title: Performance assessment of different constraining potentials in computational structure prediction for disulfide-bridged proteins.
abstract: The presence of disulfide bonds in proteins has very important implications on the three-dimensional structure and folding of proteins. An adequate treatment of disulfide bonds in de-novo protein simulations is therefore very important. Here we present a computational study of a set of small disulfide-bridged proteins using an all-atom stochastic search approach and including various constraining potentials to describe the disulfide bonds. The proposed potentials can easily be implemented in any code based on all-atom force fields and employed in simulations to achieve an improved prediction of protein structure. Exploring different potential parameters and comparing the structures to those from unconstrained simulations and to experimental structures by means of a scoring function we demonstrate that the inclusion of constraining potentials improves the quality of final structures significantly. For some proteins (1KVG and 1PG1) the native conformation is visited only in simulations in presence of constraints. Overall, we found that the Morse potential has optimal performance, in particular for the β-sheet proteins.
authors.affiliation: Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Karlsruhe, Germany. ivan.kondov@kit.edu
authors.forename: Ivan
authors.initials: I
authors.lastname: Kondov
authors.forename: Abhinav
authors.initials: A
authors.lastname: Verma
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Wenzel
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004220:Disulfides / Q000737:chemistry*; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D004220:Disulfides; D011506:Proteins