A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

T, Lee; Radak, Brian K.; Pabis, Anna; York, Darrin M.

doi:10.1021/ct300703z

Cited by 99 publications

(152 citation statements)

References 84 publications

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“…One additional window at 3.75 Å was needed for the G33N1 − profile to improve sampling at the top of the barrier between the "Stacked" and "Triple" states. The free energy profiles were built using vFEP 38 and are presented in Figure 4. In order to estimate the statistical error of these calculations, 100 random subsamples of 10% of the data were collected.…”

Section: Methodsmentioning

confidence: 99%

Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation

Gaines

York

2016

J. Am. Chem. Soc.

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We present results from molecular dynamics simulations and free energy calculations of the twister ribozyme at different stages along the reaction path in order to gain insight into its mechanism. Results, together with recent biochemical experiments, provide support for a mechanism involving general acid catalysis by a conserved adenine residue in the active site. Although adenine has been previously implicated as a general acid acting through the N1 position in other ribozymes such as the hairpin and VS ribozymes, in the twister ribozyme there may be - a twist. Biochemical experiments suggest that general acid catalysis may occur through the N3 position, which has never before been implicated in this role; however, there currently lacks a detailed structural model for the active state of the twister ribozyme in solution that is consistent with these and other experiments. Simulations in a crystalline environment reported here are consistent with X-ray crystallographic data, and suggest that crystal packing contacts trap the RNA in an inactive conformation with U-1 in an extruded state that is incompatible with an in-line attack to the scissile phosphate. Simulations in solution, on the other hand, reveal this region to be dynamic and able to adopt a conformation where U-1 is stacked with G33. In this state, the nucleophile is in line with the scissile phosphate, and the N1 position of G33 and N3 position of A1 are poised to act as general base and acid, respectively, as supported by mutational experiments. Free energy calculations further predict the electrostatic environment causes a shift of the microscopic pKa at the N3 position of A1 toward neutrality by approximately 5 pKa units. These results offer a unified interpretation of a broad range of currently available experimental data that points to a novel mode of general acid catalysis through the N3 position of an adenine nucleobase, thus expanding the repertoire of known mechanistic strategies employed by small nucleolytic ribozymes.

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Section: Methodsmentioning

confidence: 99%

Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation

Gaines

York

2016

J. Am. Chem. Soc.

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“…Generation of free 140 energy profiles from umbrella sampling simulations was achieved using vFEP. 4 …”

Section: Supplementary Methods 2 MD Additional Details 135mentioning

confidence: 99%

Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA

et al. 2016

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While DNA is mostly a primary carrier of genetic information and displays a regular duplex structure, RNA can form very complicated and conserved 3D structures displaying a large variety of functions, such as being an intermediary carrier of the genetic information, translating such information into the protein machinery of the cell, or even acting as a chemical catalyst. At the base of such functional diversity is the subtle balance between different backbone, nucleobase, and ribose conformations, finely regulated by the combination of hydrogen bonds and stacking interactions. Although an apparently simple chemical modification, the presence of the 2'OH in RNA has a profound effect in the ribonucleotide conformational balance, adding an extra layer of complexity to the interactions network in RNA. In the present work, we have combined database analysis with extensive molecular dynamics, quantum mechanics, and hybrid QM/MM simulations to provide direct evidence on the dramatic impact of the 2'OH conformation on sugar puckering. Calculations provide evidence that proteins can modulate the 2'OH conformation to drive sugar repuckering, leading then to the formation of bioactive conformations. In summary, the 2'OH group seems to be a primary molecular switch contributing to specific protein-RNA recognition.

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“…QM treatments range from computationally economical semi-empirical approaches [31] to more accurate and computationally expensive density functional and ab inito methods [32]. Development of both fast and accurate multi-scale methods has great potential to facilitate analysis of free energy surfaces for rigorous comparison with experimental measurements and for identification of alternative mechanisms of RNA transphosphorylation [33,34]. …”

Section: Transition States Of Solution Rna 2′-o-transphosphorylationmentioning

confidence: 99%

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2′-O-transphosphorylation

Kellerman

York

Piccirilli

et al. 2014

Current Opinion in Chemical Biology

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Although there have been great strides in defining the mechanisms of RNA strand cleavage by 2′-O-transphosphorylation, long-standing questions remain. How do different catalytic modes such as acid/base and metal ion catalysis influence transition state charge distribution? Does the large rate enhancement characteristic of biological catalysis result in different transition states relative to solution reactions? Answering these questions is important for understanding biological catalysis in general, and revealing principles for designing small molecule inhibitors. Recent application of linear free energy relationships and kinetic isotope effects together with multi-scale computational simulations are providing tentative answers to these questions for this fundamentally important class of phosphoryl transfer reactions.

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A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

Cited by 99 publications

References 84 publications

Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation

Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation

Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2′-O-transphosphorylation

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