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Organic & Biomolecular Chemistry Vol -6

Organic & Biomolecular Chemistry Vol -5

Organic & Biomolecular Chemistry Vol -4

Organic & Biomolecular Chemistry Vol -3

Organic & Biomolecular Chemistry Vol -2

Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases

Content Provider	Royal Society of Chemistry (RSC)
Author	Williams, Ian H. Ruggiero, Giuseppe D. Pernía, J. Javier Ruiz Soliman, Mahmoud E. S. Greig, Ian R.
Copyright Year	2009
Abstract	Molecular dynamics simulations have been performed for non-covalent complexes of phenyl β-xylobioside with the retaining endo-β-1,4-xylanase from B. circulans (BCX) and its Tyr69Phe mutant using a hybrid QM/MM methodology. A trajectory initiated for the wild-type enzyme–substrate complex with the proximal xylose ring bound at the –1 subsite (adjacent to the scissile glycosidic bond) in the 4C1 chair conformation shows spontaneous transformation to the 2,5B boat conformation, and potential of mean force calculations indicate that the boat is ∼30 kJ mol−1 lower in free energy than the chair. Analogous simulations for the mutant lacking one oxygen atom confirm the key role of Tyr69 in stabilizing the boat in preference to the 4C1 chair conformation, with a relative free energy difference of about 20 kJ mol−1, by donating a hydrogen bond to the endocyclic oxygen of the proximal xylose ring. QM/MM MD simulations for phenyl β-xyloside in water, with and without a propionate/propionic acid pair to mimic the catalytic glutamate/glutamic acid pair of the enzyme, show the 4C1 chair to be stable, although a hydrogen bond between the OH group at C2 of xylose and the propionate moiety seems to provide some stabilization for the 2,5B conformation.
Starting Page	460
Ending Page	468
Page Count	9
File Format	HTM / HTML PDF
ISSN	14770520
Volume Number	7
Issue Number	3
Journal	Organic & Biomolecular Chemistry
DOI	10.1039/b814695k
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Glutamic acid Gibbs free energy Scissile bond Enzyme Molecular dynamics Propionate Phenyl group Xylose Glycosidic bond Xylanase Carboxylic acid Conformational isomerism Mutation Cyclohexane conformation Nucleophile Hydrogen bond
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Biochemistry Physical and Theoretical Chemistry

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