Acharya Rudresh, Gupta Madhvi, Ramakumar Suryanarayanarao, Ramagopal Udupi A, Chauhan Virander S
Department of Physics, Indian Institute of Science, Bangalore, India.
BMC Struct Biol. 2007 Aug 1;7:51. doi: 10.1186/1472-6807-7-51.
The de novo design of peptides and proteins has recently surfaced as an approach for investigating protein structure and function. This approach vitally tests our knowledge of protein folding and function, while also laying the groundwork for the fabrication of proteins with properties not precedented in nature. The success of these studies relies heavily on the ability to design relatively short peptides that can espouse stable secondary structures. To this end, substitution with alpha, beta-dehydroamino acids, especially alpha, beta-dehydrophenylalanine (Delta Phe) comes in use for spawning well-defined structural motifs. Introduction of Delta Phe induces beta-bends in small and 3(10)-helices in longer peptide sequences.
The present report is an investigation of the effect of incorporating two glycines in the middle of a DeltaPhe containing undecapeptide. A de novo designed undecapeptide, Ac-Gly1-Ala2-Delta Phe3-Leu4-Gly5-Delta Phe6-Leu7-Gly8-Delta Phe9-Ala10-Gly11-NH2, was synthesized and characterized using X-ray diffraction and Circular Dichroism spectroscopic methods. Crystallographic studies suggest that, despite the presence of L-amino acid (L-Ala and L-Leu) residues in the middle of the sequence, the peptide adopts a 3(10)-helical conformation of ambidextrous screw sense, one of them a left-handed (A) and the other a right-handed (B) 3(10)-helix with A and B being antiparallel to each other. However, CD studies reveal that the undecapeptide exclusively adopts a right-handed 3(10)-helical conformation. In the crystal packing, three different interhelical interfaces, Leu-Leu, Gly-Gly and Delta Phe-Delta Phe are observed between the helices A and B. A network of C-H...O hydrogen bonds are observed at Delta Phe-Delta Phe and Gly-Gly interhelical interfaces. An important feature observed is the occurrence of glycine zipper motif at Gly-Gly interface. At this interface, the geometric pattern of interhelical interactions seems to resemble those observed between helices in transmembrane (TM) proteins.
The present design strategy can thus be exploited in future work on de novo design of helical bundles of higher order and compaction utilizing Delta Phe residues along with GXXG motif.
肽和蛋白质的从头设计最近已成为一种研究蛋白质结构和功能的方法。这种方法至关重要地检验了我们对蛋白质折叠和功能的认识，同时也为制造具有自然界中前所未有的特性的蛋白质奠定了基础。这些研究的成功在很大程度上依赖于设计出能够呈现稳定二级结构的相对短的肽的能力。为此，用α,β-脱氢氨基酸，尤其是α,β-脱氢苯丙氨酸（ΔPhe）进行取代，可用于产生明确的结构基序。引入ΔPhe会在短肽中诱导β-转角，并在较长肽序列中诱导3(10)-螺旋。
本报告研究了在含ΔPhe的十一肽中间掺入两个甘氨酸的效果。合成了一个从头设计的十一肽Ac-Gly1-Ala2-ΔPhe3-Leu4-Gly5-ΔPhe6-Leu7-Gly8-ΔPhe9-Ala10-Gly11-NH2，并使用X射线衍射和圆二色光谱法对其进行了表征。晶体学研究表明，尽管序列中间存在L-氨基酸（L-Ala和L-Leu）残基，但该肽采用了具有左右手螺旋方向的3(10)-螺旋构象，其中一个是左手（A）3(10)-螺旋，另一个是右手（B）3(10)-螺旋，A和B相互反平行。然而，圆二色性研究表明，该十一肽仅采用右手3(10)-螺旋构象。在晶体堆积中，在螺旋A和B之间观察到三种不同的螺旋间界面，即Leu-Leu、Gly-Gly和ΔPhe-ΔPhe。在ΔPhe-ΔPhe和Gly-Gly螺旋间界面观察到C-H...O氢键网络。观察到的一个重要特征是在Gly-Gly界面出现了甘氨酸拉链基序。在这个界面上，螺旋间相互作用的几何模式似乎类似于跨膜（TM）蛋白中螺旋之间观察到的模式。
因此，在未来利用ΔPhe残基和GXXG基序进行高阶螺旋束的从头设计和压实的工作中，可以采用本设计策略。
