Special Issue "Entropy and RNA Structure, Folding and Mechanics"
A special issue of Entropy (ISSN 1099-4300).
Deadline for manuscript submissions: closed (30 April 2015)
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
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
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
Manuscript Submission Information
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