Shine A, Shenoy J, Jayan Parvathy, Jiji A C, Vijayan Vinesh
School of Chemistry, IISER, Thiruvananthapuram Maruthamala PO, Vithura, Kerala, India.
Chemphyschem. 2020 May 5;21(9):888-894. doi: 10.1002/cphc.201901100. Epub 2020 Apr 7.
Although the conformation of the polymer chain of Ubiquitin (Ub) mainly depends on the type of isopeptide linkage connecting two Ub molecules, the non-covalent (noncovalent) interaction between two Ub molecules within the chain could also tune their conformational preference. Here, we studied the conformation of noncovalently formed Ub dimers in solution using residual dipolar couplings (RDCs). Comparing the RDC derived alignment tensor of the noncovalently formed dimer with the two most abundant (K11 and K48) covalent linked Ub dimers revealed that the conformation of K11 linked and noncovalent Ub dimers were similar. Between the various NMR and crystal structures of K11 linked Ub dimers, RDC tensor analysis showed that the structure of K11 linked dimer crystalized at neutral pH is similar to noncovalent dimer. Analogous to the experimental study, the comparison of predicted order matrix of various covalent Ub dimers with that of the experimentally determined order matrix of noncovalent Ub dimer also suggests that the conformation of K11 linked dimers crystalized at neutral pH is similar to the noncovalent dimer.
尽管泛素（Ub）聚合物链的构象主要取决于连接两个Ub分子的异肽键类型，但链内两个Ub分子之间的非共价相互作用也可以调节它们的构象偏好。在这里，我们使用残余偶极耦合（RDC）研究了溶液中非共价形成的Ub二聚体的构象。将非共价形成的二聚体的RDC衍生排列张量与两种最丰富的（K11和K48）共价连接的Ub二聚体进行比较，结果表明K11连接的和非共价Ub二聚体的构象相似。在K11连接的Ub二聚体的各种NMR和晶体结构之间，RDC张量分析表明在中性pH下结晶的K11连接二聚体的结构与非共价二聚体相似。与实验研究类似，将各种共价Ub二聚体的预测序矩阵与非共价Ub二聚体的实验测定序矩阵进行比较，也表明在中性pH下结晶的K11连接二聚体的构象与非共价二聚体相似。
