Polysaccharide-Protein Complexes in a Coarse-Grained Model.

Area of Science:

• Computational chemistry
• Biophysics
• Molecular modeling

Background:

• Coarse-grained (CG) models simplify complex molecular systems for large-scale simulations.
• Accurate CG models are crucial for studying carbohydrate-protein interactions, particularly in biological contexts like cellulose degradation.

Purpose of the Study:

• To construct and validate two CG models of hexaoses (six-monosaccharide units).
• To determine effective stiffness constants and nonbonded interaction parameters for these models.
• To investigate the interactions between hexaoses and proteins within catalytic complexes.

Main Methods:

• Construction of two CG models: one based on monomer centers of mass, another on C4 atoms.
• Determination of stiffness constants using all-atom simulations, Boltzmann inversion (BI), and an energy-based (EB) method.
• Modeling nonbonded interactions using Lennard-Jones potentials.
• Analysis of hexaose-Man5B catalytic complexes and their contact energies.

Main Results:

• The C4-atom-based CG model demonstrated better definition and suitability for protein interactions.
• Effective stiffness constants varied between hexaoses and differed from crystalline cellulose Iβ.
• Nonbonded couplings in hexaoses were stronger than protein hydrogen bonds, with EB method showing better agreement with experimental data.
• Contact energies in hexaose-Man5B complexes were significantly stronger than protein hydrogen bonds.

Conclusions:

• The C4-atom-based CG model provides a robust framework for studying carbohydrate-protein interactions.
• The determined parameters highlight the strength of inter-sugar interactions, impacting enzymatic processes.
• Coarse-grained simulations of hexaose-protein complexes are consistent with all-atom studies.