Effects of disulfide bonds on folding behavior and mechanism of the beta-sheet protein tendamistat.
Effects of disulfide bonds on folding behavior and mechanism of the beta-sheet protein tendamistat.
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DOI：
10.1529/biophysj.105.063552
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发表时间：
2006
影响因子：
3.4
通讯作者：
M. Qin;Jian Zhang;Wei Wang
中科院分区：
文献类型：
--
作者：
M. Qin;Jian Zhang;Wei Wang
利用改进的Gō-like模型研究了Tendamistat（一种小的二硫键β折叠蛋白）及其三个单/双二硫键突变体，旨在了解二硫键蛋白的折叠机制以及去除二硫键对折叠过程的影响。我们的模拟结果表明，tendamistat和它的两个单二硫键突变体都是双态文件夹，与实验观察一致。结果表明，在N端loop-0和strand-6之间的二硫键以及三个氢键对于tendamistat的折叠具有重要意义。没有这些相互作用，它们的两态行为变得不稳定，模型的预测与实验不一致。此外，通过比较野生型tendamistat及其两个突变体，研究了二硫键对折叠过程的影响，发现C11-C27或C45-C73二硫键的去除都会导致未折叠状态下的分子稳定性大幅下降和结构丢失，且前者的影响比后者更强。这些模拟结果与实验结果吻合良好，从而验证了我们的模型。基于相同的模型，研究了野生型tendamistat和两个突变体的详细折叠途径，并讨论了二硫键对折叠动力学的影响。所获得的结果提供了这些蛋白质的详细折叠图片和补充实验结果。最后，本工作首次鉴定了预测存在于该蛋白tendamistat及其突变体中的折叠核。原子核的位置与实验研究中所讨论的一致。因此，一个成核/生长折叠机制，可以解释两个状态的折叠方式是明确的特点。此外，去除每个二硫键对折叠热力学和动力学的影响也可以从它们对折叠核的影响来很好地解释。这一工作的实施表明，改进的Gō-like模型真实地描述了蛋白质tendamistat的折叠行为，并可用于研究其他二硫键蛋白质的折叠。
Tendamistat, a small disulfide-bonded beta-sheet protein, and its three single/double-disulfide mutants are investigated by using a modified Gō-like model, aiming to understand the folding mechanism of disulfide-bonded protein as well as the effects of removal of disulfide bond on the folding process. Our simulations show that tendamistat and its two single-disulfide mutants are all two-state folders, consistent with the experimental observations. It is found that the disulfide bonds as well as three hydrogen bonds between the N-terminal loop-0 and strand-6 are of significant importance for the folding of tendamistat. Without these interactions, their two-state behaviors become unstable and the predictions of the model are inconsistent with experiments. In addition, the effect of disulfide bonds on the folding process are studied by comparing the wild-type tendamistat and its two mutants; it is found that the removal of either of the C11-C27 or C45-C73 disulfide bond leads to a large decrease in the thermodynamical stability and loss of structure in the unfolded state, and the effect of the former is stronger than that of the later. These simulation results are in good agreement with experiments and, thus, validate our model. Based on the same model, the detailed folding pathways of the wild-type tendamistat and two mutants are studied, and the effect of disulfide bonds on the folding kinetics are discussed. The obtained results provide a detailed folding picture of these proteins and complement experimental findings. Finally, the folding nuclei predicted to be existent in this protein tendamistat as well as its mutants are firstly identified in this work. The positions of the nucleus are consistent with those argued in experimental studies. Therefore, a nucleation/growth folding mechanism that can explain the two-state folding manner is clearly characterized. Moreover, the effect by the removal of each disulfide bond on the folding thermodynamics and dynamics can also be well interpreted from their influence on the folding nucleus. The implementation of this work indicates that the modified Gō-like model really describes the folding behavior of protein tendamistat and could be used to study the folding of other disulfide-bonded proteins.