Deptartment of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America.
PLoS One. 2011;6(7):e20937. doi: 10.1371/journal.pone.0020937. Epub 2011 Jul 6.
Some protein design tasks cannot be modeled by the traditional single state design strategy of finding a sequence that is optimal for a single fixed backbone. Such cases require multistate design, where a single sequence is threaded onto multiple backbones (states) and evaluated for its strengths and weaknesses on each backbone. For example, to design a protein that can switch between two specific conformations, it is necessary to to find a sequence that is compatible with both backbone conformations. We present in this paper a generic implementation of multistate design that is suited for a wide range of protein design tasks and demonstrate in silico its capabilities at two design tasks: one of redesigning an obligate homodimer into an obligate heterodimer such that the new monomers would not homodimerize, and one of redesigning a promiscuous interface to bind to only a single partner and to no longer bind the rest of its partners. Both tasks contained negative design in that multistate design was asked to find sequences that would produce high energies for several of the states being modeled. Success at negative design was assessed by computationally redocking the undesired protein-pair interactions; we found that multistate design's accuracy improved as the diversity of conformations for the undesired protein-pair interactions increased. The paper concludes with a discussion of the pitfalls of negative design, which has proven considerably more challenging than positive design.
有些蛋白质设计任务不能通过传统的单一状态设计策略来建模，这种策略是找到一个对单个固定骨架最优的序列。这种情况下需要多态设计，其中一个序列被穿到多个骨架（状态）上，并在每个骨架上评估其优缺点。例如，要设计一种能够在两种特定构象之间切换的蛋白质，就需要找到一种与两种骨架构象都兼容的序列。本文提出了一种通用的多态设计实现方法，适用于广泛的蛋白质设计任务，并在两个设计任务中展示了其在计算上的能力：一个是重新设计一个必需的同源二聚体为必需的异源二聚体，使得新单体不会形成同源二聚体；另一个是重新设计一个杂乱的界面，只与一个伴侣结合，不再与其余伴侣结合。这两个任务都包含了负面设计，即多态设计被要求找到会产生多个模型状态高能量的序列。通过计算重新对接不需要的蛋白质相互作用来评估负面设计的成功，我们发现随着不需要的蛋白质相互作用的构象多样性增加，多态设计的准确性提高了。本文最后讨论了负面设计的陷阱，事实证明，负面设计比正面设计更具挑战性。
