Cohanim Amir B, Trifonov Edward N, Kashi Yechezkel
Department of Biotechnology and Food Engineering, Technion, Haifa, 32000, Israel.
J Mol Evol. 2006 Sep;63(3):393-400. doi: 10.1007/s00239-005-0258-1. Epub 2006 Jul 28.
Prokaryotic sequences are responsible for more than just protein coding. There are two 10- to 11-base periodical patterns superimposed on the protein coding message within the same sequence. Positional auto- and cross-correlation analysis of the sequences shows that these two patterns are a short-range counter-phase oscillation of AA and TT dinucleotides and a medium-range in-phase oscillation of the same dinucleotides, spanning distances of up to approximately 30 and approximately 100 bases, respectively. The short-range oscillation is encoded by the amino acid sequences themselves, apparently, due to the presence of amphipathic alpha-helices in the proteins. The medium-range oscillation, related to DNA folding in the cell, is created largely by a special choice of the bases in the third positions of the codons. Interestingly, the amino acid sequences do contribute to that signal as well. That is, the very amino acid sequences are, to some extent, degenerate to serve the same oscillating pattern that is associated with the degenerate third codon positions.
原核生物序列的作用不止于蛋白质编码。在同一序列的蛋白质编码信息上叠加着两种10至11个碱基的周期性模式。对这些序列的位置自相关和交叉相关分析表明，这两种模式分别是AA和TT二核苷酸的短程反相振荡以及相同二核苷酸的中程同相振荡，其跨度分别可达约30个碱基和约100个碱基。短程振荡显然是由氨基酸序列本身编码的，这是由于蛋白质中存在两亲性α螺旋。与细胞内DNA折叠相关的中程振荡很大程度上是由密码子第三位碱基的特殊选择造成的。有趣的是，氨基酸序列也对该信号有贡献。也就是说，氨基酸序列在某种程度上是简并的，以服务于与简并的第三位密码子位置相关的相同振荡模式。
