Guanine-adenine (GA) base pairs play important roles in determining the structure, dynamics, and stability of RNA. In RNA internal loops, GA base pairs often occur in tandem arrangements and their structure is context and sequence dependent. Calculations reported here test the thermodynamic integration (TI) approach with the amber99 force field by comparing computational predictions of free energy differences with the free energy differences expected on the basis of NMR determined structures of the RNA motifs (5'-GCGGACGC-3')(2), (5'-GCiGGAiCGC-3')(2), (5'-GGCGAGCC-3')(2), and (5'-GGiCGAiGCC-3')(2). Here, iG and iC denote isoguanosine and isocytidine, which have amino and carbonyl groups transposed relative to guanosine and cytidine. The NMR structures show that the GA base pairs adopt either imino (cis Watson-Crick/Watson-Crick A-G) or sheared (trans Hoogsteen/Sugar edge A-G) conformations depending on the identity and orientation of the adjacent base pair. A new mixing function for the TI method is developed that allows alchemical transitions in which atoms can disappear in both the initial and final states. Unrestrained calculations gave DeltaG degrees values 2-4 kcal/mol different from expectations based on NMR data. Restraining the structures with hydrogen bond restraints did not improve the predictions. Agreement with NMR data was improved by 0.7 to 1.5 kcal/mol, however, when structures were restrained with weak positional restraints to sample around the experimentally determined NMR structures. The amber99 force field was modified to partially include pyramidalization effects of the unpaired amino group of guanosine in imino GA base pairs. This provided little or no improvement in comparisons with experiment. The marginal improvement is observed when the structure has potential cross-strand out-of-plane hydrogen bonding with the G amino group. The calculations using positional restraints and a nonplanar amino group reproduce the signs of DeltaG degrees from the experimental results and are, thus, capable of providing useful qualitative insights complementing the NMR experiments. Decomposition of the terms in the calculations reveals that the dominant terms are from electrostatic and interstrand interactions other than hydrogen bonds in the base pairs. The results suggest that a better description of the backbone is key to reproducing the experimental free energy results with computational free energy predictions.

Department of Physics and Astronomy Department of Chemistry and Department of Pediatrics University of Rochester Rochester New York 14627 and Institute of Biophysics Academy of Sciences of the Czech Republic v v i Královopolská 135 61265 Brno Czech Republic

Zobrazit více v PubMed

Krasovska M. V.; Sefcikova J.; Spackova N.; Sponer J.; Walter N. G. Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. J. Mol. Biol. 2005, 351, 731. PubMed

Csaszar K.; Spackova N.; Stefl R.; Sponer J.; Leontis N. B. 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. J. Mol. Biol. 2001, 313, 1073. PubMed

Auffinger P.; Hashem Y. Nucleic acid solvation: from outside to insight. Curr. Opin. Struct. Biol. 2007, 17, 325. PubMed

McDowell S. E.; Spackova N.; Sponer J.; Walter N. G. Molecular dynamics simulations of RNA: An in silico single molecule approach. Biopolymers 2007, 85, 169. PubMed PMC

Trylska J.; Tozzini V.; McCammon J. A. Exploring global motions and correlations in the ribosome. Biophys. J. 2005, 89, 1455. PubMed PMC

Zagrovic B.; Pande V. Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study. J. Comput. Chem. 2003, 24, 1432. PubMed

Russell R.; Millettt I. S.; Tate M. W.; Kwok L. W.; Nakatani B.; Gruner S. M.; Mochrie S. G. J.; Pande V.; Doniach S.; Herschlag D.; Pollack L. Rapid compaction during RNA folding. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 4266. PubMed PMC

Zagrovic B.; Sorin E. J.; Pande V. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 2001, 313, 151. PubMed

Duan Y.; Kollman P. A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998, 282, 740. PubMed

Cornell W. D.; Cieplak P.; Bayly C. I.; Gould I. R.; Merz K. M.; Ferguson D. M.; Spellmeyer D. C.; Fox T.; Caldwell J. W.; Kollman P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179.

MacKerell A. D.; Bashford D.; Bellott M.; Dunbrack R. L.; Evanseck J. D.; Field M. J.; Fischer S.; Gao J.; Guo H.; Ha S.; Joseph-McCarthy D.; Kuchnir L.; Kuczera K.; Lau F. T. K.; Mattos C.; Michnick S.; Ngo T.; Nguyen D. T.; Prodhom B.; Reiher W. E.; Roux B.; Schlenkrich M.; Smith J. C.; Stote R.; Straub J.; Watanabe M.; Wiorkiewicz-Kuczera J.; Yin D.; Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586. PubMed

Scott W. R. P.; Hunenberger P. H.; Tironi I. G.; Mark A. E.; Billeter S. R.; Fennen J.; Torda A. E.; Huber T.; Kruger P.; van Gunsteren W. F. The GROMOS biomolecular simulation program package. J. Phys. Chem. A 1999, 103, 3596.

