scholarly journals Ground-State Destabilization Controls the Selectivity of a Cofactor-Free Decarboxylase

2020 ◽  
Author(s):  
Michal Biler ◽  
Anna K. Schweiger ◽  
Robert Kourist ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Ground State ◽  
Valence Bond ◽  
Optical Purity ◽  
Interaction Network ◽  
Enzyme Engineering ◽  
Molecular Processes ◽  
Solvent Exposure ◽  
Empirical Valence Bond ◽  
High Optical Purity ◽  
Insight Into

<div> <div> <div> <p>Bacterial arylmalonate decarboxylase (AMDase) and evolved variants have become a valuable tool with which to access both enantiomers of a broad range of chiral arylaliphatic acids with high optical purity. Yet, the molecular principles responsible for the substrate scope, activity and selectivity of this enzyme are only poorly understood to this day, greatly hampering the predictability and design of improved enzyme variants for specific applications. In this work, empirical valence bond simulations were performed on wild-type AMDase and variants thereof, to obtain a better understanding of the underlying molecular processes determining reaction outcome. Our results clearly reproduce the experimentally observed substrate scope, and support a mechanism driven by ground-state destabilization of the carboxylate group being cleaved by the enzyme. In addition, our results indicate that, in the case of the non-converted or poorly-converted substrates studied in this work, increased solvent exposure of the active site upon binding of these substrates can disturb the vulnerable network of interactions responsible for facilitating the AMDase-catalyzed cleavage of CO2. Our results thus allow insight into the tight interaction network determining AMDase selectivity, which in turn provides guidance for the identification of target residues for future enzyme engineering. </p> </div> </div> </div>

scholarly journals Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor- Free Decarboxylase

2020 ◽  
Author(s):  
Michal Biler ◽  
Rory Crean ◽  
Anna K. Schweiger ◽  
Robert Kourist ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Ground State ◽  
Active Site ◽  
Valence Bond ◽  
Optical Purity ◽  
Interaction Network ◽  
Enzyme Engineering ◽  
Carboxylate Group ◽  
Solvent Exposure ◽  
Preferential Cleavage ◽  
High Optical Purity

<div> <div> <p> </p><div> <div> <div> <p>Bacterial arylmalonate decarboxylase (AMDase) and evolved variants have become a valuable tool with which to access both enantiomers of a broad range of chiral arylaliphatic acids with high optical purity. Yet, the molecular principles responsible for the substrate scope, activity and selectivity of this enzyme are only poorly understood to this day, greatly hampering the predictability and design of improved enzyme variants for specific applications. In this work, empirical valence bond and metadynamics simulations were performed on wild-type AMDase and variants thereof, to obtain a better understanding of the underlying molecular processes determining reaction outcome. Our results clearly reproduce the experimentally observed substrate scope, and support a mechanism driven by ground-state destabilization of the carboxylate group being cleaved by the enzyme. In addition, our results indicate that, in the case of the non-converted or poorly-converted substrates studied in this work, increased solvent exposure of the active site upon binding of these substrates can disturb the vulnerable network of interactions responsible for facilitating the AMDase-catalyzed cleavage of CO2. Finally, our results indicate a switch from preferential cleavage of the pro-(R) to the pro-(S) carboxylate group in the CLG-IPL variant of AMDase for all substrates studied. This appears to be due to the emergence of a new hydrophobic pocket generated by the insertion of the six amino acid substitutions, into which the pro-(S) carboxylate binds. Our results allow insight into the tight interaction network determining AMDase selectivity, which in turn provides guidance for the identification of target residues for future enzyme engineering. </p> </div> </div> </div> </div> </div>

scholarly journals Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor- Free Decarboxylase

2020 ◽  
Author(s):  
Michal Biler ◽  
Rory Crean ◽  
Anna K. Schweiger ◽  
Robert Kourist ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Ground State ◽  
Active Site ◽  
Valence Bond ◽  
Optical Purity ◽  
Interaction Network ◽  
Enzyme Engineering ◽  
Carboxylate Group ◽  
Solvent Exposure ◽  
Preferential Cleavage ◽  
High Optical Purity

<div> <div> <p> </p><div> <div> <div> <p>Bacterial arylmalonate decarboxylase (AMDase) and evolved variants have become a valuable tool with which to access both enantiomers of a broad range of chiral arylaliphatic acids with high optical purity. Yet, the molecular principles responsible for the substrate scope, activity and selectivity of this enzyme are only poorly understood to this day, greatly hampering the predictability and design of improved enzyme variants for specific applications. In this work, empirical valence bond and metadynamics simulations were performed on wild-type AMDase and variants thereof, to obtain a better understanding of the underlying molecular processes determining reaction outcome. Our results clearly reproduce the experimentally observed substrate scope, and support a mechanism driven by ground-state destabilization of the carboxylate group being cleaved by the enzyme. In addition, our results indicate that, in the case of the non-converted or poorly-converted substrates studied in this work, increased solvent exposure of the active site upon binding of these substrates can disturb the vulnerable network of interactions responsible for facilitating the AMDase-catalyzed cleavage of CO2. Finally, our results indicate a switch from preferential cleavage of the pro-(R) to the pro-(S) carboxylate group in the CLG-IPL variant of AMDase for all substrates studied. This appears to be due to the emergence of a new hydrophobic pocket generated by the insertion of the six amino acid substitutions, into which the pro-(S) carboxylate binds. Our results allow insight into the tight interaction network determining AMDase selectivity, which in turn provides guidance for the identification of target residues for future enzyme engineering. </p> </div> </div> </div> </div> </div>

scholarly journals Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor- Free Decarboxylase

