蛋白合成的终止在细菌中能以很高的保真性实现，这个时候mRNA上的“终止密码子”与释放因子RF1 和 RF2结合，而不是与另一种带有一个氨基酸的tRNA相结合，同时一个新合成的蛋白被释放出来。生物谷启用新域名 www.bioon.net
随着最近几种终止复合物的晶体结构的发表，现在有可能对“终止密码子”能量状态的读出结果进行计算分析，同时搞清释放因子结合的这种高准确性的起源。
对14种不同终止复合物进行的分子动态模拟显示，“终止密码子”的读出结果取决于几个以前没有被识别出的互动和识别开关，这些开关不能用三肽反密码子“tRNA mimicry”模型来描述。(生物谷Bioon.net)
生物谷推荐原文出处：
Nature doi:10.1038/nature09082
Principles of stop-codon reading on the ribosome
Johan Sund, Martin Andér & Johan ?qvist
In termination of protein synthesis, the bacterial release factors RF1 and RF2 bind to the ribosome through specific recognition of messenger RNA stop codons and trigger hydrolysis of the bond between the nascent polypeptide and the transfer RNA at the peptidyl-tRNA site, thereby releasing the newly synthesized protein. The release factors are highly specific for a U in the first stop-codon position1 and recognize different combinations of purines in the second and third positions, with RF1 reading UAA and UAG and RF2 reading UAA and UGA. With recently determined crystal structures of termination complexes2, 3, 4, it has become possible to decipher the energetics of stop-codon reading by computational analysis and to clarify the origin of the high release-factor binding accuracy. Here we report molecular dynamics free-energy calculations on different cognate and non-cognate termination complexes. The simulations quantitatively explain the basic principles of decoding in all three codon positions and reveal the key elements responsible for specificity of the release factors. The overall reading mechanism involves hitherto unidentified interactions and recognition switches that cannot be described in terms of a tripeptide anticodon model. Further simulations of complexes with tRNATrp, the tRNA recognizing the triplet codon for Trp, explain the observation of a ‘leaky’ stop codon5 and highlight the fundamentally different third position reading by RF2, which leads to a high stop-codon specificity with strong discrimination against the Trp codon. The simulations clearly illustrate the versatility of codon reading by protein, which goes far beyond tRNA mimicry.