Sponer J.; Riley K. E.; Hobza P. Nature and magnitude of aromatic stacking of nucleic acid bases. Phys. Chem. Chem. Phys. 2008, 10, 2595. PubMed

Gautheret D. F.; Konings D.; Gutell R. R. A major family of motifs involving G·A mismatches in ribosomal RNA. J. Mol. Biol. 1994, 242, 1. PubMed

Gutell R. R.; Gray M. W.; Schnare M. N. A compilation of large subunit (23S- and 23S-like) ribosomal-RNA structures: 1993. Nucleic Acids Res. 1993, 21, 3055. PubMed PMC

Gutell R. R.; Weiser B.; Woese C. R.; Noller H. F. Comparative anatomy of 16S-like ribosomal-RNA. Prog. Nucleic Acid Res. Mol. Biol. 1985, 32, 155. PubMed

Cannone J. J.; Subramanian S.; Schnare M. N.; Collett J. R.; D’Souza L. M.; Du Y. S.; Feng B.; Lin N.; Madabusi L. V.; Muller K. M.; Pande N.; Shang Z. D.; Yu N.; Gutell R. R. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 2002, 3, 2. PubMed PMC

Pley H. W.; Flaherty K. M.; McKay D. B. 3-Dimensional structure of a hammerhead ribozyme. Nature 1994, 372, 68. PubMed

Pley H. W.; Flaherty K. M.; McKay D. B. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 1994, 372, 111. PubMed

Biou V.; Yaremchuk A.; Tukalo M.; Cusack S. The 2.9 Angstrom crystal structure of T. thermophilus Seryl-tRNA synthetase complexed with tRNA(Ser). Science 1994, 263, 1404. PubMed

Murphy F. L.; Cech T. R. GAAA tetraloop and conserved bulge stabilize tertiary structure of a Group-I Intron domain. J. Mol. Biol. 1994, 236, 49. PubMed

Michel F.; Westhof E. Modeling of the 3-Dimensional architecture of Group-I Catalytic Introns based on comparative sequence-analysis. J. Mol. Biol. 1990, 216, 585. PubMed

Zwieb C. Recognition of a tetranucleotide loop of signal recognition particle RNA by protein-Srp19. J. Biol. Chem. 1992, 267, 15650. PubMed

SantaLucia J.; Kierzek R.; Turner D. H. Effects of GA mismatches on the structure and thermodynamics of RNA internal loops. Biochemistry 1990, 29, 8813. PubMed

SantaLucia J. Jr.; Turner D. H. Structure of r(GGCGAGCC)2 in solution from NMR and restrained molecular dynamics. Biochemistry 1993, 32, 12612. PubMed

Wu M.; Turner D. H. Solution structure of r(GCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry 1996, 35, 9677. PubMed

Villescas-Diaz G.; Zacharias M. Sequence context dependence of tandem Guanine-Adenine mismatch conformations in RNA: A continuum solvent analysis. Biophys. J. 2003, 85, 416. PubMed PMC

Yildirim I.; Turner D. H. RNA challenges for computational chemists. Biochemistry 2005, 44, 13225. PubMed PMC

Kollman P. A. Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93, 2395.

Chen G.; Kierzek R.; Yildirim I.; Krugh T. R.; Turner D. H.; Kennedy S. D. Stacking effects on local structure in RNA: Changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs. J. Phys. Chem. B 2007, 111, 6718. PubMed PMC

Hobza P.; Sponer J. Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chem. Rev. 1999, 99, 3247. PubMed

Sponer J.; Mokdad A.; Sponer J. E.; Spackova N.; Leszczynski J.; Leontis N. B. Unique tertiary and neighbor interactions determine conservation patterns of cis Watson-Crick A/G base-pairs. J. Mol. Biol. 2003, 330, 967. PubMed

Sponer J.; Florian J.; Hobza P.; Leszczynski J. Nonplanar DNA base pairs. J. Biomol. Struct. Dyn. 1996, 13, 827. PubMed

Wang J. M.; Cieplak P.; Kollman P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules. J. Comput. Chem. 2000, 21, 1049.

Case D. A.; Darden T. A.; Cheatham T. E. I.; Simmerling C. L.; Wang J.; Duke R. E.; Luo R.; Merz K. M.; Pearlman D. A.; Crowley M.; Walker R. C.; Zhang W.; Wang B.; Hayik S.; Roitberg A.; Seabra G.; Wong K. F.; Paesani F.; Wu X.; Brozell S.; Tsui V.; Gohlke H.; Yang L.; Tan C.; Mongan J.; Hornak V.; Cui G.; Beroza P.; Mathews D. H.; Schafmeister C.; Ross W. S.; Kollman P. A.. AMBER 9, University of California: San Francisco, CA; 2006.

Simonson T.; Carlsson J.; Case D. A. Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models. J. Am. Chem. Soc. 2004, 126, 4167. PubMed

Shirts M. R.; Pitera J. W.; Swope W. C.; Pande V. S. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins. J. Chem. Phys. 2003, 119, 5740.

