*** README1.jlittl	Thu May 16 10:06:40 1991
--- README1.jlittl.bak	Thu May 16 09:40:48 1991
***************
*** 68,74 ****
  HE <-----> E <-----> Estar -----> products
  
  The equations are as in lexfitB.c, but with terms in Kestar deleted (setting
! pKestar low is formally equivalent to deletion of these terms).
  
  If Kconf is large and the pH is low, the significant species are:
  	HE and E*
--- 68,74 ----
  HE <-----> E <-----> Estar -----> products
  
  The equations are as in lexfitB.c, but with terms in Kestar deleted (setting
! pKestar = 8.5 or lower is formally equivalent to deletion of these terms).
  
  If Kconf is large and the pH is low, the significant species are:
  	HE and E*
***************
*** 85,91 ****
  traditional square of equilibria as we have, by implication attributing
  both pKe and pKestar to the same protein group.  Indeed, pKestar may be
  effectively absent (see below)! And the pK of the lysine providing,
! presumably, pKe, may be shifted to a higher value in E*!
  
  It is also important to keep in mind that E* is detected in steady state
  kinetic experiments.  It may not be in equilibrium with E, i.e. it might
--- 85,91 ----
  traditional square of equilibria as we have, by implication attributing
  both pKe and pKestar to the same protein group.  Indeed, pKestar may be
  effectively absent (see below)! And the pK of the lysine providing,
! presumably, pKe, may by shifted to a higher value in E*!
  
  It is also important to keep in mind that E* is detected in steady state
  kinetic experiments.  It may not be in equilibrium with E, i.e. it might
***************
*** 129,135 ****
               H
  
  If other information determines that pKestar must be much lower
! than 8.5, then ascribing it to a lysine becomes questionable.
  
  
  2. How about the following possibility for E*? the tetrahedral intermediate
--- 129,135 ----
               H
  
  If other information determines that pKestar must be much lower
! that 8.5, then ascribing it to a lysine becomes questionable.
  
  
  2. How about the following possibility for E*? the tetrahedral intermediate
***************
*** 265,274 ****
  3. What are the thermodynamics of the E --> E* equilibrium and the
  E* breakdown? 
  
! There appears to be odd chemistry; for wt LexA:
  
  	delH(k_limit) = 15 kcal/mol 
! 		< delG(k_limit) by about 6 kcal/mol
  	delS(k_limit) = -21 cal/K.mol
  
  This is a bit curious -- for amide hydrolysis catalyzed by a protease,
--- 265,274 ----
  3. What are the thermodynamics of the E --> E* equilibrium and the
  E* breakdown? 
  
! There appears to be odd chemistry:
  
  	delH(k_limit) = 15 kcal/mol 
! 		< delG(k_limit) for wt, by about 6 kcal/mol
  	delS(k_limit) = -21 cal/K.mol
  
  This is a bit curious -- for amide hydrolysis catalyzed by a protease,
***************
*** 331,337 ****
  
  	d. examination of homologies and mutants with the question in
  		mind: are there main chain/side chain groups that
! 		are critical for function and that could interact (oxyanion
  		hole, ...) as in cht/subtilisin?
  
  	e. DFP reaction of trp mutant and its pH dependence; if formation 
--- 331,337 ----
  
  	d. examination of homologies and mutants with the question in
  		mind: are there main chain/side chain groups that
! 		are critical for function and that could interact oxyanion
  		hole, ...) as in cht/subtilisin?
  
  	e. DFP reaction of trp mutant and its pH dependence; if formation