Dehury Budheswar, Mishra Sarbani, Panda Sunita, Singh Mahender Kumar, Simha Nischal L, Pati Sanghamitra
Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.
Bioinformatics Division I Microbiology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India.
J Cell Biochem. 2025 Jan;126(1):e30693. doi: 10.1002/jcb.30693.
B0AT1 (SLC6A19) is a major sodium-coupled neutral amino acid transporter that relies on angiotensin converting enzyme 2 (ACE2) or collectrin for membrane trafficking. Despite its significant role in disorders associated with amino acid metabolism, there is a deficit of comprehensive structure-function understanding of B0AT1 in lipid environment. Herein, we have employed molecular dynamics (MD) simulations to explore the architectural characteristics of B0AT1 in two distinct environments: a simplified POPC bilayer and a complex lipid system replicating the native membrane composition. Notably, our B0AT1 analysis in terms of structural stability and regions of maximum flexibility shows consistency in both the systems with enhanced structural features in the case of complex lipid system. Our findings suggest that diacylglycerol phospholipids significantly alter the pore radius, hydrophobic index, and surface charge distribution of B0AT1, thereby affecting the flexibility of transmembrane helices TM7, TM12, and loop connecting TM7-TM8, crucial for ACE2-B0AT1 interaction. Pro41, Ser190, Arg214, Arg240, Ser413, Pro414, Cys463, and Val582 are among the most prominent lipid binding residues that might influence B0AT1 functionality. We also perceive notable lipid mediated deviation in the degree of tilt and loss of helicity in TM1 and TM6 which might affect the substrate binding sites S1 and S2 in B0AT1. Considerably, destabilization in the structure of B0AT1 in lipid environment was evident upon mutation in TM domain, associated with Hartnup disorder through various structure-based protein stability tools. Our two-tiered approach allowed us to validate the use of POPC as a baseline for initial analyses of SLC transporters. Altogether, our all-atoms MD study provides a platform for future investigations into the structure-function mechanism of B0AT1 in realistic lipid mimetic bilayers and offers a framework for developing new therapeutic agents targeting this transporter.
B0AT1（SLC6A19）是一种主要的钠偶联中性氨基酸转运体，其膜转运依赖于血管紧张素转换酶2（ACE2）或collectrin。尽管它在与氨基酸代谢相关的疾病中发挥着重要作用，但在脂质环境中，人们对B0AT1的结构-功能缺乏全面的了解。在此，我们采用分子动力学（MD）模拟来探索B0AT1在两种不同环境中的结构特征：简化的POPC双层膜和复制天然膜组成的复杂脂质系统。值得注意的是，我们对B0AT1在结构稳定性和最大灵活性区域方面的分析表明，在这两种系统中结果一致，在复杂脂质系统的情况下，其结构特征有所增强。我们的研究结果表明，二酰基甘油磷脂显著改变了B0AT1的孔径、疏水指数和表面电荷分布，从而影响跨膜螺旋TM7、TM12以及连接TM7-TM8的环的灵活性，而这些对于ACE2-B0AT1相互作用至关重要。Pro41、Ser190、Arg214、Arg240、Ser413、Pro414、Cys463和Val582是最突出的可能影响B0AT1功能的脂质结合残基。我们还观察到TM1和TM6的倾斜程度和螺旋度丧失存在明显的脂质介导偏差，这可能会影响B0AT1中的底物结合位点S1和S2。值得注意的是，通过各种基于结构的蛋白质稳定性工具，在TM结构域发生突变时，脂质环境中B0AT1的结构明显不稳定，这与Hartnup病相关。我们的两层方法使我们能够验证将POPC用作SLC转运体初始分析基线的可行性。总之，我们的全原子MD研究为未来研究B0AT1在实际脂质模拟双层膜中的结构-功能机制提供了一个平台，并为开发针对该转运体的新治疗药物提供了一个框架。
