S-Adenosylmethionine conformations in solution and in protein complexes: Conformational influences of the sulfonium group

S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR and computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes with proteins. S-Methylmethionine and S-dimethylsulfonioproprionate adopt a variety of conformations in aqueous solution; a conformation with an electrostatic interaction between the sulfonium sulfur and the carboxylate group is not noticeably favored, in contrast to the preferred conformation found by in vacuo calculations. Nuclear Overhauser effect measurements and computational results for AdoMet indicate a predominantly anti conformation about the glycosidic bond with a variety of conformations about the methionyl C-alpha-C-beta and C-beta-C-gamma bonds. An AdoMet conformation in which the positively charged sulfonium sulfur is near an electronegative oxygen in the ribose ring is common. Comparisons of NMR results for AdoMet with those for the uncharged S-adenosylhomocysteine and 5'-methylthioadenosine, and the anionic ATP, indicate that the solution conformations are not dictated mainly by molecular charge. In 20 reported structures of AdoMet-protein complexes, both anti and syn glycosidic torsional angles are found. The methionyl group typically adopts an extended conformation in complexes with enzymes that transfer the methyl group from the sulfonium center, but is more folded in complexes with proteins that do not catalyze reactions involving the sulfur and which can use the sulfonium sulfur solely as a binding site. The conformational energies of AdoMet in these crystal structures are comparable to those found for AdoMet in solution. The sulfonium sulfur is in van der Waals contact with a protein heteroatom in the structures of four proteins, which reflects an energetically favorable contact. Interactions of the sulfonium with aromatic rings are rarely observed.