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2 TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2 2014

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Mechanical unfolding of Ddfln4 studied by coarse-grained knowledge-based cabs model

Kouza M., Jamroz M., Gront D., Kmiecik S., Koliński A.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2014

Vol. 18, No 4

373--378

Mechanical unfolding of the fourth domain of Distyostelium discoideum fi lamin ( DDFLN 4) was studied using a CABS – coarse-grained knowledge-based protein model. Our study demonstrates that CABS is capable of reproducing the unfolding free energy landscape of protein unfolding and highlights an important role of non-native interacti ons in the protein unfolding process. The obtained three peaks in the force-extension profile suggest a four-state picture of DDFLN 4 protein unfolding and correspond reasonably to the results of the all-at om simulation in explicit solvent.

Coarse-grained modeling of protein structure, dynamics and protein-protein interactions

Koliński A., Kmiecik S., Jamróz M., Błaszczyk M., Kouza M., Kurciński M.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2014

Vol. 18, No 3

219--229

Theoretical prediction of protein structures and dynamics is essent ial for understanding the molecular basis of drug action, metabolic and signaling pathway s in living cells, designing new technologies in the life science and material sciences . We developed and validated a novel multiscale methodology for the study of protein folding proces ses including flexible docking of proteins and peptides. The new modeling technique starts fr om coarse-grained large-scale simulations, followed by selection of the most plausible final structu res and intermediates and, finally, by an all-atom rectification of the obtained structures. Except f or the most basic bioinformatics tools, the entire computational methodology is based on the models an d algorithms developed in our lab. The coarse-grained simulations are based on a high-resol ution lattice representation of protein structures, a knowledge based statistical for ce field and efficient Monte Carlo dynamics schemes, including Replica Exchange algorithms. This p aper focuses on the description of the coarse-grained CABS model and its selected applications.