Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
J Am Chem Soc. 2022 Aug 10;144(31):14150-14160. doi: 10.1021/jacs.2c03819. Epub 2022 Jul 29.
Peptide-RNA coacervates can result in the concentration and compartmentalization of simple biopolymers. Given their primordial relevance, peptide-RNA coacervates may have also been a key site of early protein evolution. However, the extent to which such coacervates might promote or suppress the exploration of novel peptide conformations is fundamentally unknown. To this end, we used electron paramagnetic resonance spectroscopy (EPR) to characterize the structure and dynamics of an ancient and ubiquitous nucleic acid binding element, the helix-hairpin-helix (HhH) motif, alone and in the presence of RNA, with which it forms coacervates. Double electron-electron resonance (DEER) spectroscopy applied to singly labeled peptides containing one HhH motif revealed the presence of dimers, even in the absence of RNA. Moreover, dimer formation is promoted upon RNA binding and was detectable within peptide-RNA coacervates. DEER measurements of spin-diluted, doubly labeled peptides in solution indicated transient α-helical character. The distance distributions between spin labels in the dimer and the signatures of α-helical folding are consistent with the symmetric (HhH)-Fold, which is generated upon duplication and fusion of a single HhH motif and traditionally associated with dsDNA binding. These results support the hypothesis that coacervates are a unique testing ground for peptide oligomerization and that phase-separating peptides could have been a resource for the construction of complex protein structures common evolutionary processes, such as duplication and fusion.
肽 - RNA 凝聚物可导致简单生物聚合物的浓缩和区室化。鉴于它们的原始相关性，肽 - RNA 凝聚物也可能是早期蛋白质进化的关键场所。然而，这种凝聚物在多大程度上促进或抑制新的肽构象的探索在根本上是未知的。为此，我们使用电子顺磁共振波谱（EPR）来单独表征和研究古老且普遍存在的核酸结合元件，即螺旋-发夹-螺旋（HhH）基序的结构和动力学，以及它与 RNA 形成凝聚物的情况。应用于含有单个 HhH 基序的单标记肽的双电子电子共振（DEER）光谱学揭示了即使在没有 RNA 的情况下也存在二聚体。此外，RNA 结合促进二聚体的形成，并且在肽 - RNA 凝聚物中可检测到。在溶液中对自旋稀释的双标记肽进行 DEER 测量表明存在瞬时α螺旋特征。二聚体中自旋标记之间的距离分布和α螺旋折叠的特征与对称（HhH）-Fold 一致，该折叠是通过单个 HhH 基序的复制和融合产生的，并且传统上与 dsDNA 结合相关。这些结果支持这样一种假设，即凝聚物是肽寡聚化的独特试验场，并且相分离肽可能是构建复杂蛋白质结构的资源，这些结构是常见的进化过程，如复制和融合的产物。
