Deprotonation of Tyrosine 164 in Lytic polysaccharide monooxygenase (LPMO) intermediates
(2019) KEMK08 20191Department of Chemistry
- Abstract
- In this thesis the enzyme Lytic polysaccharide monooxygenase (LPMO) is investigated. The LPMOs have captured the interest of the biofuel industry due to their ability to boost the breakdown of cellulose. Researchers have progressed in mapping out the mechanism behind this oxidative reaction. However, there are still many uncertainties concerning the intermediates involved and the role of certain amino acids close to the LPMO active site. In this thesis we investigate the formation of three intermediates formed by deprotonation of the tyrosine (Tyr164), denoted [CuOH-TyrO]^(+), (1b), [CuOH_2-TyrO]^(2+), (2b), and [CuOH_2-TyrO]^(+), (3b), to test weather these intermediates are energetically and structurally feasible.Tyr164 is located close... (More)
- In this thesis the enzyme Lytic polysaccharide monooxygenase (LPMO) is investigated. The LPMOs have captured the interest of the biofuel industry due to their ability to boost the breakdown of cellulose. Researchers have progressed in mapping out the mechanism behind this oxidative reaction. However, there are still many uncertainties concerning the intermediates involved and the role of certain amino acids close to the LPMO active site. In this thesis we investigate the formation of three intermediates formed by deprotonation of the tyrosine (Tyr164), denoted [CuOH-TyrO]^(+), (1b), [CuOH_2-TyrO]^(2+), (2b), and [CuOH_2-TyrO]^(+), (3b), to test weather these intermediates are energetically and structurally feasible.Tyr164 is located close to the copper in the active site. It is uncertain What the role of this amino acid plays in the reaction mechanism. One suggestion is that Tyr164 is deprotonated. A combination of quantum and molecular mechanics (QM/MM) was used. We employed density functional theory (DFT) and also investigated the effect of different functionals on computed energies. Additionally UV-Vis spectra for [CuOH-TyrO]^(+) (1b) were calculated using time-dependent density functional theory (TD-DFT). We investigated how the calculated spectra depend on the size of the system specified, and how the calculated UV-Vis spectra compare to experimental observations of the same intermediate. A spin density analysis was also carried out to suggest possible oxidation states of the copper component of the intermediates. The thesis found that all investigated intermediates were energetically feasible. We also showed that the system size affected the calculated UV-Vis spectrum in that a variation could be seen, but the spectra were qualitatively the same. Analysis of the computed spectra showed good agreement with experimental observations. The results support that the hypothesis that all three intermediates examined are feasible in the deprotonation pathway of Tyr164 in LPMOs. Further investigation of the involvement of the deprotonation of Tyr164 is warranted. (Less)
- Popular Abstract (Swedish)
- I dagens samhälle är ett hållbart alternativ till fossiltbränsle högt efterfrågat. Biobränsle är ett alternativ, men om detta alternativ ska vara optimalt, måste det härstamma från ett billigt och lättillgängligt material, som t.ex. cellulosa. Cellulosa finns i bl.a. växtcellväggar och är uppbyggd av sockerenheter (glykos) i en väldigt stabil struktur vilket är en bra egenskap när den sitter i växtcellväggen. Dessvärre i vårt syfte att extrahera energi blir det lite svårare. Man har hittat att vissa bakterier och svampar har egenskapen att bryta ner cellolusa. Efter närmare undersökning visar det sig att de använder sig av enzymet \textit{Lytic polysaccharide monooxygenase (LPMO)}. Just hur detta enzymet gör och vad som får processen att... (More)
