'Computer-Chemistry' Yields New Insight into a Puzzle of Cell Division

　　'计算化学' 为细胞分裂之谜给出新见解(中英对照)

　　Interdisciplinary team searched through one thousand trillion possible ways two molecules could match up, then made the molecules wiggle

　　跨学科研究小组在1000万亿种可能性中搜寻两个分子可能匹配的途径， 然后使分子发生摆动

　　Thursday, December 8, 2005

　　周四， 2005年12月8日

　　来源:杜克大学

　　Durham, N.C. -- Duke University biochemists aided by Duke computer scientists and computational chemists have identified the likely way two key enzymes dock in an intricate three-dimensional puzzle-fit to regulate cell division. Solving the docking puzzle could lead to anticancer drugs to block the runaway cell division behind some cancers, said the researchers. 达Durham, N.C. -杜克大学的生物化学家在该校计算机科学家和计算化学家的帮助下已经鉴定出了两个关键性酶在一个复杂的三维结构中可能的对接方式，该三维结构形成的作用是调节细胞分裂。解决对接之谜将可能用抗癌药物来阻止一些癌症细胞分裂失控，研究人员说。

　　
      From left, Herbert Edelsbrunner, Johannes Rudolph and Weitao Yang with color-coded molecule models

　　从左至右分别是Herbert Edelsbrunner ，Johannes Rudolph和Weitao Yang，当然，还有用他们的颜色标记的分子模型

　　Significantly, their insights arose not just from meticulous biochemical studies, but also from using sophisticated simulation techniques to perform "chemistry in the computer."

　　有意义的是，他们的见解不是单纯从细致的生化研究中产生的，还利用了复杂的模拟技术“在计算机上进行化学反应”。

　　" In a paper published Nov. 24, 2005 online in the journal Biochemistry, members of the interdisciplinary collaboration described how they discovered the probable orientation required for a Cdc25B phosphatase enzyme to "dock" with and activate a cyclin-dependent kinase protein complex that also functions as an enzyme, known as Cdk2-pTpY--CycA. The work was funded by the National Institutes of Health.

　　生物化学(Biochemistry)网刊2005年11月24日发表的一篇论文中，跨学科团队成员描述了他们如何发现使得Cdc25B磷酸酶"对接" 和激活Cdk2-pTpY—CycA的可能取向的过程。 Cdk2-pTpY—CycA是一种细胞周期蛋白依赖性激酶蛋白复合物，也是一种酶。这项工作是由美国国家卫生研究所赞助的。

　　Detailed study of such docking is important because uncontrolled overreaction of the Cdc25 family of enzymes has been associated with the development of various cancers. Anti-cancer drugs that jam the enzyme, preventing its docking with the kinase, could halt cell over proliferation to treat such cancers. However, developing such drugs has been hampered by lack of detailed understanding of how the Cdc25s fit with their associated kinases.

　　对该对接的深入研究是重要的，因为无节制过度反应的cdc25家族的酶与各种癌症的发生相关。干扰此酶的抗癌药物防止它与激酶对接，可以阻止细胞过度增殖， 从而治疗这种癌症。但是，因缺乏对cdc25s与其相关激酶契合的详细了解，限制了这类药物的开发。

　　"To me this is the culmination of my six years here at Duke," said Johannes Rudolph, the Duke assistant professor of chemistry and biochemistry who led the research. "It's very exciting. I think it's a really hard problem."

　　"对我来说，这是我在杜克大学六年工作历程的巅峰"，领导这项研究的杜克大学化学与生物化学助理教授Johannes Rudolph 说，"这非常令人兴奋。我觉得这是一个颇具挑战性的问题。 "

　　A successful docking between the two enzymes not only requires the "active sites" -- where chemical reactions occur --on the phosphatase and the kinase to link precisely, Rudolph said. The two molecules' component parts, or "residues," must also orient in a tongue-and-groove fit at a few other special places, which the researchers dubbed 'hot spots," on the irregular molecular surfaces.

　　Rudolph认为两个酶之间的成功对接不仅要求产生化学反应的磷酸酶和激酶的"活性位点"精确结合，而且两个分子组成部分，即"残基"，还必须在不规则分子表面的其他几个特别的位点，以榫槽方式契合，研究者称这些位点为“热点”(hot spot)。

　　Only when active sites and hot spots fit correctly can this brief docking accomplish its role in the cell division cycle, said Rudolph. That biochemical role is for the enzyme to remove the phosphates from two phosphate-bearing amino acids on the protein.

