A MOLECULAR DYNAMICS STUDY OF CLOSED CONFORMATIONAL STRUCTURE OF HUMAN PLASMINO

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 人纤溶酶原，又称谷氨酸纤溶酶原(Glu-纤溶酶原，Glu-PG)，由N-末端的Glu1-Val79、5个kringle结构域和C-末端的丝氨酸蛋白酶结构域组成。Glu-PG形成一个封闭的结构，推测是NTP-kringle结合的结果。有实验证据表明，Glu-PG的封闭构象是通过Kringle5和NTP结合而保持的。借助这些实验信息，分子动力学(MD)研究对于阐明纤溶过程中纤溶酶原构象变化的详细机制是非常有用的。虽然计算研究可以非常有助于理解结合机制，但搜索整个自由能空间来表征它们的结合过程是困难和繁琐的。因此，我们将通过接近NTP的Lys50来研究Kringle5的赖氨酸结合位点(LBSS)附近可能的结合区域。尽管进行了大量的实验研究，但整个纤溶酶原分子结构尚未确定。因此，其余的未知结构将被添加到某些环的晶体X射线结构中，通过能量最小化和平衡来调整整个结构。五个Kringes和NTP(541个残基)在水中的平衡几何构型将通过将氯/钠离子和40,000个TIP3P水分子放置在正交周期框中来确定。CHARMM力场将用于所有MD模拟。在平衡过程中，将对符合条件的结合位点之间的距离进行特殊的谐和约束。这将通过在运行的前0.4 ns期间将与约束相关联的力常数减小到零来缓慢完成。在它们被移除后，MD模拟将继续进行额外的1 ns，以跟踪没有约束的结合原子对的距离的轨迹。为了成功地对如此大型的生物系统进行MD模拟，我们在PSC BIGBEN平台上要求10,000个SU。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Human plasminogen, so-called Glu-plasminogen (Glu-Pg), consists of an N-terminal peptide (NTP) Glu1-Val79, followed by five kringle domains and a serine-protease domain at the C-terminal end. Glu-Pg forms a closed structure postulated to result from NTP-kringle binding. There is experimental evidence that the closed conformation of Glu-Pg is maintained via kringle 5 and NTP binding. With the aid of this experimental information, the molecular dynamics (MD) study can be very useful in elucidating detail mechanisms of conformational change of plasminogen in the fibrinolysis. While computational studies can be very helpful to understanding binding mechanisms, it is difficult and tedious to search the entire free energy space to characterize their binding processes. Thus, we will investigate possible binding regions near lysine-binding sites (LBSs) of kringle 5 by approaching Lys50 of NTP. Despite numerous experimental studies, the structure of an entire plasminogen molecule has not been determined. Thus, the rest of unknown structures will be added to crystallographic X-ray structures of some kringles, adjusting entire structures via energy-minimization and equilibration. Equilibrium geometries of five kringes and NTP (541 residues) in water will be determined with chloride/sodium ions and 40,000 TIP3P water molecules placed in an orthorhombic periodic box. CHARMM force field will be used for all MD simulations. During equilibration, ad hoc harmonic constraints on distance between eligible binding sites, will be implemented. This will be done slowly by decreasing force constants associated with the constraints to zero during the first 0.4 ns of the run. After their removal, MD simulations will be continued for an additional 1 ns to trace trajectories of the distances of the binding atom pairs without the constraints. To conduct successfully MD simulations for such a large biosystem, we request 10,000 SU on the PSC BIGBEN platform.