| 1. |
- Bauer, Paul, et al.
(författare)
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Q6 : A comprehensive toolkit for empirical valence bond and related free energy calculations
- 2018
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Ingår i: SoftwareX. - : Elsevier. - 2352-7110. ; 7, s. 388-395
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Tidskriftsartikel (refereegranskat)abstract
- Atomistic simulations have become one of the main approaches to study the chemistry and dynamicsof biomolecular systems in solution. Chemical modelling is a powerful way to understand biochemistry,with a number of different programs available to perform specialized calculations. We present here Q6, anew version of the Q software package, which is a generalized package for empirical valence bond, linearinteraction energy, and other free energy calculations. In addition to general technical improvements, Q6extends the reach of the EVB implementation to fast approximations of quantum effects, extended solventdescriptions and quick estimation of the contributions of individual residues to changes in the activationfree energy of reactions.
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| 2. |
- Hong, Nan-Sook, et al.
(författare)
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The evolution of multiple active site configurations in a designed enzyme
- 2018
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.
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| 3. |
- Purg, Miha, 1988-
(författare)
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Computational Modeling of the Mechanisms and Selectivity of Organophosphate Hydrolases
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Computational modeling is becoming an increasingly integral part of (bio)chemistry, providing a powerful complementary view into the dynamics, binding, and reactivity of biochemical systems. In particular, molecular simulations based on multiscale models are now regularly employed in studies of enzymatic reactions, offering invaluable mechanistic insight through the lens of molecular energy landscapes. In this thesis, I used the empirical valence bond (EVB) and related methods to study the mechanisms and selectivity of organophosphate hydrolases.Organophosphate hydrolases are a diverse class of enzymes capable of degrading some of the most toxic compounds known to mankind, including pesticides and chemical warfare agents. They are particularly interesting from a mechanistic and evolutionary point of view, having evolved the ability to catalyze the hydrolysis of compounds which were introduced to nature less than a century ago. Moreover, they show promise as effective organophosphate decontamination agents and a thorough understanding of their function is fundamental to the future design of efficient and selective biocatalysts. As organophosphate hydrolases are metal-dependent enzymes, a reliable metal model was a prerequisite to our simulations. First, I present the development of force-field independent parameters for several alkaline-earth and transition-metal ions described using the nonbonded cationic dummy model. The model was subsequently employed in EVB simulations to probe the origin of metal-ion activity and selectivity patterns observed in methyl parathion hydrolase (MPH) and to provide mechanistic insight into its paraoxonase and promiscuous arylesterase activities. I further set out to resolve open mechanistic questions surrounding diisopropyl fluorophosphatase (DFPase) by performing extensive simulations of two mechanistic pathways proposed in literature, including calculating the effects of mutations, temperature, and protonation states on the rate of hydrolysis. Using this knowledge, I address the origin of cross-selectivity between DFPase and a structurally similar enzyme serum paraoxonase 1 (PON1). Finally, I present the latest developments in the software used to perform the simulations.
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| 4. |
- Purg, Miha, et al.
(författare)
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Empirical Valence Bond Simulations of Organophosphate Hydrolysis : Theory and Practice
- 2018
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Ingår i: PHOSPHATASES. - : ELSEVIER ACADEMIC PRESS INC. - 9780128138816 ; , s. 3-51
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Bokkapitel (refereegranskat)abstract
- Recent years have seen an explosion of interest in understanding the mechanisms of phosphate ester hydrolysis in biological systems, using a range of computational approaches, each with different advantages and limitations. In this contribution, we present the empirical valence bond (EVB) approach as a powerful tool for modeling biochemical reactivity, using the example of organophosphate hydrolysis by diisopropyl fluorophosphatase as our model reaction. We walk the reader through the protocol for setting up and performing EVB simulations, as well as key technical considerations that need to be taken into account. Finally, we provide examples of the applications of the EVB approach to understanding different experimental observables.
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