Accurate Proton Affinity and Gas-Phase Basicity Values for Molecules Important in Biocatalysis

Moser, Adam; Range, Kevin; York, Darrin M.

doi:10.1021/jp107450n

Cited by 141 publications

(168 citation statements)

References 109 publications

(193 reference statements)

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“…If this is set equal to −145.7−(0 to 3.1) + E b (GluH) − E b (H3O), we obtain E b (GluH)= 316 to 319 kcal/mol. For comparison, the gas phase proton affinity of Glu is 347.2 kcal/mol 65 .…”

Section: Resultsmentioning

confidence: 99%

Classical Molecular Dynamics with Mobile Protons

Lazaridis

Hummer

2017

J. Chem. Inf. Model.

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An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton diffusion in bulk water and carbon nanotubes, and on proton conductance in the gramicidin A channel. Using hopping parameters determined from proton diffusion in bulk water, the model reproduces the enhanced proton diffusivity in carbon nanotubes and gives a reasonable estimate of the proton conductance in gramicidin A.

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Section: Resultsmentioning

confidence: 99%

Classical Molecular Dynamics with Mobile Protons

Lazaridis

Hummer

2017

J. Chem. Inf. Model.

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“…[27][28][29][30][31][32] For analytes with lower proton a nity, such as carbohydrates, the ionization e ciency drops by a few orders of magnitude to 10 −7 -10 −8 . 23,33,34) A better understanding of mechanisms leads to improvements in the ionization e ciency and increases its e ectiveness toward more elds.…”

Section: Ion Production In Maldimentioning

confidence: 99%

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry: Mechanistic Studies and Methods for Improving the Structural Identification of Carbohydrates

Lai

Wang

2017

Mass Spectrometry

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Although matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is one of the most widely used so ionization methods for biomolecules, the lack of detailed understanding of ionization mechanisms restricts its application in the analysis of carbohydrates. Structural identi cation of carbohydrates achieved by MALDI mass spectrometry helps us to gain insights into biological functions and pathogenesis of disease. In this review, we highlight mechanistic details of MALDI, including both ionization and desorption. Strategies to improve the ion yield of carbohydrates are also reviewed. Furthermore, commonly used fragmentation methods to identify the structure are discussed.

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“…As such, new fluorescent and Raman crystallographic approaches serve to pinpoint and quantify shifts in base p K a values, providing a greater understanding of how conformational changes fine-tune ionization for catalysis. These data provide benchmarks for calculations that require p K a values to simulate chemical mechanisms [45]. Additional efforts should look to the use of sulfur probes to assess the importance of leaving-group lability [46], which can shed light on the assignment of general acid catalysts [46,47].…”

Section: Conclusion and Future Prospectsmentioning

confidence: 99%

Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world

Liberman

Wedekind

2011

Current Opinion in Structural Biology

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Genome sequencing has produced thousands of non-protein coding (nc)RNA sequences including new ribozymes and riboswitches. Such RNAs are notable for their extraordinary functionality, which entails exquisite folding that culminates in biocatalytic or ligand-binding capabilities. Here we discuss advances in relating ncRNA form to function with an emphasis on base-pKa shifting by the hairpin and hepatitis delta virus ribozymes. We then describe ligand binding by the two smallest riboswitches, which target preQ1 and S-adenosyl-(L)-homocysteine, followed by an analysis of a second-messenger riboswitch that binds cyclic-di-GMP. Each riboswitch is then compared to a protein that binds the same ligand to contrast binding properties. The results showcase the breadth of functionality attainable from ncRNAs, as well as molecular features notable for antibacterial design.

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Accurate Proton Affinity and Gas-Phase Basicity Values for Molecules Important in Biocatalysis

Cited by 141 publications

References 109 publications

Classical Molecular Dynamics with Mobile Protons

Classical Molecular Dynamics with Mobile Protons

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry: Mechanistic Studies and Methods for Improving the Structural Identification of Carbohydrates

Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world

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