ArticleInternational journal of molecular sciences2018
Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids.
Article in International journal of molecular sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 24 citations in OpenAlex.
- DPPC Membrane Under Lateral Compression and Stretching to Extreme Limits: Phase Transitions and Rupture.Membranes · 2025Article
- Charge distribution and helicity tune the binding of septin's amphipathic helix domain to membranes.Biophysical journal · 2025Article
- Exploring the Binding Mechanism of ADGRG2 Through Metadynamics and Biochemical Analysis.International journal of molecular sciences · 2024Article
- Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer.The journal of physical chemistry. B · 2024Article
- Computer simulations of protein-membrane systems.Progress in molecular biology and translational science · 2020Article
- Energy Landscapes of Ligand Motion Inside the Tunnel-Like Cavity of Lipid Transfer Proteins: The Case of the Pru p 3 Allergen.International journal of molecular sciences · 2019Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
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Abstract
Thermodynamics of the permeation of amino acids from water to lipid bilayers is an important first step for understanding the mechanism of cell-permeating peptides and the thermodynamics of membrane protein structure and stability. In this work, we employed bias-exchange metadynamics simulations to simulate the membrane permeation of all 20 amino acids from water to the center of a dipalmitoylphosphatidylcholine (DPPC) membrane (consists of 256 lipids) by using both directional and torsion angles for conformational sampling. The overall accuracy for the free energy profiles obtained is supported by significant correlation coefficients (correlation coefficient at 0.5-0.6) between our results and previous experimental or computational studies. The free energy profiles indicated that (1) polar amino acids have larger free energy barriers than nonpolar amino acids; (2) negatively charged amino acids are the most difficult to enter into the membrane; and (3) conformational transitions for many amino acids during membrane crossing is the key for reduced free energy barriers. These results represent the first set of simulated free energy profiles of membrane crossing for all 20 amino acids.
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