title: A path planning-based study of protein folding with a case study of hairpin formation in protein G and L.
abstract: We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMS). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structure, assuming we know the native fold. A feature of our PRM-based framework is that the large sets of folding pathways in the roadmaps it produces, in a few hours on a desktop PC, provide global information about the protein's energy landscape. This is an advantage over other simulation methods such as molecular dynamics or Monte Carlo methods which require more computation and produce only a single trajectory in each run. In our initial studies, we obtained encouraging results for several small proteins. In this paper, we investigate more sophisticated techniques for analyzing the folding pathways in our roadmaps. In addition to more formally revalidating our previous results, we present a case study showing our technique captures known folding differences between the structurally similar proteins G and L.
authors.affiliation: Department of Computer Science, Texas A&M University, College Station, TX 77843-3112, USA. gsong@cs.tamu.edu
authors.forename: Guang
authors.initials: G
authors.lastname: Song
authors.forename: Shawna
authors.initials: S
authors.lastname: Thomas
authors.forename: Ken A
authors.initials: KA
authors.lastname: Dill
authors.forename: J Martin
authors.initials: JM
authors.lastname: Scholtz
authors.forename: Nancy M
authors.initials: NM
authors.lastname: Amato
mesh_terms: D001426:Bacterial Proteins; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D009010:Monte Carlo Method; D009419:Nerve Tissue Proteins / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C029152:G-substrate; C116593:L-protein, Peptococcus magnus; D009419:Nerve Tissue Proteins