Simulating the behavior of proteins and nucleic acids - Lennart Nilsson
Molecular dynamics simulations of the tRNA anticodon and mRNA codon, inside the ribosome 30S subunit, show that the common tRNA modifications cmo5U34 and m6A37 in tRNAVal, which allow all four nucleotides to be successfully read at the wobble position in a codon, may work through two mechanisms: The further reach of the cmo5U34 modification allows an alternative conformation to be formed for the noncognate base pairs, and increased contacts between tRNA, mRNA, and the ribosome. One intricate issue that requires much attention is the corretct handling, and placement of Mg2+ ions.
Polymerization of the amyloid β-peptide (Ab) requires the helical structure of Ab to unfold. The effects of two ligands, which were designed to bind to and stabilize the helix, on unfolding of the Ab central helix were investigated by MD simulations.We quantitatively showed that both ligands increase the stability of the Ab helix, which correlates well with previous experiments for these ligands.
The dissociation mechanism of thioredoxin (Trx) mixed disulfide complexes is unknown We studied mixed disulfide dissociation in arsenate reductase using theoretical reactivity analysis, molecular dynamics simulations, and biochemical complex formation experiments with Cys-mutants. This lead to a universal thiol/disulfide exchange reaction mechanism that results in reduced substrate and oxidized Trx.
Consensus structure of the -Cys-X1-X2-Cys- active site motif in glutaredoxins.