Threading As a Tool For Ab Initio Prediction Of 3D Folds Of Proteins:
Possibility And Limitations

Dmitry S. Rykunov Institute of Theoretical & Experimental Biophysics
RAS, Pushchino, Moscow reg., 142292 Russia

Aim: Our aim is to apply threading approach to ab initioprediction of
protein folds. As the target folds for treading, we use the sets of
folding patterns that are partly observed and partly not observed in
natural protein. Each set is obtained from some native protein core
using extrapolations of its secondary structure elements and all the
reasonable modifications of the core topology, i.e. a variety chain
pathways through this core. The computations are based on the self
consistent molecular field theory and on the statistical mechanics of
chain molecules. The molecular field summarizes the action of
long-range interactions. Statistical mechanics finds the stable state
and fluctuations of the chain in this field.

Results: The developed computer program and the set of generated
frameworks are used to single out the stable folds of a number of
protein chains. It is shown that extrapolation of secondary structure
segments improves recognition of cognate proteins, and that extension
of target fold library by reconnectingof secondary structures of known
protein folds is useful for recognition of "new", previously not
observed protein folds. However, in a general case the native fold is
recognized as one of the most stable, but rarely as the most stable
chain fold.

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