| 1. |
- de Visser, Sam P., et al.
(författare)
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Computational modelling of oxygenation processes in enzymes and biomimetic model complexes
- 2014
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Ingår i: Chemical Communications. - 1364-548X. ; 50, s. 262-282
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Forskningsöversikt (refereegranskat)abstract
- With computational resources becoming more efficient and more powerful and at the same time cheaper, computational methods have become more and more popular for studies on biochemical and biomimetic systems. Although large efforts from the scientific community have gone into exploring the possibilities of computational methods on large biochemical systems, such studies are not without pitfalls and often cannot be routinely done but require expert execution. In this review we summarize and highlight advances in computational methodology and its application to enzymatic and biomimetic model systems. In particular, we emphasize on topical and state-of-the-art methodologies that are able to either reproduce experimental findings, e.g., spectroscopic parameters and rate constants, accurately or give predictions on short-lived intermediates and fast reaction processes in nature. Moreover, we give examples of processes where certain computational methods dramatically fail.
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| 2. |
- Groenhof, Gerrit, et al.
(författare)
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Photoactivation of the photoactive yellow protein : why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein.
- 2004
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 126:13, s. 4228-4233
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Tidskriftsartikel (refereegranskat)abstract
- Atomistic QM/MM simulations have been carried out on the complete photocycle of Photoactive Yellow Protein, a bacterial photoreceptor, in which blue light triggers isomerization of a covalently bound chromophore. The "chemical role" of the protein cavity in the control of the photoisomerization step has been elucidated. Isomerization is facilitated due to preferential electrostatic stabilization of the chromophore's excited state by the guanidium group of Arg52, located just above the negatively charged chromophore ring. In vacuo isomerization does not occur. Isomerization of the double bond is enhanced relative to isomerization of a single bond due to the steric interactions between the phenyl ring of the chromophore and the side chains of Arg52 and Phe62. In the isomerized configuration (ground-state cis), a proton transfer from Glu46 to the chromophore is far more probable than in the initial configuration (ground-state trans). It is this proton transfer that initiates the conformational changes within the protein, which are believed to lead to signaling.
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| 3. |
- Himo, Fahmi, et al.
(författare)
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Status report on the quantum chemical cluster approach for modeling enzyme reactions
- 2022
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Ingår i: Communications Chemistry. - : Springer Science and Business Media LLC. - 2399-3669. ; 5
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The cluster approach is a very valuable technique for elucidating reaction mechanisms of enzymes. Here, the authors discuss the current status of this methodology, highlighting its strengths and weaknesses, and argue that it should be the method of choice for investigating enzymatic reaction mechanisms.
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