Interplay between conformational entropy and solvation entropy in protein–ligand binding

ML Verteramo, O Stenstrom, MM Ignjatovic… - Journal of the …, 2019 - ACS Publications
Understanding the driving forces underlying molecular recognition is of fundamental
importance in chemistry and biology. The challenge is to unravel the binding …

Human adipose glycerol flux is regulated by a pH gate in AQP10

K Gotfryd, AF Mósca, JW Missel, SF Truelsen… - Nature …, 2018 - nature.com
Obesity is a major threat to global health and metabolically associated with glycerol
homeostasis. Here we demonstrate that in human adipocytes, the decreased pH observed …

pH-responsive antimicrobial peptide with selective killing activity for bacterial abscess therapy

Z Wang, Q Li, J Li, L Shang, J Li, S Chou… - Journal of Medicinal …, 2022 - ACS Publications
The unusual acidic pH of the abscess milieu is an adverse factor that decreases the
therapeutic efficacy of traditional antibiotics. Moreover, avoiding both the undesired killing of …

Entropy–Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C

J Wallerstein, V Ekberg, MM Ignjatović, R Kumar… - JACS Au, 2021 - ACS Publications
Molecular recognition is fundamental to biological signaling. A central question is how
individual interactions between molecular moieties affect the thermodynamics of ligand …

Protonation states of homocitrate and nearby residues in nitrogenase studied by computational methods and quantum refinement

L Cao, O Caldararu, U Ryde - The Journal of Physical Chemistry …, 2017 - ACS Publications
Nitrogenase is the only enzyme that can break the triple bond in N2 to form two molecules of
ammonia. The enzyme has been thoroughly studied with both experimental and …

QM/MM study of the reaction mechanism of the dehydratase domain from mammalian fatty acid synthase

FE Medina, RPP Neves, MJ Ramos… - ACS Catalysis, 2018 - ACS Publications
Dehydratase (DH) is a catalytic domain of the mammalian fatty acid synthase (mFAS), a
multidomain enzyme with seven different active sites that work in tandem to carry out the …

F pocket flexibility influences the tapasin dependence of two differentially disease‐associated MHC Class I proteins

ET Abualrous, S Fritzsche, Z Hein… - European Journal of …, 2015 - Wiley Online Library
The human MHC class I protein HLA‐B* 27: 05 is statistically associated with ankylosing
spondylitis, unlike HLA‐B* 27: 09, which differs in a single amino acid in the F pocket of the …

Potts Hamiltonian Models and Molecular Dynamics Free Energy Simulations for Predicting the Impact of Mutations on Protein Kinase Stability

A Thakur, J Gizzio, RM Levy - The Journal of Physical Chemistry …, 2024 - ACS Publications
Single-point mutations in kinase proteins can affect their stability and fitness, and
computational analysis of these effects can provide insights into the relationships among …

Catalytic reaction mechanism of glyoxalase II: A quantum mechanics/molecular mechanics study

J Shirazi, S Jafari, U Ryde, M Irani - The Journal of Physical …, 2023 - ACS Publications
Methylglyoxal (MG) is a reactive and toxic compound produced in carbohydrate, lipid, and
amino acid metabolism. The glyoxalase system is the main detoxifying route for MG and …

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

S Genheden, U Ryde… - Journal of Computational …, 2015 - Wiley Online Library
The most general way to improve the accuracy of binding‐affinity calculations for protein–
ligand systems is to use quantum‐mechanical (QM) methods together with rigorous …