Biology subjects

Soler, J.

Publications and source records attributed to Soler, J..

3 recordsLinked to original sources

bioRxiv2024

A computationally designed panel of diverse and selective peroxygenases for terpene oxyfunctionalization

Enzyme engineering has a critical role in the transition to economical, low-energy and environmentally friendly chemical production. Current approaches relying on costly iterations of mutation and selection are limited to reactions with a straightforward experimental readout and struggle to address mutational epistasis. We focus on unspecific peroxygenases (UPOs), prized engineering targets due to their ability to oxyfunctionalize diverse organic molecules of industrial and environmental value. To address the lack of scalable screening for UPO functions, we applied enzyme-design calculations to focus experiments. Starting from an AlphaFold2 model of MthUPO, the automated FuncLib algorithm generated 50 diverse active-site multipoint designs--all of which were functional. Screening against nine diverse terpenes revealed large improvements and new oxyfunctionalization products, resulting in molecules of high pharmaceutical and industrial value. We rationalized observed specificity changes using AI-based docking and molecular dynamics simulations, providing molecular insights that could generalize to engineering other UPOs. Thus, computational design and modeling can dramatically accelerate the urgently needed green transition of the chemical industry. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/615329v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@3f8dceorg.highwire.dtl.DTLVardef@76ee48org.highwire.dtl.DTLVardef@15f2a7org.highwire.dtl.DTLVardef@edba31_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

Structural and mechanistic views of enzymatic, heme-dependent nitrogen-nitrogen bond formation

Molecules with nitrogen-nitrogen (N-N) bonds constitute a large group of clinically important drugs, and various synthetic approaches have been developed to construct functional groups like hydrazines, diazos, pyrazoles, and N-nitrosos. While hundreds of N-N-containing specialized natural metabolites have also been discovered, little is known about the underlying enzymatic mechanisms that have evolved for N-N bond formation. In order to directly form a single N(sp3)-N(sp3) bond, enzymes must reverse the typical nucleophilicity of one nitrogen. Here, we report structural and mechanistic interrogations of the piperazate synthase PipS, a heme-dependent enzyme that catalyzes an N-N bond forming cyclization of N5-OH-L-ornithine to give the non-proteinogenic amino acid L-piperazic acid. We show that PipS can process a variety of N-substituted hydroxylamines, to give either an imine or an N-N bond, in a substrate-specific manner. Using a combination of structural and biochemical experiments, computational studies, and spectroscopic characterization, we propose that heme-dependent dehydration and N-N bond formation in PipS proceed through divergent pathways, which may stem from a shared nitrenoid intermediate that effectively reverses the nucleophilicity of the hydroxylamine nitrogen. Our work expands the current knowledge of enzymatic N-N bond formation, and delineates the catalytic versatility of a heme cofactor, paving the way for future development of genetically encoded biocatalysts for N-N bond formation.

biochemistry↗

bioRxiv2020

Modeling invasion patterns in the glioblastoma battlefield

Glioblastoma is the most aggressive tumor of the central nervous system, due to its great infiltration capacity. Understanding the mechanisms that regulate the Glioblastoma invasion front is a major challenge with preeminent potential clinical relevance. In the in1ltration front, the key features of its dynamics relate to biochemical and biomechanical aspects, which result in extended cellular protrusions, known as tumor microtubes. The coordination of metalloproteinase expression, extracellular matrix degradation, and integrin activity emerges as leading mechanism that facilitates Glioblastoma expansion and in1ltration in uncontaminated brain regions. We propose a novel multidisciplinary approach, based on in vivo experiments in Drosophila and mathematical models, for the proteins dynamics at the front of Glioblastoma, with a predictive value of the tumor progression.

cancer biology↗