Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 19, Issue 3, Pages -Publisher
MDPI
DOI: 10.3390/ijms19030885
Keywords
metadynamics simulation; permeation of amino acids; translocation free energy
Funding
- National Natural Science Foundation of China [31670727, 11447004, 11504043, 61271378, 61671107, 61540025]
- Natural Science Foundation of Shandong Province, China [ZR2016CQ15, ZR2014AL014, ZR2014JL006]
- Taishan Scholars Program of Shandong province of China
- Technology Development Project of Shandong Province [2014GNC110025]
- National Health and Medical Research Council of Australia [1059775]
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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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