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QM/MM study of the ...
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Caldararu, OctavLund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH
(author)
QM/MM study of the reaction mechanism of sulfite oxidase
- Article/chapterEnglish2018
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2018-03-16
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Springer Science and Business Media LLC,2018
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LIBRIS-ID:oai:lup.lub.lu.se:7e77d999-7309-45b6-adcd-7c2275fb93f5
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https://lup.lub.lu.se/record/7e77d999-7309-45b6-adcd-7c2275fb93f5URI
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https://doi.org/10.1038/s41598-018-22751-6DOI
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Language:English
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Summary in:English
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Subject category:art swepub-publicationtype
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Subject category:ref swepub-contenttype
Notes
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Sulfite oxidase is a mononuclear molybdenum enzyme that oxidises sulfite to sulfate in many organisms, including man. Three different reaction mechanisms have been suggested, based on experimental and computational studies. Here, we study all three with combined quantum mechanical (QM) and molecular mechanical (QM/MM) methods, including calculations with large basis sets, very large QM regions (803 atoms) and QM/MM free-energy perturbations. Our results show that the enzyme is set up to follow a mechanism in which the sulfur atom of the sulfite substrate reacts directly with the equatorial oxo ligand of the Mo ion, forming a Mo-bound sulfate product, which dissociates in the second step. The first step is rate limiting, with a barrier of 39-49 kJ/mol. The low barrier is obtained by an intricate hydrogen-bond network around the substrate, which is preserved during the reaction. This network favours the deprotonated substrate and disfavours the other two reaction mechanisms. We have studied the reaction with both an oxidised and a reduced form of the molybdopterin ligand and quantum-refinement calculations indicate that it is in the normal reduced tetrahydro form in this protein.
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Feldt, MilicaUniversity of Göttingen
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Cioloboc, DanielaLund University
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Van Severen, Marie CélineLund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH(Swepub:lu)teok-mvr
(author)
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Starke, KerstinLund University,Lunds universitet,Kemisk fysik,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Chemical Physics,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH(Swepub:lu)chem-kis
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Mata, Ricardo A.University of Göttingen
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Nordlander, EbbeLund University,Lunds universitet,Kemisk fysik,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Chemical Physics,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH(Swepub:lu)ook1-eno
(author)
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Ryde, UlfLund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH(Swepub:lu)teok-ury
(author)
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BeräkningskemiEnheten för fysikalisk och teoretisk kemi
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In:Scientific Reports: Springer Science and Business Media LLC8:12045-2322
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