Correction to: Large-scale analysis of 48 DNA and 48 RNA tetranucleotides studied by 1 μs explicit-solvent molecular dynamics simulations (Journal of Chemical Theory and Computation (2015) 11:12 (5906-5917) DOI: 10.1021/acs.jctc.5b00899);Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations

Journal of Chemical Theory and Computation

Volumn 11, Issue 12, 2015, Pages 5906-5917

  Schrodt, Michael V ^a   Andrews, Casey T ^a   Elcock, Adrian H ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA; SOLVENT;

CHEMISTRY; CONFORMATION; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; THERMODYNAMICS;

BASE SEQUENCE; DNA; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; RNA; SOLVENTS; THERMODYNAMICS;

EID: 84949656411     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.8b00595     Document Type: Erratum

References (53)

1. Cheatham, T. E., III; Case, D. A. Twenty-five years of nucleic acid simulations Biopolymers 2013, 99, 969-77 10.1002/bip.22331
2. Šponer, J.; Banáš, P.; Jurečka, P.; Zgarbová, M.; Kührová, P.; Havrila, M.; Krepl, M.; Stadlbauer, P.; Otyepka, M. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome J. Phys. Chem. Lett. 2014, 5, 1771-1782 10.1021/jz500557y
3. Cheatham, T. E., III; Cieplak, P.; Kollman, P. A. A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat J. Biomol. Struct. Dyn. 1999, 16, 845-862 10.1080/07391102.1999.10508297
4. Pérez, A.; Marchán, I.; Svozil, D.; Šponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers Biophys. J. 2007, 92, 3817-3829 10.1529/biophysj.106.097782
5. Yildirim, I.; Stern, H. A.; Kennedy, S. D.; Tubbs, J. D.; Turner, D. H. Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine J. Chem. Theory Comput. 2010, 6, 1520-1531 10.1021/ct900604a
6. Banáš, P.; Hollas, D.; Zgarbová, M.; Jurečka, P.; Orozco, M.; Cheatham, T. E., III; Šponer, J. i.; Otyepka, M. Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins J. Chem. Theory Comput. 2010, 6, 3836-3849 10.1021/ct100481h
7. Zgarbová, M.; Otyepka, M.; Šponer, J.; Mládek, A.; Banáš, P.; Cheatham, T. E., III; Jurečka, P. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles J. Chem. Theory Comput. 2011, 7, 2886-2902 10.1021/ct200162x
8. Mlýnský, V.; Banáš, P.; Hollas, D.; Réblová, K.; Walter, N. G.; Šponer, J.; Otyepka, M. Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H+ Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme J. Phys. Chem. B 2010, 114, 6642-6652 10.1021/jp1001258
9. Banáš, P.; Sklenovský, P.; Wedekind, J. E.; Šponer, J.; Otyepka, M. Molecular Mechanism of preQ1 Riboswitch Action: A Molecular Dynamics Study J. Phys. Chem. B 2012, 116, 12721-12734 10.1021/jp309230v
10. Ode, H.; Matsuo, Y.; Neya, S.; Hoshino, T. Force field parameters for rotation around χ torsion axis in nucleic acids J. Comput. Chem. 2008, 29, 2531-2542 10.1002/jcc.21006
11. Krepl, M.; Zgarbová, M.; Stadlbauer, P.; Otyepka, M.; Banáš, P.; Koča, J.; Cheatham, T. E., III; Jurečka, P.; Šponer, J. Reference simulations of noncanonical nucleic acids with different chi variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA J. Chem. Theory Comput. 2012, 8, 2506-2520 10.1021/ct300275s
12. Yildirim, I.; Kennedy, S. D.; Stern, H. A.; Hart, J. M.; Kierzek, R.; Turner, D. H. Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs J. Chem. Theory Comput. 2012, 8, 172-181 10.1021/ct200557r
13. Zgarbová, M.; Luque, F. J.; Šponer, J.; Cheatham, T. E., III; Otyepka, M.; Jurečka, P. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters J. Chem. Theory Comput. 2013, 9, 2339-2354 10.1021/ct400154j
