小擎子 (2023-05-31 23:05):
#paper 10.1126/science.1257481 Science, 2014 , High thermodynamic stability of parametrically designed helical bundles 参数化设计的螺旋束的高热力学稳定性。通过参数化骨架生成与Rosetta蛋白质设计相结合的方法,生成非常稳定的蛋白质结构。不依赖已知序列基序的情况下轻松生成具有精细几何形状的超稳定蛋白质,有助于基于蛋白质的纳米结构、疗法和催化剂的设计。核心是参数化设计,依靠的是对Crick Coiled-coil方程做参数扰动。0.1埃的扰动可以生成成千上万个α螺旋设计骨架。文章找了几种低能量的设计做测试,实验验证,晶体结构与设计一致,且稳定性超好,堪称“砖头”。ps 因文章较早,用的是Rosetta设计序列,如果改用ProteinMPNN,可以生成有更多活性表达的蛋白质序列。
High thermodynamic stability of parametrically designed helical bundles
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Abstract:
We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil-generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔGfold > 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.
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