Physical Origins of Codon Positions That Strongly Influence Cotranslational Folding: A Framework for Controlling Nascent-Protein Folding

An
emerging paradigm in the field of in vivo protein biophysics
is that nascent-protein behavior is a type of nonequilibrium phenomenon,
where translation-elongation kinetics can be more important in determining
nascent-protein behavior than the thermodynamic properties of the
protein. Synonymous codon substitutions, which change the translation
rate at select codon positions along a transcript, have been shown
to alter cotranslational protein folding, suggesting that evolution
may have shaped synonymous codon usage in the genomes of organisms
in part to increase the amount of folded and functional nascent protein.
Here, we develop a Monte Carlo-master-equation method that allows
for the control of nascent-chain folding during translation through
the rational design of mRNA sequences to guide the cotranslational
folding process. We test this framework using coarse-grained molecular
dynamics simulations and find it provides optimal mRNA sequences to
control the simulated, cotranslational folding of a protein in a user-prescribed
manner. With this approach we discover that some codon positions in
a transcript can have a much greater impact on nascent-protein folding
than others because they tend to be positions where the nascent chain
populates states that are far from equilibrium, as well as being dependent
on a complex ratio of time scales. As a consequence, different cotranslational
profiles of the same protein can have different critical codon positions
and different numbers of synonymous mRNA sequences that encode for
them. These findings explain that there is a fundamental connection
between the nonequilibrium nature of cotranslational processes, nascent-protein
behavior, and synonymous codon usage.

体内蛋白质生物物理学领域的新兴范式指出，新生蛋白（nascent-protein）行为属于一类非平衡现象（nonequilibrium phenomenon），翻译延伸动力学（translation-elongation kinetics）在决定新生蛋白行为的过程中，往往比蛋白质的热力学特性更为关键。同义密码子替换（synonymous codon substitutions）——即改变转录本（transcript）上特定密码子位点的翻译速率——已被证实可改变共翻译蛋白质折叠（cotranslational protein folding）过程，这表明生物基因组中的同义密码子使用偏好（synonymous codon usage）在一定程度上是进化塑造的结果，其目的是提升具备完整折叠结构与功能的新生蛋白的占比。本研究开发了一种蒙特卡洛主方程方法（Monte Carlo-master-equation method），可通过合理设计mRNA序列来调控翻译过程中的新生链折叠，进而引导共翻译折叠进程。我们采用粗粒度分子动力学模拟（coarse-grained molecular dynamics simulations）对该框架进行了验证，结果表明该方法可生成最优mRNA序列，以用户指定的方式实现对蛋白质模拟共翻译折叠过程的调控。借助该方法，我们发现转录本中的部分密码子位点对新生蛋白折叠的影响远大于其他位点：这是因为这些位点往往对应新生链处于远离平衡态的构象，且其影响程度还取决于复杂的时间尺度比例关系。由此可见，同一蛋白质的不同共翻译特征谱（cotranslational profiles）会拥有不同的关键密码子位点，且编码这些特征谱的同义mRNA序列的数量也各不相同。上述研究结果揭示了共翻译过程的非平衡特性、新生蛋白行为与同义密码子使用偏好三者之间存在本质联系。