Determining critical amino acid contacts for knotted protein folding

• Autorzy: Dąbrowski-Tumański P. , Niewieczerzał S. , Sułkowska J. I.
• Języki publikacji: EN

Abstrakty

EN

Proteins with a non-trivial topological structure are currently well recognized, while a knotted protein chain represents a new motif in protein three dimensional folds. Recent comprehensive analysis of the Protein Data Base shows that knotted proteins represent 1.5% of known protein structures. Determination of a free energy landscape of knotted proteins, and its understanding provides a serious challenge for both experimentalists and theoreticians. Moreover the role of a knot for biological activity of protein still remains elusive. In this work we study the smallest knotted proteins ( PDB code 2efv) to understand/investigate their free energy landscape, by means of extensive molecular dynamics simulations. We explore the dependence of the thermodynamics, kinetics and protein folding pathways on the native-likes contact maps and on the length of the chain. We analyze two sets of native-like contacts , which differ by a number of long range interactions, and we consider the 2efv protein with two different lengths of its C-terminus end. We identify the subset of native contacts sufficient to explore the entire free energy landscape. Then, we analyze the influence of the remaining set of native contacts – we show that the set of additional contacts may enhance folding kinetics, and that it has an influence on folding pathways.

Słowa kluczowe

EN

knotted protein; slipknot; 2efv folding; contact map; native; non-native

PL

wiązanie białek; slipknot; 2efv; mapa kontaktowa

• Wydawca: Politechnika Gdańska
• Czasopismo: TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
• Rocznik: 2014
• Tom: Vol. 18, No 3
• Strony: 265--279
• Opis fizyczny: Bibliogr. 38 poz., rys., tab., wykr.

Twórcy

autor

Dąbrowski-Tumański P.

• Departament of Chemistry, University of Warsaw Pasteura 1, 02-093 Warsaw, Poland
• Centre of New Technologies, University of Warsaw Banacha 2c, 02-097 Warsaw, Poland

autor

Niewieczerzał S.

• Departament of Chemistry, University of Warsaw Pasteura 1, 02-093 Warsaw, Poland

autor

Sułkowska J. I.

• Departament of Chemistry, University of Warsaw Pasteura 1, 02-093 Warsaw, Poland

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