My project is binding energy calculation using mmpbsa for protein-protein interaction. I have used g_mmpbsa for binding energy calculation. I am getting very irrelevant energy for 1BRS (581..562 KJ/mol) and its mutant 1BRS_R59A (398.652 KJ/mol )and 1BRS_H102A (492.685 kj/mol) using dielectric constant 2
Did you calculate the average binding free energy? How many snapshots did you use, and what are the contributions of different terms, polar and non-polar, to the total average binding free energy? These kind of analyses may help you to identify the problem with your values.
What if explicit treatment of water-mediated hydrogen-bonding network at the protein-protein interface is of crucial importance for obtaining reliable binding free energies?
Hiqmet Kamberaj Sir, Here is my protocol
Molecular Dynamics Simulations. The MD simulations were performed using the gromacs with the Duan et al. force field. Simulation were performed using TIP3P explicit water molecules. Complex was solvated by explicit waters that extended 10 Å from any edge of the box to the protein atoms. Counterions were added to the boxes to neutralize the system. In each of the simulations, the system was initially minimized to remove bad contacts using the steepest descent algorithm followed by conjugated gradient. The systems were then subjected to 2 ns of heating (in NVT ensemble) in which the temperature was gradually raised to 300 K, followed by 6 ns runs in the NPT ensemble. The equations of motion were integrated with a 2 fs time-step and the nonbonded interactions were 10 Å cutoff in explicit solvent simulations, respectively. After that 10 ns md_production.
For mmpbsa calculation. I have removed the water from the trajectory and used 2000 frames from 1 ns - 10 ns. solute dielectric constant - 4
Dielectric constant - 4
md_production: 1ns-10ns (2000frame)
WILD_FLT
van der Waal energy = -230.195 +/- 31.781 kJ/mol
Electrostattic energy = -253.937 +/- 41.826 kJ/mol
Polar solvation energy = 381.113 +/- 99.424 kJ/mol
SASA energy = -6.810 +/- 0.905 kJ/mol
Binding energy (delta_G) = -109.829 +/- 59.096 kJ/mol
1FLT_K16A
van der Waal energy = -304.134 +/- 29.615 kJ/mol
Electrostattic energy = -264.362 +/- 34.798 kJ/mol
Polar solvation energy = 330.799 +/- 73.629 kJ/mol
SASA energy = -8.234 +/- 0.841 kJ/mol
Binding energy (delta_G) = -245.931 +/- 53.127 kJ/mol
mutant_delta_G - wild_delta_G (delta_delta_G) :136.102 kj/mol (32.53 kcal/mol)
WILD_BRS
van der Waal energy = -344.251 +/- 21.823 kJ/mol
Electrostattic energy = -518.020 +/- 39.872 kJ/mol
Polar solvation energy = 693.293 +/- 73.071 kJ/mol
SASA energy = -8.703 +/- 0.547 kJ/mol
Binding energy (delta_G) = -177.682 +/- 48.838 kJ/mol
BRS_R59A
van der Waal energy = -264.138 +/- 21.982 kJ/mol
Electrostattic energy = -347.904 +/- 37.609 kJ/mol
Polar solvation energy = 467.050 +/- 90.165 kJ/mol
SASA energy = -6.909 +/- 0.758 kJ/mol
Binding energy (delta_G) = -151.901 +/- 62.346 kJ/mol
mutant_delta_G - wild_delta_G (delta_delta_G) = 25.781 kj/mol ( 6.161 kcal/mol)
BRS_H102A
van der Waal energy = -318.438 +/- 27.896 kJ/mol
Electrostattic energy = -568.160 +/- 34.770 kJ/mol
Polar solvation energy = 843.424 +/- 83.187 kJ/mol
SASA energy = -9.039 +/- 0.649 kJ/mol
Binding energy (delta_G)= -52.212 +/- 53.247 kJ/mol
mutant_delta_G - wild_delta_G (delta_delta_G) =125.47 kj/mol (29.988 kcal/mol)
The number of frames analyzed (2000) is extremely small: Collect structures every (let's say) 10 MD steps, i.e. every 20 fs (450,000 frames per 9 ns): Find out that MMPBSA is not less time-consuming than are the methods based on linear response theory . . . not to mention that the latter offer better prospects of actually providing accurate binding free energies . . .
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Decimal places in the energies (expressed in kcal/mol or kJ/mol) carry no useful information: Round the final binding free energies to integer values.
Hi.
I performed similar analysis for a protein protein complex with 424 and 248 residues for each protomer but with solvent. The trajectory length was 10ns. Dielectric constant was 2 and solvent dielectric was set to 75. The result was vague. The binding energy was almost +900 kj/mol.
g_mmpbsa -f xtc -s tpr -n ndx -i pbsa.mdp -pdie 2 -pbsa -decomp`
group chosen :13 and 14 [ Chain A and chain B respectively]
Do I do anything wrong?
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