Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.

锌指蛋白 (ZFP) 在细胞过程中发挥重要作用。ZFP的DNA结合区由3个通过氨基酸接头连接的锌指DNA结合域组成，序列TGQKP连接ZF1和ZF2，TGEKP连接ZF2和ZF3。接头的作用是将锌指蛋白调整到正确的位置以结合其 DNA 靶标，氨基酸残基的类型和接头的长度反映了 ZF1-ZF2-ZF3 的相互作用，并有助于 ZF 蛋白对其 DNA 的搜索和识别过程目标。通过 MD 模拟和 MM_GB(PB)SA 研究了接头突变和所得突变体对特定和非特异性 DNA 靶标的亲和力。突变体对 DNA 的亲和力因氨基酸残基的类型和位置而异。TGQKP 中的 K 突变导致亲和力丧失，因为失去了与磷酸盐的正 K 相互作用，G 的突变显示对 DNA、WT 蛋白的亲和力丧失，并且所有接头突变体显示对非特异性 DNA 靶标的亲和力丧失，这一发现证实了先前的报告将这种亲和力的损失解释为由于 ZF1 具有锚定作用，而 ZF3 在结合机制中扮演探索者的角色。鉴于蛋白质结构和接头残基在结合中的作用，讨论了 ZFP-DNA 亲和力与接头突变的变化。ZF3在绑定机制中扮演探索者角色。鉴于蛋白质结构和接头残基在结合中的作用，讨论了 ZFP-DNA 亲和力与接头突变的变化。ZF3在绑定机制中扮演探索者角色。鉴于蛋白质结构和接头残基在结合中的作用，讨论了 ZFP-DNA 亲和力与接头突变的变化。