A molecular dynamics simulation of the flavin mononucleotide-RNA aptamer complex

Evolution of Vitamin B2 Biosynthesis. A Novel Class of Riboflavin Synthase in Archaea

“…It has been shown that artificial RNA sequences (aptamers) can bind FMN with very high affinity. 44,45 It has also been shown that the regulation of the riboflavin biosynthesis operon in Bacillaceae is based on the interaction of FMN with the mRNA specified by the rib operon resulting in premature transcription termination. 46 A hypothetical RNA world would most probably have required catalytic redox processes, and flavin derivatives would have been excellent candidates due to the fact that the isoalloxazine chromophore can arise by a highly unusual reaction in the absence of any catalyst.…”

SELEX—A (r)evolutionary method to generate high-affinity nucleic acid ligands

“…Furthermore, the three-dimensional binding structure of aptamer and target has to be clarified. In this regard methods like nuclear magnetic resonance (NMR) spectroscopy, X-ray structure analysis, and crystallization are usually applied (Forster et al, 2006;Kelly et al, 1996;Schneider and Suhnel, 1999;Soukup and Breaker, 1999).…”

1,2,5-Oxadiazole analogues of leflunomide and related compounds

“…AMBER FF99 parameters were assigned to protein atoms and GAFF parameters to the co-crystallized inhibitor and orotate, while atom-centred point charges were fitted to the quantum-mechanical electrostatic potential according to the RESP method [33]. Equilibrium internal coordinates, forcefield parameters and electrostatic charges for the FMN cofactor were taken from literature [34]. After removing the co-crystallized inhibitor, docking of compounds 3b, 3c, 10b, 10c, 14b, 14c was carried out using AutoDock 4.0.…”