A MOLECULAR DYNAMICS STUDY OF CLOSED CONFORMATIONAL STRUCTURE OF HUMAN PLASMINO

人纤溶酶闭合构象结构的分子动力学研究

• 批准号: 7601532
• 负责人: H-Y KIM
• 金额: $ 0.03万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601532
• 关键词: Binding; Binding Sites; Boxing; C-terminal; Chloride Ion; Chlorides; Computer Retrieval of Information on Scientific Projects Database; Equilibrium; Excision; Fibrinolysis; Free Energy; Funding; Glutamyl Plasminogen; Grant; Human; Institution; Kringles; Lysine; Molecular Conformation; N-terminal; Peptides; Plasminogen; Process; Protease Domain; Research; Research Personnel; Resources; Rest; Roentgen Rays; Running; Serine Protease; Source; Structure; United States National Institutes of Health; Water; computer studies; molecular dynamics; research study; sodium ion

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.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 人纤溶酶原，即所谓的Glu-纤溶酶原（Glu-Pg），由N-末端肽（NTP）Glu 1-Val 79，随后是五个Kringle结构域和在C-末端的丝氨酸-蛋白酶结构域组成。Glu-Pg形成闭合结构，推测是由NTP-kringle结合引起的。有实验证据表明Glu-Pg的闭合构象通过Kringle 5和NTP结合来维持。借助这些实验信息，分子动力学（MD）研究将有助于阐明纤溶酶原在纤溶过程中构象变化的详细机制。虽然计算研究对理解结合机制非常有帮助，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Lys 50来研究kringle 5的赖氨酸结合位点（LBS）附近的可能结合区域。尽管有许多实验研究，但整个纤溶酶原分子的结构尚未确定。因此，其余的未知结构将被添加到一些Kringles的晶体学X射线结构中，通过能量最小化和平衡来调整整个结构。将用氯离子/钠离子和40，000个TIP 3 P水分子放置在正交周期盒中，测定水中五种kringes和NTP（541种残留物）的平衡几何形状。CHARMM力场将用于所有MD模拟。在平衡过程中，将对合格结合位点之间的距离实施特别谐波约束。这将通过在运行的第一个0.4 ns期间将与约束相关的力常数降低到零来缓慢完成。在它们被移除后，MD模拟将继续额外的1 ns，以追踪没有约束的结合原子对的距离的轨迹。为了成功地对这样一个大型生物系统进行MD模拟，我们在PSC BIGBEN平台上请求10，000 SU。