ArticleJournal of chemical theory and computation2021
Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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Who cites it
12 citing papers in PubMed, 30 citations in OpenAlex.
- Does Complexation of Plasma Membrane Cholesterol with Phospholipids Determine its Transbilayer Distribution?The Journal of membrane biology · 2026Article
- Sequence constraints predispose Class D GPCRs to follow an atypical activation mechanism.bioRxiv : the preprint server for biology · 2026Article
- Effects of Membrane Cholesterol on the Structure and Function of Selected Class A GPCRs─Challenges and Future Perspectives.Biochemistry · 2025Review
- A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1.Nature communications · 2024Article
- Estimating the Cholesterol Affinity of Integral Membrane Proteins from Experimental Data.Biochemistry · 2024Article
- LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.Nature communications · 2023Article
- Hepatocyte cholesterol content modulates glucagon receptor signalling.Molecular metabolism · 2022Article
- The role of cholesterol binding in the control of cholesterol by the Scap-Insig system.European biophysics journal : EBJ · 2022Article
- Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?Bioscience reports · 2022Article
- PyLipID: A Python Package for Analysis of Protein-Lipid Interactions from Molecular Dynamics Simulations.Journal of chemical theory and computation · 2022Article
- Towards design of drugs and delivery systems with the Martini coarse-grained model.QRB discovery · 2022Review
- Regulation of Cholesterol Binding to the Receptor Patched1 by its interactions With the Ligand Sonic Hedgehog (Shh).Frontiers in molecular biosciences · 2022Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-electron microscopy (cryo-EM) densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities using experimental or simulation methods. Here, we develop a method for determining protein-lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our results with free energies obtained from density-based equilibrium methods and with potential of mean force calculations, getting good agreement with respect to the ranking of affinities for different sites. Thus, our binding saturation method provides a robust, high-throughput alternative for determining the relative consequence of individual sites seen in, e.g., cryo-EM derived membrane protein structures surrounded by an array of ancillary lipid densities.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.