论文信息 - Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings.

Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings.

HiRE-RNA is a coarse-grained model for RNA structure prediction and the dynamical study of RNA folding. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking, we show that noncanonical and multiple base interactions are necessary to capture the full physical behavior of complex RNAs. In this paper, we give a full account of the model and present results on the folding, stability, and free energy surfaces of 16 systems with 12 to 76 nucleotides of increasingly complex architectures, ranging from monomers to dimers, using a total of 850 μs of simulation time.

[1] D. Turner,et al. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation , 2006, Nucleic acids research.

[2] J. Rottler,et al. A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality. , 2009, The Journal of chemical physics.

[3] L. Jaeger,et al. Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin , 2007, Nucleic acids research.

[4] Ignacio Tinoco,et al. Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of –1 ribosomal frameshifting , 2009, Proceedings of the National Academy of Sciences.

[5] A. Liwo,et al. Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. , 2013, Physical review letters.

[6] Shi-Jie Chen,et al. Physics-based de novo prediction of RNA 3D structures. , 2011, The journal of physical chemistry. B.

[7] David H. Mathews,et al. RNAstructure: web servers for RNA secondary structure prediction and analysis , 2013, Nucleic Acids Res..

[8] 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.

[9] J. Maizel,et al. RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA , 2008, Journal of biomolecular structure & dynamics.

[10] D Thirumalai,et al. Folding of human telomerase RNA pseudoknot using ion-jump and temperature-quench simulations. , 2011, Journal of the American Chemical Society.

[11] Marc Baaden,et al. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. , 2014, Chemical Society reviews.

[12] P. Derreumaux,et al. HiRE-RNA: a high resolution coarse-grained energy model for RNA. , 2010, The journal of physical chemistry. B.

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

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

[15] D. Giedroc,et al. Non-nearest neighbor effects on the thermodynamics of unfolding of a model mRNA pseudoknot. , 1998, Journal of molecular biology.

[16] Loren Dean Williams,et al. Cations in charge: magnesium ions in RNA folding and catalysis. , 2012, Current opinion in structural biology.

[17] C. A. Theimer,et al. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. , 2005, Molecular cell.

[18] Russ B Altman,et al. Turning limited experimental information into 3D models of RNA. , 2010, RNA.

[19] Flavio Romano,et al. A nucleotide-level coarse-grained model of RNA. , 2014, The Journal of chemical physics.

[20] Ken A Dill,et al. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. , 2007, Journal of chemical theory and computation.

[21] A. Rich,et al. Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22] K. Weeks. Advances in RNA structure analysis by chemical probing. , 2010, Current opinion in structural biology.

[23] A. Serganov,et al. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. , 2004, Chemistry & biology.

[24] Pengyu Y. Ren,et al. Coarse-grained model for simulation of RNA three-dimensional structures. , 2010, The journal of physical chemistry. B.

[25] T. Schlick,et al. Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. , 2003, Nucleic acids research.

[26] J. Šponer,et al. Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations? , 2010, The journal of physical chemistry. B.

[27] Eckart Bindewald,et al. CyloFold: secondary structure prediction including pseudoknots , 2010, Nucleic Acids Res..

[28] P. Derreumaux,et al. A coarse‐grained protein force field for folding and structure prediction , 2007, Proteins.

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

[30] Pengyu Ren,et al. RNA 3D structure prediction by using a coarse-grained model and experimental data. , 2013, The journal of physical chemistry. B.

[31] Stephen R Holbrook,et al. RNA structure: the long and the short of it , 2005, Current Opinion in Structural Biology.

[32] Brice Felden,et al. NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation , 2006, Nucleic acids research.

[33] H. Schwalbe,et al. NMR-spectroscopic characterisation of phosphodiester bond cleavage catalyzed by the minimal hammerhead ribozyme , 2008, RNA biology.

[34] Ignacio Tinoco,et al. How RNA unfolds and refolds. , 2008, Annual review of biochemistry.

[35] A Xayaphoummine,et al. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[36] P. Fraser,et al. No-Nonsense Functions for Long Noncoding RNAs , 2011, Cell.

[37] D. Turner,et al. A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. , 1994, Biochemistry.

[38] Jun Feng,et al. Cooperative and directional folding of the preQ1 riboswitch aptamer domain. , 2011, Journal of the American Chemical Society.

[39] 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.

[40] Kevin E. Riley,et al. Nature and magnitude of aromatic stacking of nucleic acid bases. , 2008, Physical chemistry chemical physics : PCCP.

[41] Giovanni Bussi,et al. The role of nucleobase interactions in RNA structure and dynamics , 2014, Nucleic acids research.

[42] E Rivas,et al. A dynamic programming algorithm for RNA structure prediction including pseudoknots. , 1998, Journal of molecular biology.

[43] Tamar Schlick,et al. Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs , 2005, Nucleic acids research.

[44] D. Wales. Discrete path sampling , 2002 .

[45] Michael Zuker,et al. Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

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

[47] Qi Zhang,et al. Solution structure and dynamics of the wild-type pseudoknot of human telomerase RNA. , 2008, Journal of molecular biology.

[48] Xiaojun Xu,et al. Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction , 2014, PloS one.

[49] Eric Westhof,et al. The non-Watson-Crick base pairs and their associated isostericity matrices. , 2002, Nucleic acids research.

[50] T. Schlick,et al. Predicting Helical Topologies in RNA Junctions as Tree Graphs , 2013, PloS one.

[51] J. Doye,et al. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. , 2010, The Journal of chemical physics.

[52] F. Ding,et al. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. , 2008, RNA.

[53] D Thirumalai,et al. Coarse-grained model for predicting RNA folding thermodynamics. , 2013, The journal of physical chemistry. B.

[54] Tao Pan,et al. RNA folding: models and perspectives. , 2003, Current opinion in structural biology.

[55] Yannick G. Spill,et al. Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model. , 2011, Journal of chemical theory and computation.

[56] D. Wales,et al. Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins. , 2014, Journal of the American Chemical Society.

[57] Samuela Pasquali,et al. Ab initio RNA folding , 2014, Journal of physics. Condensed matter : an Institute of Physics journal.

[58] P. Derreumaux,et al. Coarse-grained simulations of RNA and DNA duplexes. , 2013, The journal of physical chemistry. B.

[59] D. Thirumalai,et al. Mechanical unfolding of RNA hairpins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[60] C. Tebbe,et al. Diversity responses of rumen microbial communities to Fusarium-contaminated feed, evaluated with rumen simulating technology. , 2008, Environmental microbiology.

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

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

[63] Wojciech Kasprzak,et al. Bridging the gap in RNA structure prediction. , 2007, Current opinion in structural biology.

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

[65] Rhiju Das,et al. Four Small Puzzles That Rosetta Doesn't Solve , 2011, PloS one.

[66] F. Major,et al. RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. , 2002, Nucleic acids research.

[67] C. Ponting,et al. Evolution and Functions of Long Noncoding RNAs , 2009, Cell.

[68] D. Giedroc,et al. Contribution of the intercalated adenosine at the helical junction to the stability of the gag-pro frameshifting pseudoknot from mouse mammary tumor virus. , 2000, RNA.

[69] D. Baker,et al. Automated de novo prediction of native-like RNA tertiary structures , 2007, Proceedings of the National Academy of Sciences.

[70] A. Aravin,et al. PIWI-interacting small RNAs: the vanguard of genome defence , 2011, Nature Reviews Molecular Cell Biology.