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
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:
Generate optimized arc files for each
(stationary point) in the mechanism. Give these files simple names, e.g.,
Step_1 - Step_6. If, as often happens, there are other possible
intermediates then these should also be given simple names, e.g., Step_6a or
Data sets for locating transition states should be given
systematic simple names. Examples would be
Step_1_2_Transition_State.mop and Step_1_3_Transition_State.mop.
Individual data sets for locating transition states should use keywordsEPS=78.4, LOCATE-TS,
Each data set should consist of only one to three lines: keywords, title
comment (also optional) lines. GEO_DATandGEO_REF should refer to ARC
files for the intermediates, not to <file>.mop files. <file>.arc files
can easily be inspected to see if they are suitable - the heat of formation
is easily seen, as is the gradient norm. If the ARC file is edited to
make a new MOP file, the potential for introducing an error is large, and
finding an error in a MOP file is not easy.
The choice of which ARC file to use for
GEO_DATand which forGEO_REFis arbitrary. The names can be
switched around at the user's discretion.
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.