Sokhansanj Bahrad A, Rodrigue Garry R, Fitch J Patrick, Wilson David M
Biology and Biotechnology Research Program, L-441, University of California, Lawrence Livermore National Laboratory, Livermore, CA 94551-9900, USA.
Nucleic Acids Res. 2002 Apr 15;30(8):1817-25. doi: 10.1093/nar/30.8.1817.
Base excision repair (BER) is a multistep process involving the sequential activity of several proteins that cope with spontaneous and environmentally induced mutagenic and cytotoxic DNA damage. Quantitative kinetic data on single proteins of BER have been used here to develop a mathematical model of the BER pathway. This model was then employed to evaluate mechanistic issues and to determine the sensitivity of pathway throughput to altered enzyme kinetics. Notably, the model predicts considerably less pathway throughput than observed in experimental in vitro assays. This finding, in combination with the effects of pathway cooperativity on model throughput, supports the hypothesis of cooperation during abasic site repair and between the apurinic/apyrimidinic (AP) endonuclease, Ape1, and the 8-oxoguanine DNA glycosylase, Ogg1. The quantitative model also predicts that for 8-oxoguanine and hydrolytic AP site damage, short-patch Polbeta-mediated BER dominates, with minimal switching to the long-patch subpathway. Sensitivity analysis of the model indicates that the Polbeta-catalyzed reactions have the most control over pathway throughput, although other BER reactions contribute to pathway efficiency as well. The studies within represent a first step in a developing effort to create a predictive model for BER cellular capacity.
碱基切除修复（BER）是一个多步骤过程，涉及多种蛋白质的顺序作用，这些蛋白质可应对自发的和环境诱导的致突变和细胞毒性DNA损伤。本文利用BER单个蛋白质的定量动力学数据建立了BER途径的数学模型。然后利用该模型评估机制问题，并确定途径通量对改变的酶动力学的敏感性。值得注意的是，该模型预测的途径通量比实验体外测定中观察到的要少得多。这一发现，结合途径协同性对模型通量的影响，支持了无碱基位点修复过程中以及脱嘌呤/脱嘧啶（AP）内切酶Ape1和8-氧鸟嘌呤DNA糖基化酶Ogg1之间存在协同作用的假设。定量模型还预测，对于8-氧鸟嘌呤和水解AP位点损伤，短补丁Polβ介导的BER占主导，转换到长补丁子途径的情况最少。模型的敏感性分析表明，Polβ催化的反应对途径通量的控制最大，尽管其他BER反应也对途径效率有贡献。本文的研究代表了创建BER细胞能力预测模型这一不断发展的努力中的第一步。
