Photoelectron Spectroscopy of Oppositely Charged Molecular Switches in the Aqueous Phase: Theory and Experiment

E Ikonnikov, M Paolino, JC Garcia-Alvarez… - The Journal of …, 2023 - ACS Publications
XUV photoelectron spectroscopy (XPS) is a powerful method for investigating the electronic
structures of molecules. However, the correct interpretation of results in the condensed …

Alternative strategy for spectral tuning of flavin-binding fluorescent proteins

MP Kabir, D Ouedraogo… - The Journal of …, 2023 - ACS Publications
iLOV is an engineered flavin-binding fluorescent protein (FbFP) with applications for in vivo
cellular imaging. To expand the range of applications of FbFPs for multicolor imaging and …

Protein conformational space at the edge of allostery: turning a nonallosteric malate dehydrogenase into an “allosterized” enzyme using evolution-guided punctual …

A Iorio, C Brochier-Armanet, C Mas… - Molecular Biology …, 2022 - academic.oup.com
We unveil the intimate relationship between protein dynamics and allostery by following the
trajectories of model proteins in their conformational and sequence spaces. Starting from a …

Ionic atmosphere effect on the absorption spectrum of a flavoprotein: a reminder to consider solution ions

BD Dratch, Y Orozco-Gonzalez, G Gadda… - The Journal of …, 2021 - ACS Publications
This study utilizes the FMN-dependent NADH: quinone oxidoreductase from Pseudomonas
aeruginosa PAO1 to investigate the effect of introducing an active site negative charge on …

Allostery and Evolution: A Molecular Journey Through the Structural and Dynamical Landscape of an Enzyme Super Family

S Coquille, CS Pereira, J Roche… - Molecular Biology …, 2025 - academic.oup.com
Allosteric regulation is a powerful mechanism for controlling the efficiency of enzymes.
Deciphering the evolutionary mechanisms by which allosteric properties have been …

An active site mutation induces oxygen reactivity in D-arginine dehydrogenase: A case of superoxide diverting protons

JA Quaye, KE Wood, C Snelgrove, D Ouedraogo… - Journal of Biological …, 2024 - ASBMB
Enzymes are potent catalysts that increase biochemical reaction rates by several orders of
magnitude. Flavoproteins are a class of enzymes whose classification relies on their ability …

Quantum‐based Modeling of Protein‐ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen

IV Polyakov, AV Nemukhin… - Molecular …, 2023 - Wiley Online Library
Modern quantum‐based methods are employed to model interaction of the flavin‐
dependent enzyme RutA with the uracil and oxygen molecules. This complex presents the …

QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase

B Grigorenko, T Domratcheva, A Nemukhin - Molecules, 2023 - mdpi.com
Oxygenase activity of the flavin-dependent enzyme RutA is commonly associated with the
formation of flavin-oxygen adducts in the enzyme active site. We report the results of …

Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase

A Iyer, RAG Reis, J Agniswamy, IT Weber… - Archives of Biochemistry …, 2022 - Elsevier
Abstract d-Arginine dehydrogenase from Pseudomonas aeruginosa (Pa DADH) catalyzes
the flavin-dependent oxidation of d-arginine and other d-amino acids. Here, we report the …

The Ionic Atmosphere Effect on the Absorption Spectrum of a Flavoprotein: A Reminder to Consider the Importance of Solution Ions

B Dratch, Y Orozco-Gonzalez, G Gadda, S Gozem - 2021 - chemrxiv.org
Ionizable residues and monoatomic ions in solution modulate enzyme catalysis and the
structural stability of proteins; however, the delicate interplay between these short-range …