ArticleBiophysical journal2006
Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch.
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 72 papers.
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72 citing papers in PubMed, 177 citations in OpenAlex.
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- Topology-Driven Discovery of Transmembrane ProteinbioRxiv : the preprint server for biology · 2024Article
- Energetics of the Transmembrane Peptide Sorting by Hydrophobic Mismatch.The journal of physical chemistry letters · 2024Article
- Sensing membrane voltage by reorientation of dipolar transmembrane peptides.Biophysical journal · 2024Article
- Functional regulation of aquaporin dynamics by lipid bilayer composition.Nature communications · 2024Article
- Studying Conformational Properties of Transmembrane Domain of KCNE3 in a Lipid Bilayer Membrane Using Molecular Dynamics Simulations.Membranes · 2024Article
- Lipoteichoic Acids Are Essential for Pneumococcal Colonization and Membrane Integrity.Journal of innate immunity · 2024Article
- Membrane defects as a generalized driving force for membrane protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Electron paramagnetic resonance spectroscopic characterization of the human KCNE3 protein in lipodisq nanoparticles for structural dynamics of membrane proteins.Biophysical chemistry · 2023Article
- Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition.bioRxiv : the preprint server for biology · 2023Article
- PEO-Biomacromolecules · 2022Article
- Spiers Memorial Lecture: Analysis andFaraday discussions · 2021Article
- Active SBiochimica et biophysica acta. Biomembranes · 2020Article
- Characterization of the Human KCNQ1 Voltage Sensing Domain (VSD) in Lipodisq Nanoparticles for Electron Paramagnetic Resonance (EPR) Spectroscopic Studies of Membrane Proteins.The journal of physical chemistry. B · 2020Article
- Insights Into ProteinFrontiers in molecular neuroscience · 2018Review
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- 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
12 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hydrophobic mismatch, which is the difference between the hydrophobic length of trans-membrane segments of a protein and the hydrophobic width of the surrounding lipid bilayer, is known to play a role in membrane protein function. We have performed molecular dynamics simulations of trans-membrane KALP peptides (sequence: GKK(LA)nLKKA) in phospholipid bilayers to investigate hydrophobic mismatch alleviation mechanisms. By varying systematically the length of the peptide (KALP15, KALP19, KALP23, KALP27, and KALP31) and the lipid hydrophobic length (DLPC, DMPC, and DPPC), a wide range of mismatch conditions were studied. Simulations of durations of 50-200 ns show that under positive mismatch, the system alleviates the mismatch predominantly by tilting the peptide and to a smaller extent by increased lipid ordering in the immediate vicinity of the peptide. Under negative mismatch, alleviation takes place by a combination of local bilayer bending and the snorkeling of the lysine residues of the peptide. Simulations performed at a higher peptide/lipid molar ratio (1:25) reveal slower dynamics of both the peptide and lipid relative to those at a lower peptide/lipid ratio (1:128). The lysine residues have favorable interactions with specific oxygen atoms of the phospholipid headgroups, indicating the preferred localization of these residues at the lipid/water interface.
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