The stochastic formalism for the Bethe-Salpeter equation (BSE) has previously been improved using an exact separation of the effective interaction, W, into W = {W - vW} + vW, where the latter is any translationally invariant, two-body interaction. This enabled an efficient stochastic evaluation of W, overcoming the most expensive part of the BSE algorithm. However, vW is system specific, requiring the computationally heavy W to still be generated for each system. Here, we present a generalized parametrization of vW for efficient and accurate time-dependent Hartree-Fock spectral calculations. This method makes use of molecular systems with similar static dielectric responses, grouping them into families. By a single parametrization of the inverse dielectric function using a fourth-order polynomial with an error-function tail, we eliminate the need for the system-specific individual fitting of vW. This approach produces BSE-quality optical spectra while significantly reducing the computational overhead, offering a versatile and transferable framework applicable to diverse molecular families. We demonstrate the effectiveness of this method across highly conjugated polymethine cyanine dyes as well as planar and curved hydrocarbons.

AMP activated protein kinase (AMPK) is a central regulator of cellular energy homeostasis, with a variety of downstream targets throughout the cell. In response to cell stress, AMPK binding to AMP and phosphorylation of AMPK by upstream kinases liver kinase B1 (LKB1) and calcium-calmodulin dependent protein kinase kinase 2 (CaMKK2) fully activate AMPK to restore metabolic homeostasis. AMPK has downstream targets throughout the cell at unique locations, but the mechanisms behind subcellular AMPK activity are still unclear. We previously developed a single-fluorophore excitation-ratiometric AMPK activity reporter (ExRai AMPKAR), which enables detection of subtle, subcellular AMPK activity. We used ExRai AMPKAR to uncover mechanisms for energy stress-induced subcellular AMPK activity. However, how other forms of stress, including oxidative stress, influence subcellular AMPK activity is largely unknown. Using ExRai AMPKAR, we find that oxidative stress induced by hydrogen peroxide results in location-specific differences in AMPK activity, which has implications for the subcellular regulation of metabolism. To understand the mechanism behind ROS induced AMPK activity, we first correlated measured subcellular AMPK dynamics with cellular oxidative state and ATP dynamics by using a hydrogen peroxide sensor to measure cellular oxidation levels and an ATP biosensor. Then, we assessed the impact of upstream kinases on subcellular ROS-induced AMPK activity, finding AMPK activity is dependent on LKB1.

Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a diverse class of natural products derived from precursor peptides through enzymatic tailoring. While bacterial RiPP biosynthesis is well studied, it remains rare in fungi, despite their rich repertoire of bioactive compounds. Phomopsins are hexapeptide mycotoxins from Phomopsis leptostromiformis that target the vinca domain of tubulin, exhibiting strong antimitotic activity and potential as antitumor leads. Phomopsin A was recently identified as a fungal RiPP, with its biosynthetic gene cluster containing several UstYa family proteins. These DUF3328 (Domain of Unknown Function) proteins are widespread in fungi and are involved in diverse chemical transformations such as oxidative cyclization, chlorination, and desaturation. In this study, we investigate a phomopsin A–like biosynthetic gene cluster from Neurospora crassa, which encodes four DUF3328 homologues: phomYb, phomYc, phomYd, and phomYf. Previous gene knockout experiments in related clusters demonstrated that homologues like phomYc and phomYd are responsible for amino acid desaturation, a novel function among UstYa proteins. We aim to heterologously express this cluster in vitro and systematically characterize the role of each DUF3328 protein in modifying the core peptide. Our work will provide new insights into the enzymatic versatility of fungal RiPP biosynthesis and expand genome mining efforts for discovering novel natural products with unique structural features.

Long-term exposure to per- and polyfluoroalkyl substances (PFAS), a class of anthropogenic synthetic chemicals, have created concerns regarding their toxicological implications and accumulation in biological systems. The PFAS family is widely used in the production of items ranging from fast-food containers to firefighting foams, making them extremely prevalent in the lives of the general population. The fluorinated-carbon structure of PFAS is responsible for their competitive protein-ligand binding and also accounts for their extreme stability and long half-lives, making them virtually non-biodegradable and reinforcing their nickname “forever chemicals”. Past projects have theorized their ability to disrupt biological processes including thyroid function, tumorigenesis, and organ disease. Given the aforementioned research and data, the current study attempts to address the challenges of past work as well as the knowledge gap in computational fields by examining how the molecular structure of PFAS impacts binding affinity in the peroxisome proliferator-activated receptor (PPAR) family of cellular nuclear receptors. Employed methods include the development of molecular mechanics force fields with ab initio calculations and free energy perturbation calculations with molecular dynamics. The use of computational methods allows the study to achieve its designed purpose by ultimately producing validated force field parameters that serve as a strong foundation for future molecular dynamic studies.

Peroxy radicals (RO₂) undergo a variety of reactions in the atmosphere, including unimolecular and bimolecular pathways. These pathways may lead to products with comparatively low vapor pressure that promote the formation of secondary organic aerosols (SOA), or can propagate the radical cycle. Typically, in atmospheric chamber experiments, compounds are oxidized by OH, O₃, Cl, or NO₃, followed by addition of O₂, to form the RO₂. Studying RO₂ with these oxidation methods comes with the caveat of dealing with the production of other radical products, such as HO₂, which makes isolated study of RO₂ difficult. This study aims to find if synthesis of alkyl halides can be used to generate precursors that create specific RO₂ radicals, in this case, CH3COCH2O2. Iodoacetone was synthesized via a halogen replacement reaction of chloroacetone and potassium iodide. We found that photolysis of synthesized iodoacetone generated substantial products consistent with the acetonyl peroxyradical. Our results demonstrate that the alternative pathway of alkyl iodide photolysis generates signals evident of RO₂ chemistry, while minimizing the levels of HO₂ that would have been generated from alternate oxidation sources. Future extensions of this project will analyze the role structure and functional groups play in RO₂ chemistry.