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

2 2016

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Molecular Dynamics and structural comparison approach to understanding the role of knots in proteins

Perlinska A. P., Macnar J. M., Sulkowska J. I.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2016

Vol. 20, No 4

373--382

The role of knots in proteins is still unclear. In this short review, we summarize the current knowledge about structural and dynamical differences between knotted and unknotted proteins. We show how the topological difference helps to distinguish the physical properties, characterize the biological activity or identify the biological function of knotted proteins. This knowledge can be used to correctly annotate protein family members and to identify new members.

Current approaches to disentagle the mystery of knotted protein folding

Dabrowski-Tumanski P., Sklodowski M., Sulkowska J. I.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2016

Vol. 20, No 4

361--372

The folding of knotted proteins remains a mystery both for theoreticians and experimentalists. Despite the development of new models, the driving force for self-tying remains elusive and the principle of minimal frustration cannot be reproduced in silico. In this paper we review different models used to understand protein self-knotting and suggest, how to improve the structure based model to observe efficient folding. Our preliminary results show, that including information about some amino acids properties, or reducing the set of physical contacts may be beneficial for modeling of the knotted protein folding.