ABC输出转运体蛋白质分子的门控机制:计算模拟研究  

Molecular mechanism underlying ABC exporter gating:a computational study

作　　者：王子 廖结楼[1] Zi Wang;Jielou Liao(Department of Chemical Physics,University of Science and Technology of China,Hefei 230026,China)

机构地区：[1]中国科学技术大学化学物理系,安徽合肥230026

出　　处：《中国科学技术大学学报》2023年第12期47-52,I0007,I0010,共8页JUSTC

基　　金：supported by the National Natural Science Foundation of China(21073170,21273209).

摘　　要：三磷酸腺苷结合盒式(ATP-binding cassette,ABC)输出转运体是一类典型的蛋白质分子机器,这类分子机器通过门控运动进行“向外打开”(outward-facing,OF)和“向内打开”(inward-facing,IF)构象态之间转换,从而把底物转运输出生物膜外。尽管结构和功能的研究已取得重大进展,但对ABC输出转运体构象门控的分子机制还没有完全理解。由于全原子分子动力学存在长时间尺度问题,因此对ABC蛋白质分子构象变化不能进行完全描述。本文应用粗粒化分子动力学(CG-MD)结合改善的抽样方法,对细菌ABC输出转运体MsbA进行计算模拟研究。本文计算得到的平均力势(potential of mean force,PMF)表明,从OF构象态到IF构象态之间的转变需要经过一个“阻塞态”(occluded state,OC),即MsbA的内门和外门都是关闭的状态。这种阻塞状态对ABC输出功能的方向单一性具有重要意义。我们的CG-MD计算模拟结果显示,随着MsbA的核苷酸结合域(nucleotide binding domain,NBD)的分离,外门的关闭和内门的打开是采用高度协作的方式。基于本文的计算模拟结果,我们提出了一个与目前文献中发表的有很大不同的机械力学模型,揭示了ABC输出转运体通过构象门控运动输运底物的分子机制。ATP-binding cassette(ABC)exporters are a class of molecular machines that transport substrates out of biological membranes by gating movements leading to transitions between outward-facing(OF)and inward-facing(IF)conformational states.Despite significant advances in structural and functional studies,the molecular mechanism underlying conformational gating in ABC exporters is not completely understood.A complete elucidation of the state transitions during the transport cycle is beyond the capability of the all-atom molecular dynamics(MD)method because of the limited time scale of MD.In the present work,a coarse-grained molecular dynamics(CG-MD)method with an improved sampling strategy is performed for the bacterial ABC exporter MsbA.The resultant potential of the mean force(PMF)along the center-of-mass(COM)distances,d_(1)and d_(2),between the two opposing subunits of the internal and external gates,respectively,are obtained,delicately showing the details of the OF→IF transition occurring via an occluded(OC)state,in which the internal and external gates are both closed.The OC state has an important role in the unidirectionality of the transport function of ABC exporters.Our CG-MD simulations dynamically show that upon NBD dissociation,the opening of the internal gate occurs in a highly cooperative manner with the closure of the external gate.Based on our PMF calculations and CG-MD simulations in this paper,we proposed a mechanistic model that is significantly different from those recently published in the literature,shedding light on the molecular mechanism by which the ABC exporter executes conformational gating for substrate translocation.

关 键 词：三磷酸腺苷结合盒式输出转运体 平均力势 粗粒化分子动力学 机械力学模型 

分 类 号：O643.1[理学—物理化学]