Biology subjects

Perry, S. L.

Publications and source records attributed to Perry, S. L..

5 recordsLinked to original sources

bioRxiv2026

Graphene Device for High-Temperature Crystallography Visualizes How Enzymatic Reactivity is Rooted in Ensemble Probability

Life exists at temperatures ranging from -20 to 122 {degrees}C. However, the majority of high-resolution structural data in the Protein Data Bank (PDB) were obtained at cryogenic temperatures, where biological function is halted due to the lack of thermal fluctuations. To overcome this fundamental problem and directly link structure to biological function, we have created a graphene-based device that significantly extends the temperature range for high-resolution macromolecular X-ray diffraction data collection. Using the new device, we obtained models of the transition state ensembles for a psychrophilic, a mesophilic, and a thermophilic homolog of the enzyme orotidine 5-monophosphate decarboxylase from -173 to 65 {degrees}C. The data reveal how the active site ensemble structure at the transition state of each homolog changes with temperature, directly visualizing how the measured catalytic rates are rooted in the ensemble probabilities of reactive distances. The multi-temperature transition state ensembles further illuminate why cryogenic data, although useful, are inaccurate for describing biological processes.

biophysics↗

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↗

bioRxiv2024

Scalable Fabrication of an Array-Type Fixed-Target Device for Automated Room Temperature X-ray Protein Crystallography

1.X-ray crystallography is one of the leading tools to analyze the 3-D structure, and therefore, function of proteins and other biological macromolecules. Traditional methods of mounting individual crystals for X-ray diffraction analysis can be tedious and result in damage to fragile protein crystals. Furthermore, the advent of serial crystallography methods explicitly require the mounting of large numbers of crystals. To address this need, we have developed a device that facilitates the straightforward mounting of protein crystals for diffraction analysis, and that can be easily manufactured at scale. Inspired by grid-style devices that have been reported in the literature, we have developed an X-ray compatible microfluidic device that can be used to trap protein crystals in an array configuration, while also providing excellent optical transparency, a low X-ray background, and compatibility with the robotic sample handling and environmental controls used at synchrotron macromolecular crystallography beamlines. At the Stanford Synchrotron Radiation Lightsource (SSRL), these capabilities allow for fully remote-access data collection at controlled humidity conditions. Furthermore, we have demonstrated continuous manufacturing of these devices via roll-to-roll fabrication to enable cost-effective and efficient large-scale production.

molecular biology↗

bioRxiv2017

Partitioning and Enhanced Self-Assembly of Actin in Polypeptide Coacervates

Biomolecules exist and function in cellular micro-environments that control their spatial organization, local concentration and biochemical reactivity. Due to the complexity of native cytoplasm, the development of artificial bioreactors and cellular mimics to compartmentalize, concentrate and control the local physicochemical properties is of great interest. Here, we employ self-assembling polypeptide coacervates to explore the partitioning of the ubiquitous cytoskeletal protein actin into liquid polymer-rich droplets. We find that actin spontaneously partitions into coacervate droplets and is enriched by up to {approx}30-fold. Actin polymerizes into micrometer-long filaments and, in contrast to the globular protein BSA, these filaments localize predominately to the droplet periphery. We observe up to a 50-fold enhancement in the actin filament assembly rate inside coacervate droplets, consistent with the enrichment of actin within the coacervate phase. Together these results suggest that coacervates can serve as a versatile platform in which to localize and enrich biomolecules to study their reactivity in physiological environments.\n\nSIGNIFICANCE STATEMENTLiving cells harbor many protein-rich membrane-less organelles, the biological functions of which are defined by compartment composition and properties. Significant differences between the physico-chemical properties of these crowded compartments and the dilute solutions in which biochemical reactions are traditionally studied pose a major challenge for understanding regulation of organelle composition and component activity. Here, we report the spontaneous partitioning and accelerated polymerization of the cytoskeletal protein actin inside model polypeptide coacervates as a proof-of-concept demonstration of coacervates as bioreactors for studying biomolecular reactions in cell-like environments. Our work introduces exciting avenues for the use of synthetic polymers to control the physical and biological properties of bioreactors in vitro, enabling studies of biochemical reactions in cell-like micro-environments.

biophysics↗