New biologically motivated knot table

被引:9
|
作者
Brasher, Reuben [1 ]
Scharein, Rob G. [2 ]
Vazquez, Mariel [1 ]
机构
[1] San Francisco State Univ, Dept Math, San Francisco, CA 94132 USA
[2] Hypnag Software, Vancouver, BC V6K 1V6, Canada
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
average crossing number; chirality; DNA knot; knot table; lattice knot; writhe; CUBIC LATTICE; TOPOISOMERASE-IV; EXCLUDED VOLUME; PHAGE CAPSIDS; CIRCULAR DNA; WRITHE; CHIRALITY; LINKS; POLYGONS;
D O I
10.1042/BST20120278
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The knot nomenclature in common use, summarized in Rolfsen's knot table [Rolfsen (1990) Knots and Links, American Mathematical Society], was not originally designed to distinguish between mirror images. This ambiguity is particularly inconvenient when studying knotted biopolymers such as DNA and proteins, since their chirality is often significant. In the present article, we propose a biologically meaningful knot table where a representative of a chiral pair is chosen on the basis of its mean writhe. There is numerical evidence that the sign of the mean writhe is invariant for each knot in a chiral pair. We review numerical evidence where, for each knot type K, the mean writhe is taken over a large ensemble of randomly chosen realizations of K. It has also been proposed that a chiral pair can be distinguished by assessing the writhe of a minimal or ideal conformation of the knot. In all cases examined to date, the two methods produce the same results.
引用
收藏
页码:606 / 611
页数:6
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