0README

Wed Jul 27 23:14:01 MST 2005


|-- lexa                        directory - analysis of measurements of the
    |					    pH dependence of the rate of 
    |					    autolysis (autocatalytic cleavage)
    |					    of wild-type and mutant lexA 
    |					    (data from John Little laboratory);
    |-- 0NOTE
    |-- 0README
    |-- 1-README.fits
    |-- 1-README1.erratum
    |-- 1-README1.jlittl
    |
    |-- Makefile			
    |-- lexfitB				executable, model B, lexa cleavage data 
    |-- lexfitB.c			C code for above
    |-- lexfitken			executable, model ken, lexa ....
    |-- lexfitken.c			C code for above
    |
    |-- bgallB				script wrapper - lexfitB -> results file
    |-- lex.prep
    |-- longprep
    |-- mk.special
    |-- mk.theory
    |-- plot.theory
    |-- plotallB			script - plot data & calcd values
    |-- prep
    |-- rawdata.lexa
    |-- runallB				script - combine bgallB and plotallB
    |-- sd.awk
    |-- theory.prep
    |
    |-- results.B			directtory - results from lexfitB
    |   |-- lexa.data.1				data, cntrl values, param set 1
    |   |-- lexa.data.1-1991
    |   |-- lexa.data.2				same, param set 2
    |   |-- lexa.data.2-1991
    |   |-- lexa.data.3				etc
    |   |-- lexa.data.3-1991
    |   |
    |   |-- lexa.out.1				fit results, parm set 1, macosx
    |   |-- lexa.out.1-1991A			old fit results, under sgi 4d30
    |   |-- lexa.out.2				etc.
    |   |-- lexa.out.2-1991
    |   |-- lexa.out.3
    |   |-- lexa.out.3-1991
    |   |
    |   |-- lexa.plot.1				plot data & calcd - parm set 1
    |   |-- lexa.plot.1-1991			etc
    |   |-- lexa.plot.2
    |   |-- lexa.plot.2-1991
    |   |-- lexa.plot.3
    |   |-- lexa.plot.3-1991
    |   |
    |   |-- lexa.plotth.1-1991			plot data & calcd curves - set 1
    |   |-- lexa.plotth.2-1991
    |   |-- lexa.plotth.3-1991
    |   |
    |   |-- bgallB -> ../bgallB
    |   |-- lex.prep -> ../lex.prep
    |   |-- lexfitB -> ../lexfitB
    |   |-- longprep -> ../longprep
    |   |-- mk.special -> ../mk.special
    |   |-- mk.theory -> ../mk.theory
    |   |-- plot.theory -> ../plot.theory
    |   |-- plotallB -> ../plotallB
    |   |-- prep -> ../prep
    |   |-- runallB -> ../runallB
    |   `-- theory.prep -> ../theory.prep
    |
    `-- results.B.corr			directory - more results lexA data fits
        |-- kendata-1992			data, cntrl, params - lexfitken
        |-- kendata.one-1992
        |-- kendatax
        |-- kendatax.one
        |
        |-- kenout-1992				4d30 results, fit with lexfitken
        |-- kenout.one-1992			etc
        |-- kenoutx				current macosx fit results
        |-- kenoutx.one				etc
        |
        |-- lexa.data.1-1992			data, cntrl, params - lexfitB
        |-- lexa.data.x
        |
        |-- lexa.out.1-1992			4d30 output
        |-- lexa.out.x				current macosx results
        |
        |-- lexa.plot.1-1992			4d30 plots of data and calcd
        |-- lexa.plot.x				macosx
        |
        |-- bgallB -> ../bgallB
        |-- lex.prep -> ../lex.prep
        |-- lexfitB -> ../lexfitB
        |-- lexfitken -> ../lexfitken
        |-- longprep -> ../longprep
        |-- mk.special -> ../mk.special
        |-- mk.theory -> ../mk.theory
        |-- plot.theory -> ../plot.theory
        |-- plotallB -> ../plotallB
        |-- prep -> ../prep
        |-- runallB -> ../runallB
        `-- theory.prep -> ../theory.prep
    

lexa
	analysis of measurements of the pH dependence of
	the rate of autolysis (autocatalytic cleavage) of
	wild-type and mutant lexA (data from John Little's
	laboratory);
		data fit by two models:
			lexfitB (lexfitB.c) 
			lexfitken (lexfitken.c)
		models have up to eight variable parameters


For details of fitting functions, see ./lexfitB.c and ./lexfitken.c;

From file headers:

*******for LEXFITB.C

/* MODEL */
/*-
 * simulation of breakdown of LexA:
 *
 * model:
 *
 *                Kestar                  kstar
 *      EstarH+    ---->        Estar     --->    products
 *
 *        ^                       ^
 *        |                       |
 *        |                       | Kconf
 *        |                       |
 *
 *       EH+       ---->          E
 *                  Ke
 *
 *
 * v = kstar . (Estar)
 *
 *   = k . (Etotal)
 *
 *
 * k = observed first order rate constant for appearance of products
 *
 * k = kstar / [ 1/Kconf + (H+)/{Kconf.Ke} + 1 + (H+)/Kestar ]
 *
 * apparent pK controlling k:
 * 	pK_app = - log( [ 1/Kconf + 1 ] / [ 1/{Kconf.Ke} + 1/Kestar ] )
 *
 * high pH limit of k:
 *	logk_limit = logkstar - log( 1/Kconf + 1 );
 */

/*-
 *
 * modification:
 *
 * assume that Ke and/or kstar vary with Kconf;
 *
 * let pKe and logkstar depend linearly on log(Kconf),
 * i.e., a linear free energy relationship;
 *
 * this is equivalent to:
 *
 * kstar = kstar,ref . (Kconf)^alpha
 * Ke = Ke,ref . (Kconf)^beta
 *
 */
[****** Kconf different for each mutant ]
[	good fit to data with only Kconf species dependent ]
[	non-zero values of alpha or beta do not significantly improve fit ]
[****** because pKestar very low << pKe, can be ignored, -> ]
[	good fit with parms pKe, kstar, Kconf for each species ]
[	= 6 parms ]


*******for LEXFITKEN.C
[ less elegant approach - not better fit ]

/* MODEL */
/*-
 * simulation of breakdown of LexA:
 *
 * model:
 *
 *                 Ke                    klim
 *      EH+       ---->        E         --->    products
 *
 *
 * v = klim  . (E)
 *
 *   = k . (Etotal)
 *
 *
 * k = observed first order rate constant for appearance of products
 *
 * k = klim / [ 1 + (H+)/{Ke} ]
 *
 */
[***** Ke and klim differ for wild type and each mutant ]



John Rupley
 rupley@u.arizona.edu -or- jar@rupley.com
 30 Calle Belleza, Tucson AZ 85716 - (520) 325-4533; fax - (520) 325-4991
 Dept. Biochemistry & Molecular Biophysics, Univ. Arizona, Tucson AZ 85721
