Raza Saad, Sarkar Daipayan, Chan Leanne Jade G, Mae Joshua, Sutter Markus, Petzold Christopher J, Kerfeld Cheryl A, Ralston Corie Y, Gupta Sayan, Vermaas Josh V
MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States.
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.
ACS Omega. 2024 Jul 18;9(33):35503-35514. doi: 10.1021/acsomega.4c02406. eCollection 2024 Aug 20.
Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria that encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form , the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We used molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found . Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed the overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.
细菌微区室(BMCs)是存在于某些细菌中的蛋白质结合细胞器,它包裹酶以增强催化活性。这些区室在空间上通过半透性外壳蛋白隔离酶,类似于许多膜结合细胞器。外壳蛋白组装成多聚体片层;六聚体、三聚体和五聚体,这些片层自组装成具有二十面体对称性的更大聚集体。虽然二十面体外壳是主要形式,但片层也可以形成纳米级圆柱体或薄片。单个多聚体片层具有中央孔,这些孔是调节跨蛋白质外壳运输的关键。我们的主要兴趣是量化纳米尺度下响应替代组分形态的孔形状变化。我们使用分子建模工具为片层的平面薄片和代表完整外壳的弯曲结构开发了原子级详细模型。随后,使用经典分子动力学模拟对这些模型进行动画处理。从得到的轨迹中,我们分析了来自模型BMC外壳的六聚体和三聚体蛋白质片层的整体结构稳定性、单个残基的水可及性、水停留时间和孔几何形状。这些详尽的分析表明,扁平外壳几何形状和弯曲外壳几何形状之间的孔结构或溶剂可及性没有实质性变化。我们还将我们的分析与羟基自由基足迹数据进行比较,以检验我们的模拟结果,突出水分子长时间结合的特定残基。尽管形态或水相互作用变化很小,但我们建议在研究通过BMC孔的渗透性时,平面形态和胶囊形态可以互换使用。