title: Modelling sequential protein folding under kinetic control.
abstract: BACKGROUND
  This study presents a novel investigation of the effect of kinetic control on cotranslational protein folding. We demonstrate the effect using simple HP lattice models and show that the cotranslational folding of proteins under kinetic control has a significant impact on the final conformation. Differences arise if nature is not capable of pushing a partially folded protein back over a large energy barrier. For this reason we argue that such constraints should be incorporated into structure prediction techniques. We introduce a finite surmountable energy barrier which allows partially formed chains to partly unfold, and permits us to enumerate exhaustively all energy pathways.
  
  
  RESULTS
  We compare the ground states obtained sequentially with the global ground states of designing sequences (those with a unique global ground state). We find that the sequential ground states become less numerous and more compact as the surmountable energy barrier increases. We also introduce a probabilistic model to describe the distribution of final folds and allow partial settling to the Boltzmann distribution of states at each stage. As a result, conformations with the highest probability of final occurrence are not necessarily the ones of lowest energy.
  
  
  BACKGROUND
  Software available on request.
authors.affiliation: Department of Statistics, Macquarie University, NSW 2109, Australia. fhuard@efs.mq.edu.au
authors.forename: Fabien P E
authors.initials: FP
authors.lastname: Huard
authors.forename: Charlotte M
authors.initials: CM
authors.lastname: Deane
authors.forename: Graham R
authors.initials: GR
authors.lastname: Wood
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins