Development of A Modeling Framework for Characterizing Protein–Polymer Bioconjugates with Enhanced Sampling Molecular Dynamics Simulations
Year: 2026
Type: preprint
Abstract: Protein–polymer bioconjugates represent a class of biomaterials that leverages the molecular specificity of proteins and the tunability of synthetic polymers. Strategic conjugation of polymers to protein surfaces can enhance key biomolecular properties such as structural stability and target affinity while preserving the biological functions of the native protein. The rational design of these hybrid biomolecules demands a detailed understanding of the underlying molecular mechanisms governing protein–polymer interfacial behavior. Critically, strong interfacial interactions can impose substantial energetic barriers that hinder conformational sampling in molecular dynamics (MD) studies of this system. Enhanced sampling methods are highly effective for overcoming such limitations in the simulation of biomolecular interfaces. However, the opportunity to apply enhanced sampling methods toward navigating the complex interfacial landscapes of protein–polymer bioconjugates has yet to be realized by the field. In this study, we showcase the development of a molecular modeling framework that leverages enhanced sampling to extensively characterize protein–polymer bioconjugates. To validate this framework, we constructed two bioconjugate models of hen egg-white lysozyme grafted with activated methoxy polyethylene glycol (mPEG) chains of varying lengths at multiple surface-exposed lysine sites. We then performed all-atom MD simulations of these PEGylated constructs, augmented with well-tempered metadynamics (WTM) to fully explore their conformational landscapes under multi-site polymer conjugation. This approach yielded converged free energy surfaces (FES) characterizing the thermodynamic favorability of grafted mPEG chain conformations at each conjugation site. We also identified key protein contact residues and site-specific non-bonded interactions responsible for bioconjugate stabilization. This study demonstrates a novel application of enhanced sampling methodologies in bioconjugate systems for characterizing site-specific conjugation effects on protein–polymer interfacial energetics and structural dynamics in the context of protein surface chemistry. More broadly, applying this methodological framework across diverse polymer chemistries and protein variants can elucidate molecular design rules for engineering bioconjugates with precise properties and functions for applications spanning biotechnology, energy, and health.
Source: ChemRxiv
Institution: University of Florida
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: G1354291523, G2586609609, G2796167598, MRI Collaborative Consortium: Acquisition of a Shared Supercomputer by the Rocky Mountain Advanced Computing Consortium, G4958434179, MRI Collaborative Consortium: Acquisition of a Shared Supercomputer by the Rocky Mountain Advanced Computing Consortium, G6942722009, G8929392486, Computational tools for new pharmaceutical paradigms
OpenAlex ID: W7221116977