title: Bridging the gap between ribosome structure and biochemistry by mechanistic computations.
abstract: The wealth of structural and biochemical data now available for protein synthesis on the ribosome presents major new challenges for computational biochemistry. Apart from technical difficulties in modeling ribosome systems, the complexity of the overall translation cycle with a multitude of different kinetic steps presents a formidable problem for computational efforts where we have only seen the beginning. However, a range of methodologies including molecular dynamics simulations, free energy calculations, molecular docking and quantum chemical approaches have already been put to work with promising results. In particular, the combined efforts of structural biology, biochemistry, kinetics and computational modeling can lead towards a quantitative structure-based description of translation.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden. aqvist@xray.bmc.uu.se
authors.forename: Johan
authors.initials: J
authors.lastname: Aqvist
authors.forename: Christoffer
authors.initials: C
authors.lastname: Lind
authors.forename: Johan
authors.initials: J
authors.lastname: Sund
authors.forename: Göran
authors.initials: G
authors.lastname: Wallin
mesh_terms: D003062:Codon / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D020558:GTP Phosphohydrolases / Q000378:metabolism; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics; D012270:Ribosomes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D003062:Codon; D010455:Peptides; D012343:RNA, Transfer; D020558:GTP Phosphohydrolases