Department of Biochemistry and Molecular Biology, Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
J Mol Recognit. 2011 Jul-Aug;24(4):647-55. doi: 10.1002/jmr.1093.
An intriguing regulatory mechanism is the ability of some proteins to recognize their binding partners in an isoform-specific manner. In this study we undertook a systematic analysis of the specificity of the tropomodulin (Tmod) interaction with tropomyosin (TM) to show that affinities of different Tmod isoforms to TM are isoform-dependent. Intrinsic disorder predictions, alignment of sequences, and circular dichroism were utilized to establish a structural basis for these isoform-specific interactions. The affinity of model peptides derived from the N-terminus of different TM isoforms to protein fragments that correspond to the two TM-binding sites of different Tmod isoforms were analyzed. Several residues were determined to be responsible for the isoform-dependent differences in affinity. We suggest that changing a set of residues rather than a single residue is needed to alter the binding affinity of one isoform to mimic the affinity of another isoform. The general intrinsic disorder predictor, PONDR® VLXT, was shown to be a useful tool for analyzing regions involved in isoform-specific binding and for predicting the residues important for isoform differences in binding. Knowing the residues responsible for isoform-specific affinity creates a tool suitable for studying the influence of Tmod/TM interactions on sarcomere assembly in muscle cells or actin dynamics in non-muscle cells.
一种有趣的调控机制是某些蛋白质以同种型特异性的方式识别其结合伴侣的能力。在这项研究中，我们对原肌球蛋白（TM）与原肌球蛋白结合的肌动蛋白调节蛋白（Tmod）的特异性进行了系统分析，结果表明不同 Tmod 同种型与 TM 的亲和力是同种型依赖性的。利用内在无序预测、序列比对和圆二色性来确定这些同种型特异性相互作用的结构基础。分析了源自不同 TM 同种型 N 端的模型肽与对应于不同 Tmod 同种型的两个 TM 结合位点的蛋白片段之间的亲和力。确定了几个残基负责亲和力的同种型依赖性差异。我们认为，需要改变一组残基而不是单个残基来改变一种同种型的结合亲和力，以模拟另一种同种型的亲和力。一般的内在无序预测器 PONDR®VLXT 被证明是一种有用的工具，可用于分析涉及同种型特异性结合的区域，并预测对结合的同种型差异重要的残基。了解导致同种型特异性亲和力的残基为研究 Tmod/TM 相互作用对肌细胞肌节组装或非肌细胞肌动蛋白动力学的影响提供了合适的工具。
