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 …

Targeting key proteins involved in transcriptional regulation for cancer therapy: Current strategies and future prospective

H Pei, W Guo, Y Peng, H Xiong… - Medicinal Research …, 2022 - Wiley Online Library
The key proteins involved in transcriptional regulation play convergent roles in cellular
homeostasis, and their dysfunction mediates aberrant gene expressions that underline the …

[HTML][HTML] Allostery: allosteric cancer drivers and innovative allosteric drugs

R Nussinov, M Zhang, R Maloney, Y Liu, CJ Tsai… - Journal of molecular …, 2022 - Elsevier
Here, we discuss the principles of allosteric activating mutations, propagation downstream of
the signals that they prompt, and allosteric drugs, with examples from the Ras signaling …

[HTML][HTML] G protein-coupled receptors (GPCRs): advances in structures, mechanisms, and drug discovery

M Zhang, T Chen, X Lu, X Lan, Z Chen… - Signal Transduction and …, 2024 - nature.com
G protein-coupled receptors (GPCRs), the largest family of human membrane proteins and
an important class of drug targets, play a role in maintaining numerous physiological …

[HTML][HTML] Protein conformational ensembles in function: roles and mechanisms

R Nussinov, Y Liu, W Zhang, H Jang - RSC Chemical Biology, 2023 - pubs.rsc.org
The sequence-structure-function paradigm has dominated twentieth century molecular
biology. The paradigm tacitly stipulated that for each sequence there exists a single, well …

Design and engineering of allosteric communications in proteins

J Chen, YL Vishweshwaraiah, NV Dokholyan - Current opinion in structural …, 2022 - Elsevier
Allostery in proteins plays an important role in regulating protein activities and influencing
many biological processes such as gene expression, enzyme catalysis, and cell signaling …

Molecular dynamics simulations establish the molecular basis for the broad allostery hotspot distributions in the tetracycline repressor

Y Yuan, J Deng, Q Cui - Journal of the American Chemical …, 2022 - ACS Publications
It is imperative to identify the network of residues essential to the allosteric coupling for the
purpose of rationally engineering allostery in proteins. Deep mutational scanning analysis …

[HTML][HTML] Machine learning approaches in predicting allosteric sites

F Nerín-Fonz, Z Cournia - Current Opinion in Structural Biology, 2024 - Elsevier
Allosteric regulation is a fundamental biological mechanism that can control critical cellular
processes via allosteric modulator binding to protein distal functional sites. The advantages …

Alchemical Free Energy Calculations on Membrane-Associated Proteins

M Papadourakis, H Sinenka, P Matricon… - Journal of Chemical …, 2023 - ACS Publications
Membrane proteins have diverse functions within cells and are well-established drug
targets. The advances in membrane protein structural biology have revealed drug and lipid …

Predicting protein–membrane interfaces of peripheral membrane proteins using ensemble machine learning

A Chatzigoulas, Z Cournia - Briefings in Bioinformatics, 2022 - academic.oup.com
Abnormal protein–membrane attachment is involved in deregulated cellular pathways and
in disease. Therefore, the possibility to modulate protein–membrane interactions represents …