- I dagens samhälle är ett hållbart alternativ till fossiltbränsle högt efterfrågat. Biobränsle är ett alternativ, men om detta alternativ ska vara optimalt, måste det härstamma från ett billigt och lättillgängligt material, som t.ex. cellulosa. Cellulosa finns i bl.a. växtcellväggar och är uppbyggd av sockerenheter (glykos) i en väldigt stabil struktur vilket är en bra egenskap när den sitter i växtcellväggen. Dessvärre i vårt syfte att extrahera energi blir det lite svårare. Man har hittat att vissa bakterier och svampar har egenskapen att bryta ner cellolusa. Efter närmare undersökning visar det sig att de använder sig av enzymet \textit{Lytic polysaccharide monooxygenase (LPMO)}. Just hur detta enzymet gör och vad som får processen att fungera undersöks noggrannare. För att kunna härma denna process på bästa sätt på en industriell skala krävs det att man vet mer om hela reaktionen. I denna uppsatsen kommer möjliga strukturer av enzymet att undersökas och för att se om dessa bidrar till enzymets funktion. I enzymets aktiva säte finns aminosyroran tyrosin (Tyr164). Närmare bestämt kommer denna tyrosinens (Tyr164) roll i reaktionen att undersökas. Kvantmekaniska beräkningar utfördes för att erhålla enzymets struktur samt energin på enzymet. Energin agerar som en indikator på om de föreslagna intermediated är 1. trolig att existera, 2. möjlig att bildas. Ytterligare försöktes ett oxidationstillstånd för koppar jonen i aktiva sätet att identifieras, även ett UV-Vis spektra replikerande experimentella spektra beräknades. Energiberäkningarna som utfördes visade att de investigerade strukturerna skulle kunna existera. Det beräknade UV-Vis spektrat visade även resultat liknande de som erhållits från experimentella mätningar. Dessa observationer stödjer att vidare undersökning av tyrosinens roll i reaktionen kan vara av intresse. (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/8988710
- author
- Mc Evoy, Aina LU
- supervisor
- organization
- course
- KEMK08 20191
- year
- 2019
- type
- M2 - Bachelor Degree
- subject
- keywords
- Theoretical chemistry, Teoretisk kemi, QM/MM, LPMO
- language
- English
- id
- 8988710
- date added to LUP
- 2019-07-04 16:25:52
- date last changed
- 2019-07-04 16:25:52
@misc{8988710,
abstract = {{In this thesis the enzyme Lytic polysaccharide monooxygenase (LPMO) is investigated. The LPMOs have captured the interest of the biofuel industry due to their ability to boost the breakdown of cellulose. Researchers have progressed in mapping out the mechanism behind this oxidative reaction. However, there are still many uncertainties concerning the intermediates involved and the role of certain amino acids close to the LPMO active site. In this thesis we investigate the formation of three intermediates formed by deprotonation of the tyrosine (Tyr164), denoted [CuOH-TyrO]^(+), (1b), [CuOH_2-TyrO]^(2+), (2b), and [CuOH_2-TyrO]^(+), (3b), to test weather these intermediates are energetically and structurally feasible.Tyr164 is located close to the copper in the active site. It is uncertain What the role of this amino acid plays in the reaction mechanism. One suggestion is that Tyr164 is deprotonated. A combination of quantum and molecular mechanics (QM/MM) was used. We employed density functional theory (DFT) and also investigated the effect of different functionals on computed energies. Additionally UV-Vis spectra for [CuOH-TyrO]^(+) (1b) were calculated using time-dependent density functional theory (TD-DFT). We investigated how the calculated spectra depend on the size of the system specified, and how the calculated UV-Vis spectra compare to experimental observations of the same intermediate. A spin density analysis was also carried out to suggest possible oxidation states of the copper component of the intermediates. The thesis found that all investigated intermediates were energetically feasible. We also showed that the system size affected the calculated UV-Vis spectrum in that a variation could be seen, but the spectra were qualitatively the same. Analysis of the computed spectra showed good agreement with experimental observations. The results support that the hypothesis that all three intermediates examined are feasible in the deprotonation pathway of Tyr164 in LPMOs. Further investigation of the involvement of the deprotonation of Tyr164 is warranted.}},
author = {{Mc Evoy, Aina}},
language = {{eng}},
note = {{Student Paper}},
title = {{Deprotonation of Tyrosine 164 in Lytic polysaccharide monooxygenase (LPMO) intermediates}},
year = {{2019}},
}