ArticleThe journal of physical chemistry letters2016
Association of Peripheral Membrane Proteins with Membranes: Free Energy of Binding of GRP1 PH Domain with Phosphatidylinositol Phosphate-Containing Model Bilayers.
Article in The journal of physical chemistry letters, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 56 citations in OpenAlex.
- The SIMDA framework maps PIP2-binding sites regulating the KCNQ1 channel.Nature communications · 2026Article
- GōMartini 3: From large conformational changes in proteins to environmental bias corrections.Nature communications · 2025Article
- Lysosomal PIPProceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations.Journal of molecular biology · 2025Review
- Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution.Nature communications · 2024Article
- Molecular dynamics simulations of human α-defensin 5 (HD5) crossing gram-negative bacterial membrane.PloS one · 2023Article
- Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C.Journal of chemical information and modeling · 2022Article
- Dissecting peripheral protein-membrane interfaces.PLoS computational biology · 2022Article
- Two cooperative binding sites sensitize PI(4,5)PScience advances · 2022Article
- Systematic simulation of the interactions of pleckstrin homology domains with membranes.Science advances · 2022Article
- Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?Bioscience reports · 2022Article
- Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design.Pharmaceuticals (Basel, Switzerland) · 2021Review
- CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations.Journal of chemical theory and computation · 2021Article
- Binding of CaStructure (London, England : 1993) · 2021Article
- Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations.Journal of chemical theory and computation · 2021Article
- Flexible pivoting of dynamin pleckstrin homology domain catalyzes fission: insights into molecular degrees of freedom.Molecular biology of the cell · 2021Article
- Capturing Choline-Aromatics Cation-π Interactions in the MARTINI Force Field.Journal of chemical theory and computation · 2020Article
- Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes.Journal of computational chemistry · 2020Article
- The energetics of protein-lipid interactions as viewed by molecular simulations.Biochemical Society transactions · 2020Review
- Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes.Science advances · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Understanding the energetics of peripheral protein-membrane interactions is important to many areas of biophysical chemistry and cell biology. Estimating free-energy landscapes by molecular dynamics (MD) simulation is challenging for such systems, especially when membrane recognition involves complex lipids, e.g., phosphatidylinositol phosphates (PIPs). We combined coarse-grained MD simulations with umbrella sampling to quantify the binding of the well-explored GRP1 pleckstrin homology (PH) domain to model membranes containing PIP molecules. The experimentally observed preference of GRP1-PH for PIP3 over PIP2 was reproduced. Mutation of a key residue (K273A) within the canonical PIP-binding site significantly reduced the free energy of PIP binding. The presence of a noncanonical PIP-interaction site, observed experimentally in other PH domains but not previously in GRP1-PH, was also revealed. These studies demonstrate how combining coarse-grained simulations and umbrella sampling can unmask the molecular basis of the energetics of interactions between peripheral membrane proteins and complex cellular membranes.
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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.