ArticleBiochimica et biophysica acta2016
Computational approaches to detect allosteric pathways in transmembrane molecular machines.
Article in Biochimica et biophysica acta, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Cholesterol allosteric modulation of the oxytocin receptor.Biophysical journal · 2025Article
- Conformational dynamics of the active state of β-arrestin 1.bioRxiv : the preprint server for biology · 2025Article
- Advances of Predicting Allosteric Mechanisms Through Protein Contact in New Technologies and Their Application.Molecular biotechnology · 2024Review
- Article
- The Structural Basis of the Activity Cliff in Modafinil-Based Dopamine Transporter Inhibitors.Biomolecules · 2024Article
- Subtle Structural Modification of a Synthetic Cannabinoid Receptor Agonist Drastically Increases its Efficacy at the CB1 Receptor.ACS chemical neuroscience · 2023Article
- Connected Component Analysis of Dynamical Perturbation Contact Networks.The journal of physical chemistry. B · 2023Article
- A Novel "Activation Switch" Motif Common to All Aminergic Receptors.Journal of chemical information and modeling · 2023Review
- The Molecular Mechanism of Positive Allosteric Modulation at the Dopamine D1 Receptor.International journal of molecular sciences · 2023Article
- The molecular mechanism of positive allosteric modulation at the dopamine D1 receptor.bioRxiv : the preprint server for biology · 2023Article
- Binding preference at the μ-opioid receptor underlies distinct pharmacology of cyclopropyl versus valeryl analogs of fentanyl.Neuropharmacology · 2023Article
- Mapping allosteric pathway in NIa-Pro using computational approach.Quantitative biology (Beijing, China) · 2023Article
- Article
- Sparse group selection and analysis of function-related residue for protein-state recognition.Journal of computational chemistry · 2022Article
- A comprehensive evaluation of the potential binding poses of fentanyl and its analogs at the µ-opioid receptor.Computational and structural biotechnology journal · 2022Article
- Exploring the putative mechanism of allosteric modulations by mixed-action kappa/mu opioid receptor bitopic modulators.Future medicinal chemistry · 2021Article
- Community Network Analysis of Allosteric Proteins.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Data-guided Multi-Map variables for ensemble refinement of molecular movies.The Journal of chemical physics · 2020Article
- A structural basis for how ligand binding site changes can allosterically regulate GPCR signaling and engender functional selectivity.Science signaling · 2020Article
- Integrated Computational Approaches and Tools forAllosteric Drug Discovery.International journal of molecular sciences · 2020Review
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Authors and funding
5 authors.
Funding
Abstract
Many of the functions of transmembrane proteins involved in signal processing and transduction across the cell membrane are determined by allosteric couplings that propagate the functional effects well beyond the original site of activation. Data gathered from breakthroughs in biochemistry, crystallography, and single molecule fluorescence have established a rich basis of information for the study of molecular mechanisms in the allosteric couplings of such transmembrane proteins. The mechanistic details of these couplings, many of which have therapeutic implications, however, have only become accessible in synergy with molecular modeling and simulations. Here, we review some recent computational approaches that analyze allosteric coupling networks (ACNs) in transmembrane proteins, and in particular the recently developed Protein Interaction Analyzer (PIA) designed to study ACNs in the structural ensembles sampled by molecular dynamics simulations. The power of these computational approaches in interrogating the functional mechanisms of transmembrane proteins is illustrated with selected examples of recent experimental and computational studies pursued synergistically in the investigation of secondary active transporters and GPCRs. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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