Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids

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...

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Main Authors:	Zanxia Cao, Yunqiang Bian, Guodong Hu, Liling Zhao, Zhenzhen Kong, Yuedong Yang, Jihua Wang, Yaoqi Zhou
Format:	Article
Language:	English
Published:	MDPI AG 2018-03-01
Series:	International Journal of Molecular Sciences
Subjects:	metadynamics simulation permeation of amino acids translocation free energy
Online Access:	http://www.mdpi.com/1422-0067/19/3/885

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spelling	doaj-136901a2f8874e6a9c1a03e5f77b76502020-11-24T21:14:31ZengMDPI AGInternational Journal of Molecular Sciences1422-00672018-03-0119388510.3390/ijms19030885ijms19030885Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino AcidsZanxia Cao0Yunqiang Bian1Guodong Hu2Liling Zhao3Zhenzhen Kong4Yuedong Yang5Jihua Wang6Yaoqi Zhou7Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, ChinaShandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, ChinaShandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, ChinaShandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, ChinaShandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, ChinaInstitute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD 4222, AustraliaShandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, ChinaShandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, ChinaThermodynamics 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.http://www.mdpi.com/1422-0067/19/3/885metadynamics simulationpermeation of amino acidstranslocation free energy
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Zanxia Cao Yunqiang Bian Guodong Hu Liling Zhao Zhenzhen Kong Yuedong Yang Jihua Wang Yaoqi Zhou
spellingShingle	Zanxia Cao Yunqiang Bian Guodong Hu Liling Zhao Zhenzhen Kong Yuedong Yang Jihua Wang Yaoqi Zhou Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids International Journal of Molecular Sciences metadynamics simulation permeation of amino acids translocation free energy
author_facet	Zanxia Cao Yunqiang Bian Guodong Hu Liling Zhao Zhenzhen Kong Yuedong Yang Jihua Wang Yaoqi Zhou
author_sort	Zanxia Cao
title	Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids
title_short	Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids
title_full	Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids
title_fullStr	Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids
title_full_unstemmed	Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids
title_sort	bias-exchange metadynamics simulation of membrane permeation of 20 amino acids
publisher	MDPI AG
series	International Journal of Molecular Sciences
issn	1422-0067
publishDate	2018-03-01
description	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.
topic	metadynamics simulation permeation of amino acids translocation free energy
url	http://www.mdpi.com/1422-0067/19/3/885
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Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids

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