Gołaś Ewa, Maisuradze Gia G, Senet Patrick, Ołdziej Stanisław, Czaplewski Cezary, Scheraga Harold A, Liwo Adam
Faculty of Chemistry, University of Gdánsk, Sobieskiego 18, 80-952 Gdánsk, Poland.
J Chem Theory Comput. 2012 May 8;8(5):1750-1764. doi: 10.1021/ct200680g. Epub 2012 Mar 15.
Heat-shock proteins 70 (Hsp70s) are key molecular chaperones which assist in the folding and refolding/disaggregation of proteins. Hsp70s, which consist of a nucleotide-binding domain (NBD, consisting of NBD-I and NBD-II subdomains) and a substrate-binding domain [SBD, further split into the β-sheet (SBD-β) and α-helical (SBD-α) subdomains], occur in two major conformations having (a) a closed SBD, in which the SBD and NBD domains do not interact, (b) an open SBD, in which SBD-α interacts with NBD-I and SBD-β interacts with the top parts of NBD-I and NBD-II. In the SBD-closed conformation, SBD is bound to a substrate protein, with release occurring after transition to the open conformation. While the transition from the closed to the open conformation is triggered efficiently by binding of adenosine triphosphate (ATP) to the NBD, it also occurs, although less frequently, in the absence of ATP. The reverse transition occurs after ATP hydrolysis. Here, we report canonical and multiplexed replica exchange simulations of the conformational dynamics of Hsp70s using a coarse-grained molecular dynamics approach with the UNRES force field. The simulations were run in the following three modes: (i) with the two halves of the NBD unrestrained relative to each other, (ii) with the two halves of the NBD restrained in an "open" geometry as in the SBD-closed form of DnaK (2KHO), and (iii) the two halves of NBD restrained in a "closed" geometry as in known experimental structures of ATP-bound NBD forms of Hsp70. Open conformations, in which the SBD interacted strongly with the NBD, formed spontaneously during all simulations; the number of transitions was largest in simulations carried out with the "closed" NBD domain, and smallest in those carried out with the "open" NBD domain; this observation is in agreement with the experimentally-observed influence of ATP-binding on the transition of Hsp70's from the SBD-closed to the SBD-open form. Two kinds of open conformations were observed: one in which SBD-α interacts with NBD-I and SBD-β interacts with the top parts of NBD-I and NBD-II (as observed in the structures of nucleotide exchange factors), and another one in which this interaction pattern is swapped. A third type of motion, in which SBD-α binds to NBD without dissociating from SBD-β was also observed. It was found that the first stage of interdomain communication (approach of SBD-β, to NBD) is coupled with the rotation of the long axes of NBD-I and NBD-II towards each other. To the best of our knowledge, this is the first successful simulation of the full transition of an Hsp70 from the SBD-closed to the SBD-open conformation.
热休克蛋白70（Hsp70s）是关键的分子伴侣，可协助蛋白质的折叠以及重新折叠/解聚。Hsp70s由一个核苷酸结合结构域（NBD，由NBD-I和NBD-II亚结构域组成）和一个底物结合结构域[SBD，进一步分为β-折叠（SBD-β）和α-螺旋（SBD-α）亚结构域]组成，以两种主要构象存在：（a）一种封闭的SBD构象，其中SBD和NBD结构域不相互作用；（b）一种开放的SBD构象，其中SBD-α与NBD-I相互作用，SBD-β与NBD-I和NBD-II的顶部相互作用。在SBD封闭构象中，SBD与底物蛋白结合，在转变为开放构象后释放。虽然从封闭构象到开放构象的转变可通过三磷酸腺苷（ATP）与NBD的结合有效触发，但在没有ATP的情况下也会发生，尽管频率较低。ATP水解后发生反向转变。在此，我们报告了使用具有UNRES力场的粗粒度分子动力学方法对Hsp70s构象动力学进行的规范和多重副本交换模拟。模拟以以下三种模式运行：（i）NBD的两半彼此不受约束；（ii）NBD的两半以“开放”几何形状受限，如同DnaK的SBD封闭形式（2KHO）；（iii）NBD的两半以“封闭”几何形状受限，如同Hsp70的ATP结合NBD形式的已知实验结构。在所有模拟过程中，均自发形成了SBD与NBD强烈相互作用的开放构象；转变次数在以“封闭”NBD结构域进行的模拟中最多，在以“开放”NBD结构域进行的模拟中最少；这一观察结果与实验观察到的ATP结合对Hsp70从SBD封闭形式向SBD开放形式转变的影响一致。观察到两种开放构象：一种是SBD-α与NBD-I相互作用，SBD-β与NBD-I和NBD-II的顶部相互作用（如在核苷酸交换因子的结构中观察到的），另一种是这种相互作用模式互换。还观察到第三种运动类型，即SBD-α在不与SBD-β解离的情况下与NBD结合。发现结构域间通讯的第一阶段（SBD-β接近NBD）与NBD-I和NBD-II的长轴彼此朝向旋转相关联。据我们所知，这是首次成功模拟Hsp70从SBD封闭构象到SBD开放构象的完整转变。
