title: Folding and unfolding characteristics of short beta strand peptides under different environmental conditions and starting configurations.
abstract: We analyze the effect of different environmental conditions, sequence lengths and starting configurations on the folding and unfolding pathways of small peptides exhibiting beta turns. We use chignolin and a sequence of peptide G as examples. A variety of different analysis tools allows us to characterize the changes in the folding pathways. It is observed that different harmonic modes dominate not only for different conditions but also for different starting points. The modes remain essentially very similar but their relative importance varies. A detailed analysis from diverse viewpoints including the influence of the particular amino acid sequence, conformational aspects as well as the associated motions yields a global picture that is consistent with experimental evidence and theoretical studies published elsewhere. Patterns of modes that remain stable over a range of temperatures might serve as an additional diagnostic to identify conformations that have reliably adopted a native fold. This could aid in reconstructing the folding process of a complete protein by identifying conformationally determined regions.
authors.affiliation: Fraunhofer Institute for Algorithms and Scientific Computing, Department of Simulation Engineering, Schloss Birlinghoven, 53754 St. Augustin, Germany.
authors.forename: Astrid
authors.initials: A
authors.lastname: Maass
authors.forename: Emine Deniz
authors.initials: ED
authors.lastname: Tekin
authors.forename: Anton
authors.initials: A
authors.lastname: Schüller
authors.forename: Ahmet
authors.initials: A
authors.lastname: Palazoglu
authors.forename: Dirk
authors.initials: D
authors.lastname: Reith
authors.forename: Roland
authors.initials: R
authors.lastname: Faller
mesh_terms: D003198:Computer Simulation; D006860:Hydrogen Bonding; D007074:Immunoglobulin G / Q000737:chemistry*; D008958:Models, Molecular; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D009842:Oligopeptides / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D025341:Principal Component Analysis; D011487:Protein Conformation; D017510:Protein Folding; D013696:Temperature
chemical_list: C029152:G-substrate; D007074:Immunoglobulin G; D009419:Nerve Tissue Proteins; D009842:Oligopeptides; D010446:Peptide Fragments; C506175:chignolin