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Curr Opin Struct Biol. 2009 Jun;19(3):321-8. doi: 10.1016/j.sbi.2009.04.009. Epub 2009 May 29.

Discrete-continuous duality of protein structure space.

Author information

1
Howard Hughes Medical Institute, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

Abstract

Recently, the nature of protein structure space has been widely discussed in the literature. The traditional discrete view of protein universe as a set of separate folds has been criticized in the light of growing evidence that almost any arrangement of secondary structures is possible and the whole protein space can be traversed through a path of similar structures. Here we argue that the discrete and continuous descriptions are not mutually exclusive, but complementary: the space is largely discrete in evolutionary sense, but continuous geometrically when purely structural similarities are quantified. Evolutionary connections are mainly confined to separate structural prototypes corresponding to folds as islands of structural stability, with few remaining traceable links between the islands. However, for a geometric similarity measure, it is usually possible to find a reasonable cutoff that yields paths connecting any two structures through intermediates.

PMID:
19482467
PMCID:
PMC3688466
DOI:
10.1016/j.sbi.2009.04.009
[Indexed for MEDLINE]
Free PMC Article

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