ArticleJournal of chemical theory and computation2018
Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- Accurate determination of the preferred aggregation number of a micelle-encapsulated membrane protein dimer.Biophysical journal · 2026Article
- Free energy of collagen-mimetic peptide dimerization and implications for fibrillization.Biophysical journal · 2026Article
- Accurate determination of the preferred aggregation number of a micelle-encapsulated membrane protein dimer.bioRxiv : the preprint server for biology · 2025Article
- STIM1 transmembrane helix dimerization captured by AI-guided transition path sampling.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Free Energy, Rates, and Mechanism of Transmembrane Dimerization in Lipid Bilayers from Dynamically Unbiased Molecular Dynamics Simulations.The journal of physical chemistry. B · 2025Article
- The Role of Cholesterol in M2 Clustering and Viral Budding Explained.Journal of chemical theory and computation · 2025Article
- Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane.Journal of chemical theory and computation · 2024Article
- A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes.Journal of chemical theory and computation · 2023Article
- The role of structural heterogeneity in the homodimerization of transmembrane proteins.The Journal of chemical physics · 2023Article
- Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer.Structure (London, England : 1993) · 2023Article
- On Computing Equilibrium Binding Constants for Protein-Protein Association in Membranes.Journal of chemical theory and computation · 2022Article
- Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide.JACS Au · 2022Article
- Modulation of adenosine A2a receptor oligomerization by receptor activation and PIPStructure (London, England : 1993) · 2021Article
- Conformational Clamping by a Membrane Ligand Activates the EphA2 Receptor.Journal of molecular biology · 2021Article
- Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors.International journal of molecular sciences · 2021Review
- Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model.Journal of chemical theory and computation · 2021Article
- Martini 3: a general purpose force field for coarse-grained molecular dynamics.Nature methods · 2021Article
- Atomistic mechanism of transmembrane helix association.PLoS computational biology · 2020Article
- Inserting Small Molecules across Membrane Mixtures: Insight from the Potential of Mean Force.Biophysical journal · 2020Article
- Cutting antiparallel DNA strands in a single active site.Nature structural & molecular biology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Atomistic simulations have recently been shown to be sufficiently accurate to reversibly fold globular proteins and have provided insights into folding mechanisms. Gaining similar understanding from simulations of membrane protein folding and association would be of great medical interest. All-atom simulations of the folding and assembly of transmembrane protein domains are much more challenging, not least due to very slow diffusion within the lipid bilayer membrane. Here, we focus on a simple and well-characterized prototype of membrane protein folding and assembly, namely the dimerization of glycophorin A, a homodimer of single transmembrane helices. We have determined the free energy landscape for association of the dimer using the CHARMM36 force field. We find that the native structure is a metastable state, but not stable as expected from experimental estimates of the dissociation constant and numerous experimental structures obtained under a variety of conditions. We explore two straightforward approaches to address this problem and demonstrate that they result in stable dimers with dissociation constants consistent with experimental data.
Indexed as
Identifiers
What OpenQuestion holds
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.