Molecular Insights into Distinct Membrane-insertion Behaviors and Mechanisms of 20 Amino Acids: an All-atom MD Simulation Study

doi:10.1007/s40242-023-3175-1

Chemical Research in Chinese Universities ›› 2023, Vol. 39 ›› Issue (5): 829-839.doi: 10.1007/s40242-023-3175-1

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Molecular Insights into Distinct Membrane-insertion Behaviors and Mechanisms of 20 Amino Acids: an All-atom MD Simulation Study

TU Wenqiang¹, DONG Xuewei^1,3, OU Luping¹, ZHANG Xinke¹, YUAN Bing², YANG Kai^1,2

1. Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, P. R. China;
2. Songshan Lake Materials Laboratory, Dongguan 523808, P. R. China;
3. State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China

Received:2023-07-30 Online:2023-10-01 Published:2023-09-26
Contact: YUAN Bing, YANG Kai E-mail:yuanbing@sslab.org.cn;yangkai@suda.edu.cn
Supported by:
This work was supported by the Open Research Fund of Songshan Lake Materials Laboratory, China (No.2021SLABFK10), the National Natural Science Foundation of China (Nos.12274307, 32230063, 21774092 and 22303060), the Natural Science Foundation of Guangdong Province, China (No.2023A1515011610) and the Open Research Fund of State Key Laboratory of Surface Physics of Fudan University, China (No.KF2023_03).

Abstract

Abstract: Interfacial interactions of proteins with cell membranes play important roles in fundamental physiological processes of cells. The binding of proteins to membranes involves interactions between amino acids and membranes. However, the mechanism underlying amino acids' membrane behavior remains elusive. Herein, all-atom molecular dynamic simulations were applied to comprehensively investigating the molecular details of interactions between 20 amino acids with DOPC membranes. Our results show that 20 amino acids exhibit distinct membrane insertion activities, which are not simply determined by the side chain properties of amino acids. Aromatic Tyr/Phe/Trp, hydrophobic Val/Ile/Leu/Met, positively-charged Arg and hydrophilic Cys exhibit significantly strong membrane insertion capacities with different characteristic insertion depths and insertion angles. Surprisingly, hydrophobic Ala, positively-charged His/Lys, hydrophilic Asn/Ser/Gln/Thr, negatively-charged Asp/Glu and Pro/Gly have low membrane insertion capabilities. Considering the chemical structures and interaction details of amino acids with membranes, we suggest that the abundance and diversity of interaction sites and types, the synergistic effect of hydrophilic and hydrophobic interactions of amino acids with membranes and the structural flexibility of amino acids are key factors for determining membrane insertion capabilities and characteristics of amino acids. Our study sheds light on the atomic mechanism of interactions between single amino acids and membranes.

Key words: Amino acid-membrane interaction, Membrane insertion capability, Insertion depth and angle, Molecular dynamic simulation

TU Wenqiang, DONG Xuewei, OU Luping, ZHANG Xinke, YUAN Bing, YANG Kai. Molecular Insights into Distinct Membrane-insertion Behaviors and Mechanisms of 20 Amino Acids: an All-atom MD Simulation Study[J]. Chemical Research in Chinese Universities, 2023, 39(5): 829-839.

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Molecular Insights into Distinct Membrane-insertion Behaviors and Mechanisms of 20 Amino Acids: an All-atom MD Simulation Study

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