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PLOS ONE  2012 

Kinetics of Bulge Bases in Small RNAs and the Effect of Pressure on It

DOI: 10.1371/journal.pone.0042052

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Abstract:

Due to their self-catalytic properties, small RNAs with bulge bases are hypothesized to be primordial molecules which could form elementary translation systems. Using molecular dynamics simulations, we study the binding propensity of small RNAs by calculating the free energy barrier corresponding to the looped out conformations of bulge bases, which presumably act as the binding sites for ligands in these small RNAs. We find that base flipping kinetics can proceed at atmospheric pressure but with a very small propensity. Furthermore, the free energy barrier associated with base flipping depends on the stacking with neighboring bases. Next, we studied the base flipping kinetics with pressure. We find that the free energy associated with base looping out increases monotonically as the pressure is increased. Furthermore, we calculate the mean first-passage time of conformational looping out of the bulge base using the diffusion of reaction coordinate associated with the base flipping on the underlying free energy surface. We find that the mean first-passage time associated with bulge looping out increases slowly upon increasing pressures up to atm but changes dramatically for atm. Finally, we discuss our results in the light of the role of hydration shell of water around RNA. Our results are relevant for the RNA world hypothesis.

References

[1]  Verlander MS (1973) The RNA world. J Mol Evol 2: 303–316.
[2]  Cech TR (1987) The chemistry of self-splicing RNA and RNA enzymes. Science 236: 1532–1539.
[3]  Wyatt JR, Puglisi JD, Tinoco I (1989) RNA folding: pseudoknots, loops and bulges. BioEssays 11: 100–106.
[4]  Hermann T, Patel DJ (2000) RNA bulges as architectural and recognition motifs. Structure 8: R47–R54.
[5]  Lustig B, Bahar I, Jernigan RL (1998) RNA bulge entropies are correlated with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access. Nucelic Acids Research 26: 5212–5217.
[6]  Patel DJ, Kozlowski SA, Marky LA, Rice JA, Broka L, et al. (1982) Extra adenosine stacks into the self-complementary d() duplex in solution. J Biochemistry 21: 445–451.
[7]  Woodson SA, Crothers DM (1989) DNA bending by the bulge defect. Bichemistry 28: 4512–4516.
[8]  Gilbert W (1986) The RNA world. Nature 309: 618.
[9]  Illangasekare M, Kovalchuke O, Yarus M (1999) A tiny RNA that catalyses both aminoacyl-RNA and peptidyl-RNA synthesis. RNA 5: 1482–1489.
[10]  Lehmann J, Reichel A, Buguin A, Libchaber A (2007) Efficiency of a self-aminoacylating ribozyme: Effect of the length and base-composition of its 3′ extension. RNA 13: 1191–1197.
[11]  Baross JA, Hoffmann SE (1985) Submarine hydrothermal vents and associated gradient environ-ments as sites for the origin and evolution of life. Orig Life Evol Biosph 15: 327–345.
[12]  Martin W, Baross J, Russell MJ (2008) Hydrothermal vents and the origin of life. Nat Rev Microbio 6: 805–814.
[13]  Barthel A, Zacharias M (2006) Conformational Transitions in RNA Single Uridine and Adenosine Bulge Structures: A Molecular Dynamics Free Energy Simulation Study. Biophys J 90: 2450–2462.
[14]  Feig M, Zacharias M, Pettitt BM (2001) Conformation of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations. Biophys J 81: 352–370.
[15]  Auffinger P, Hashem Y (2007) Nucleic acid solvation: from outside to insight. Current Opinion in Structural Biology 17: 325–333.
[16]  Tanford C (1980) The Hydrophobic Effect: Formation ofMicelles and BiologicalMembranes. Wiley, New York, second edition.
[17]  Dill KA (1990) Dominant forces in protein folding. Biochemistry 29: 7133–7155.
[18]  Lum K, Chandler D, Weeks J (1999) Hydrophobicity at small and large length scales. J Phys Chem B 103: 4570–4577.
[19]  Ashbaugh HS, Truskett TM, Debenedetti PG (2002) A simple molecular thermodynamic theory of hydrophobic hydration. J Chem Phys 116: 2907–2921.
[20]  Hummer G, Garde S, Garcia AE, Phorille A, Pratt LR (1996) An information theory model of hydrophobic interactions. Proc Nat Acad Sci USA 93: 8951–8955.
[21]  Widom B, Bhimalapuram P, Koga K (2003) The hydrophobic effect. Phys Chem Chem Phys 5: 3085–3093.
[22]  Buldyrev SV, Pradeep Kumar, Debenedetti PG, Rossky PJ, Stanley HE (2007) Water-like salvation thermodynamics in a spherically symmetric solvent model with two characteristic lengths. Proc Nat Acad Sci USA 104: 20177–20182.
[23]  Berendsen HJC, Van Der Spoel D, Drunen R van (1995) Gromacs: A message-passing parallel molecular dynamics implementation. Comp Phys Comm 91: 43–56.
[24]  Lindahl E, Hess B, Spoel D van der (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis. J Mol Mod 7: 306–317.
[25]  Case DA, Cheatham T, Darden T, Gohlke H, Luo R, et al. (2005) The Amber biomolecular simu-lation programs. J Computat Chem 26: 1668–1688.
[26]  Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Computat Chem 26: 1781–1802.
[27]  Kumar S, Rosenberg JM, Djamal Bouzida, Swendsen RH, Kollman PA (1992) The weighted his-togram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem 13: 1011–1021.
[28]  Van Kampen NG (1981) Stochastic Processes in Physics and Chemistry. North-Holland Personal Library, third edition.
[29]  Gardiner C (2009) Stochastic Methods. Springer.
[30]  Chau PL, Hardwick AJ (1998) A new order parameter for tetrahedral configurations. Mol Phys 93: 511–518.
[31]  Errington JR, Debenedetti PG (2001) Relationship between structural order and the anomalies of liquid water. Nature 9: 318–321.
[32]  Pradeep Kumar, Buldyrev SV, Stanley HE (2009) A tetrahedral entropy for water. Proc Nat Acad Sci USA 106: 22130–22134.
[33]  Franks F (1972–1982) Water: A comprehensive Treatise., volume 1–7. New York Plenum.
[34]  Debenedetti PG, Stanley HE (2003) Supercooled and Glassy Water. Physics Today 56: 40–46.
[35]  Maeda YT, Buguin A, Libchaber A (2011) Thermal separation: interplay between the Soret effect and entropic force gradient. Phys Rev Lett 107: 0338301.
[36]  Kumar Pradeep (2010) Dynamics of 2D Monolayer Confined Water in Hydrophobic and Charged Environments. Cond-Mat Arxiv Available: http://arxivorg/abs/10052380, Accessed 2010 May 13

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