A SAAM30 BAM.S 5/8/92
C REF- HENSLEY, P. ET AL. THE TIME-RESOLVED KINETICS OF SUPERHELICAL
C DNA CLEAVAGE BY BAM HI RESTRICTION ENDONUCLEASE.
C J. BIOL. CHEM. 265, 25,15300-153-7, 1990.
H PAR
C 10 NM OF SUBSTRATE INCUBATED WITH DIFFERENT ENZYME CONCENTRATIONS
C RANGING FROM 6 NM TO 0.4 NM
C
C COMPARTMENT 1 - BOUND ES
C COMPARTMENT 2 - BOUND NICKED DNA
C COMPARTMENT 3 - LINEAR DNA
C COMPARTMENT 4 - FREE NICKED DNA
C COMPARTMENT 5 - FREE SUPERHELICAL DNA
C COMPARTMENT 6 - FREE ENZYME
IC(1)=P(1)
IC(4)=P(2)
IC(3)=P(3)
IC(5)=P(5)
C P(6) IS INITIAL ENZYME CONCENTRATION
IC(6)=P(6)
P(6) 6
P(1) 0.000000E+00
P(2) 4.200000E-01
P(3) 7.700000E-01
P(5) 8.710000E+00 0.000000E+00 1.200000E+01
L(2,1) 7.760000E-01 1.000000E-03 1.000000E+01
L(1,5) 4.260000E-02 1.303682E-02 1.173314E-01 *F6
L(3,2) 1.867000E+00 4.842153E-01 4.357938E+00
L(4,2) 2.320000E-01 2
L(2,4) 1.870000E-02 6.487773E-03 5.838996E-02 *F6
L(5,1)=L(1,5)*.01
C ACCOUNTING FOR FREE ENZYME (METHOD 1)
C L(6,1)=L(5,1)
C L(0,1)=-L(5,1)
C L(6,2)=L(4,2)+L(3,2)
C L(0,2)=-L(6,2)
C L(0,6)=1 *G40
C
C ACCOUNTING FOR FREE ENZYME (METHOD 2)
C COMPARTMENT 7 - ENZYME BOUND TO SUBSTRATE
C COMPARTMENT 8 - ENZYME BOUND TO NICKED
H PAR
L(7,6)=L(1,5) *F5
L(6,7)=L(5,1)
L(8,7)=L(2,1)
L(8,6)=L(2,4) *F4
L(6,8)=L(4,2)+L(3,2)
H DAT
XG(40)= (L(1,5)*F(5))+(L(2,4)*F(4))
XG(1) = F(1) + F(5)
XG(2) = F(2) + F(4)
C G(20), G(21) AND G(22) ARE SUMS OF P'S
C G(20) IS AVERAGE INTIAL CONDITION IN COMPARTMENT 5
XG(20)=(P(5)+P(30)+P(31)+P(32)+P(33)+P(34))/6
C G(21) IS AVERAGE VALUE OF L(2,4)
XG(21)=(L(2,4)+P(20)+P(21)+P(22)+P(23))/5
C G(21) IS AVERAGE VALUE OF L(1,5)
XG(22)=(L(1,5)+P(40)+P(41)+P(42)+P(43)+P(44))/6
100
G(20)
G(21)
G(22)
106
0.
2 1 40
H DAT TC(2)
T
116F(6)
0.
2 2 30
H DAT TC(4)
T
126F(6)
0.
2 2 35
H DAT TC(6)
T
136F(6)
0.
2 5 23
H DAT TC(8)
T
146F(6)
0.
2 5 36
H DAT TC(10)
T
156F(6)
0.
2 5 52
H ICC TC(2)
I I
H ICC TC(4)
I I
H ICC TC(6)
I I
H ICC TC(8)
I I
H ICC TC(10)
I I
C *********************END OF MOD.6 ***************
H PAR
P(20) 2.127000E-02 5.100000E-03 4.590000E-02
P(21) 2.188000E-02 5.100000E-03 4.590000E-02
P(22) 1.050000E-02 5.100000E-03 4.590000E-02
P(23) 1.048000E-02 5.100000E-03 4.590000E-02
P(24) 0.000000E+00
P(30) 9.167000E+00 0.000000E+00 1.200000E+01
P(31) 9.120000E+00 0.000000E+00 1.200000E+01
P(32) 9.138000E+00 0.000000E+00 1.200000E+01
P(33) 9.046000E+00 0.000000E+00 1.200000E+01
P(34) 8.867000E+00 0.000000E+00 1.200000E+01
P(40) 3.800000E-02 1.000000E-02 6.000000E-02
P(41) .045 1.000000E-02 6.000000E-02
P(42) 3.180000E-02 1.000000E-02 6.000000E-02
P(43) 3.070000E-02 1.000000E-02 6.000000E-02
P(44) 2.500000E-02 1.000000E-02 6.000000E-02
H PCC TC(2)
P 2 0. .39
P 3 0. .50
L 2 4 1. P20
L01 5 1. P40
P 5 1. P30
P 6 0. 3.
H PCC TC(4)
P 2 0. 0.18
P 3 0. 0.65
L 2 4 1. P21
L01 5 1. P41
P05 1. P31
P06 0. 2.
