(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:

• Generate optimized arc files for each candidate intermediate (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 Step_7.
  
  
• If several keywords are common to each data set, e.g.,  EPS=78.4, MOZYME, CHARGE=1, CVB(1000:-1001), GNORM=20, T=1W, then create a file, e.g., SETUP.TXT, containing these keywords, and use keyword SETUP to indicate that the set of keywords is to be read in.
  
  
• 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 keywords EPS=78.4, LOCATE-TS, GEO_DAT and GEO_REF. Each data set should consist of only one to three lines: keywords, title (optional), and comment (also optional) lines. GEO_DAT and GEO_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_DAT and which for GEO_REF is 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.