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首页> 外文期刊>Acta crystallographica.Section D. Biological crystallography >Meaningful refinement of polyalanine models using rigid-body simulated annealing: application to the structure determination of the A31P Rop mutant.
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Meaningful refinement of polyalanine models using rigid-body simulated annealing: application to the structure determination of the A31P Rop mutant.

机译：有意义的改进polyalanine模型使用刚体模拟退火:应用程序的结构测定A31P罗普突变体。

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摘要

Conventional refinement methods, when applied to even correctly positioned polyalanine models of a target structure, result in a systematic distortion of the molecular geometry and to a concomitant increase in the mean phase difference from the correct phase set. Here, it is shown that iterative rigid-body simulated-annealing refinement of polyalanine models employing successively fewer residues per rigid body (down to one alanine residue per body) at a very high initial temperature (of the order of T0 = 10000 K) and with the geometric energy terms switched on, not only preserves the geometry of the model but can also converge to an essentially correct polyalanine trace of the target structure, even when the starting model deviates systematically and significantly from the sought structure. As an example of the application of the method, details are presented of the structure determination of the Ala31Pro mutant of the Rop protein, where an initial roughly positioned polyalanine model (giving an average phase difference of 78.2 degrees from the final phase set) was successfully refined against a 1.8 A resolution native data set, leading to an essentially correct model of the main chain with an average displacement of its atomic positions from the final model of 0.275 A. The phases calculated from this refined polyalanine model had an average difference of 43.8 degrees from the final phase set (corresponding to a mean figure of merit of 0.72) and gave a readily interpretable electron-density map.
机译：传统的优化方法,在应用的时候出现即使正确定位polyalanine模型目标结构,导致系统分子的几何和扭曲伴随的增加意味着相位差从正确的阶段。,迭代刚体模拟退火细化polyalanine模型的使用先后每个刚体(更少的残留一丙氨酸残基的身体)非常高初始温度(T0 = 10000K)和几何能量交换,不仅保留了模型的几何形状但从本质上说,还可以收敛于一个正确polyalanine跟踪目标的结构,甚至当起始模型系统地偏离并从寻求结构明显。应用程序的方法的一个例子,结构的细节了确定Ala31Pro罗普的突变蛋白,最初的大致位置polyalanine模型(给平均阶段差异78.2度的最后阶段集)成功提炼1.8解决本地数据集,导致本质上正确的主链模型平均原子位置的位移从0.275的最终模型。从这个精制polyalanine模型计算平均43.8度的区别最后阶段集(对应于一个意思图0.72)的优点和容易可说明的电子密度图。

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