Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding.

[1]  Feng Ding,et al.  RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. , 2012, RNA.

[2]  T. Schlick,et al.  Tertiary motifs revealed in analyses of higher-order RNA junctions. , 2009, Journal of molecular biology.

[3]  S. Nakamura,et al.  Dynamics of transfer RNAs analyzed by normal mode calculation. , 1994, Nucleic acids research.

[4]  P. Stadler,et al.  Structure of transfer RNAs: similarity and variability , 2012, Wiley interdisciplinary reviews. RNA.

[5]  D. Crothers,et al.  The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. , 1974, Journal of molecular biology.

[6]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[7]  K. Dill,et al.  Cooperativity in protein-folding kinetics. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[8]  D. Thirumalai,et al.  Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures , 2012, Nucleic acids research.

[9]  Eckart Bindewald,et al.  RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign , 2007, Nucleic Acids Res..

[10]  P. Schimmel,et al.  Novel transfer RNAs that are active in Escherichia coli. , 1992, Biochemistry.

[11]  C. Brooks,et al.  Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. , 2011, Current opinion in structural biology.

[12]  Active suppressor tRNAs with a double helix between the D- and T-loops. , 2007, Journal of molecular biology.

[13]  Christopher A. Lavender,et al.  Three-Dimensional RNA Structure Refinement by Hydroxyl Radical Probing , 2012, Nature Methods.

[14]  Michael Levitt,et al.  Clustering to identify RNA conformations constrained by secondary structure , 2011, Proceedings of the National Academy of Sciences.

[15]  J. Kjems,et al.  An Unusual Topological Structure of the HIV-1 Rev Response Element , 2013, Cell.

[16]  M. Sekine,et al.  Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group. , 1992, Biochemistry.

[17]  H. Al‐Hashimi,et al.  Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation , 2010, Science.

[18]  Carsten O. Daub,et al.  The mutual information: Detecting and evaluating dependencies between variables , 2002, ECCB.

[19]  Hashim M. Al-Hashimi,et al.  Functional complexity and regulation through RNA dynamics , 2012, Nature.

[20]  Hashim M. Al-Hashimi,et al.  Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges , 2014, The journal of physical chemistry. B.

[21]  J. Lobry,et al.  Relationships Between Genomic G+C Content, RNA Secondary Structures, and Optimal Growth Temperature in Prokaryotes , 1997, Journal of Molecular Evolution.

[22]  D Gautheret,et al.  Reproducing the three-dimensional structure of a tRNA molecule from structural constraints. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Canonical analysis of correlated atomic motions in DNA from molecular dynamics simulation. , 1994, Biophysical chemistry.

[24]  Magdalena A. Jonikas,et al.  Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. , 2009, RNA.

[25]  D. Crothers,et al.  Conformational changes of transfer RNA. The role of magnesium(II). , 1976, Biochemistry.

[26]  D Gautheret,et al.  Identification of base-triples in RNA using comparative sequence analysis. , 1995, Journal of molecular biology.

[27]  S. Harvey,et al.  Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques. , 1994, Biophysical journal.

[28]  E. Westhof,et al.  Topology of three-way junctions in folded RNAs. , 2006, RNA.

[29]  D. Lilley,et al.  The folding of the hairpin ribozyme: dependence on the loops and the junction. , 2000, RNA.

[30]  R L Jernigan,et al.  Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. , 1998, Journal of molecular biology.

[31]  Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations. , 2001, Biochemistry.

[32]  D. Crothers,et al.  Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. , 1972, Biochemistry.

[33]  Henri Grosjean,et al.  tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. , 2002, RNA.

[34]  A. S. Krasilnikov,et al.  Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium. , 2006, RNA.

[35]  S. Woodson,et al.  Crowders perturb the entropy of RNA energy landscapes to favor folding. , 2013, Journal of the American Chemical Society.

[36]  R Giegé,et al.  Search for characteristic structural features of mammalian mitochondrial tRNAs. , 2000, RNA.

[37]  I. Tinoco,et al.  RNA folding causes secondary structure rearrangement. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Stephan H Bernhart,et al.  RNA structure prediction. , 2011, Methods in molecular biology.

[39]  R. Gutell,et al.  Folding of circularly permuted transfer RNAs. , 1991, Science.

[40]  J. Richardson,et al.  Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Dominique Barth,et al.  Automated prediction of three-way junction topological families in RNA secondary structures , 2012, Comput. Biol. Chem..

[42]  E. Phizicky,et al.  Identification of yeast tRNA Um(44) 2'-O-methyltransferase (Trm44) and demonstration of a Trm44 role in sustaining levels of specific tRNA(Ser) species. , 2007, RNA.

[43]  S. Butcher,et al.  The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. , 2011, Accounts of chemical research.

[44]  E. Westhof,et al.  Hierarchy and dynamics of RNA folding. , 1997, Annual review of biophysics and biomolecular structure.

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

[46]  J. Richardson,et al.  De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. , 1990, Science.

[47]  D. Mathews,et al.  Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots , 2013, Proceedings of the National Academy of Sciences.

[48]  O. Uhlenbeck,et al.  Selection for active E. coli tRNA(Phe) variants from a randomized library using two proteins. , 1993, The EMBO journal.