14. Bevilacqua, P. C.; Blose, J. M. Structures, Kinetics, Thermodynamics, and Biological Functions of RNA Hairpins Annu. Rev. Phys. Chem. 2008, 59, 79-103 10.1146/annurev.physchem.59.032607.093743
15. Yildirim, I.; Stern, H. A.; Tubbs, J. D.; Kennedy, S. D.; Turner, D. H. Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised chi torsions J. Phys. Chem. B 2011, 115, 9261-70 10.1021/jp2016006
16. Tubbs, J. D.; Condon, D. E.; Kennedy, S. D.; Hauser, M.; Bevilacqua, P. C.; Turner, D. H. The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics Biochemistry 2013, 52, 996-1010 10.1021/bi3010347
17. Condon, D. E.; Yildirim, I.; Kennedy, S. D.; Mort, B. C.; Kierzek, R.; Turner, D. H. Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU) J. Phys. Chem. B 2014, 118, 1216-28 10.1021/jp408909t
18. Condon, D. E.; Kennedy, S. D.; Mort, B. C.; Kierzek, R.; Yildirim, I.; Turner, D. H. Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics J. Chem. Theory Comput. 2015, 11, 2729-2742 10.1021/ct501025q
19. Henriksen, N. M.; Roe, D. R.; Cheatham, T. E., III Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations J. Phys. Chem. B 2013, 117, 4014-27 10.1021/jp400530e
20. Bergonzo, C.; Henriksen, N. M.; Roe, D. R.; Swails, J. M.; Roitberg, A. E.; Cheatham, T. E., III Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide J. Chem. Theory Comput. 2014, 10, 492-499 10.1021/ct400862k
21. Roe, D. R.; Bergonzo, C.; Cheatham, T. E., III Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods J. Phys. Chem. B 2014, 118, 3543-52 10.1021/jp4125099
22. Gil-Ley, A.; Bussi, G. Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering J. Chem. Theory Comput. 2015, 11, 1077-1085 10.1021/ct5009087
23. Chakraborty, K.; Mantha, S.; Bandyopadhyay, S. Molecular dynamics simulation of a single-stranded DNA with heterogeneous distribution of nucleobases in aqueous medium J. Chem. Phys. 2013, 139, 075103 10.1063/1.4818537
24. Ghosh, S.; Dixit, H.; Chakrabarti, R. Ion assisted structural collapse of a single stranded DNA: A molecular dynamics approach Chem. Phys. 2015, 459, 137-147 10.1016/j.chemphys.2015.07.038
25. Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: Fast, flexible, and free J. Comput. Chem. 2005, 26, 1701-1718 10.1002/jcc.20291
26. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447 10.1021/ct700301q
27. Kührová, P.; Banáš, P.; Best, R. B.; Šponer, J.; Otyepka, M. Computer Folding of RNA Tetraloops? Are We There Yet? J. Chem. Theory Comput. 2013, 9, 2115-2125 10.1021/ct301086z
28. Stadlbauer, P.; Krepl, M.; Cheatham, T. E., III; Koča, J.; Šponer, J. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations Nucleic Acids Res. 2013, 41, 7128-43 10.1093/nar/gkt412
29. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew J. Chem. Phys. 2004, 120, 9665-9678 10.1063/1.1683075
30. Brown, R. F.; Andrews, C. T.; Elcock, A. H. Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment J. Chem. Theory Comput. 2015, 11, 2315-2328 10.1021/ct501170h
31. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935 10.1063/1.445869
32. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins: Struct., Funct., Genet. 2006, 65, 712-725 10.1002/prot.21123
33. Li, D.-W.; Brüschweiler, R. NMR-Based Protein Potentials Angew. Chem., Int. Ed. 2010, 49, 6778-6780 10.1002/anie.201001898
34. Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Improved side-chain torsion potentials for the Amber ff99SB protein force field Proteins: Struct., Funct., Genet. 2010, 78, 1950-1958 10.1002/prot.22711
35. Beauchamp, K. A.; Lin, Y.-S.; Das, R.; Pande, V. S. Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements J. Chem. Theory Comput. 2012, 8, 1409-1414 10.1021/ct2007814
36. Joung, I. S.; Cheatham, T. E., III Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations J. Phys. Chem. B 2008, 112, 9020-9041 10.1021/jp8001614
37. Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method J. Appl. Phys. 1981, 52, 7182-7190 10.1063/1.328693
38. Nosé, S. A unified formulation of the constant temperature molecular dynamics methods J. Chem. Phys. 1984, 81, 511-519 10.1063/1.447334
39. Hoover, W. G. Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695-1697 10.1103/PhysRevA.31.1695
40. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 1997, 18, 1463-1472 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.3.CO;2-L
41. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A smooth particle mesh Ewald method J. Chem. Phys. 1995, 103, 8577 10.1063/1.470117
42. Norberg, J.; Nilsson, L. Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates Biophys. J. 1995, 69, 2277-2285 10.1016/S0006-3495(95)80098-6
43. Norberg, J.; Nilsson, L. Stacking Free Energy Profiles for All 16 Natural Ribodinucleoside Monophosphates in Aqueous Solution J. Am. Chem. Soc. 1995, 117, 10832-10840 10.1021/ja00149a006
44. Vokáčová, Z.; Buděšínský, M.; Rosenberg, I.; Schneider, B.; Šponer, J.; Sychrovský, V. Structure and Dynamics of the ApA, ApC, CpA, and CpC RNA Dinucleoside Monophosphates Resolved with NMR Scalar Spin-Spin Couplings J. Phys. Chem. B 2009, 113, 1182-1191 10.1021/jp809762b
45. Jafilan, S.; Klein, L.; Hyun, C.; Florián, J. Intramolecular Base Stacking of Dinucleoside Monophosphate Anions in Aqueous Solution J. Phys. Chem. B 2012, 116, 3613-3618 10.1021/jp209986y
46. Schneider, B.; Morávek, Z.; Berman, H. M. RNA conformational classes Nucleic Acids Res. 2004, 32, 1666-1677 10.1093/nar/gkh333
47. Le Faucheur, X.; Hershkovits, E.; Tannenbaum, R.; Tannenbaum, A. Nonparametric clustering for studying RNA conformations IEEE/ACM Trans. Comput. Biol. Bioinf. 2011, 8, 1604-1619 10.1109/TCBB.2010.128
48. Chen, H.; Meisburger, S. P.; Pabit, S. A.; Sutton, J. L.; Webb, W. W.; Pollack, L. Ionic strength-dependent persistence lengths of single-stranded RNA and DNA Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 799-804 10.1073/pnas.1119057109
49. Ke, C.; Humeniuk, M.; S-Gracz, H.; Marszalek, P. E. Direct Measurements of Base Stacking Interactions in DNA by Single-Molecule Atomic-Force Spectroscopy Phys. Rev. Lett. 2007, 99, 018302 10.1103/PhysRevLett.99.018302
50. Ke, C.; Loksztejn, A.; Jiang, Y.; Kim, M.; Humeniuk, M.; Rabbi, M.; Marszalek; Piotr, E. Detecting Solvent-Driven Transitions of poly(A) to Double-Stranded Conformations by Atomic Force Microscopy Biophys. J. 2009, 96, 2918-2925 10.1016/j.bpj.2008.12.3939
51. Chen, A. A.; García, A. E. High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 16820-16825 10.1073/pnas.1309392110
52. Šponer, J.; Mládek, A.; Špačková, N.; Cang, X.; Cheatham, T. E., III; Grimme, S. Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations J. Am. Chem. Soc. 2013, 135, 9785-9796 10.1021/ja402525c
53. Kruse, H.; Havrila, M.; Šponer, J. QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches J. Chem. Theory Comput. 2014, 10, 2615-2629 10.1021/ct500183w