Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains

The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in function or regulatory properties.

真核生物（eukaryote）基因组编码的绝大多数蛋白质都包含不止一个蛋白质结构域（protein domain）。多结构域蛋白质在各类生物中广泛存在，其原因被认为是相较于单结构域蛋白质，它们具备更高的稳定性、更优越的功能与折叠优势。尽管具备这些优势，仍有许多蛋白质仅由单个结构域构成，而它们的同源结构域却属于多结构域蛋白质。本研究中，我们探讨了单结构域与多结构域系统中蛋白质结构域的性质差异，及其对蛋白质功能的影响。我们选取了20对完全相同的蛋白质结构域，它们以两种形式完成结晶：(a) 与其他蛋白质结构域融合锚定；(b) 相较于(a)仅连接更少的蛋白质结构域，或未与任何蛋白质结构域锚定。研究结果表明，多结构域蛋白质中结构域的锚定连接，会影响其组成蛋白质结构域的结构、动态学与能量学性质。在这些蛋白质结构域对中，50%展现出显著的结构偏差，90%存在动态学性质差异，另有12%的氨基酸残基表现出能量学层面的差异。为进一步探究锚定连接对结构域功能的影响，我们选取了4对同源蛋白质结构域进行研究：其中一对的其中一个成员为全长单结构域蛋白质，另一个成员则是多结构域蛋白质的组成部分。分析结果显示，同源蛋白质结构域中完全相同且结构等价的功能性氨基酸残基，其动态学性质存在差异；不过我们观察到，计算机模拟（in silico）生成的嵌合蛋白质与天然多结构域蛋白质的动态学性质相近。基于上述观察结果，同源蛋白质功能层面的差异可归因于其结构域的锚定连接状态。综上，我们得出结论：多结构域蛋白质中的锚定结构域，不仅能为蛋白质带来稳定性或折叠优势，还可通过影响信号通路，导致蛋白质功能或调控性质出现差异。