Javanainen Matti, Ollila O H Samuli, Martinez-Seara Hector
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
Computational Physics Laboratory, Tampere University, Tampere 33720, Finland.
J Phys Chem B. 2020 Apr 16;124(15):2994-3001. doi: 10.1021/acs.jpcb.0c00884. Epub 2020 Apr 1.
Membrane proteins travel along cellular membranes and reorient themselves to form functional oligomers and protein-lipid complexes. Following the Saffman-Delbrück model, protein radius sets the rate of this diffusive motion. However, it is unclear how this model, derived for ideal and dilute membranes, performs under crowded conditions of cellular membranes. Here, we study the rotational motion of membrane proteins using molecular dynamics simulations of coarse-grained membranes and 2-dimensional Lennard-Jones fluids with varying levels of crowding. We find that the Saffman-Delbrück model captures the size-dependency of rotational diffusion under dilute conditions where protein-protein interactions are negligible, whereas stronger scaling laws arise under crowding. Together with our recent work on lateral diffusion, our results reshape the description of protein dynamics in native membrane environments: The translational and rotational motions of proteins with small transmembrane domains are rapid, whereas larger proteins or protein complexes display substantially slower dynamics.
膜蛋白沿着细胞膜移动并重新定向自身,以形成功能性寡聚体和蛋白质 - 脂质复合物。根据萨夫曼 - 德尔布吕克模型,蛋白质半径决定了这种扩散运动的速率。然而,尚不清楚这个为理想且稀薄的膜推导出来的模型,在细胞膜拥挤的条件下表现如何。在这里,我们使用具有不同拥挤程度的粗粒化膜和二维 Lennard-Jones 流体的分子动力学模拟来研究膜蛋白的旋转运动。我们发现,萨夫曼 - 德尔布吕克模型在蛋白质 - 蛋白质相互作用可忽略不计的稀薄条件下捕捉到了旋转扩散的尺寸依赖性,而在拥挤条件下会出现更强的标度律。结合我们最近关于横向扩散的工作,我们的结果重塑了天然膜环境中蛋白质动力学的描述:具有小跨膜结构域的蛋白质的平移和旋转运动很快,而较大的蛋白质或蛋白质复合物表现出明显较慢的动力学。