Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 89

121. Roychowdhury-Saha M, Burke DH. Distinct reaction pathway promoted by non-
divalent-metal cations in a tertiary stabilized hammerhead ribozyme. RNA .2007;
13:841-848.
122. Ward WL, DeRose VJ. Ground-state coordination of a catalytic metal to the scissile
phosphate of a tertiary-stabilized hammerhead ribozyme. RNA . 2012;18:16-23.
123. Imhof P, No´ F, Fischer S, Smith JC. AM1/d Parameters for magnesium in

metalloenzymes. J Chem Theory Comput. 2006;2:1050-1056.
124. Perez A, Marchan I, Svozil D, et al. Refinement of the AMBER force field for nucleic
acids: improving the description of a / g conformers. Biophys J. 2007;92:3817-3829.
125. Horn HW, Swope WC, Pitera JW, et al. Development of an improved four-site water
model for biomolecular simulations: TIP4P-Ew. J Chem Phys. 2004;120:9665-9678.
126. Joung IS, Cheatham III TE. Determination of alkali and halide monovalent ion param-
eters for use in explicitly solvated biomolecular simulations. J Phys Chem B .

2008;112:9020-9041.
127. Torrie GM, Valleau JP. Nonphysical sampling distributions in Monte Carlo free-
energy estimation: Umbrella sampling. J Comput Phys. 1977;23:187-199.
128. Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM. The weighted his-
togram analysis method for free-energy calculations on biomolecules. I. The method.
J Comput Chem. 1992;13:1011-1021.
129. Roux B. The calculation of the potential of mean force using computer simulations.
Comput Phys Commun. 1995;91:275-282.
130. Murray JB, Seyhan AA, Walter NG, Burke JM, Scott WG. The hammerhead, hairpin
and VS ribozymes are catalytically proficient in monovalent cations alone. Chem Biol.
1998;5:587-595.
131. O'Rear JL, Wang S, Feig AL, Beigelman L, Uhlenbeck OC, Herschlag D. Comparison
of the hammerhead cleavage reactions stimulated by monovalent and divalent cations.
RNA . 2001;7:537-545.
132. Curtis EA, Bartel DP. The hammerhead cleavage reaction in monovalent cations.
RNA . 2001;7:546-552.
133. Lee T-S, Giamba¸u GM, Sosa CP, Martick M, Scott WG, York DM. Threshold occu-
pancy and specific cation binding modes in the hammerhead ribozyme active site are
required for active conformation. J Mol Biol. 2009;388:195-206.
134. Schnabl J, Sigel RK. Controlling ribozyme activity by metal ions. Curr Opin Chem Biol.
2010;14:269-275.
135. Torres RA, Bruice TC. Molecular dynamics study displays near in-line attack confor-
mations in the hammerhead ribozyme self-cleavage reaction. Proc Natl Acad Sci USA.
1998;95:11077-11082.
136. MacQueen J. Some methods for classification and analysis of multivariate observations.
In: Le Cam LM, Neyman J, eds. Proceedings of the 5th Berkeley Symposium on Mathematical
Statistics and Probability , Vol. 1. Berkeley, CA: University of California Press;
1967:281-297.
137. Davis JH, Foster TR, Tonelli M, Butcher SE. Role of metal ions in the tetraloop-
receptor complex as analyzed by NMR. RNA . 2007;13:76-86.
138. Vogt M, Lahiri S, Hoogstraten CG, Britt DR, DeRose VJ. Coordination environment
of a site-bound metal ion in the hammerhead ribozyme determined by 15N and 2H
ESEEM spectroscopy. J Am Chem Soc. 2006;128:16764-16770.
139. Burke DH, Greathouse ST. Low-magnesium, trans-cleavage activity by type III, ter-
tiary stabilized hammerhead ribozymes with stem 1 discontinuities. BMC Biochem.
2005;6:14.
140. Persson TK, Hartmann R, Eckstein F. Selection of hammerhead ribozyme variants
with low Mg 2 þ requirement: importance of stem-loop II. Chembiochem . 2002;

3:1066-1071.