Free energy methods for the description of molecular processes

C Chipot - Annual Review of Biophysics, 2023 - annualreviews.org
Efforts to combine theory and experiment to advance our knowledge of molecular processes
relevant to biophysics have been considerably enhanced by the contribution of statistical …

Along the allostery stream: Recent advances in computational methods for allosteric drug discovery

D Ni, Z Chai, Y Wang, M Li, Z Yu, Y Liu… - Wiley …, 2022 - Wiley Online Library
Allostery is a universal, biological phenomenon in which orthosteric sites are fine‐tuned by
topologically distal allosteric sites triggered by perturbations, such as ligand binding, residue …

[HTML][HTML] Delineating the activation mechanism and conformational landscape of a class BG protein-coupled receptor glucagon receptor

Y Wang, M Li, W Liang, X Shi, J Fan, R Kong… - Computational and …, 2022 - Elsevier
Class BG protein-coupled receptors (GPCRs) are important targets in the treatment of
metabolic syndrome and diabetes. Although multiple structures of class B GPCRs–G protein …

Hazardous shortcuts in standard binding free energy calculations

M Blazhynska… - The Journal of …, 2022 - ACS Publications
Calculating the standard binding free energies of protein–protein and protein–ligand
complexes from atomistic molecular dynamics simulations in explicit solvent is a problem of …

Autopromotion of K-Ras4B feedback activation through an SOS-mediated long-range allosteric effect

X He, K Du, Y Wang, J Fan, M Li, D Ni, S Lu… - Frontiers in Molecular …, 2022 - frontiersin.org
The Ras-specific guanine nucleotide exchange factors Son of Sevenless (SOS) regulates
Ras activation by converting inactive GDP-bound to active GTP-bound states. The catalytic …

Understanding the P-loop conformation in the determination of inhibitor selectivity toward the hepatocellular carcinoma-associated dark kinase STK17B

C Liu, Z Li, Z Liu, S Yang, Q Wang… - Frontiers in Molecular …, 2022 - frontiersin.org
As a member of the death-associated protein kinase family of serine/threonine kinases, the
STK17B has been associated with diverse diseases such as hepatocellular carcinoma …

Insights into the allosteric effect of SENP1 Q597A mutation on the hydrolytic reaction of SUMO1 via an integrated computational study

M Ji, Z Chai, J Chen, G Li, Q Li, M Li, Y Ding, S Lu, G Ju… - Molecules, 2022 - mdpi.com
Small ubiquitin-related modifier (SUMO)-specific protease 1 (SENP1) is a cysteine protease
that catalyzes the cleavage of the C-terminus of SUMO1 for the processing of SUMO …

Decoupling the dynamic mechanism revealed by FGFR2 mutation-induced population shift

Y Zhang, XL Yin, M Ji, Y Chen… - Journal of Biomolecular …, 2024 - Taylor & Francis
The fibroblast growth factor receptor 2 (FGFR2) is a key component in cellular signaling
networks, and its dysfunctional activation has been implicated in various diseases including …

Improving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple …

M Blazhynska… - Journal of Chemical …, 2023 - ACS Publications
Accurate evaluation of protein–ligand binding free energies in silico is of paramount
importance for understanding the mechanisms of biological regulation and providing a …

Tetracycline derivatives inhibit plasmodial cysteine protease falcipain-2 through binding to a distal allosteric site

JE Hernandez Gonzalez, LN Alberca… - Journal of Chemical …, 2021 - ACS Publications
Allosteric inhibitors regulate enzyme activity from remote and usually specific pockets. As
they promise an avenue for less toxic and safer drugs, the identification and characterization …