Active Site Dehydration In Catalysis by RNA Polymerase

多亚基RNA聚合酶是一种从DNA模板合成RNA聚合物的酶，在进化过程中高度保守，具有高度的动态性。因为RNA聚合酶在RNA合成时沿着DNA模板移动，所以它们被认为是“分子马达”，以单碱基增量移动。RNA聚合酶利用四种核苷三磷酸底物将碱基掺入生长的RNA聚合物中。在每次碱基添加期间，所添加的底物由DNA模板的序列指定。超级计算机模拟被用来理解RNA聚合酶在RNA聚合和RNA聚合酶易位过程中的原子运动。为了更好地模拟聚合反应和RNA聚合酶沿模板DNA的沿着移动，分别模拟了反应的不同阶段。为了合并反应中的连续步骤，使用称为“复制品交换”的方法，其中模拟两个反应步骤之间的最可能轨迹。由于模拟是在水和离子浴中进行的，因此可以预测结构中最可能的水位置。在聚合反应期间，RNA聚合酶排除水。一个主要的努力是学习的重要性，水排斥在聚合和保持聚合的准确性。RNA聚合酶中的许多氨基酸变化导致蛋白质功能改变。为了更好地理解这些变化，将研究改变的蛋白质的聚合和易位功能，然后通过计算机模拟进行分析，以确保化学测试的结果得到预测的原子运动的支持。 更广泛的影响多亚基RNA聚合酶是生物系统中精确遗传信息流所必需的。因此，RNA合成的机制、动力学和准确性是复杂生命系统的基础。复杂的计算机模拟应用于现代生物学中最大和最困难的问题之一。受训者将成为生物化学，遗传学和计算方法的专家，使他们成为灵活的跨学科科学家。计算机模拟数据将被纳入密歇根州立大学的本科教学中。将尽一切努力招募有才华的本科生和代表性不足的群体进入这一研究计划，例如，通过MSU IDEAS研究计划（www.bmb.msu.edu/~ugrad/research/res-oppor-minority.htm）。

Intellectual meritMulti-subunit RNA polymerases, which synthesize an RNA polymer from a DNA template, are highly conserved in evolution and are highly dynamic. Because RNA polymerases move along a DNA template as RNA is synthesized, they are considered to be 'molecular motors', moving in single base increments. RNA polymerases utilize four nucleoside triphosphate substrates to incorporate bases into the growing RNA polymer. During each base addition, the substrate added is specified by the sequence of the DNA template. Supercomputer simulation is used to understand the atomic motions of RNA polymerase during RNA polymerization and during RNA polymerase translocation. In order to better simulate the polymerization reaction and RNA polymerase movement along template DNA, different stages of the reaction are simulated separately. To merge consecutive steps in the reaction, a method termed 'replica exchange' is used in which the likeliest trajectory between two reaction steps is simulated. Because simulations are done in a bath of water and ions, predictions are obtained for the likeliest water placements in the structure. During the polymerization reaction, RNA polymerases exclude water. A major effort is to learn the importance of water exclusion in polymerization and in maintaining the accuracy of polymerization. Many amino acid changes have been made in RNA polymerases resulting in altered protein function. To better understand these changes, altered proteins will be studied for their polymerization and translocation functions, and then analyzed by computer simulation to ensure that results from chemical tests are supported by predicted atomic motions. Broader impactsMulti-subunit RNA polymerases are necessary for accurate genetic information flow in biological systems. As such, the mechanism, dynamics and accuracy of RNA synthesis are fundamental to complex living systems. Sophisticated computer simulation is applied to one of the largest and most difficult problems in modern biology. Trainees will become expert in biochemical, genetic and computational methods, preparing them as flexible, interdisciplinary scientists. Computer simulation data will be incorporated into undergraduate teaching at Michigan State University. Every effort will be made to recruit talented undergraduates and underrepresented groups into this research program, for instance, through the MSU IDEAS research program (http://www.bmb.msu.edu/~ugrad/research/res-oppor-minority.htm ).