Biology subjects

Sarupria, S.

Publications and source records attributed to Sarupria, S..

3 recordsLinked to original sources

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↗

bioRxiv2021

Rational engineering of low temperature activity in thermoalkalophilic Geobacillus thermocatenulatus lipase

While thermophilic enzymes have thermostability desired for broad industrial applications, they can lose activity at ambient temperatures far from their optimal. Engineering cold activity into thermophilic enzymes has the potential to broaden the range of temperatures resulting in significant activity (i.e., decreasing the temperature dependence of kcat). Even though it has been widely suggested that cold temperature enzyme activity results from active flexibility that is at odds with the rigidity necessary for thermostable enzymes; however, directed evolution experiments have shown us these properties are not mutually exclusive. In this study, rational protein engineering was used to introduce flexibility inducing mutations around the active sites of Geobacillus thermocatenulatus lipase (GTL). Two mutants were found to have enhanced specific activity compared to wild-type at temperatures between 283 K to 363 K with p-nitrophenol butyrate but not with larger substrates. Kinetics assay revealed both mutations resulted in psychrophilic traits, such as lower activation enthalpy and more negative entropy values compared to wild type in all substrates. Furthermore, the mutants had significantly improved thermostability compared to wild type enzyme, which proves that it is feasible to improve the cold activity without trade-off. Our study provides insight into the enzyme cold adaptation mechanism and design principles for engineering cold activity into thermostable enzymes.

biochemistry↗