Gresh N
Département de Pharmacochimie Moléculaire et Structurale U266 INSERM - URA D1500 CNRS UFR des Sciences Pharmaceutiques et Biologiques, Faculté de Pharmacie, Paris, France.
J Biomol Struct Dyn. 1996 Oct;14(2):255-73. doi: 10.1080/07391102.1996.10508117.
Proline-rich peptides are known to adopt preferentially the extended polyproline II (PPII) helical conformation, which is involved in several protein-protein recognition events. By resorting to molecular modelling techniques, we wished to investigate the extent to which PPII helices could be used for the formation of isochelical peptide-DNA complexes leading to the selective recognition of the major groove of B-DNA. For that purpose, we have grafted to a cationic intercalator, 9-amino-acridine, an oligopeptide having the sequence: Pro- Arg-Pro-Pro-Arg-Pro-Pro-Arg-Pro-Pro-Asp-Pro-Pro. Each residue in the sequence was set in the D configuration, to prevent enzymatic hydrolysis, and each Arg residue was designed to target O6/N7 of a guanine base following the intercalation site. The Asp residue was designed to target a cytosine base, whilst simultaneously forming a bidentate complex with the Arg three residues upstream. Energy-minimization, using the JUMNA procedure, led to the following conclusions : 1) major groove binding is favoured over minor groove or exclusive binding to the phosphates by large energy differences, of over 50 and 90 kcal/mole, respectively: 2) the two best bound sequences are those having three successive guanine bases on the same DNA strand, immediately adjacent to the intercalation site. Sequence d(CGGGC G), encountered in the Primer Binding Site of the HIV retrovirus, thus ranks amongst the best-bound sequences; 3) replacement of an individual guanine amongst the three ones upstream of the intercalation site, by an adenine base, weakens by > 6 kcal/mole the binding energetics; 4) the conformational rigidity of the DNA-bound PPII helix should enable for a modulation of the base sequence selectivity, by appropriate replacements of the Arg and Asp residues. Thus sequence CGGCAAG, also encountered in the HIV genome, could be targeted by an oligopeptide having the sequence Pro-Arg-Pro-Pro-Asp-Pro-Pro-Asn-Pro-Pro-Asn-Pro-Pro-Arg-Ala.
富含脯氨酸的肽优先采用延伸的聚脯氨酸II（PPII）螺旋构象，这种构象参与了多种蛋白质-蛋白质识别事件。通过运用分子建模技术，我们希望研究PPII螺旋在多大程度上可用于形成等螺旋的肽-DNA复合物，从而实现对B-DNA大沟的选择性识别。为此，我们将一个具有如下序列的寡肽嫁接到阳离子嵌入剂9-氨基吖啶上：Pro-Arg-Pro-Pro-Arg-Pro-Pro-Arg-Pro-Pro-Asp-Pro-Pro。序列中的每个残基都设定为D构型，以防止酶促水解，并且每个精氨酸残基设计为在嵌入位点之后靶向鸟嘌呤碱基的O6/N7。天冬氨酸残基设计为靶向胞嘧啶碱基，同时与上游三个残基处的精氨酸形成双齿复合物。使用JUMNA程序进行能量最小化得出以下结论：1）大沟结合比小沟结合或仅与磷酸基团结合更受青睐，能量差异分别超过50和90千卡/摩尔；2）两个结合最佳的序列是在同一DNA链上紧邻嵌入位点有三个连续鸟嘌呤碱基的序列。HIV逆转录病毒引物结合位点中出现的序列d（CGGGC G）因此位列结合最佳的序列之中；3）将嵌入位点上游三个鸟嘌呤中的一个替换为腺嘌呤碱基，会使结合能减弱超过6千卡/摩尔；4）与DNA结合的PPII螺旋的构象刚性应能够通过适当替换精氨酸和天冬氨酸残基来调节碱基序列选择性。因此，HIV基因组中也出现的序列CGGCAAG可被一个具有如下序列的寡肽靶向：Pro-Arg-Pro-Pro-Asp-Pro-Pro-Asn-Pro-Pro-Asn-Pro-Pro-Arg-Ala。
