(325a) Enhanced Sampling Molecular Simulations of Protein-Polymer Interactions in Pegylated Lysozyme Bioconjugates

Protein-polymer bioconjugates are a class of hybrid biological molecules that strategically utilize the natural specificity of proteins and the synthetic modularity of polymers. Recently, the design and assembly of protein-polymer bioconjugates have gained much attention due to the potential applications of these bioconjugates in drug therapeutics, biomineralization, and biosensing. The conjugation of polymers to protein surfaces can enhance key properties of the biomolecule such as its structural stability and affinity for specific targets, while maintaining its natural biological functions. To optimally design and synthesize these hybrid molecules, the underlying mechanisms that influence their enhanced thermodynamic and kinetic properties must be understood at the molecular level. Computational approaches such as molecular dynamics (MD) simulations provide an excellent entry point for such studies, via the development of accurate and compatible molecular models for studying broad variations of the protein-polymer bioconjugate system.

Previously, we showcased the development of a computational framework for systematically building and testing models of protein-polymer bioconjugates that can be readily scaled for high-throughput processing. This methodological workflow encompasses various in silico tools such as Python, C++, CGENFF, Gaussian, Avogadro, ChemDraw, VMD, and GROMACS. Herein, we built and tested this framework on hen egg-white lysozyme conjugated with activated methoxy polyethylene glycol (mPEG) at two chain lengths. MD simulations were carried out on these PEG-ylated lysozymes to elucidate structural changes stemming from multi-sited conjugation in the context of protein thermostability and solubility. Furthermore, we performed enhanced sampling (well-tempered metadynamics) MD simulations to fully explore the configurational space of conjugated polymers and its influence from protein surface chemistries. To this end, we successfully constructed configurational free energy landscapes to determine the conformational favorability of individual conjugated polymer chains within the specific biochemical environment of their conjugation sites. We then identified residue-specific protein-polymer contacts and various non-bonded interactions (hydrogen-bonding, hydrophobic/hydrophilic, electrostatic) driven by features of the protein surface chemistry. In this work, we demonstrated that such a computational framework, when combined with fundamental analysis methods such as MD, can support the rational design of novel bioconjugates with improved efficacy. From the direct implementation of this framework, we gained new atomistic insights into bioconjugate structural properties and the biochemical effects of protein surface residues in driving conjugated polymer behavior.