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Rosetta Cartesian_ddG: 更快更准确的蛋白质稳定性预测方法


计算单点突变自由能是分子稳定性改造的”老套路”。FoldX以及ddg_monomer application已经久经实战考验(具体用法参考前人总结:http://bioengx.hk1.91site.net/rosetta-ddg_monomer/)。今天我们就来说说Rosetta新一代的预测方法: Cartesian_ddG。

1 Cartesian_ddG方法概述

参考: Hahnbeom Park, Philip Bradley, Per Greisen Jr., Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, and Frank DiMaio (2016) “Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules”, JCTC.





2 Cartesian_ddG的使用方法



2.1 预优化野生型蛋白结构


-nstruct 20
-relax:cartesian-score:weights ref2015_cart # 务必设为ref2015_cart
-relax:min_type lbfgs_armijo_nonmonotone # 能量最小化的算法
-relax:script cart2.script

repeat 2
ramp_repack_min 0.02 0.01 1.0 50
ramp_repack_min 0.250 0.01 0.5 50
ramp_repack_min 0.550 0.01 0.0 100
ramp_repack_min 1 0.00001 0.0 200

relax.mpi.macosclangrelease -s $pdb @relax_flag

2.2 准备mutfile文件

total 1 # mutfile中总突变数量
1 # 本轮突变氨基酸个数,单点突变设置为1.
T 89 A # 将89位的T突变为A

2.3 运行Cartesian_ddG
Cartesian_ddG有两种运行模式: 蛋白稳定性预测模式(Protein stability mode)和 相互作用界面模式(Interface mode)。

1)蛋白稳定性预测模式(Protein stability mode)
创建cartddg_flag文件, 内容如下:

-ddg:iterations 5 # 默认为3,可以根据自身计算资源调整。
-ddg::dump_pdbs False # 是否输出突变后的蛋白PDB文件,推荐False,否则文件夹会很乱
-bbnbrs 1 # 骨架自由度,额外考虑线性邻居氨基酸的数目,1代表 邻近的3个氨基酸骨架自由度被考虑在计算中。
-fa_max_dis 9.0 # 控制范德华和溶剂化能量计算的范围,默认为6埃以内的氨基酸被考虑。
-score:weights ref2015_cart # 务必设为ref2015_cart

cartesian_ddg.linuxgccrelease -s [inputpdb] @cartddg_flag -ddg:mut_file T89A.mutfile

2 )相互作用界面模式(Interface mode)
该模式开发者并未做详细测试,斟酌使用,此处笔者未做测试。如有需要请参考: https://www.rosettacommons.org/docs/latest/cartesian-ddG

3 结果分析


COMPLEX: Round1: WT: -333.782 fa_atr: -840.140 fa_rep: ………….
COMPLEX: Round2: WT: -333.782 fa_atr: -840.140 fa_rep: ………….
COMPLEX: Round3: WT: -333.782 fa_atr: -840.140 fa_rep: ………….
COMPLEX: Round4: WT: -333.782 fa_atr: -840.140 fa_rep: ………….
COMPLEX: Round5: WT: -333.782 fa_atr: -840.140 fa_rep: ………….
COMPLEX: Round1: MUT_89ALA: -330.352 fa_atr: -834.516 ………….
COMPLEX: Round2: MUT_89ALA: -330.352 fa_atr: -834.516 ………….
COMPLEX: Round3: MUT_89ALA: -330.352 fa_atr: -834.516 ………….
COMPLEX: Round4: MUT_89ALA: -330.352 fa_atr: -834.516 ………….
COMPLEX: Round5: MUT_89ALA: -330.352 fa_atr: -834.516 ………….





∆∆G < -1.0 代表点突变为蛋白带来稳定效应; ∆∆G > 1.0 代表点突变为蛋白带来不稳定效应;

备注: 如果需要批量分析和点突变扫描,请使用脚本生成多个mutfile,然后按照以上流程进行计算。

作者: Rosetta研习社

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  14. 创建relax_flag文件,文件内容如下:

    -nstruct 20
    -relax:cartesian-score:weights ref2015_cart # 务必设为ref2015_cart
    -relax:min_type lbfgs_armijo_nonmonotone # 能量最小化的算法
    -relax:script cart2.script

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    -score:weights ref2015_cart # 务必设为ref2015_cart
    -relax:min_type lbfgs_armijo_nonmonotone # 能量最小化的算法
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