ArticleProtein science : a publication of the Protein Society2006
Positioning of proteins in membranes: a computational approach.
Article in Protein science : a publication of the Protein Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 papers, 1 of them a synthesis that pooled it.
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
118 citing papers in PubMed, 1 synthesis or guideline pooled it, 256 citations in OpenAlex.
- Meta-Analysis of Permeability Literature Data Shows Possibilities and Limitations of Popular Methods.Molecular pharmaceutics · 2025Pooled it
- Structure and Membrane Interactions of Two Helices from Mycobacterium tuberculosis FtsL, One Transmembrane and One Amphipathic.Journal of the American Chemical Society · 2026Article
- Structural basis for the ion selectivity of potassium-chloride cotransporter KCC4 revealed by cryo-EM titration.Biophysics reports · 2026Article
- PRED-TMSdeep: Prediction of Transmembrane Topology and Signal Peptides Using Deep Learning.Biology · 2026Article
- A membrane insertion code for intrinsically disordered proteins.bioRxiv : the preprint server for biology · 2026Article
- MPLID (Membrane Protein-Lipid Interaction Database): A Large-Scale Experimental Resource of Residue-Level Protein-Lipid Contacts.GigaScience · 2026Article
- Allosteric Modulation of Cannabinoid Type 1 Receptor by ZCZ011: Integration of In Vitro Pharmacology and Molecular Dynamics Simulation.ACS bio & med chem Au · 2025Article
- Wzy 3D structural models correlate with inter-repeat unit glycosidic bond configuration in pneumococcal capsule polysaccharides.Microbiology spectrum · 2025Article
- Prediction of αBiophysical journal · 2025Article
- X-Ray Crystal and Cryo-Electron Microscopy Structure Analysis Unravels How the Unique Thylakoid Lipid Composition Is Utilized by CytochromeMembranes · 2025Article
- Flexibility-Induced Collective Behavior Drives Symmetry Breaking in Discrimination of Undesired Ions.JACS Au · 2025Article
- Functional characterization and phenotyping of RAB2A and Lactadherin/MFGE8 as boar sperm zona pellucida binding proteins.Frontiers in cell and developmental biology · 2025Article
- Activation of the Influenza B M2 Proton Channel (BM2).Biochemistry · 2024Article
- Activation of the influenza B M2 proton channel (BM2).bioRxiv : the preprint server for biology · 2024Article
- In Silico drug repurposing pipeline using deep learning and structure based approaches in epilepsy.Scientific reports · 2024Article
- The structure assessment web server: for proteins, complexes and more.Nucleic acids research · 2024Article
- Extracellular Kir2.1Circulation research · 2024Article
- Structure and mechanisms of transport of human Asc1/CD98hc amino acid transporter.Nature communications · 2024Article
- EncoMPASS: An encyclopedia of membrane proteins analyzed by structure and symmetry.Structure (London, England : 1993) · 2024Article
- Viper Venom Phospholipase A2 Database: The Structural and Functional Anatomy of a Primary Toxin in Envenomation.Toxins · 2024Article
58 more citing papers are in PubMed but not listed here.
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 at 2 institutions in 1 country.
Funding
Abstract
A new computational approach has been developed to determine the spatial arrangement of proteins in membranes by minimizing their transfer energies from water to the lipid bilayer. The membrane hydrocarbon core was approximated as a planar slab of adjustable thickness with decadiene-like interior and interfacial polarity profiles derived from published EPR studies. Applicability and accuracy of the method was verified for a set of 24 transmembrane proteins whose orientations in membranes have been studied by spin-labeling, chemical modification, fluorescence, ATR FTIR, NMR, cryo-microscopy, and neutron diffraction. Subsequently, the optimal rotational and translational positions were calculated for 109 transmembrane, five integral monotopic and 27 peripheral protein complexes with known 3D structures. This method can reliably distinguish transmembrane and integral monotopic proteins from water-soluble proteins based on their transfer energies and membrane penetration depths. The accuracies of calculated hydrophobic thicknesses and tilt angles were approximately 1 A and 2 degrees, respectively, judging from their deviations in different crystal forms of the same proteins. The hydrophobic thicknesses of transmembrane proteins ranged from 21.1 to 43.8 A depending on the type of biological membrane, while their tilt angles with respect to the bilayer normal varied from zero in symmetric complexes to 26 degrees in asymmetric structures. Calculated hydrophobic boundaries of proteins are located approximately 5 A lower than lipid phosphates and correspond to the zero membrane depth parameter of spin-labeled residues. Coordinates of all studied proteins with their membrane boundaries can be found in the Orientations of Proteins in Membranes (OPM) database:http://opm.phar.umich.edu/.
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.