MARVEL BIOMED/NIH GRANT

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。 项目1：DNA解旋酶PcrA的作用机制 在过去的一年里，理论和计算生物物理学小组使用了 PSC强大的Jonas集群，以研究DNA解旋的机制 在嗜热脂肪芽孢杆菌的DNA解旋酶PcrA中。DNA解旋 PcrA的作用是由解旋酶沿沿着单链DNA移位引起的， 这是由腺苷三磷酸（ATP）在单一的水解驱动的。 催化部位 我们使用了量子力学/分子力学（QM/MM） 模拟研究ATP水解反应途径及其耦合， PcrA解旋酶中蛋白质构象的变化。仿真系统 由大约20，000个原子组成，其中77个原子被量子力学处理， 在B3 LYP/6- 31 G理论水平上;经典部分使用 琥珀94力场为了模拟这样一个大型QM/MM系统，我们依赖于 关键在于PSC的Jonas集群的可用性， 内存架构，这使得我们的代码能够高效运行 多达32个处理器。 类似于我们以前对F1-ATPase中ATP水解的研究， 中继机制被确定为生理相关的质子转移 亲核攻击过程中的路径。来自一个人的“精氨酸指”残基R287可以是来自一个人的精氨酸指。 邻近催化位点的蛋白质结构域被发现对 过渡状态稳定化，从而增加了相似性列表 PcrA和F1-ATPase在催化位点水平上的相互作用。在计算机中使用 突变研究，可以表明，Q254的位置相对于 ATP的末端磷酸基团对ATP的能量有很大的影响 水解产物状态，因为侧链长度稍微减少 （突变Q254 N）改变了反应能量分布，从吸热的，在 从野生型到能量几乎相等这表明蛋白质 由DNA易位引起的构象变化与DNA的构象变化有关。 PcrA结合位点的催化反应。

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. Project 1: Mechanism of DNA helicase PcrA Over the past year, the Theoretical and Computational Biophysics Group has used the powerful Jonas cluster at PSC to investigate the mechanism of DNA unwinding in the DNA helicase PcrA from Bacillus stearothermophillus. The DNA unwinding action of PcrA is caused by helicase translocation along single stranded DNA, which is driven by the hydrolysis of adenosine tri-phosphate (ATP) in a single catalytic site. We have used combined quantum mechanical/molecular mechanical (QM/MM) simulations to study the ATP hydrolysis reaction pathway and its coupling to protein conformational changes in PcrA helicase. The simulation system consisted of about 20,000 atoms, 77 of which were treated quantum mechanically at the B3LYP/6-31G level of theory; the classical part was modeled using the AMBER94 force field. In order to simulate such a large QM/MM system, we relied crucially on the availability of the Jonas cluster at PSC with its large shared memory architecture, which allowed our code to run efficiently on up to 32 processors. Analogous to our previous studies of ATP hydrolysis in F1-ATPase, a proton relay mechanism was identified as the physiologically relevant proton transfer pathway during nucleophilic attack. The "arginine finger" residue R287 from a protein domain neighboring the catalytic site was found to be crucial for transition state stabilization, thereby, adding to the list of similarities between PcrA and F1-ATPase at the catalytic site level. Employing in silico mutation studies, it could be shown that the position of Q254 with respect to the terminal phosphate group of ATP greatly influences the energy of the ATP hydrolysis product state, since a slight decrease in side chain length (mutation Q254N) changed the reaction energy profile from endothermic in the wild type to almost equi-energetic. This suggests a mechanism by which protein conformational changes induced by DNA translocation are coupled to the catalytic reaction in the binding site of PcrA.