Michnick S W, Shakhnovich E
Département de biochime, Université de Montréal, Quebec.
Fold Des. 1998;3(4):239-51. doi: 10.1016/S1359-0278(98)00035-2.
Nucleation-growth theory predicts that fast-folding peptide sequences fold to their native structure via structures in a transition-state ensemble that share a small number of native contacts (the folding nucleus). Experimental and theoretical studies of proteins suggest that residues participating in folding nuclei are conserved among homologs. We attempted to determine if this is true in proteins with highly diverged sequences but identical folds (superfamilies).
We describe a strategy based on comparisons of residue conservation in natural superfamily sequences with simulated sequences (generated with a Monte-Carlo sequence design strategy) for the same proteins. The basic assumptions of the strategy were that natural sequences will conserve residues needed for folding and stability plus function, the simulated sequences contain no functional conservation, and nucleus residues make native contacts with each other. Based on these assumptions, we identified seven potential nucleus residues in ubiquitin superfamily members. Non-nucleus conserved residues were also identified; these are proposed to be involved in stabilizing native interactions. We found that all superfamily members conserved the same potential nucleus residue positions, except those for which the structural topology is significantly different.
Our results suggest that the conservation of the nucleus of a specific fold can be predicted by comparing designed simulated sequences with natural highly diverged sequences that fold to the same structure. We suggest that such a strategy could be used to help plan protein folding and design experiments, to identify new superfamily members, and to subdivide superfamilies further into classes having a similar folding mechanism.
成核-生长理论预测，快速折叠的肽序列通过过渡态集合中的结构折叠成其天然结构，这些结构共享少量天然接触（折叠核）。对蛋白质的实验和理论研究表明，参与折叠核的残基在同源物中是保守的。我们试图确定在具有高度不同序列但相同折叠结构的蛋白质（超家族）中是否也是如此。
我们描述了一种基于比较天然超家族序列与相同蛋白质的模拟序列（采用蒙特卡罗序列设计策略生成）中残基保守性的策略。该策略的基本假设是，天然序列将保留折叠、稳定性和功能所需的残基，模拟序列不包含功能保守性，并且核残基彼此形成天然接触。基于这些假设，我们在泛素超家族成员中鉴定出七个潜在的核残基。还鉴定出了非核保守残基；这些残基被认为参与稳定天然相互作用。我们发现，除了那些结构拓扑有显著差异的成员外，所有超家族成员都保留了相同的潜在核残基位置。
我们的结果表明，通过将设计的模拟序列与折叠成相同结构的天然高度不同序列进行比较，可以预测特定折叠结构核的保守性。我们认为，这样的策略可用于帮助规划蛋白质折叠和设计实验、识别新的超家族成员，以及将超家族进一步细分为具有相似折叠机制的类别。
