Prediction and control of protein stability using computer experiments

本项目的目的是（1）在不受用户干扰的情况下，自动计算突变蛋白质的稳定自由能。(2)通过在并行机上并行化程序来加速自由能计算。(3)将计算诱变方法扩展到不同种类之间的氨基酸突变。（4）在实验观察突变蛋白之前，定量预测突变蛋白的稳定性。(1)通过制作unix shell来控制计算过程，实现了稳定自由能的自动计算，计算诱变>分子动力学模拟>自由能计算。(2)通过在富士通VPP 5000上并行化程序COSMOS 90，实现了计算速度的提高，用于分子动力学模拟，这是稳定性计算中最耗时的部分。(3)通过对Myb R2结构域和α-乳清蛋白进行从瓦尔（疏水氨基酸）到Thr（亲水氨基酸）的氨基添加突变，成功地进行了计算诱变的扩展。(4)对Myb R2结构域的瓦尔>Met和瓦尔>Thr突变进行稳定性的预测计算。计算成功地预测了瓦尔>Met突变体的稳定性，但不能预测瓦尔>Thr突变体。澄清了瓦尔>Thr计算结果不一致的原因，重新计算得到了正确的结果。

The purpose of this project were(1) Automatically calculating the stability free energies of mutant proteins without interrupting by a user.(2) Speed up free energy calculations by parallelizing the programs on parallel machines.(3) Expanding the computational mutagenesis methodology to amino acid mutations between different kinds(4) Quantitatively predicting the stability of mutant proteins before experimentally observing it.These purpose were achieved as follows.(1) Automatic calculation of stability free energy was achieved by making unix shells to control the calculation processes, i.e., computational mutagenesis > molecular dynamics simulation > free energy calculation.(2) Speed up of calculation was achieved by parallelizing the program COSMOS90 on fujitsu VPP5000 for the molecular dynamics simulation that is the most time consuming part of the stability calculation.(3) Expansion of computational mutagenesis was successfully performed by amino add mutation from Val (hydrophobia amino acid) to Thr (hydrophilic amino acid) for Myb R2 domain and alpha-lactalbumin.(4) Predictive calculation of stability was performed to Val>Met and Val>Thr mutations for Myb R2 domain. The calculations successfully predicted the stability of Val>Met mutant but not Val>Thr mutant. The reason of this discrepancy for the Val>Thr calculation was clarified and recalculation gave the correct result.