Premium
Coarse‐Grained and Atomistic MD Simulations of RNA and DNA Folding
Author(s) -
Leuchter Jessica D.,
Green Adam T.,
Gilyard Julian,
Rambarat Cecilia G.,
Cho Samuel S.
Publication year - 2014
Publication title -
israel journal of chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.908
H-Index - 54
eISSN - 1869-5868
pISSN - 0021-2148
DOI - 10.1002/ijch.201400022
Subject(s) - nucleic acid , chemistry , folding (dsp implementation) , molecular dynamics , protein folding , rna , dna , nucleic acid structure , energy landscape , computational biology , nanotechnology , computational chemistry , biochemistry , biology , materials science , electrical engineering , gene , engineering
Although the main features of the protein folding problem are coming into clearer focus, the microscopic viewpoint of nucleic acid folding mechanisms is only just beginning to be addressed. Experiments, theory, and simulations are pointing to complex thermodynamic and kinetic mechanisms. As is the case for proteins, molecular dynamics (MD) simulations continue to be indispensable tools for providing a molecular basis for nucleic acid folding mechanisms. In this review, we provide an overview of biomolecular folding mechanisms focusing on nucleic acids. We outline the important interactions that are likely to be the main determinants of nucleic acid folding energy landscapes. We discuss recent MD simulation studies of empirical force field and Go‐type MD simulations of RNA and DNA folding mechanisms to outline recent successes and the theoretical and computational challenges that lie ahead.