Mruk Karen, Farley Brian M, Ritacco Alan W, Kobertz William R
Department of Biochemistry and Molecular Pharmacology and Programs in Chemical Biology and Neuroscience, and.
Department of Scientific and Research Computing, University of Massachusetts Medical School, Worcester, MA 01605.
J Gen Physiol. 2014 Jul;144(1):105-14. doi: 10.1085/jgp.201311140. Epub 2014 Jun 16.
The calcium-binding protein calmodulin (CaM) directly binds to membrane transport proteins to modulate their function in response to changes in intracellular calcium concentrations. Because CaM recognizes and binds to a wide variety of target sequences, identifying CaM-binding sites is difficult, requiring intensive sequence gazing and extensive biochemical analysis. Here, we describe a straightforward computational script that rapidly identifies canonical CaM-binding motifs within an amino acid sequence. Analysis of the target sequences from high resolution CaM-peptide structures using this script revealed that CaM often binds to sequences that have multiple overlapping canonical CaM-binding motifs. The addition of a positive charge discriminator to this meta-analysis resulted in a tool that identifies potential CaM-binding domains within a given sequence. To allow users to search for CaM-binding motifs within a protein of interest, perform the meta-analysis, and then compare the results to target peptide-CaM structures deposited in the Protein Data Bank, we created a website and online database. The availability of these tools and analyses will facilitate the design of CaM-related studies of ion channels and membrane transport proteins.
钙结合蛋白钙调蛋白（CaM）直接与膜转运蛋白结合，以响应细胞内钙浓度的变化来调节其功能。由于CaM能识别并结合多种靶序列，因此识别CaM结合位点很困难，需要深入的序列审视和广泛的生化分析。在此，我们描述了一个简单的计算脚本，它能快速识别氨基酸序列中的典型CaM结合基序。使用该脚本对高分辨率CaM-肽结构的靶序列进行分析发现，CaM通常与具有多个重叠典型CaM结合基序的序列结合。在此荟萃分析中加入正电荷鉴别器，得到了一种能在给定序列中识别潜在CaM结合域的工具。为了让用户能够在感兴趣的蛋白质中搜索CaM结合基序、进行荟萃分析，然后将结果与蛋白质数据库中存储的靶肽-CaM结构进行比较，我们创建了一个网站和在线数据库。这些工具和分析的可用性将有助于设计与CaM相关的离子通道和膜转运蛋白研究。
