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 (31 August 2013)

Special Issue Editor

Guest Editor
Dr. Wayne K. Dawson
Asai Laboratory, Department of Computational Biology, Faculty of Frontier Science, University of Tokyo, AIST Tokyo Waterfront BIO-IT Research Building, 2-4-7 Aomi, Koto-Ku, Tokyo, 135-0064, Japan
E-Mail: dawson@bi.a.u-tokyo.ac.jp
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 1200 CHF (Swiss Francs).


Published Papers (3 papers)

Entropy 2014, 16(3), 1331-1348; doi:10.3390/e16031331
Received: 6 August 2013; in revised form: 15 January 2014 / Accepted: 21 February 2014 / Published: 3 March 2014
Show/Hide Abstract | Download PDF Full-text (3639 KB)

Entropy 2013, 15(12), 5362-5383; doi:10.3390/e15125362
Received: 13 September 2013; in revised form: 19 November 2013 / Accepted: 22 November 2013 / Published: 3 December 2013
Show/Hide Abstract | Download PDF Full-text (1704 KB) |  Supplementary Files
abstract graphic

Entropy 2013, 15(8), 3088-3099; doi:10.3390/e15083088
Received: 13 June 2013; in revised form: 15 July 2013 / Accepted: 22 July 2013 / Published: 31 July 2013
Show/Hide Abstract | Download PDF Full-text (180 KB)

Last update: 18 February 2013

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