Induced Fit or Conformation Selection for Specific Recognition between RNA/DNA Hybrid and RNA Polymerase

【作者】 叶纬； 张健； 陈海峰；

【Author】 Wei Ye~1,Fang Qin~1,Yixue Li~(2,*),Jian Zhang~(3,*), Hai-Feng Chen~(1,2,’*) 1State Key Laboratory of Microbial metabolism,College of Life Sciences and Biotechnology,Shanghai Jiaotong University,800 Dongchuan Road,Shanghai,200240,China 2Shanghai Center for Bioinformation Technology,100 Qinzhou Road,Shanghai,200235,China 3Department of Pathophysiology,Key Laboratory of Cell Differentiation andApoptosis of Chinese Ministry of Education,School of Medicine,Shanghai Jiaotong University,Shanghai 200025,China

【机构】 State Key Laboratory of Microbial metabolism,College of Life Sciences and Biotechnology,Shanghai Jiaotong University,800 Dongchuan Road,Shanghai,200240,China； Department of Pathophysiology,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,School of Medicine,Shanghai Jiaotong University,Shanghai 200025,China； Shanghai Center for Bioinformation Technology,100 Qinzhou Road,Shanghai,200235,China；

【摘要】 <正>RNA polymerase catalyzes transcription with a high fidelity.If a DNA-RNA mismatch or DNA damage occurs downstream,a backtracked RNA polymerase can proofread this situation. However,the mechanism of backtracking is still poorly understood.Here we have performed explicit-solvent molecular dynamics(MD) simulations on bound and apo DNA/RNA hybrid to study the kinetics.MD simulations at 298K suggest that the conformation of bound DNA/RNA hybrid has significant adjustment and becomes more stable upon the enzyme binding.This is consistent with previous experiments.Kinetics analysis of MD simulations at 498K shows that bound and apo DNA/RNA hybrid unfold via a two-state process.Both kinetics and free energy landscape analyses indicate that bound DNA-RNA hybrid folds in the order of DNA/RNA contracting,the tertiary folding and the enzyme binding.The average rmsd values between the bound structures and the corresponding apo structures and Kolmogorov-Smirnov(KS) P test analyses indicate that the folding of DNA/RNA hybrid might follow an induced fit mechanism.The predictedΦ-values suggest that G8,G9,dT13,dC15 and dT16 are key bases for bound DNA/RNA hybrid folding.Furthermore,this method could be used to relative studies of specific recognition between nucleic acid and protein.更多还原

【Abstract】 RNA polymerase catalyzes transcription with a high fidelity.If a DNA-RNA mismatch or DNA damage occurs downstream,a backtracked RNA polymerase can proofread this situation. However,the mechanism of backtracking is still poorly understood.Here we have performed explicit-solvent molecular dynamics(MD) simulations on bound and apo DNA/RNA hybrid to study the kinetics.MD simulations at 298K suggest that the conformation of bound DNA/RNA hybrid has significant adjustment and becomes more stable upon the enzyme binding.This is consistent with previous experiments.Kinetics analysis of MD simulations at 498K shows that bound and apo DNA/RNA hybrid unfold via a two-state process.Both kinetics and free energy landscape analyses indicate that bound DNA-RNA hybrid folds in the order of DNA/RNA contracting,the tertiary folding and the enzyme binding.The average rmsd values between the bound structures and the corresponding apo structures and Kolmogorov-Smirnov(KS) P test analyses indicate that the folding of DNA/RNA hybrid might follow an induced fit mechanism.The predictedΦ-values suggest that G8,G9,dT13,dC15 and dT16 are key bases for bound DNA/RNA hybrid folding.Furthermore,this method could be used to relative studies of specific recognition between nucleic acid and protein.更多还原