(Modeling proteins)

Locating and Refining Transition States in Proteins

The task of locating and refining transition states in enzyme-catalyzed reactions has normally been regarded as very difficult, if not impossible.  Hopefully, this has changed now that a fully automatic procedure, LOCATE-TS, has been developed.  LOCATE-TS was developed specifically for locating transition states in proteins; it will work for some other types of reactions, but be aware that it has been optimized for protein work.

LOCATE-TS was tested using the chymotrypsin mechanism.  The default setting worked for locating most transition states, for the rest, trial-and-error methods for locating transition states were used.  These resulted in all the stationary points between intermediates being located.

The chymotrypsin mechanism was used as the example in modeling proteins.  Some features of this example are common to all projects involving modeling enzyme mechanisms.  Among these are:

All possible combinations of intermediates were used in modeling the chymotrypsin mechanism, however only the transition states connecting adjacent pairs of intermediates are meaningful; the rest were included in this example to illustrate different types of reactions. Transition states connected by a red dot are not meaningful.