ArticleBiophysical journal2007
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- In Silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices.Journal of computational chemistry · 2017Article
- Atomic-level description of protein-lipid interactions using an accelerated membrane model.Biochimica et biophysica acta · 2016Review
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.Biochimica et biophysica acta · 2016Review
- Exploring the Formation and the Structure of Synaptobrevin Oligomers in a Model Membrane.Biophysical journal · 2016Article
- Structural Characterizations of the Fas Receptor and the Fas-Associated Protein with Death Domain Interactions.The protein journal · 2016Article
- Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution.The Journal of membrane biology · 2015Review
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- Membrane-induced structural rearrangement and identification of a novel membrane anchor in talin F2F3.Biophysical journal · 2014Article
- 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
- Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers.Journal of computational chemistry · 2014Article
- Atomistic detailed mechanism and weak cation-conducting activity of HIV-1 Vpu revealed by free energy calculations.PloS one · 2014Article
- Article
- Molecular dynamics simulations reveal the HIV-1 Vpu transmembrane protein to form stable pentamers.PloS one · 2013Article
- Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model.Biophysical journal · 2012Article
- The intertransmembrane region of Kaposi's sarcoma-associated herpesvirus modulator of immune recognition 2 contributes to B7-2 downregulation.Journal of virology · 2012Article
- In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV.Journal of molecular modeling · 2012Article
- Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides.Cellular and molecular life sciences : CMLS · 2011Review
- ORF8a of SARS-CoV forms an ion channel: experiments and molecular dynamics simulations.Biochimica et biophysica acta · 2011Article
- Viral channel forming proteins - modeling the target.Biochimica et biophysica acta · 2011Review
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3 authors.
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Abstract
The assembly of simple transmembrane helix homo-oligomers is studied by combining a generalized Born implicit membrane model with replica exchange molecular dynamics simulations to sample the conformational space of various oligomerization states and the native oligomeric conformation. Our approach is applied to predict the structures of transmembrane helices of three proteins--glycophorin A, the M2 proton channel, and phospholamban--using only peptide sequence and the native oligomerization state information. In every case, the methodology reproduces native conformations that are in good agreement with available experimental structural data. Thus, our method should be useful in the prediction of native structures of transmembrane domains of other peptides. When we ignore the experimental constraint on the native oligomerization state and attempt de novo prediction of the structure and oligomerization state based only on sequence and simple energetic considerations, we identify the pentamer as the most stable oligomer for phospholamban. However, for the glycophorin A and the M2 proton channels, we tend to predict higher oligomers as more stable. Our studies demonstrate that reliable predictions of the structure of transmembrane helical oligomers can be achieved when the observed oligomerization state is imposed as a constraint, but that further efforts are needed for the de novo prediction of both structure and oligomeric state.
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