Modeling Chromatography Binding through Molecular Dynamics Simulations with Resin Fragments.

ABSTRACT: Accurate atomistic modeling of the interactions of a chromatography resin with a solute can inform the selection of purification conditions for a product, an important problem in the biotech and pharmaceutical industries. We present a molecular dynamics simulation-based approach for the qualitative prediction of interaction sites (specificity) and retention times (affinity) of a protein for a given chromatography resin. We mimicked the resin with an unrestrained ligand composed of the resin headgroup coupled with successively larger fragments of the agarose backbone. The interactions of the ligand with the protein are simulated in an explicit solvent using the Replica Exchange Molecular Dynamics enhanced sampling approach in conjunction with Hydrogen Mass Repartitioning (REMD-HMR). We comp

SUBMITTER: Stanevich V 

PROVIDER: S-EPMC11181327 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature