Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids
Zanxia Cao 1,2
, Yunqiang Bian 1, Guodong Hu 1,2, Liling Zhao 1,2, Zhenzhen Kong 1,3, Yuedong Yang 4,5, Jihua Wang 1,2,* and Yaoqi Zhou 1,4,*
, Yunqiang Bian 1, Guodong Hu 1,2, Liling Zhao 1,2, Zhenzhen Kong 1,3, Yuedong Yang 4,5, Jihua Wang 1,2,* and Yaoqi Zhou 1,4,*
1
Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
2
College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China
3
College of Life Science, Shandong Normal University, Jinan 250014, China
4
Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, Australia
5
School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(3), 885; https://doi.org/10.3390/ijms19030885
Received: 13 February 2018 / Revised: 11 March 2018 / Accepted: 12 March 2018 / Published: 16 March 2018
(This article belongs to the Special Issue Computational Studies of Structure-Dynamics-Function Relationships in Biomolecules)
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. View Full-Text
Graphical abstract
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Cao, Z.; Bian, Y.; Hu, G.; Zhao, L.; Kong, Z.; Yang, Y.; Wang, J.; Zhou, Y. Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids. Int. J. Mol. Sci. 2018, 19, 885.
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