Dutta Angshu, Patel Smit, Kanaujia Shankar Prasad
Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
Comput Struct Biotechnol J. 2025 May 24;27:2074-2097. doi: 10.1016/j.csbj.2025.05.031. eCollection 2025.
MlaC is involved in the transportation of phospholipids between the inner and outer membranes of Gram-negative bacteria. This MlaC-mediated transport safeguards the outer membrane asymmetry thereby preserving its integrity and shielding effect against antibiotics, detergents, etc. MlaC is constituted by two domains, viz. nuclear transport factor 2-like and phospholipid-binding protein. These unique structural properties contribute to a novel ligand binding process and a diverse conformational landscape, which still remains a marginally investigated subject. In order to fill this knowledge gap, comprehensive molecular docking and simulation studies were performed. The docking experiments performed using these structures against different phospholipids reveal, for the first time, their preference for certain substrate sizes and organizations of binding planes. The conformational dynamicity of MlaC was studied by simulation using 13 different systems in different liganded states for 1000 ns each. A distinct behavioural pattern was observed between the apo open and holo open states, with the former being conformationally more flexible. A time-dependent study of the changes in binding-pocket volume further substantiated the differences in the protein dynamics. The study further aided in the identification of global and local movements, paving the path for the investigation of coordinated motions. The extensive analyses performed on different liganded systems disclose (anti-)correlated motions that have helped in the understanding of the motions and enigmatic conformational landscape of MlaC. Further, an unanticipated MlaC crystal state that further adds to the understanding of MlaC flexibility.
MlaC参与革兰氏阴性菌内膜与外膜之间磷脂的转运。这种由MlaC介导的转运可保护外膜不对称性，从而保持其完整性以及对抗生素、去污剂等的屏蔽作用。MlaC由两个结构域组成，即核转运因子2样结构域和磷脂结合蛋白结构域。这些独特的结构特性促成了一种新颖的配体结合过程和多样的构象态势，而这仍是一个研究较少的课题。为了填补这一知识空白，我们进行了全面的分子对接和模拟研究。利用这些结构针对不同磷脂进行的对接实验首次揭示了它们对特定底物大小和结合平面组织的偏好。通过对13个处于不同配体状态的不同系统分别进行1000纳秒的模拟，研究了MlaC的构象动力学。在无配体开放状态和有配体开放状态之间观察到了明显不同的行为模式，前者在构象上更具灵活性。对结合口袋体积变化的时间依赖性研究进一步证实了蛋白质动力学的差异。该研究还有助于识别全局和局部运动，为研究协同运动铺平了道路。对不同配体系统进行的广泛分析揭示了（反）相关运动，这有助于理解MlaC的运动和神秘的构象态势。此外，一种意外的MlaC晶体状态进一步增进了对MlaC灵活性的理解。