[49]  Walter N. Moss,et al.  Folding and finding RNA secondary structure. , 2010, Cold Spring Harbor perspectives in biology.

[50]  Michael Feig,et al.  MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. , 2004, Journal of molecular graphics & modelling.

[51]  T. Schlick,et al.  Analysis of four-way junctions in RNA structures. , 2009, Journal of molecular biology.

[52]  S. Holbrook.  Structural principles from large RNAs. , 2008, Annual review of biophysics.

[53]  M. Bina-Stein,et al.  Conformational changes of transfer ribonucleic acid. The pH phase diagram under acidic conditions. , 1974, Biochemistry.

[54]  C. Brooks,et al.  New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation , 2011, Nucleic acids research.

[55]  V. Pande,et al.  Do conformational biases of simple helical junctions influence RNA folding stability and specificity? , 2009, RNA.

[56]  Changbong Hyeon,et al.  Theory of RNA Folding: From Hairpins to Ribozymes , 2009 .

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

[58]  K. M. Harrington,et al.  Many of the conserved nucleotides of tRNA(Phe) are not essential for ternary complex formation and peptide elongation. , 1994, The EMBO journal.

[59]  T. Schlick,et al.  Graph-based sampling for approximating global helical topologies of RNA , 2014, Proceedings of the National Academy of Sciences.

[60]  Edmund K. Burke,et al.  RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures , 2010, BMC Bioinformatics.

[61]  Kevin M Weeks,et al.  RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts. , 2005, Journal of the American Chemical Society.

[62]  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.

[63]  L. Cohen,et al.  The role of magnesium. , 2002, The Israel Medical Association journal : IMAJ.

[64]  Peter F. Stadler,et al.  tRNAdb 2009: compilation of tRNA sequences and tRNA genes , 2008, Nucleic Acids Res..

[65]  Z. Luthey-Schulten,et al.  Experimental and computational determination of tRNA dynamics , 2010, FEBS letters.

[66]  D. Millar,et al.  Helical junctions as determinants for RNA folding: origin of tertiary structure stability of the hairpin ribozyme. , 2000, Biochemistry.

[67]  S. Woodson,et al.  Cooperative Tertiary Interaction Network Guides RNA Folding , 2012, Cell.

[68]  Rongzhong Li,et al.  Sequence-dependent base-stacking stabilities guide tRNA folding energy landscapes. , 2013, The journal of physical chemistry. B.

[69]  F. Michel,et al.  Frequent use of the same tertiary motif by self‐folding RNAs. , 1995, The EMBO journal.

[70]  C. Brooks,et al.  3D maps of RNA interhelical junctions , 2011, Nature Protocols.

[71]  Eric Westhof,et al.  The Dynamic Landscapes of RNA Architecture , 2009, Cell.

[72]  Cinque S. Soto,et al.  Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[73]  P. Privalov,et al.  Thermodynamic analysis of transfer RNA unfolding. , 1978, Journal of molecular biology.

[74]  Eric J. Sorin,et al.  Does native state topology determine the RNA folding mechanism? , 2004, Journal of molecular biology.

[75]  N. Walter,et al.  Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction , 1999, Nature Structural Biology.

[76]  David H Mathews,et al.  Predicting helical coaxial stacking in RNA multibranch loops. , 2007, RNA.

[77]  J. Frank,et al.  Transfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data , 2007, Proceedings of the National Academy of Sciences.

[78]  Feng Ding,et al.  On the significance of an RNA tertiary structure prediction. , 2010, RNA.

[79]  Raymond F. Gesteland,et al.  Life Before DNA. (Book Reviews: The RNA World. The Nature of Modern RNA Suggests a Prebiotic RNA World.) , 1993 .

[80]  Feng Ding,et al.  Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. , 2010, Biochemistry.

[81]  S. Woodson,et al.  Compact intermediates in RNA folding. , 2010, Annual review of biophysics.

[82]  David H. Mathews,et al.  Automated RNA tertiary structure prediction from secondary structure and low‐resolution restraints , 2011, J. Comput. Chem..

[83]  Adelene Y. L. Sim,et al.  Modeling nucleic acids. , 2012, Current opinion in structural biology.

[84]  Taekjip Ha,et al.  A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[85]  Richard Giegé,et al.  Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase , 1993, Nucleic Acids Res..

[86]  Thomas A. Steitz,et al.  RNA tertiary interactions in the large ribosomal subunit: The A-minor motif , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[87]  D. Herschlag,et al.  A repulsive field: advances in the electrostatics of the ion atmosphere. , 2008, Current opinion in chemical biology.

[88]  I. Tinoco,et al.  How RNA folds. , 1999, Journal of molecular biology.

[89]  D. Herschlag,et al.  Direct measurement of tertiary contact cooperativity in RNA folding. , 2008, Journal of the American Chemical Society.

[90]  C. Brooks,et al.  Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. , 1993, Biochemistry.

[91]  R. Batey,et al.  Non-protein coding RNAs , 2009 .

[92]  Changbong Hyeon,et al.  Capturing the essence of folding and functions of biomolecules using coarse-grained models. , 2011, Nature communications.