Recognition of Selective DNA Sequences by Cooperative Binding Peptides

通过协同结合肽识别选择性 DNA 序列

• 批准号: 09680569
• 负责人: MORII Takashi
• 金额: $ 2.3万
• 依托单位: KYOTO UNIVERSITY
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 1997
• 资助国家: 日本
• 起止时间: 1997 至 1998
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-09680569/
• 关键词: Molecular Recognition; Host-Guest Inclusion Complex; Oligopeptides; Cooperativity; DNA Recognition; DNA Cleavage; ホストーゲスト

Sequence-specific DNA binding proteins generally consist of more than two DNA contacting regions to ensure the selectivity of recognition. The multiple DNA binding modules are connected either through the covalent linker or through the noncovalent dimerization domain, We have compared the DNA binding of peptide dimers with covalent and noncovalent dimerization domains to explore the potential advantage of each linkage on the sequence-specific DNA binding. Three sets of head-to-tail peptide dimers were synthesized by using the same basic region peptide to target the same DNA sequence : one dimer was assembled with a bridged biphenyl derivative as a covalent dimerization domain and other two dimers with the cyclodextrin-guest noncovalent dimerization domains. One of the noncovalent dimers was a heterodimer consisted of cyclodextrin- and guest-peptides, while the other was a homodimer consisted of peptides bearing both cyclodextrin and the guest molecule within the same chain. Both noncov … More alent dimers formed the specific DNA complexes within narrower ranges of peptide concentrations and showed higher sequence selectivity than the covalent dimer did. Among the three dimers, the noncovalent homodimer that can form an intramolecular inclusion complex showed the highest sequence-selectivity. Because the noncovalent homodimer with the higher stability of the circular intramolecular inclusion complex revealed the higher sequence-selectivity, it was concluded that an equilibrium involving a conformational transition of a monomeric peptide effectively reduced the stability of its non-specific binding complex hence increasing the efficacy of cooperative dimer formation at the specific DNA sequence. The basic region peptides with five different guest molecules were synthesized and their equilibrium dissociation constants with a peptide possessing b-cyclodextrin were determined. These values, ranging from 1.3 to 15 muM, were used to estimate the stability of the complexes between the dimers with various guest/cyclodextrin dimerization domains and GCN4 target sequences. An efficient cooperative formation of the dimer complexes at the GCN4 binding sequence was observed when the adamantyl group was replaced with the norbornyl or noradamantyl group, but not with the cyclohexyl group that formed a b-cyclodextrin complex with an order of magnitude lower stability than the adamantyl group. Thus, cooperative formation of the stable dimer-DNA complex appeared to be effected by the stability of dimerization domain. Less

序列特异性DNA结合蛋白通常由两个以上的DNA接触区组成，以确保识别的选择性。多个DNA结合模块通过共价连接区或非共价二聚结构域连接，我们比较了多肽二聚体与共价和非共价二聚结构域的DNA结合，以探索每个连接在序列特异性DNA结合上的潜在优势。利用相同的碱基区多肽靶向同一DNA序列，合成了三组头尾二聚体：一组二聚体与桥联联苯衍生物组装为共价二聚体结构域，另两组二聚体与环糊精客体非共价二聚体结构域组装在一起。其中一个非共价二聚体是由环糊精和客体多肽组成的杂二聚体，另一个是由环糊精和客体分子在同一链上的多肽组成的同源二聚体。两个非覆盖…更多的Alent二聚体在较窄的肽浓度范围内形成特定的DNA复合体，并显示出比共价二聚体更高的序列选择性。在三个二聚体中，能够形成分子内包合物的非共价同源二聚体显示出最高的序列选择性。由于环状分子内包合物稳定性较高的非共价均二聚体表现出较高的序列选择性，因此可以得出结论，涉及单体多肽构象转变的平衡有效地降低了其非特异性结合络合物的稳定性，从而提高了在特定DNA序列上合作形成二聚体的效率。合成了具有5种不同客体分子的碱性区肽，并测定了它们与含有b-环糊精的多肽的平衡解离常数。这些值的范围从1.3到15微米，用于评估具有不同客体/环糊精二聚结构域的二聚体与GCN4靶序列之间的络合物的稳定性。当金刚烷基被降冰片基或去金刚烷基取代时，在GCN4结合序列上观察到有效的二聚体络合物的协同形成，而与形成稳定性比金刚烷基低一个数量级的b-环糊精络合物的环己基不同。因此，稳定的二聚体-DNA复合体的协同形成似乎受到二聚化结构域稳定性的影响。较少

项目成果

Yasunori Aizawa 他: "Comparison of the Sequence-Selective DNA Binding by Peptide Dimers with Covalent and Noncovalent Dimerization Domains." Biochemistry. 38. 1626-1632 (1999)

Yasunori Aizawa 等人：“肽二聚体与共价和非共价二聚化结构域的序列选择性 DNA 结合的比较。”38. 1626-1632 (1999)

Y.Aizawa, Y.Sugiura and T.Morii: "Comparison of the Sequence-Selective DNA Binding by Peptide Dimers with Covalent and Noncovalent Dimeriza-tion Domains." Biochemistry. 38. 1626-1632 (1999)

Y.Aizawa、Y.Sugiura 和 T.Morii：“具有共价和非共价二聚化结构域的肽二聚体的序列选择性 DNA 结合的比较”。

Y.Aizawa, Y.Sugiura, M.Ueno, Y.Mori, K.Imoto, K.Makino and T.Morii: "Stability of the Dimeriza-tion Domains Effects the Cooperative DNA Bind-ing of Short Petides." Biochemistry. 38. 4008-4017 (1999)

Y.Aizawa、Y.Sugiura、M.Ueno、Y.Mori、K.Imoto、K.Makino 和 T.Morii：“二聚化结构域的稳定性影响短肽的协同 DNA 结合。”

Yasunori, Aizawa他: "Selective Recognition of Tandemly Repeated DNA Sequences by Homo and Hetero-Dimers of Short Peptides." Nucleic Acids Symposium Series. 37. 311-312 (1997)

Yasunori, Aizawa 等人：“短肽同源和异源二聚体对串联重复 DNA 序列的选择性识别”。核酸研讨会系列 37. 311-312 (1997)。

Yasunori Aizawa 他: "Cooperative DNA Binding by Short Peptides." Nucleic Acids Symposium Series. 39. 67-68 (1998)

Yasunori Aizawa 等人：“短肽的协同 DNA 结合”。39. 67-68 (1998)