Joshi Sadhna, Rana Soumendra, Wangikar Pramod, Durani Susheel
Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076 India.
Biopolymers. 2006 Oct 5;83(2):122-34. doi: 10.1002/bip.20537.
Artificial proteins potentially barrier-free in the folding kinetics are approached computationally under the guidance of protein-folding theories. The smallest and fastest folding globular protein triple-helix-bundle (THB) is so modified as to minimize or eliminate its presumed barriers in folding speed. As the barriers may reside in the ordering of either secondary or tertiary structure, the elements of both secondary and tertiary structure in the protein are targeted for prenucleation with suitable stereochemically constrained amino acid residues. The required elements of topology and sequence for the THB are optimized independently; first the topology is optimized with simulated annealing in polypeptides of highly simplified alphabet; next, the sequence in side chains is optimized using the standard inverse design methods. The resultant three best-adapted THBs, variable in topology and distinctive in sequences, are assessed by comparing them with a few benchmark proteins. The results of mainly molecular dynamics (MD) comparisons, undertaken in explicit water at different temperatures, show that the designed sequences are favorably placed against the chosen benchmarks as THB proteins potentially thermostable in the native folds. Folding simulation experiments with MD establish that the designed sequences are rapid in the folding of individual helices, but not in the evolution of tertiary structure; energetic cum topological frustrations remain but could be the artifacts of the starting conformations that were chosen in the THBs in the folding simulations. Overall, a practical high-throughput approach for de novo protein design has been developed that may have fruitful application for any type of tertiary structure.
在蛋白质折叠理论的指导下，通过计算方法构建了在折叠动力学中可能无屏障的人工蛋白质。最小且折叠速度最快的球状蛋白质三螺旋束（THB）经过修饰，以最小化或消除其在折叠速度方面可能存在的屏障。由于这些屏障可能存在于二级结构或三级结构的排序中，因此蛋白质二级和三级结构的元素都被作为目标，通过合适的立体化学受限氨基酸残基进行预成核。THB所需的拓扑结构和序列元素分别进行优化；首先，在高度简化字母表的多肽中使用模拟退火优化拓扑结构；接下来，使用标准的反向设计方法优化侧链中的序列。通过将得到的三种适应性最佳的THB（拓扑结构不同，序列独特）与一些基准蛋白质进行比较来评估它们。主要在不同温度的明确水环境中进行的分子动力学（MD）比较结果表明，作为可能在天然折叠状态下具有热稳定性的THB蛋白质，设计的序列相对于所选基准具有优势。MD折叠模拟实验表明，设计的序列在单个螺旋的折叠过程中速度很快，但在三级结构的演化中并非如此；能量和拓扑挫折仍然存在，但可能是折叠模拟中THB起始构象选择的人为产物。总体而言，已经开发出一种实用的高通量从头蛋白质设计方法，该方法可能对任何类型的三级结构都有丰硕的应用成果。
