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Peptide Folding: When Simulation Meets Experiment
Mol. dynamics simulation studies on the folding of beta-peptides H-beta3-HVal-beta3-HAla-beta3-HLeu-(S,S)-beta3-HAla(alphaMe)-beta3-HVal-beta3-HAla-beta3-HLeu-OH and
The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane
TLDR
Purified MCR from Methanothermobacter marburgensis converts methane into methyl-coenzyme M under equilibrium conditions with apparent Vmax and Km values consistent with the observed in vivo kinetics of the anaerobic oxidation of methane with sulphate, which supports the hypothesis of ‘reverse methanogenesis’.
Reversible peptide folding in solution by molecular dynamics simulation.
TLDR
Long-standing questions on how peptides fold are addressed by the simulation at different temperatures of the reversible folding of a peptide in solution in atomic detail, implying that the search problem in peptide (or even protein) folding is surmountable using dynamics simulations.
Structure of an F430 variant from archaea associated with anaerobic oxidation of methane.
TLDR
Equilibration of the pentaacids under acid catalysis showed that the more stable (17(2)R) isomer is the naturally occurring albeit thermodynamically less stable one and is an isolation artifact generated under the acidic conditions necessary for the isolation of the cofactors from the calcium carbonate-encrusted mats.
The structure of a TNA-TNA complex in solution: NMR study of the octamer duplex derived from alpha-(L)-threofuranosyl-(3'-2')-CGAATTCG.
TLDR
Using NMR spectroscopy, the structure of a duplex consisting entirely of TNA nucleotides is determined and the helix parameters, in particular the slide and x-displacement, place the TNA duplex in the structural vicinity of A-type DNA and RNA.
Methylation of the nucleobases in RNA oligonucleotides mediates duplex-hairpin conversion.
TLDR
It can be concluded that nucleobase methylations at the Watson-Crick base pairing site provide the potential not only to modulate but to substantially affect RNA structure by formation of different secondary structure motifs.
Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on the formation and anaerobic oxidation of methane.
TLDR
These values are consistent with isotope effects reported for oxidative cleavage/reductive coupling occurring at transition metal centers during C-H activation but are also in the range expected for the radical substitution mechanism proposed by Siegbahn et al.
Probing the reactivity of Ni in the active site of methyl-coenzyme M reductase with substrate analogues
TLDR
Experiments with methyl-coenzyme M analogues showing how they affect the activity and the MCR-red1 signal of MCR from Methanothermobacter marburgensis concluded that the Ni-based EPR spectra of both inactive forms were not affected in the presence of high concentrations of these two potent inhibitors.
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