- Tytuł:
- Determining critical amino acid contacts for knotted protein folding
- Autorzy:
-
Dąbrowski-Tumański, P.
Niewieczerzał, S.
Sułkowska, J. I. - Powiązania:
- https://bibliotekanauki.pl/articles/1954247.pdf
- Data publikacji:
- 2022-02-01
- Wydawca:
- Politechnika Gdańska
- Tematy:
-
knotted protein
slipknot
2efv folding
contact map
native
non-native - Opis:
- 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.
- Źródło:
-
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 265--279
1428-6394 - Pojawia się w:
- TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
- Dostawca treści:
- Biblioteka Nauki
Artykuł