ArticleBioscience reports2022
Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?
Article in Bioscience reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 46 citations in OpenAlex.
- Binding orientation of weakly associating membrane peripheral proteins via membrane paramagnetic relaxation enhancement NMR.Communications chemistry · 2026Article
- Spider venom phospholipase D toxin structure: Interfacial binding site, mechanism, activation, and head group preference.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Decoding Protein-Membrane Binding Interfaces from Surface-Fingerprint-Based Geometric Deep Learning and Molecular Dynamics Simulations.Journal of chemical information and modeling · 2026Article
- Characterization of Membrane Binding and Protein-Lipid Interactions at the Atomic Level with an Accelerated HMMM Model.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales.Current opinion in structural biology · 2025Review
- The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations.Journal of molecular biology · 2025Review
- Atomistic Mechanism of Lipid Membrane Binding for Blood Coagulation Factor VIII with Molecular Dynamics Simulations on a Microsecond Time Scale.The journal of physical chemistry. B · 2025Article
- Review
- BioDolphin as a comprehensive database of lipid-protein binding interactions.Communications chemistry · 2024Article
- A Membrane-Assisted Mechanism for the Release of Ceramide from the CERT START Domain.The journal of physical chemistry. B · 2024Article
- Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM.PLoS computational biology · 2024Article
- Comprehensive Characterization of LAT1 Cholesterol-Binding Sites.Journal of chemical theory and computation · 2024Article
- Elucidating the Membrane Binding Process of a Disordered Protein: Dynamic Interplay of Anionic Lipids and the Polybasic Region.ACS physical chemistry Au · 2024Article
- Cooperative Membrane Binding of HIV-1 Matrix Proteins.The journal of physical chemistry. B · 2024Article
- Molecular dynamics simulations of HIV-1 matrix-membrane interactions at different stages of viral maturation.Biophysical journal · 2024Article
- The role of Phafin proteins in cell signaling pathways and diseases.Open life sciences · 2024Review
- Alchemical Free Energy Calculations on Membrane-Associated Proteins.Journal of chemical theory and computation · 2023Review
- Article
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- A coarse-grained molecular dynamics investigation on spontaneous binding of AβComputational and structural biotechnology journal · 2023Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. To provide a detailed molecular view of PMP interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. Here, we outline recent attempts to characterise these binding interactions, focusing on both intracellular proteins, such as phosphatidylinositol phosphate (PIP)-binding domains, and extracellular proteins such as glycolipid-binding bacterial exotoxins. We compare methods used to identify and analyse lipid-binding sites from simulation data and highlight recent work characterising the energetics of these interactions using free energy calculations. We describe how improvements in methodologies and computing power will help MD simulations to continue to contribute to this field in the future.
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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 OpenQuestion graph.