Regensburg 2013 – scientific programme
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BP: Fachverband Biologische Physik
BP 8: Posters: Proteins
BP 8.26: Poster
Monday, March 11, 2013, 17:30–19:30, Poster B2
Analyzing protein folding by high-throughput simulations — •Claude Sinner1,2, Benjamin Lutz1,2, Abhinav Verma1, and Alexander Schug1 — 1Steinbuch Centre for Computing (SCC),Karlsruher Institut für Technologie (KIT), 76128 Karlsuhe, Germany — 2Fakultät für Physik, Karlsruher Institut für Technologie (KIT), 76128 Karlsruhe, Germany
Molecular Dynamics allows investigating the dynamical properties of biomolecules. Protein folding simulations are computationally challenging when simulating all involved (solvent) atoms considering timescales of ms or slower. Native structure based models (SBM,’Go-models’) reduce computational complexity and have shown to be a robust and efficient way for exploring the protein folding process. They are based on energy landscape theory and the principle of minimal frustration. Using this framework, we simulate protein folding for a large set (∼ 200) of non-homologous monomeric proteins sized from 50-150 amino acids in coarse-grained simulations. A fully automatized workflow implemented with the help of ESBMTools guides these simulations. From the simulations, we extract typical folding properties like phi-values, folding free energy landscape and transition state ensembles. We repeat the simulations for a variant SBM with flavored contact strengths pending on amino acid composition. The resulting database estimates the robustness of folding parameters, quantifies the folding behavior, compares the behavior to existing experimental data and can serve as a baseline for comparison to future experiments or simulations of protein folding.