′-Cyclic GMP spontaneously nonenzymatically polymerizes in a base-catalyzed reaction affording G oligonucleotides. When reacted with fully or partially sequence-complementary RNA (oligo C), the abiotically generated oligo G RNA displays a typical ribozyme activity consisting of terminal ligation accompanied by cleavage of an internal phosphate site of the donor oligonucleotide stem upon attack of the acceptor 3′ terminal OH. This reaction is dubbed Ligation following Intermolecular Cleavage (LIC). In a prebiotic perspective, the ability of oligo G polynucleotides to react with other sequences outlines a simple and possible evolutionary scenario based on the autocatalytic properties of RNA. Full article
(This article belongs to the Special Issue Entropy and RNA Structure, Folding and Mechanics)
Figures

Open AccessArticle Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers
Entropy 2013, 15(8), 3088-3099; doi:10.3390/e15083088
Received: 13 June 2013 / Revised: 15 July 2013 / Accepted: 22 July 2013 / Published: 31 July 2013
Cited by 3 | PDF Full-text (180 KB) | HTML Full-text | XML Full-text
Abstract
To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales. We employ kinetic Monte Carlo simulation to model the time-dependent folding during transcription of thiamine pyrophosphate (TPP) riboswitch expression platforms. According to
[...] Read more.
To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales. We employ kinetic Monte Carlo simulation to model the time-dependent folding during transcription of thiamine pyrophosphate (TPP) riboswitch expression platforms. According to our simulations, riboswitch transcriptional terminators, which must adopt a specific hairpin configuration by the time they have been transcribed, fold with higher efficiency than Shine-Dalgarno sequesterers, whose proper structure is required only at the time of ribosomal binding. Our findings suggest both that riboswitch transcriptional terminator sequences have been naturally selected for high folding efficiency, and that sequesterers can maintain their function even in the presence of significant misfolding. Full article
(This article belongs to the Special Issue Entropy and RNA Structure, Folding and Mechanics)

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