Free Energy Landscape and Multiple Folding Pathways of an H-Type RNA Pseudoknot

How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA.

[1]  Jian Zhang,et al.  Atomistic analysis of pseudoknotted RNA unfolding. , 2011, Journal of the American Chemical Society.

[2]  J. Šponer,et al.  Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding. , 2001, Journal of molecular biology.

[3]  E. Siggia,et al.  Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[4]  A. Laio,et al.  Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science , 2008 .

[5]  J. Dinman,et al.  Single-molecule measurements of the CCR5 mRNA unfolding pathways. , 2014, Biophysical journal.

[6]  Syma Khalid,et al.  Single-stranded DNA within nanopores: conformational dynamics and implications for sequencing; a molecular dynamics simulation study. , 2012, Biophysical journal.

[7]  Shi-Jie Chen,et al.  Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. , 2007, Journal of molecular biology.

[8]  J. Wen,et al.  Folding a stable RNA pseudoknot through rearrangement of two hairpin structures , 2014, Nucleic acids research.

[9]  D Thirumalai,et al.  Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures , 2009, Proceedings of the National Academy of Sciences.

[10]  Daniel Herschlag,et al.  Multiple Native States Reveal Persistent Ruggedness of an RNA Folding Landscape , 2010, Nature.

[11]  Song Cao,et al.  Predicting RNA pseudoknot folding thermodynamics , 2006, Nucleic acids research.

[12]  Jie Liang,et al.  Discrete state model and accurate estimation of loop entropy of RNA secondary structures. , 2008, The Journal of chemical physics.

[13]  Massimiliano Bonomi,et al.  PLUMED: A portable plugin for free-energy calculations with molecular dynamics , 2009, Comput. Phys. Commun..

[14]  Shi-Jie Chen,et al.  Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte. , 2005, The Journal of chemical physics.

[15]  Shi-Jie Chen,et al.  Computing the conformational entropy for RNA folds. , 2010, The Journal of chemical physics.

[16]  Alessandro Laio,et al.  A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations , 2009, PLoS Comput. Biol..

[17]  Xiaojun Xu,et al.  Kinetic Mechanism for the Conformational Switch Between Bistable RNA Hairpins , 2012 .

[18]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[19]  R. Micura,et al.  Pseudoknot preorganization of the preQ1 class I riboswitch. , 2012, Journal of the American Chemical Society.

[20]  Shi-Jie Chen,et al.  Predicting loop-helix tertiary structural contacts in RNA pseudoknots. , 2010, RNA.

[21]  D. Thirumalai,et al.  Kinetics of Folding of Proteins and RNA , 1996 .

[22]  Yong Wang,et al.  Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme , 2011, PLoS Comput. Biol..

[23]  A. Laio,et al.  Optimizing the performance of bias-exchange metadynamics: folding a 48-residue LysM domain using a coarse-grained model. , 2010, The journal of physical chemistry. B.

[24]  Jun Wang,et al.  On the accuracy of metadynamics and its variations in a protein folding process , 2015 .

[25]  Shi-jie Chen,et al.  Ion-mediated nucleic acid helix-helix interactions. , 2006, Biophysical journal.

[26]  Cheng Tan,et al.  Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex , 2014, PLoS Comput. Biol..

[27]  A. Garcia,et al.  Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin. , 2008, Journal of the American Chemical Society.

[28]  D. Draper,et al.  RNA folding: thermodynamic and molecular descriptions of the roles of ions. , 2008, Biophysical journal.

[29]  D. Draper,et al.  Ions and RNA folding. , 2005, Annual review of biophysics and biomolecular structure.

[30]  Ya-Zhou Shi,et al.  A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect. , 2014, The Journal of chemical physics.

[31]  Shi-jie Chen,et al.  RNA helix stability in mixed Na+/Mg2+ solution. , 2007, Biophysical journal.

[32]  D. Draper,et al.  Folding of an mRNA pseudoknot required for stop codon readthrough: effects of mono- and divalent ions on stability. , 1997, Biochemistry.

[33]  Shi-jie Chen.  RNA folding: conformational statistics, folding kinetics, and ion electrostatics. , 2008, Annual review of biophysics.

[34]  I. Tinoco,et al.  Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. , 2007, RNA.

[35]  Shi-jie Chen,et al.  Coarse-Grained Prediction of RNA Loop Structures , 2012, PloS one.

[36]  S. Woodson.  Metal ions and RNA folding: a highly charged topic with a dynamic future. , 2005, Current opinion in chemical biology.

[37]  Leonidas J. Guibas,et al.  Structural Insight into RNA Hairpin Folding Intermediates , 2008, Journal of the American Chemical Society.

[38]  Yangyu Huang,et al.  Automated and fast building of three-dimensional RNA structures , 2012, Scientific Reports.

[39]  D. Thirumalai,et al.  Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA. , 2011, Journal of the American Chemical Society.

[40]  F. Major,et al.  The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data , 2008, Nature.

[41]  Michael D. Stone,et al.  Single-molecule FRET reveals the folding dynamics of the human telomerase RNA pseudoknot domain. , 2012, Angewandte Chemie.

[42]  Michael R. Shirts,et al.  Native-like mean structure in the unfolded ensemble of small proteins. , 2002, Journal of molecular biology.

[43]  D. Turner,et al.  Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.

[44]  Angel E García,et al.  High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations , 2013, Proceedings of the National Academy of Sciences.

[45]  Wei Wang,et al.  Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation. , 2009, RNA.

[46]  A. Laio,et al.  A bias-exchange approach to protein folding. , 2007, The journal of physical chemistry. B.

[47]  David E Draper,et al.  Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions. , 2007, Biochemistry.

[48]  Ignacio Tinoco,et al.  Characterization of the Mechanical Unfolding of RNA Pseudoknots , 2007, Journal of Molecular Biology.

[49]  A. Ansari,et al.  Fast folding of RNA pseudoknots initiated by laser temperature-jump. , 2011, Journal of the American Chemical Society.

[50]  D. W. Staple,et al.  Open access, freely available online Primer Pseudoknots: RNA Structures with Diverse Functions , 2022 .