Abstract The composition and residue--residue interactions of knotted
proteins, compared with those of other proteins, can provide
considerable insight into the driver of the knots in proteins. In
this paper, we calculate the probabilities of 20 amino acids in 273
knotted entries from the Protein Data Bank (PDB). The collection of
273 entries contains all knotted structures in the PDB, and it is
not a subset. With an appropriate value of Rc, the numbers of all
residue--residue contacts are counted in all 273 knotted structures.
To make an accurate comparison, we count up to 9000 other entries
from the PDB as well, and these entries spread over all sorts. In
knotted structures, Leu occupies a maximal proportion of 9.62%
among all 20 amino acids, and Leu, Phe, Trp, Gly, His, Gln, Asp, Lys
and Pro may all play a more important role. Also, we analyse the
effects of amino acid residues on the long-range contacts. We
observe a larger average number of long-range contacts in the
knotted structures than that in other ones, implying their important
role in achieving the knots. Accordingly, the average number of
short-range contacts becomes small when the structure becomes
knotted because it depends mainly on the short-haul sequence of
amino acids to form the short-range contact. In addition, the shape
distribution of knotted proteins and the contrast with the other
proteins are also presented. A comparison shows that the knots may
make structures more globular because the average shape factor is
0.059 for the knotted proteins, which is only about 1/3 of the
average shape factor for the other proteins.
Received: 17 April 2008
Revised: 13 July 2008
Published: 20 April 2009
(Folding: thermodynamics, statistical mechanics, models, and pathways)
Fund: Project
supported by the National Natural Science Foundation of China (Grant
Nos 20574052 and 20774066), the Program for New Century Excellent
Talents in University, China (Grant No NCET-05-0538) and the Natural
Science Foundation of Zhejiang Province, Ch
Cite this article:
Wang Xiang-Hong, Shen Yu, Zhang Lin-Xi Structural statistical properties of knotted proteins 2009 Chin. Phys. B 18 01684
