Zajac, J. W. P. | bioRxiv Science

bioRxiv2026

Protein-Solvent Shape Complementarity as a Unifying Principle in Excipient-Mediated Protein Thermal Stability

Excipient effects on protein stability are critical for biological formulations, yet their selection remains largely empirical. Here, we use molecular dynamics simulations to define unifying metrics of protein-excipient interactions at atomistic resolution. Enhanced sampling simulations of fast-folding miniproteins, including Trpzip, WAAAH-helix (an alanine-rich -helix), and Trp-Cage, were performed to capture folding transitions across diverse excipient conditions. We identified a general stabilization mechanism based on shape complementarity between protein networks and surrounding solvent networks. Stabilizing excipients were found to form solvent structures that preferentially complement each protein, as well as residues central to known folding pathways. This framework enables a unifying approach to mechanism-based excipient selection across diverse protein and solvent chemistries. More broadly, by treating protein and solvent as dynamically coupled partners, it provides a transferable strategy for understanding solvent-mediated effects in complex molecular systems.

biophysics↗

bioRxiv2025

Cracking the Capsid Code: A Computationally-Feasible Approach for Investigating Virus-Excipient Interactions in Biologics Design

The efficacy and equitable distribution of viral biologics, including vaccines and virus-like particles, is hindered due to their inherently low shelf life. To increase the longevity of such products, formulations are typically developed with small molecule additives known as excipients. Finding the correct excipients for a biological formulation is a costly and time-consuming process due to the large excipient design space and unknown mechanisms underlying excipient-virus interactions. Molecular dynamics simulations are, in theory, well-equipped to efficiently investigate these mechanisms. However, the massive size of fully assembled viral capsids, the protein shell that encapsulates the viral genome, demands computational resources well beyond the requirements of conventional simulations. There exists a need for a novel method that enables high-throughput investigations of virus-excipient interactions at the molecular level and at atomistic resolution. Here, we introduce CapSACIN -- a computational framework for Capsid Surface Abstraction and Computationally-Induced Nanofragmentation. We demonstrate the applicability of this workflow to a model non-enveloped virus, porcine parvovirus (PPV). Through simulations of PPV surface models, we observe that the 2-fold axis of symmetry is significantly weaker at the molecular level than the 3- or 5-fold axes of symmetry. Further, we present results demonstrating excellent agreement with experimentally determined excipient effects on PPV thermal stability.

biophysics↗