　　只有当活性位点与热点正确契合时，这种短暂的对接才能实现其在细胞分裂周期中的作用，Rudolph说。此生化作用是该酶从该蛋白质的两个磷酸化氨基酸残基上移除的磷酸基团。

　　Those removals alter electrical charges in a way that allows the protein to pick up other phosphate-containing chemical groups to pass along as part of a molecular bucket brigade.

　　移除的过程将在一定程度上改变电荷，从而使得该蛋白可以摄取其他含磷酸基的化学基团，作为分子桶桥的一部分继续向前移动。

　　Rudolph initially knew the kinase's and phosphatase's general topographies as well as the locations of their active sites. "But it was literally a guessing game trying to find which residues might be important in this interaction," he said.

　　Rudolph起初知道激酶和磷酸酶总拓朴图以及活性位点的位置。“但是那只是一个猜想游戏，只是试着找出在这一相互作用中到底哪些残基是重要的”他说。

　　"Somehow these two large complicated molecules had to also interact specifically somewhere other than the site where the chemistry occurs."

　　“不知为何这两个复杂大分子不得不在发生化学反应的活性位点以外的地方发生特定的相互作用。”

　　Biochemists traditionally answer such questions by laboriously making "mutant" versions of a protein in which a single residue is altered and lab-testing whether the resulting subtle change in the protein's shape or chemistry changes the way the molecules interact with each other, he said. If there is no change, they then move on to the next residue.

　　对生物化学家而言，解决这些问题的传统办法就是煞费苦力地制作蛋白质的"突变体"，其中单一残基有所改变，然后实验检测是否该突变带来的蛋白结构和化学性质的微妙变化改变了分子间相互作用的方式，他说。如果没有变化，它们又转向其它残基。

　　"So my students started to make these mutants randomly and test their activities, one at a time," Rudolph said. "Each of these experiments is pretty hard, and pretty tedious."

　　“所以，我的学生开始随机制造突变体，测试突变体的活动，每次只做一个”，Rudolph说。“每个实验都很难，而且相当繁琐。”

　　After this trial-and-error search remained fruitless, Rudolph, his graduate students Jungsan Sohn, Kolbrun Kristjansdottir and Alexias Safi and his post-doctoral investigator Gregory Burhman began collaborating with a team led by computer science and mathematics professor Herbert Edelsbrunner.

　　经过试错法检索仍然徒劳无功，Rudolph和他的研究生Jungsan Sohn, Kolbrun Kristjansdottir ，Alexias Safi以及他的博士后研究员Gregory Burhman开始了与计算机兼数学教授Herbert Edelsbrunner领导的一个研究小组的合作。

　　Edelsbrunner, who has developed techniques and computational programs for modeling and analyzing complex molecular shapes, used a large cluster of computers and custom software to analyze about one thousand trillion different conceivable shape match-ups between the molecules.

　　Edelsbrunner 为建模和分析复杂的分子形状开发了相关方法和计算程序，用了一个大计算机群和定制软件来分析约1000万亿不同的分子两两结合可能的形状。

　　That initial mega-analysis reduced the potential molecular combinations to about 1,000 possibilities, which Rudolph called both "encouraging" and "discouraging."

　　初始的巨型分析使得潜在的分子组合减少到约一千种可能性，Rudolph称之为既“鼓舞人心”又“令人气馁”。

　　Edelsbrunner's group, which included programmer Paul Brown, then began narrowing that search further. They did so by using a different software program that could identify the highest and lowest places on the molecules' surfaces, and where "highest" on one might fit into the "deepest" on the other. "That's not easy, because there is no point of reference on those complicated shapes," Rudolph said.

　　程序员Paul Brown所在的Edelsbrunner研究小组开始进一步缩小搜寻范围。他们能用不同的软件程序找出分子表面的最高处和最低处，一个分子的“最高处”可以与另一个分子的“最深处”匹配。“这相当不容易，在那些复杂的形状上没有任何参考点，”Rudolph说。

　　The researchers finally winnowed the possibilities to what Rudolph called "one reasonable guess" by enlisting another Duke group led by chemistry professor Weitao Yang.

　　在争取到杜克大学另一个以化学教授Weitao Yang带头的研究小组的加入后，研究人员最终筛选出了这些可能性，被Rudolph称之为 “一个合理的猜想”

　　Yang's team, including his graduate student Jerry Parks, uses another bank of computers to calculate how components of molecules behave in small spaces -- in this case "how they wiggle," Rudolph said. By allowing both molecules to move -- as they would in the real world -- the researchers could evaluate whether match-ups that looked right when motionless were actually off the mark.

　　Yang的团队，他的研究生Jerry Parks也在里面，利用另一个计算机系统来计算分子组分在狭小空间的行为，应该称之为"如何摆动"，Rudolph说。通过使得两个分子移动(如同在真实世界一样)，研究者可