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Title: A Computational Study of RNA Tetraloop Thermodynamics, Including Misfolded States

Journal Article · · Journal of Physical Chemistry. B

An important characteristic of RNA folding is the adoption of alternative configurations of similar stability, often referred to as misfolded configurations. These configurations are considered to compete with correctly folded configurations, although their rigorous thermodynamic and structural characterization remains elusive. Tetraloop motifs found in large ribozymes are ideal systems for an atomistically detailed computational quantification of folding free energy landscapes and the structural characterization of their constituent free energy basins, including nonnative states. In this work, we studied a group of closely related 10-mer tetraloops using a combined parallel tempering and metadynamics technique that allows a reliable sampling of the free energy landscapes, requiring only knowledge that the stem folds into a canonical A-RNA configuration. Here we isolated and analyzed unfolded, folded, and misfolded populations that correspond to different free energy basins. We identified a distinct misfolded state that has a stability very close to that of the correctly folded state. This misfolded state contains a predominant population that shares the same structural features across all tetraloops studied here and lacks the noncanonical A-G base pair in its loop portion. Further analysis performed with biased trajectories showed that although this competitive misfolded state is not an essential intermediate, it is visited in most of the transitions from unfolded to correctly folded states. Moreover, the tetraloops can transition from this misfolded state to the correctly folded state without requiring extensive unfolding.

Research Organization:
Princeton Univ., NJ (United States)
Sponsoring Organization:
USDOE Office of Science (SC); National Science Foundation (NSF)
Grant/Contract Number:
SC0019394; CHE-1856704
OSTI ID:
1994991
Journal Information:
Journal of Physical Chemistry. B, Vol. 125, Issue 50; ISSN 1520-6106
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English

References (80)

RNA Chaperones and the RNA Folding Problem journal September 1995
Constant pressure molecular dynamics for molecular systems journal December 1983
Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena journal November 1982
Folding of RNA involves parallel pathways journal October 1997
A Network of Heterogeneous Hydrogen Bonds in GNRA Tetraloops journal December 1996
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix journal January 2006
Free-energy landscape of a hyperstable RNA tetraloop journal May 2016
RNA folding pathways in stop motion journal April 2016
Exposing the kinetic traps in RNA folding journal June 1999
Free Energy Landscape of GAGA and UUCG RNA Tetraloops journal September 2016
GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation journal February 2008
RNA force field with accuracy comparable to state-of-the-art protein force fields journal January 2018
Recognition of Planar and Nonplanar Ligands in the Malachite Green-RNA Aptamer Complex journal December 2003
Isolation of new ribozymes from a large pool of random sequences [see comment] journal September 1993
How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?: Atomistic molecular dynamics simulations of RNA and protein-RNA complexes journal November 2016
Mapping the Universe of RNA Tetraloop Folds journal July 2017
Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops". journal November 1990
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields journal June 2015
Tertiary Motifs in RNA Structure and Folding journal August 1999
Free Energy Profile of RNA Hairpins: A Molecular Dynamics Simulation Study journal February 2010
Promoting transparency and reproducibility in enhanced molecular simulations journal July 2019
Involvement of a GNRA tetraloop in long-range RNA tertiary interactions journal March 1994
Exceptionally Stable Nucleic Acid Hairpins journal June 1995
Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides journal May 2020
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins journal April 1998
Native contacts determine protein folding mechanisms in atomistic simulations journal October 2013
Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions journal March 2019
Structural Motifs in RNA journal June 1999
Structural Insight into RNA Hairpin Folding Intermediates journal July 2008
PLUMED 2: New feathers for an old bird journal February 2014
Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics journal March 2010
Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing journal September 1996
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules journal May 1995
Empirical Corrections to the Amber RNA Force Field with Target Metadynamics journal May 2016
Direct Revelation of Multiple Conformations in RNA by Femtosecond Dynamics journal April 2007
Exploring the Energy Landscape of a Small RNA Hairpin journal February 2006
CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. journal March 1988
Insights into RNA structure and function from genome-wide studies journal May 2014
Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics journal October 2006
A molecular dynamics method for simulations in the canonical ensemble journal June 1984
Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops journal July 1991
Loop and stem dynamics during RNA hairpin folding and unfolding journal October 2010
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations journal September 2013
GROMACS: A message-passing parallel molecular dynamics implementation journal September 1995
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations journal May 2018
Structures, Kinetics, Thermodynamics, and Biological Functions of RNA Hairpins journal May 2008
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method journal January 2008
Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics journal July 2015
Quality Threshold Clustering of Molecular Dynamics: A Word of Caution journal September 2019
The molecular configuration of deoxyribonucleic acid journal April 1960
Enhanced Sampling in the Well-Tempered Ensemble journal May 2010
The Paradoxical Behavior of a Highly Structured Misfolded Intermediate in RNA Folding journal October 2006
Dynamics of the RNA Hairpin GNRA Tetraloop journal April 2000
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies journal August 2016
Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations journal January 2012
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers journal June 2007
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins journal November 2010
Folding intermediates of a self-splicing RNA: mispairing of the catalytic core journal July 1998
Polymorphic transitions in single crystals: A new molecular dynamics method journal December 1981
Integrating NMR and simulations reveals motions in the UUCG tetraloop journal May 2020
Fitting Corrections to an RNA Force Field Using Experimental Data journal April 2019
Balance between α and β Structures in Ab Initio Protein Folding journal June 2010
A Time-Independent Free Energy Estimator for Metadynamics journal July 2014
Canonical dynamics: Equilibrium phase-space distributions journal March 1985
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles journal August 2011
Geometric deep learning of RNA structure journal August 2021
Visualizing transient low-populated structures of RNA journal October 2012
Computer Folding of RNA Tetraloops? Are We There Yet? journal March 2013
Peptide Folding: When Simulation Meets Experiment journal January 1999
RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop 1 1Edited by J. Dovdna journal April 2002
Thermodynamics of DNA Hybridization from Atomistic Simulations journal January 2021
A smooth particle mesh Ewald method journal November 1995
The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models journal April 2019
The Ribosome Is a Ribozyme journal August 2000
Revised AMBER Parameters for Bioorganic Phosphates journal October 2012
Escaping free-energy minima journal September 2002
Hierarchy and Dynamics of rna Folding journal June 1997
A boundary correction algorithm for metadynamics in multiple dimensions journal August 2013
Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering journal February 2015
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States journal April 2015

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