Cysteine oxidation in proteins: structure, biophysics, and simulation

D Garrido Ruiz, A Sandoval-Perez, AV Rangarajan… - Biochemistry, 2022 - ACS Publications
Cysteine side chains can exist in distinct oxidation states depending on the pH and redox
potential of the environment, and cysteine oxidation plays important yet complex regulatory …

Constant ph molecular dynamics simulations: Current status and recent applications

VM de Oliveira, R Liu, J Shen - Current opinion in structural biology, 2022 - Elsevier
Many important protein functions are carried out through proton-coupled conformational
dynamics. Thus, the ability to accurately model protonation states dynamically has wide …

GPU-accelerated all-atom particle-mesh Ewald continuous constant pH molecular dynamics in Amber

JA Harris, R Liu, V Martins de Oliveira… - Journal of chemical …, 2022 - ACS Publications
Constant pH molecular dynamics (MD) simulations sample protonation states on the fly
according to the conformational environment and user specified pH conditions; however, the …

Widespread, reversible cysteine modification by methylglyoxal regulates metabolic enzyme function

JS Coukos, CW Lee, KS Pillai, KJ Liu… - ACS Chemical …, 2022 - ACS Publications
Methylglyoxal (MGO), a reactive metabolite byproduct of glucose metabolism, is known to
form a variety of posttranslational modifications (PTMs) on nucleophilic amino acids. For …

Why all the fury over furin?

EEA Osman, A Rehemtulla… - Journal of medicinal …, 2021 - ACS Publications
Analysis of the SARS-CoV-2 sequence revealed a multibasic furin cleavage site at the
S1/S2 boundary of the spike protein distinguishing this virus from SARS-CoV. Furin, the best …

Chemoselective Caging of Carboxyl Groups for On‐Demand Protein Activation with Small Molecules

YD Petri, CS Gutierrez… - Angewandte Chemie …, 2023 - Wiley Online Library
Tools for on‐demand protein activation enable impactful gain‐of‐function studies in
biological settings. Thus far, however, proteins have been chemically caged at primarily Lys …

The physiological role of thiol‐based redox sensors in plant defense signaling

HB Chae, SB Bae, SK Paeng, SD Wi… - New …, 2023 - Wiley Online Library
Plants have developed multilayered defense strategies to adapt and acclimate to the
kaleidoscopic environmental changes that rapidly produce reactive oxygen species (ROS) …

One-pot biocatalytic synthesis of nylon monomers from cyclohexanol using Escherichia coli-based concurrent cascade consortia

S Sarak, TP Khobragade, H Jeon, AD Pagar, P Giri… - Green …, 2021 - pubs.rsc.org
We developed a multienzyme biocatalytic cascade with high atom efficiency and a self-
sufficient redox network for the synthesis of nylon monomers without adding auxiliary …

Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors

DT Patel, PJ Stogios, L Jaroszewski… - Molecular Systems …, 2024 - embopress.org
Legionella pneumophila utilizes the Dot/Icm type IVB secretion system to deliver hundreds
of effector proteins inside eukaryotic cells to ensure intracellular replication. Our …

PEP-patch: electrostatics in protein–protein recognition, specificity, and antibody developability

VJ Hoerschinger, F Waibl, ND Pomarici… - Journal of Chemical …, 2023 - ACS Publications
The electrostatic properties of proteins arise from the number and distribution of polar and
charged residues. Electrostatic interactions in proteins play a critical role in numerous …