Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment

Wong, Kin Yiu; Gu, Hong; Zhang, Shuming; Piccirilli, Joseph A.; Harris, Michael E.; York, Darrin M.

doi:10.1002/anie.201104147

Cited by 53 publications

(112 citation statements)

References 43 publications

(93 reference statements)

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“…Experiment and computation together indicate that RNase A stabilizes a product-like transition state that is very similar to the anionic solution mechanism catalyzed by specific base in solution[12, 34, 36, 60]. Nonetheless, the enzyme significantly alters leaving group bonding attributable to general acid catalysis from His119.…”

Section: Discussionmentioning

confidence: 98%

“…Computational studies of nucleophilic attack on diesters including cyclization reactions has consistently illustrated the potential for stepwise mechanism for RNA transphosphorylation with a transient monoanionic phosphorane intermediate[32–36]. Recently, density-functional calculations[33] were used to analyze a series of transphosphorylation models with different leaving groups to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state (Fig.…”

Section: Mechanisms and Transition States Of Solution Rna 2’-o-tramentioning

confidence: 99%

“…The substrate dinucleotide RNA molecule is selected in the first round of mass spectrometry, and the fragments of this parent ion resulting from inert gas collision are analyzed by a second round of mass spectrometry. The enhanced signal to noise allows the 16 O/ 18 O ratio to be measured with sufficient precision to allow mechanistic interpretations[12, 34, 36, 60]. The tandem MS/MS analysis of whole RNA molecules permits the KIE on the 2’O nucleophile to be measured, which is more difficult to obtain using the remote label approach.…”

Section: Evidence For Acid/base Catalytic Modes In the Active Sitementioning

confidence: 99%

See 2 more Smart Citations

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism

Harris

Piccirilli

York

2015

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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The well-studied mechanism of ribonuclease A is believed to involve concerted general acid–base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2’-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5’O-P bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5’O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2’O-P bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2’O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains.

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Section: Discussionmentioning

confidence: 98%

Section: Mechanisms and Transition States Of Solution Rna 2’-o-tramentioning

confidence: 99%

Section: Evidence For Acid/base Catalytic Modes In the Active Sitementioning

confidence: 99%

See 1 more Smart Citation

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism

Harris

Piccirilli

York

2015

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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“…Most importantly, KIEs are very sensitive to changes in transition state bonding environment, and ultimately encode information about the transition state that allows validation of predicted pathways that pass through it, which in turn provides insight into enzyme mechanism (Harris & Cassano, 2008; Lassila, Zalatan, & Herschlag, 2011). Nonetheless, a detailed interpretation of KIE data in terms of structure and bonding in the transition state requires the use of computational quantum mechanical models (Wong et al, 2012; H. Chen et al, 2014).…”

Section: Computing Kinetic Isotope Effects To Verify Transition Stamentioning

confidence: 99%

Multiscale Methods for Computational RNA Enzymology

Panteva

Dissanayake

Chen

et al. 2015

Methods in Enzymology

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RNA catalysis is of fundamental importance to biology and yet remains ill-understood due to its complex nature. The multi-dimensional “problem space” of RNA catalysis includes both local and global conformational rearrangements, changes in the ion atmosphere around nucleic acids and metal ion binding, dependence on potentially correlated protonation states of key residues and bond breaking/forming in the chemical steps of the reaction. The goal of this article is to summarize and apply multiscale modeling methods in an effort to target the different parts of the RNA catalysis problem space while also addressing the limitations and pitfalls of these methods. Classical molecular dynamics (MD) simulations, reference interaction site model (RISM) calculations, constant pH molecular dynamics (CpHMD) simulations, Hamiltonian replica exchange molecular dynamics (HREMD) and quantum mechanical/molecular mechanical (QM/MM) simulations will be discussed in the context of the study of RNA backbone cleavage transesterification. This reaction is catalyzed by both RNA and protein enzymes, and here we examine the different mechanistic strategies taken by the hepatitis delta virus ribozyme (HDVr) and RNase A.

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“…[26,27] Subsequently, additional approaches were introduced in the study of enzyme reactions, such as variational TST with the multidimensional tunneling approach of Truhlar and co-workers, [14,70] and wave function based methods of HammesSchiffer and co-workers. [71] Following in the footsteps of the Warshel group, we [29][30][31][32]34,72,73] and others [74][75][76][77][78] further developed the Feynman PI approach for enzyme simulations. PIs are particularly suitable for enzyme simulations because they are readily applicable to multidimensional systems and may be employed in mixed quantumÀclassical systems.…”

Section: The Feynman Path-integral Approach and The Qcpmentioning

confidence: 99%

Multiscale Quantum‐Classical Simulations of Enzymes

Doron¹,

Weitman²,

Vardi-Kilshtain³

et al. 2014

Israel Journal of Chemistry

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Enzymes are remarkably efficient catalysts evolved to perform well‐defined and highly specific chemical transformations. Studying the nature of enzymatic rate enhancements is highly important from several aspects, including the rational design of synthetic catalysts and transition‐state inhibitors. Herein, we describe recent progress in our group in the development of multiscale simulation methods and their application to several enzyme systems. In particular, we describe the use of combined quantum mechanics/molecular mechanics (QM/MM) methods in classical and quantum simulations. The development of various novel path‐integral methods is reviewed. These methods are tailor‐made for enzyme systems, where only a few degrees of freedom involved in the chemistry need to be quantized. The application of the hybrid QM/MM quantum‐classical simulation approach to three case studies is presented. The first case involves proton transfer in nitroalkane oxidase, where the enzyme employs tunneling as a catalytic fine‐tuning tool. The second case presented involves orotidine 5′‐monophosphate decarboxylase, where multidimensional free energy simulations together with kinetic isotope effects are combined in the study of the reaction mechanism. Finally, we discuss the monoterpene cyclase bornyl diphosphate synthase, where non‐statistical dynamics is a key component in enzyme function.

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Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment

Cited by 53 publications

References 43 publications

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism

Multiscale Methods for Computational RNA Enzymology

Multiscale Quantum‐Classical Simulations of Enzymes

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