Hi,
I am working on DNA duplex models with subsitutued benzene rings. When I
calculated the binding free energies for the duplex formations (say strand
A and complimetary strand B), I got comparable values for MMGBA and MMPBSa
outputs. But the E(El) and E(GBor PB) values are very high but with
opposite signs and are of very closer in magnitude.
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -52.6968 4.8595
0.0486
EEL 1453.4885 43.6661
0.4367
EGB -1445.0181 41.7015
0.4170
ESURF -5.3338 0.1814
0.0018
DELTA G gas 1400.7917 43.6956
0.4370
DELTA G solv -1450.3519 41.6927
0.4169
DELTA G binding = -49.5602 +/- 4.9116
0.0491
-------------------------------------------------------------------------------
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -52.6968 4.8595
0.0486
EEL 1453.4885 43.6661
0.4367
EPB -1444.5930 41.6394
0.4164
ECAVITY -4.3753 0.2063
0.0021
DELTA G gas 1400.7917 43.6956
0.4370
DELTA G solv -1448.9683 41.6264
0.4163
DELTA G binding = -48.1765 +/- 5.4109
0.0541
My questions:
[1] How do we interpret these values EEL of 1453.4885 and EGB of
-1445.0181 (or EPB of 1444.5930).
As negative sign indicates repulsive interactions, EEL of 1453.4885 shows a
repulsive binding energy for the formation of DNA duplex from its strands.
So it means solvation stabilzes the DNA duplex. Am I right?
Also wen I replaced with more number of benzene rings with A-T pairs in the
duplex, I expected there will be loss of electrostatic interactions as the
subsituted benzene rings cannot form a strong hydrogen bonds. Again EEl and
EGB are similar magniude with opposite sign.
What I should give an explanation for these observation.
Energy
Component
A-T
Bz1
Bz2
Bz3
Bz4
MM (Gas)
Evdw
-51.6
-52.7
-52.6
-49.4
-64.5
Eelec
1459.6
1453.5
1453.1
1447.4
1440.2
Egas
1408.0
1400.8
1400.5
1398.0
1375.7
GBSA (Solvation)
EGB
-1460.0
-1445.0
-1439.2
-1427.6
-1399.0
Esur
-5.3
-5.3
-5.5
-5.5
-7.0
ΔGsol
-1465.3
-1450.4
-1444.7
-1433.2
-1406.1
PBSA (Solvation)
EGB
-1462.1
-1444.6
-1440.8
-1428.5
-1404.9
Esurf
-4.2
-4.4
-4.5
-4.6
-6.0
ΔGsol
-1466.3
-1449.0
-1445.3
-1433.1
-1410.9
Total Binding Free Energy
ΔGMMGBSA
-57.3
-49.6
-44.2
-35.1
-30.4
ΔGMMPBSA
-58.3
-48.2
-44.8
-35.1
-35.2
T
--
Dr. Rajesh Kumar Raju
Research Associate
Texas A & M University
College Station, TX 77840
#979-422-5647
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Received on Sat Feb 15 2014 - 04:30:02 PST