Simonson T. Free-Energy of particle insertion - an exact analysis of the origin singularity for simple liquids. Mol. Phys. 1993, 80, 441.

Wolfram Research, Inc.Mathematica Edition, Version 5.2; Wolfram Research, Inc.: Champaign, IL, 2005.

Pitera J. W.; Van Gunsteren W. F. A comparison of non-bonded scaling approaches for free energy calculations. Mol. Simul. 2002, 28, 45.

Zacharias M.; Straatsma T. P.; McCammon J. A. Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration. J. Chem. Phys. 1994, 100, 9025.

Cieplak P.; Cornell W. D.; Bayly C.; Kollman P. A. Application of the multimolecule and multiconformational RESP Methodology to biopolymers - Charge derivation for DNA, RNA, and Proteins. J. Comput. Chem. 1995, 16, 1357.

Cornell W. D.; Cieplak P.; Bayly C. I.; Kollman P. A. Application of RESP charges to calculate conformational energies, hydrogen-bond energies, and free-energies of solvation. J. Am. Chem. Soc. 1993, 115, 9620.

Bayly C. I.; Cieplak P.; Cornell W. D.; Kollman P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - the Resp Model. J. Phys. Chem. 1993, 97, 10269.

Frisch M. J.; Trucks G. W.; Schlegel H. B.; Scuseria G. E.; Robb M. A.; Cheeseman J. R.; Montgomery J. A., Jr.; Vreven T.; Kudin K. N.; Burant J. C.; Millam J. M.; Iyengar S. S.; Tomasi J.; Barone V.; Mennucci B.; Cossi M.; Scalmani G.; Rega N.; Petersson G. A.; Nakatsuji H.; Hada M.; Ehara M.; Toyota K.; Fukuda R.; Hasegawa J.; Ishida M.; Nakajima T.; Honda Y.; Kitao O.; Nakai H.; Klene M.; Li X.; Knox J. E.; Hratchian H. P.; Cross J. B.; Bakken V.; Adamo C.; Jaramillo J.; Gomperts R.; Stratmann R. E.; Yazyev O.; Austin A. J.; Cammi R.; Pomelli C.; Ochterski J. W.; Ayala P. Y.; Morokuma K.; Voth G. A.; Salvador P.; Dannenberg J. J.; Zakrzewski V. G.; Dapprich S.; Daniels A. D.; Strain M. C.; Farkas O.; Malick D. K.; Rabuck A. D.; Raghavachari K.; Foresman J. B.; Ortiz J. V.; Cui Q.; Baboul A. G.; Clifford S.; Cioslowski J.; Stefanov B. B.; Liu G.; Liashenko A.; Piskorz P.; Komaromi I.; Martin R. L.; Fox D. J.; Keith T.; Al-Laham M. A.; Peng C. Y.; Nanayakkara A.; Challacombe M.; Gill P. M. W.; Johnson B.; Chen W.; Wong M. W.; Gonzalez C. ; Pople J. A.. Gaussian 03, Revision C.02; Gaussian, Inc.: Wallingford CT,2004.

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.

Ryjacek F.; Kubar T.; Hobza P. New parameterization of the Cornell et al. empirical force field covering amino group nonplanarity in nucleic acid bases. J. Comput. Chem. 2003, 24, 1891. PubMed

Ryckaert J. P.; Ciccotti G.; Berendsen H. J. C. Numerical-Integration of cartesian equations of motion of a system with constraints: Molecular-Dynamics of N-Alkanes. J. Comput. Phys. 1977, 23, 327.

Jeffrey G. A.An Introduction to Hydrogen Bonding; Oxford University Press:New York, 1997; pp 11−32.

Chen X.; Kierzek R.; Turner D. H. Stability and structure of RNA duplexes containing isoguanosine and isocytidine. J. Am. Chem. Soc. 2001, 123, 1267. PubMed

Leontis N. B.; Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA 2001, 7, 499. PubMed PMC

Grossfield A.; Ren P. Y.; Ponder J. W. Ion solvation thermodynamics from simulation with a polarizable force field. J. Am. Chem. Soc. 2003, 125, 15671. PubMed

Ren P. Y.; Ponder J. W. Polarizable atomic multipole water model for molecular mechanics simulation. J. Phys. Chem. B 2003, 107, 5933.

Babin V.; Baucom J.; Darden T. A.; Sagui C. Molecular dynamics simulations of DNA with polarizable force fields: Convergence of an ideal B-DNA structure to the crystallographic structure. J. Phys. Chem. B 2006, 110,, 11571. PubMed

Gresh N.; Sponer J. E.; Spackova N.; Leszczynski J.; Sponer J. Theoretical study of binding of hydrated Zn(II) and Mg(II) cations to 5′-guanosine monophosphate. Toward polarizable molecular mechanics for DNA and RNA. J. Phys. Chem. B 2003, 107, 8669.

Humphrey W.; Dalke A.; Schulten K. VMD: Visual molecular dynamics. J. Mol. Graph. 1996, 14, 33. PubMed

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?

A measure of bending in nucleic acids structures applied to A-tract DNA