H PCC TC(6)
P 2 0. .51
P 3 0. .36
L 2 4 1. P22
L01 5 1. P42
P05 1. P32
P06 0. 1.
H PCC TC(8)
P 2 0. .59
P 3 0. .34
L 2 4 1. P23
L01 5 1. P43
P05 1. P33
P06 0. 0.75
H PCC TC(10)
P 2 0. .66
P 3 0. .41
L 2 4 1. P24
L01 5 1. P44
P05 1. P34
P06 0. 0.4
C *********************END OF MOD.3 ***************
C EXP4 SUBSTRATE = 10 NMOLAR
C ENZYME = 6 NMOLAR
H DAT
101G(1) FSD=.2
0.
.25 8.740
.5 8.442
.75 8.242
1. 8.024
1.5 7.654
2. 7.157
2.5 6.595
3. 6.109
3.5 5.786
4. 5.390
4.5 4.968
5. 4.506
5.5 4.065
6. 3.860
6.5 3.495
7. 3.260
8. 2.675
9. 2.181
10. 1.788
11. 1.360
12. 1.049
101G(1) FSD=.5
13. 0.842
14. 0.633
15. 0.484
17. 0.264
20. 0.083
25. 0.041
30. 0.029
102G(2) FSD=.2
0.
.25 0.581
.5 0.615
.75 0.659
1. 0.703
1.5 0.764
2. .810
2.5 .900
3. .963
3.5 1.041
4. 1.050
4.5 1.060
5. 1.033
5.5 1.052
6. 1.034
6.5 1.028
7. 1.036
8. 1.050
9. 1.039
10. .889
11. .849
12. .811
13. .827
14. .649
15. .610
17. .477
20. .385
25. .242
30. .197
103 FSD=.2
0.
.25 .678
.5 .943
.75 1.099
1. 1.272
1.5 1.582
2. 2.057
2.5 2.505
3. 2.928
C 3.5 3.173
4. 3.560
4.5 3.971
C 5. 4.461
5.5 4.883
6. 5.106
6.5 5.477
7. 4.704
8. 6.275
9. 6.780
10. 7.323
11. 7.791
12. 8.141
13. 8.394
14. 8.718
15. 8.906
17. 9.259
20. 9.532
25. 9.716
30. 9.774
C EXP5 [E] = 3 nM, [S] APPROX 10 nM
H DAT TC(2)
T
111G(1) FSD=.2
0
0.5 9.031
1.0 8.815
1.5 8.506
2 8.377
2.5 8.049
3 7.633
3.5 7.539
4 7.164
4.5 6.961
5 6.703
6 6.328
7 5.889
8 5.308
9 5.086
10 4.631
12 3.821
14 3.296
16 2.636
18 2.109
20 1.724
25 1.063
30 .674
111G(1) FSD=2
35 .387
40 .230
45 .186
50 .133
60 .137
112G(2) FSD=.2
0
0.5 .489
1 .559
1.5 .662
2 .635
2.5 .660
3 .807
3.5 .704
4 .805
5 .848
6 .873
7 .909
8 .964
9 .981
10 1.032
12 1.088
14 1.002
16 .964
18 .930
20 .842
25 .620
30 .597
35 .312
40 .260
45 .261
50 .229
60 .174
113F(3) FSD=.2
0
0.5 .480
1 .626
1.5 .832
2 .988
2.5 1.290
3 1.560
3.5 1.757
4 2.031
4.5 2.197
5 2.449
6 2.799
7 3.202
C 8 3.728
9 3.933
10 4.337
C 12 5.090
14 5.703
C 16 6.400
18 6.961
20 7.434
25 8.317
30 8.730
113F(3) FSD=2
35 9.301
C 40 9.511
45 9.553
50 9.638
60 9.669
C DATA FROM PBR322 AND BAMH1 OLD DAYS EXP1 THE EARLY YEARS
H DAT TC(4)
T
121G(1) FSD=.2
.5 9.266
1. 8.984
1.5 8.831
2.0 8.516
2.5 8.407
3.0 8.240
3.5 7.907
4.0 7.725
5.0 7.235
6.0 6.580
7.0 6.405
8.0 6.091
9.0 5.633
10. 5.250
12. 4.713
14. 4.449
18. 3.116
25. 1.829
30. 1.285
121G(1) FSD=1
35. 0.880
40. 0.530
45. 0.450
50. 0.305
121G(1) FSD=2
60. 0.150
70. 0.130
122G(2)
50. .305
122G(2) FSD=.2
.5 .276
1.0 0.293
1.5 0.315
2.0 0.458
2.5 0.399
3.0 0.375
3.5 0.5
4.0 0.53
5.0 0.55
6.0 0.6
7.0 0.7
8.0 0.680
9.0 0.7
10. 0.58
12. 0.730
14. 0.760
18. 0.7
25. 0.65
30. 0.590
35. 0.6
40. 0.520
45. 0.5
122G(2) FSD=1
C 50. 0.18
60 0.21
70. 0.120
123F(3)
0.5 0.260
123F(3) FSD=.2
1.0 0.722
1.5 0.854
2.0 1.025
2.5 1.194
3.0 1.386
3.5 1.589
4.0 1.743
5.0 2.217
6.0 2.823
7.0 2.895
8.0 3.225
9.0 3.665
10. 3.822
12. 4.561
14. 4.792
18. 6.214
25. 7.52
30. 8.122
35. 8.706
40. 8.879
45. 9.089
50. 9.562
60. 9.635
70. 9.747
C ENZ CONC = 1 NM SUBSTRATE = NOMINALLY 10 NM
H DAT TC(6)
T
131G(1) FSD=.2
1. 8.978
1.5 8.963
2. 8.889
2.5 8.848
3. 8.808
4. 8.506
5. 8.349
8. 7.837
12. 7.176
16. 6.571
20. 6.047
25. 5.349
30. 4.765
35. 4.280
40. 3.682
45. 3.249
50. 2.8
55. 2.448
60. 2.129
65. 1.733
70. 1.583
75. 1.311
80. 1.128
90. .901
100. .657
115. .388
132G(2) FSD=.2
0.
