Exploring a New Approach for Discovery of Conformational Heterogeneity in Homeodomain-DNA Complexes.
Exploring a New Approach for Discovery of Conformational Heterogeneity in Homeodomain-DNA Complexes.
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探索发现同源结构域-DNA 复合物构象异质性的新方法。
DOI：
10.1021/acs.biochem.7b00760
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发表时间：
2017
期刊：
影响因子：
2.9
通讯作者：
Rance,Mark
中科院分区：
文献类型：
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作者：
Rance,Mark
蛋白质与−相互作用的分子基础一直是结构生物学领域研究的重要课题。特别是，这种相互作用需要进一步探索的一个方面是关于构象异质性和分子动力学对分子识别和结合亲和力的贡献的一般问题。尽管已经报道了大量关于蛋白质−DNA体系的结构和热力学研究，但在我们对分子动力学和灵活性在蛋白质−DNA相互作用中所扮演的角色的理解上存在着关键的和实质性的差距。分子识别领域的一个普遍问题是，结构研究揭示的关于络合物形成自由能的熵分量相对较少。因此，通过开展研究来补充可用的结构信息是非常重要的，该研究旨在阐明有关蛋白质−DNA界面中侧链动力学的细节。正如Fraenkel和Pabo在他们对Antennapedia同源结构域DNADNA复合体的工作中所提到的那样，“当我们试图整合X射线和−数据以了解灵活性和离散的有利接触在大分子识别中的各自作用时，比较其他蛋白质/DNADNA复合体将是有趣的”。1比勒特等人。假设ANTP通过一个波动的短期接触网络实现特异性，这使得它能够识别DNA，而不会产生如果侧链固定在DNA结合上所产生的熵成本。2到目前为止，同源结构域及其与DNA的络合物的详细结构研究主要是通过X射线结晶学和核磁共振(核磁共振)光谱进行的。然而，在Romesberg团队最近的一篇论文中，3他们指出红外(IR)光谱可以作为一种有价值的补充工具来发现蛋白质−DNA复合体的构象异质性。红外光谱的一个主要优势是它提供了亚皮秒的时间分辨率，这意味着它可以潜在地捕捉到在生物相关时间尺度上发生的任何构象异质性。Romesberg团队方法的一个关键是加入了非微扰、特定位置的光谱探针，即Carbon−Deurium(C−D)键，这消除了原本因重叠吸收而存在的问题。以前已经确定，D取代H的同位素将IR拉伸吸收转移到一个没有其他信号的光谱区域(见参考文献4了解这种方法的起源)。
The molecular basis of protein− DNA interactions con-tinues to be a very important subject of investigation in the field of structural biology. In particular, one aspect of such interactions that requires further exploration is the general question regarding the contributions of conformational heterogeneity and molecular dynamics to molecular recognition and binding affinity. Despite the large number of structural and thermodynamic studies that have been reported for a variety of protein− DNA systems, critical and substantial gaps exist in our understanding of the roles played by molecular dynamics and flexibility in protein− DNA interactions. A general problem in the field of molecular recognition is that structural studies reveal relatively little about the entropic component of the free energy of complex formation. Thus, it is very important to complement available structural information by undertaking studies designed to elucidate details concerning side-chain dynamics in the protein− DNA interface. As mentioned by Fraenkel and Pabo in their work on the Antennapedia (Antp) homeodomain− DNA complex,“it will be interesting to compare other protein/DNA complexes as we try to integrate X-ray and NMR data to understand the respective roles of flexibility and of discrete, favorable contacts in macromolecular recognition”. 1 Billeter et al. hypothesized that Antp achieves specificity through a fluctuating network of short-lived contacts that allows it to recognize the DNA without the entropic cost that would result if side chains were immobilized upon DNA binding. 2 To date, detailed structural studies of homeodomains and their complexes with DNA have predominantly been performed via X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. However, in a recent paper from Romesberg’s group, 3 they indicated that infrared (IR) spectroscopy can be a valuable, complementary tool for discovering conformational heterogeneity in protein− DNA complexes. A principal advantage of IR spectroscopy is the subpicosecond time resolution it offers, which means that it can potentially capture any conformational heterogeneity that occurs on biologically relevant time scales. A key to the approach of Romesberg’s group was the incorporation of nonperturbing, site-specific spectroscopic probes, namely, carbon− deuterium (C− D) bonds, which eliminates the problems that would otherwise exist because of overlapping absorptions. It had been established previously that isotopic substitution of D for H shifts the IR stretching absorptions into a spectral region that is free of other signals (see ref 4 for the origins of this approach).