Elucidating the Membrane Binding Process of a Disordered Protein: Dynamic Interplay of Anionic Lipids and the Polybasic Region

IF 3.7 Q2 CHEMISTRY, PHYSICAL ACS Physical Chemistry Au Pub Date : 2024-01-18 DOI:10.1021/acsphyschemau.3c00051
Azadeh Alavizargar*, Maximilian Gass, Michael P. Krahn and Andreas Heuer, 
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Abstract

Intrinsically disordered regions of proteins are responsible for many biological processes such as in the case of liver kinase B1 (LKB1)─a serine/threonine kinase relevant for cell proliferation and cell polarity. LKB1 becomes fully activated upon recruitment to the plasma membrane by binding of its disordered C-terminal polybasic motif consisting of eight lysines/arginines to phospholipids. Here, we present extensive molecular dynamics (MD) simulations of the polybasic motif interacting with a model membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleyl phosphatidic acid (PA) and cell culture experiments. Protein–membrane binding effects are due to the electrostatic interactions between the polybasic amino acids and PAs. For significant binding, the first three lysines turn out to be dispensable, which was also recapitulated in cell culture using transfected GFP-LKB1 variants. LKB1–membrane binding results in nonmonotonous changes in the structure of the protein as well as the membrane, in particular, accumulation of PAs and reduced thickness at the protein–membrane contact area. The protein–lipid binding turns out to be highly dynamic due to an interplay of PA–PA repulsion and protein–PA attraction. The thermodynamics of this interplay is captured by a statistical fluctuation model, which allows the estimation of both energies. Quantification of the significance of each polar amino acid in the polybasic provides detailed insights into the molecular mechanism of protein–membrane binding of LKB1. These results can likely be transferred to other proteins, which interact by intrinsically disordered polybasic regions with anionic membranes.

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阐明紊乱蛋白质的膜结合过程:阴离子脂质与多基态区域的动态相互作用
蛋白质的内在无序区对许多生物过程都有影响,例如肝激酶 B1(LKB1)--一种与细胞增殖和细胞极性有关的丝氨酸/苏氨酸激酶。肝激酶 B1(LKB1)是一种与细胞增殖和细胞极性相关的丝氨酸/苏氨酸激酶。LKB1 通过其无序的 C 端由八个赖氨酸/精氨酸组成的多基序与磷脂结合而被招募到质膜上,从而被完全激活。在这里,我们展示了多基序与由 1-棕榈酰-2-油酰-sn-甘油-3-磷酸胆碱(POPC)和 1-棕榈酰-2-油酰磷脂酸(PA)组成的模型膜相互作用的大量分子动力学(MD)模拟以及细胞培养实验。蛋白质与膜的结合效应是由于多碱性氨基酸和 PA 之间的静电作用。要实现明显的结合,前三个赖氨酸是不可或缺的,这一点在使用转染的 GFP-LKB1 变体进行细胞培养时也得到了证实。LKB1 与膜结合会导致蛋白质结构和膜结构发生非单调变化,特别是 PA 的积累和蛋白质与膜接触区域厚度的减少。由于 PA-PA 相斥和蛋白质-PA 相吸的相互作用,蛋白质-脂质的结合被证明是高度动态的。这种相互作用的热力学是通过统计波动模型捕捉到的,该模型可以估算出两种能量。通过量化多碱基中每个极性氨基酸的重要性,可以详细了解 LKB1 蛋白质与膜结合的分子机制。这些结果很可能会应用于其他蛋白质,这些蛋白质通过内在无序的多基区与阴离子膜相互作用。
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3.70
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期刊介绍: ACS Physical Chemistry Au is an open access journal which publishes original fundamental and applied research on all aspects of physical chemistry. The journal publishes new and original experimental computational and theoretical research of interest to physical chemists biophysical chemists chemical physicists physicists material scientists and engineers. An essential criterion for acceptance is that the manuscript provides new physical insight or develops new tools and methods of general interest. Some major topical areas include:Molecules Clusters and Aerosols; Biophysics Biomaterials Liquids and Soft Matter; Energy Materials and Catalysis
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