Del Val Coral, Royuela-Flor José, Milenkovic Stefan, Bondar Ana-Nicoleta
Department of Computer Science and Artificial Intelligence, University of Granada, 18071 Granada, Spain.
Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, 14195 Berlin, Germany.
Biochim Biophys Acta. 2014 May;1837(5):643-55. doi: 10.1016/j.bbabio.2013.11.005. Epub 2013 Nov 16.
Channelrhodopsins are microbial-type rhodopsins that function as light-gated cation channels. Understanding how the detailed architecture of the protein governs its dynamics and specificity for ions is important, because it has the potential to assist in designing site-directed channelrhodopsin mutants for specific neurobiology applications. Here we use bioinformatics methods to derive accurate alignments of channelrhodopsin sequences, assess the sequence conservation patterns and find conserved motifs in channelrhodopsins, and use homology modeling to construct three-dimensional structural models of channelrhodopsins. The analyses reveal that helices C and D of channelrhodopsins contain Cys, Ser, and Thr groups that can engage in both intra- and inter-helical hydrogen bonds. We propose that these polar groups participate in inter-helical hydrogen-bonding clusters important for the protein conformational dynamics and for the local water interactions. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
视紫红质通道蛋白是微生物型视紫红质，其功能为光门控阳离子通道。了解该蛋白质的详细结构如何控制其动力学以及对离子的特异性很重要，因为这有可能有助于设计用于特定神经生物学应用的定点视紫红质通道蛋白突变体。在这里，我们使用生物信息学方法来获得视紫红质通道蛋白序列的准确比对，评估序列保守模式并在视紫红质通道蛋白中找到保守基序，并使用同源建模来构建视紫红质通道蛋白的三维结构模型。分析表明，视紫红质通道蛋白的螺旋C和D含有可参与螺旋内和螺旋间氢键的半胱氨酸、丝氨酸和苏氨酸基团。我们提出，这些极性基团参与了对蛋白质构象动力学和局部水相互作用很重要的螺旋间氢键簇。本文是名为：视网膜蛋白——老狗也能学新招 的特刊的一部分。