1. .614
1.5 .610
2. .604
2.5 .616
3. .580
4. .665
5. .673
8. .776
12. .799
16. .890
20. .91
25. .958
30. .997
35. .996
40. .998
45. .965
50. 1.087
55. .975
60. .945
65. .982
70. .857
75. .950
80. .865
90. .833
100. .778
115. .685
133F(3) FSD=.2
0
1 .408
1.5 .428
2 .506
2.5 .536
3 .613
4 .829
5 .978
8 1.386
12 2.025
16 2.539
20 3.043
25 3.694
30 4.238
35 4.725
40 5.320
45 5.786
50 6.112
55 6.577
60 6.926
65 7.285
70 7.560
75 7.739
80 8.007
90 8.267
100 8.565
115 8.927
C EXP7 ENZYME CONC = 0.75 nM
H DAT TC(8)
T
141G(1) FSD=.2
0
1. 9.107
2. 8.815
4. 8.587
6. 8.375
8. 8.096
10. 7.790
13. 7.347
15 7.162
20 6.542
25 5.959
30 5.374
35 4.854
40 4.522
45 4.106
50 3.717
55 3.378
60 3.109
70 2.509
80 2.037
90 1.603
100 1.279
110 1.048
120 0.881
130 0.685
150 0.552
165 0.428
180 0.316
142G(2) FSD=.2
0
1 0.543
2 0.721
4 0.714
6 0.643
8 0.745
10 0.805
13 0.901
15 0.854
20 0.897
25 0.939
30 1.035
35 1.036
40 1.094
45 1.035
50 1.025
55 1.005
60 1.038
70 0.983
80 0.972
90 0.939
100 1.025
110 0.953
120 0.864
130 0.798
150 0.752
165 0.687
180 0.604
143F(3) FSD=.2
0
1 0.350
2 0.464
4 0.7
6 0.982
8 1.159
10 1.406
13 1.752
15 1.984
20 2.561
25 3.103
30 3.591
35 4.110
40 4.383
45 4.859
50 5.258
55 5.617
60 5.853
70 6.508
80 6.991
90 7.458
100 7.696
110 7.999
120 8.255
130 8.518
150 8.695
165 8.884
180 9.079
C THIS IS EXPERIMENT 8, ENZ CONC IS 0.4 NM SUBSTRATE CONC IS 10 NM,
H DAT TC(10)
T
151G(1) FSD=.2
1. 8.924
2. 8.906
4. 8.81
6. 8.298
8. 8.579
10. 8.451
15. 8.123
20. 7.741
25. 7.412
30. 7.069
35. 6.789
40. 6.38
45. 6.169
50. 6.026
60. 5.492
70. 5.094
80. 4.631
90. 4.307
100. 3.93
120. 3.315
140. 2.75
160. 2.398
180. 2.012
200. 1.679
220. 1.463
240. 1.186
260. 0.982
152G(2) FSD=.2
1. 0.714
C 2. 0.697
4. 0.698
C 6. 0.709
8. 0.719
C 10. 0.703
15. 0.710
C 20. 0.827
25. 0.840
C 30. 0.844
35. 0.921
C 40. 0.972
45. 1.
C 50. 0.954
60. 1.076
C 70. 1.023
80. 1.027
C 90. 1.075
100. 1.072
C 120. 1.083
140. 1.363
C 160. 1.3
180. 1.362
C 200. 1.460
220. 1.293
C 240. 1.518
260. 1.593
153F(3) FSD=1
1. 0.364
C 2. 0.397
4. 0.494
C 6. 0.575
8. 0.702
C 10. 0.846
153F(3) FSD=.2
15. 1.167
C 20. 1.432
25. 1.748
C 30. 2.087
35. 2.290
C 40. 2.649
45. 2.831
C 50. 3.020
60. 3.432
C 70. 3.904
80. 4.342
C 90. 4.618
100. 4.998
C 120. 5.602
140. 5.887
C 160. 6.302
180. 6.625
C 200. 6.86
220. 7.292
240. 7.296
C 260. 7.426
C ********** THIS IS THE END OF THE DATA ************