Exploring The Recognation Mechanism Of Wilms' Tumour Surppressor Protein And DNA Triplets By Molecular Dynamics Simulation And Free Energy Analysis

DNA and protein are the most important biological macromolecules in organisms.There is an inseparable relationship between protein and DNA.The synthesis of protein depends on the genetic information in DNA,and the realization of biological function needs protein as a carrier.In this paper,we mainly focus on the zinc finger protein WT1.WT1 was initially identified as a tumour suppressor gene by virtue of its capacity to prevent paediatric renal cancer.As a transcription factor,WT1 could act as an oncogene that plays multifaceted roles in the processes of cancer initiation,development,and progression.WT1 consists of 10 exons,the N-terminus comprises domains for dimerization and transcription activation and repression,the C-terminus comprises four ZFs in tandem.Exon 9 represents a pivotal target for germline mutations associated with Denys–Drash syndrome(DDS).Alternative splicing at the end of exon 9 results in the insertion of the tripeptide Lys-Thr-Ser(KTS),which may have a profound effect on both the DNA-binding affinity and specificity of WT1.In this study,the initial crystal structure of the WT1(-KTS)protein-DNA complex was obtained from the Protein Data Bank(PDB code: 2PRT),and 3 different mutant complexes(E427Q,Q369 H and +KTS)for further MD simulation were also prepared based on the crystal structure(PDB code: 2PRT).Here,we present molecular dynamics simulation combined with MM-PBSA calculations to investigate the recognation mechanism between Wilms' tumour surppressor protein and DNA triplets.The results show that mutation can change the decomposition of key residues of WT1 protein,make the hydrogen bond that plays a stabilizing role on the whole structure disappear or weaken,further affect the recognition ability of the whole protein and DNA.We also found that some residues(Lys351,Arg366,Arg375 and Arg376 in ZF2,Lys399 and Arg403 in ZF3,as well as Arg424 and Arg430 in ZF4)have significant influence on recognition and binding to DNA.These results represent the first step towards a thorough characterization of the WT1 recognition mechanisms,providing a better understanding of the structure-function relationship of proteins.