Engineering topics

Kim, Hoshin

Publications and source records attributed to Kim, Hoshin.

10 records

DOE OSTI2024

SAXS of murine amelogenin identifies a persistent dimeric species from pH 5.0 to 8.0

Amelogenin is an intrinsically disordered protein essential to tooth enamel formation in mammals. Here, using advanced small angle X-ray scattering (SAXS) capabilities at synchrotrons and computational models, we revisited measuring the quaternary structure of murine amelogenin as a function of pH and phosphorylation at serine-16. The SAXS data shows that at the pH extremes, amelogenin exists as an extended monomer at pH 3.0 (R g = 38.4 Å) and nanospheres at pH 8.0 (R g = 84.0 Å), consistent with multiple previous observations. At pH 5.0 and above there was no evidence for a significant population of monomeric species. Instead, at pH 5.0 ~ 80% of the population is a heterogenous dimeric species that increases to ~ 100% at pH 5.5. The dimer population was observed at all pH > 5 conditions in dynamic equilibrium with a species in the pentamer range at pH < 6.5 and nanospheres at pH 8.0. At pH 8.0 ~ 40% of the amelogenin still remained in the dimeric state. In general, serine-16 phosphorylation of amelogenin appears to modestly stabilize the population of the dimeric species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Chemical diversity in angiosperms − monoterpene synthases control complex reactions that provide the precursors for ecologically and commercially important monoterpenoids

SUMMARY Monoterpene synthases (MTSs) catalyze the first committed step in the biosynthesis of monoterpenoids, a class of specialized metabolites with particularly high chemical diversity in angiosperms. In addition to accomplishing a rate enhancement, these enzymes manage the formation and turnover of highly reactive carbocation intermediates formed from a prenyl diphosphate substrate. At each step along the reaction path, a cationic intermediate can be subject to cyclization, migration of a proton, hydride, or alkyl group, or quenching to terminate the sequence. However, enzymatic control of ligand folding, stabilization of specific intermediates, and defined quenching chemistry can maintain the specificity for forming a signature product. This review article will discuss our current understanding of how angiosperm MTSs control the reaction environment. Such knowledge allows inferences about the origin and regulation of chemical diversity, which is pertinent for appreciating the role of monoterpenoids in plant ecology but also for aiding commercial efforts that harness the accumulation of these specialized metabolites for the food, cosmetic, and pharmaceutical industries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

X-ray absorption spectroscopy and theoretical investigations of the effect of extended ligands in potassium organic matter interaction

Potassium (K) is an essential nutrient for plant growth, and despite its abundance in soil, most of the K is structurally bound in minerals, limiting its bioavailability and making this soil K reservoir largely inaccessible to plants. Microbial biochemical weathering has been shown to be a promising pathway to sustainably increase plant available K. However, the mechanisms underpinning microbial K uptake, transformation, storage, and sharing are poorly resolved. Here, to better understand the controls on microbial K transformations, we performed K K-edge x-ray absorption near-edge structure (XANES) spectroscopy on K-organic salts, including acetate, citrate, nitrate, oxalate, and tartrate, which are frequently observed as low molecular weight organic acids secreted by soil microbes, as well as humic acid, which acts as a proxy for higher molecular weight organic acids. The organic salts display feature-rich K XANES spectra, each demonstrating numerous unique features spanning ~13 eV range across the absorption edge. In contrast, the spectra for humic acid have one broad, wide feature across the same energy range. We used a combination of time-dependent density functional theory and the Bethe–Salpeter equation based approach within the OCEAN code to simulate the experimental spectra for K-nitrate (KNO 3 ) and K-citrate [K 3 (C 6 H 5 O 7 )·H 2 O] to identify the electronic transitions that give rise to some of the outlying and unique spectral features in the organic salts. KNO 3 has both the lowest and highest lying energy features, and K 3 (C 6 H 5 O 7 )·H 2 O is produced by several soil microbes and is effective at mineral weathering. Our results analyze the K-organic salt bonding in detail to elucidate why the spectral shapes differ and indicate that the K K-edge XANES spectra are associated with the entire ligand despite similar first-shell bonding environments around the K center. The improved understanding of K bonding environments with organic ligands and their use for interpretation of the K-XANES spectra provides an important toolkit to understand how K is transformed by microbial processes and made bioavailable for plant uptake.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023