Stabilizing effect of knots on proteins

Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2008-12, Vol.105 (50), p.19714-19719
Main Authors: Sułkowska, Joanna I, Sułkowski, Piotr, Szymczak, P, Cieplak, Marek
Format: Article
Language:English
Subjects:
Active sites
Amino acids
Atoms
Biological Sciences
Computer Simulation
Disulfides
Disulfides - chemistry
Enzymes
Hot Temperature
Humans
Lead
Models, Chemical
Molecular structure
Molecules
Ornithine Carbamoyltransferase - chemistry
Protein Folding
Protein Structure, Secondary
Proteins
Stress, Mechanical
Studies
Temperature dependence
Topology
Trajectories
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Summary:Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0805468105