Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics...

Area of Science:

• Computational chemistry
• Biophysics
• Molecular modeling

Background:

• Accurately calculating protein-carbohydrate binding energies computationally is difficult.
• Hevein is a plant lectin that binds to monosaccharides and disaccharides.

Purpose of the Study:

• To estimate binding energies of hevein with GlcNAc and (GlcNAc)2 using expanded ensemble molecular dynamics (EEMD) simulations.
• To calculate enthalpy and entropy components of binding energy.
• To compare EEMD accuracy with other computational methods.

Main Methods:

• Expanded ensemble molecular dynamics (EEMD) simulation with double decoupling.
• Calculation of binding energies, enthalpy, and entropy.
• Comparison with thermodynamic integration and MM/GBSA.

Main Results:

• EEMD estimated binding energies for hevein-carbohydrate interactions were within ±0.5 kcal of experimental data.
• EEMD demonstrated higher accuracy compared to thermodynamic integration and MM/GBSA.
• This is the first report of EEMD for biomolecular binding energy estimation.

Conclusions:

• EEMD is a highly accurate computational method for determining protein-carbohydrate binding energies.
• The approach provides reliable enthalpy and entropy contributions.
• EEMD offers a promising alternative for studying biomolecular interactions.