ArticleBiophysical journal2006
Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques.
Article in Biophysical journal, 2006. 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, 60 citations in OpenAlex.
- Membrane Protein Folding and Biogenesis: Insights from Single-Molecule Force Spectroscopy.Chemical reviews · 2026Review
- Study of Protein-Protein Interactions in Septin Assembly: Multiple amphipathic helix domains cooperate in binding to the lipid membrane.PLoS computational biology · 2026Article
- Charge distribution and helicity tune the binding of septin's amphipathic helix domain to membranes.Biophysical journal · 2025Article
- Implicit model to capture electrostatic features of membrane environment.PLoS computational biology · 2024Article
- Diverse Scientific Benchmarks for Implicit Membrane Energy Functions.Journal of chemical theory and computation · 2021Article
- Prediction of amphipathic helix-membrane interactions with Rosetta.PLoS computational biology · 2021Article
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- Chirality-Dependent Adsorption between Amphipathic Peptide and POPC Membrane.International journal of molecular sciences · 2019Article
- Tuneable poration: host defense peptides as sequence probes for antimicrobial mechanisms.Scientific reports · 2018Article
- Engineering monolayer poration for rapid exfoliation of microbial membranes.Chemical science · 2017Article
- Peptide Folding in Translocon-Like Pores.The Journal of membrane biology · 2015Article
- Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association.Journal of chemical theory and computation · 2014Article
- More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization.The Journal of chemical physics · 2014Article
- Probing the orientational distribution of dyes in membranes through multiphoton microscopy.Biophysical journal · 2012Article
- Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions.Structure (London, England : 1993) · 2012Article
- Beyond modeling: all-atom olfactory receptor model simulations.Frontiers in genetics · 2012Article
- Effects of clinically relevant MPL mutations in the transmembrane domain revealed at the atomic level through computational modeling.PloS one · 2011Article
- A comparative study on the ability of two implicit solvent lipid models to predict transmembrane helix tilt angles.The Journal of membrane biology · 2011Article
- Viruses: incredible nanomachines. New advances with filamentous phages.European biophysics journal : EBJ · 2010Review
- Construction of an implicit membrane environment for the lattice Monte Carlo simulation of transmembrane protein.Biophysical chemistry · 2010Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
A computational method to calculate the orientation of membrane-associated alpha-helices with respect to a lipid bilayer has been developed. It is based on a previously derived implicit membrane representation, which was parameterized using the structures of 46 alpha-helical membrane proteins. The method is validated by comparison with an independent data set of six transmembrane and nine antimicrobial peptides of known structure and orientation. The minimum energy orientations of the transmembrane helices were found to be in good agreement with tilt and rotation angles known from solid-state NMR experiments. Analysis of the free-energy landscape found two types of minima for transmembrane peptides: i), Surface-bound configurations with the helix long axis parallel to the membrane, and ii), inserted configurations with the helix spanning the membrane in a perpendicular orientation. In all cases the inserted configuration also contained the global energy minimum. Repeating the calculations with a set of solution NMR structures showed that the membrane model correctly distinguishes native transmembrane from nonnative conformers. All antimicrobial peptides investigated were found to orient parallel and bind to the membrane surface, in agreement with experimental data. In all cases insertion into the membrane entailed a significant free-energy penalty. An analysis of the contributions of the individual residue types confirmed that hydrophobic residues are the main driving force behind membrane protein insertion, whereas polar, charged, and aromatic residues were found to be important for the correct orientation of the helix inside the membrane.
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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.