2020 ◽  
Author(s):  
Michal Biler ◽  
Rory Crean ◽  
Anna K. Schweiger ◽  
Robert Kourist ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Ground State ◽  
Active Site ◽  
Valence Bond ◽  
Optical Purity ◽  
Interaction Network ◽  
Enzyme Engineering ◽  
Carboxylate Group ◽  
Solvent Exposure ◽  
Preferential Cleavage ◽  
High Optical Purity

<div> <div> <p> </p><div> <div> <div> <p>Bacterial arylmalonate decarboxylase (AMDase) and evolved variants have become a valuable tool with which to access both enantiomers of a broad range of chiral arylaliphatic acids with high optical purity. Yet, the molecular principles responsible for the substrate scope, activity and selectivity of this enzyme are only poorly understood to this day, greatly hampering the predictability and design of improved enzyme variants for specific applications. In this work, empirical valence bond and metadynamics simulations were performed on wild-type AMDase and variants thereof, to obtain a better understanding of the underlying molecular processes determining reaction outcome. Our results clearly reproduce the experimentally observed substrate scope, and support a mechanism driven by ground-state destabilization of the carboxylate group being cleaved by the enzyme. In addition, our results indicate that, in the case of the non-converted or poorly-converted substrates studied in this work, increased solvent exposure of the active site upon binding of these substrates can disturb the vulnerable network of interactions responsible for facilitating the AMDase-catalyzed cleavage of CO2. Finally, our results indicate a switch from preferential cleavage of the pro-(R) to the pro-(S) carboxylate group in the CLG-IPL variant of AMDase for all substrates studied. This appears to be due to the emergence of a new hydrophobic pocket generated by the insertion of the six amino acid substitutions, into which the pro-(S) carboxylate binds. Our results allow insight into the tight interaction network determining AMDase selectivity, which in turn provides guidance for the identification of target residues for future enzyme engineering. </p> </div> </div> </div> </div> </div>

The Atomic Exciton Model for the Excited States of p-Electron Systems

1985 ◽  
Vol 38 (10) ◽  
pp. 1529
Author(s):  
PE Schipper
Keyword(s):  
Excited States ◽  
Ground State ◽  
Valence Bond ◽  
Essential Difference ◽  
Electron Systems ◽  
Exciton Model ◽  
Valence Bond Theory ◽  
Bond Theory ◽  
Atomic Excitations ◽  
Insight Into

A new model is presented to describe the π-π* excitations of π-electron systems in terms of intra-atomic excitations. The atomic exciton model combines features of conventional exciton and valence bond theory, reducing to the former in the non-exchanging limit, and the latter in the ground-state limit with covalent structures. The model is ideally suited to the approximate or exact incorporation of exchange, and highlights the opposition of excitation and electron interchange in determining the energetics of the excitation manifold, eliciting thereby the essential difference between ground and excited states. Applications to some simple π-systems are considered, providing new insight into their excited states.

scholarly journals Epoxide hydrolysis as a model system for understanding flux through a branched reaction scheme

IUCrJ ◽  
2018 ◽  
Vol 5 (3) ◽  
pp. 269-282 ◽  
Author(s):  
Åsa Janfalk Carlsson ◽  
Paul Bauer ◽  
Doreen Dobritzsch ◽  
Shina C. L. Kamerlin ◽  
Mikael Widersten
Keyword(s):  
Steady State ◽  
Valence Bond ◽  
Reaction Scheme ◽  
Epoxide Ring ◽  
Empirical Valence Bond ◽  
Catalyzed Reactions ◽  
Hydrolysis Of ◽  
Insight Into ◽  
Enzyme Intermediate ◽  
Combined Data

The epoxide hydrolase StEH1 catalyzes the hydrolysis oftrans-methylstyrene oxide to 1-phenylpropane-1,2-diol. The (S,S)-epoxide is exclusively transformed into the (1R,2S)-diol, while hydrolysis of the (R,R)-epoxide results in a mixture of product enantiomers. In order to understand the differences in the stereoconfigurations of the products, the reactions were studied kinetically during both the pre-steady-state and steady-state phases. A number of closely related StEH1 variants were analyzed in parallel, and the results were rationalized by structure–activity analysis using the available crystal structures of all tested enzyme variants. Finally, empirical valence-bond simulations were performed in order to provide additional insight into the observed kinetic behaviour and ratios of the diol product enantiomers. These combined data allow us to present a model for the flux through the catalyzed reactions. With the (R,R)-epoxide, ring opening may occur at either C atom and with similar energy barriers for hydrolysis, resulting in a mixture of diol enantiomer products. However, with the (S,S)-epoxide, although either epoxide C atom may react to form the covalent enzyme intermediate, only thepro-(R,S) alkylenzyme is amenable to subsequent hydrolysis. Previously contradictory observations from kinetics experiments as well as product ratios can therefore now be explained for this biocatalytically relevant enzyme.

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