TY - JOUR
T1 - Discrete-continuous duality of protein structure space
AU - Sadreyev, Ruslan I.
AU - Kim, Bong Hyun
AU - Grishin, Nick V.
PY - 2009/6
Y1 - 2009/6
N2 - 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.
AB - 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.
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U2 - 10.1016/j.sbi.2009.04.009
DO - 10.1016/j.sbi.2009.04.009
M3 - Review article
C2 - 19482467
AN - SCOPUS:66549094316
SN - 0959-440X
VL - 19
SP - 321
EP - 328
JO - Current Opinion in Structural Biology
JF - Current Opinion in Structural Biology
IS - 3
ER -