Lu Jianli, Deutsch Carol
Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6085, USA.
Nat Struct Mol Biol. 2005 Dec;12(12):1123-9. doi: 10.1038/nsmb1021. Epub 2005 Nov 20.
Helicity of membrane proteins can be manifested inside the ribosome tunnel, but the determinants of compact structure formation inside the tunnel are largely unexplored. Using an extended nascent peptide as a molecular tape measure of the ribosomal tunnel, we have previously demonstrated helix formation inside the tunnel. Here, we introduce a series of consecutive polyalanines into different regions of the tape measure to monitor the formation of compact structure in the nascent peptide. We find that the formation of compact structure of the polyalanine sequence depends on its location. Calculation of free energies for the equilibria between folded and unfolded nascent peptides in different regions of the tunnel shows that there are zones of secondary structure formation inside the ribosomal exit tunnel. These zones may have an active role in nascent-chain compaction.
膜蛋白的螺旋性可在核糖体通道内表现出来，但通道内紧密结构形成的决定因素在很大程度上尚未得到探索。我们之前利用一段延伸的新生肽作为核糖体通道的分子卷尺，证明了通道内会形成螺旋。在此，我们将一系列连续的多聚丙氨酸引入卷尺的不同区域，以监测新生肽中紧密结构的形成。我们发现，多聚丙氨酸序列紧密结构的形成取决于其位置。对通道不同区域折叠和未折叠新生肽之间平衡的自由能计算表明，核糖体出口通道内存在二级结构形成区域。这些区域可能在新生链的压缩过程中发挥积极作用。
