Grell D, Richardson J S, Richardson D C, Mutter M
Institute of Organic Chemistry, University of Lausanne, Switzerland.
J Mol Graph Model. 2000 Jun;18(3):290-8, 309-10. doi: 10.1016/s1093-3263(00)00049-8.
Experience has shown that protein redesigns (using the backbone from a known protein structure) are far more likely to produce well-ordered, native-like structures than are true de novo designs. Therefore, to design a four-helix bundle made of identical short helices, we here proceed by an extensive redesign of the ROP protein. A fully symmetrical SymROP sequence derived from ROP was chosen by modeling ideal-geometry side chains, including hydrogens, while maintaining the "goodness-of-fit" of side-chain packing by calculating all-atom contact surfaces with the Reduce and Probe programs. To estimate the probable extent of backbone movement and side-chain mobility, restrained molecular dynamics simulations were compared for candidate sequences and controls, including substitution of Abu for all or half the core Ala residues. The resulting 17-residue designed sequence is 41% identical to the relevant regions in ROP. SymROP is intended for construction by the Template Assembled Synthetic Proteins approach, to control the bundle topology, to use short helices, and to allow blocked termini and unnatural amino acids. ROP protein has been a valuable system for studying helical protein structure because of its simplicity and regularity within a structure large enough to have a real hydrophobic core. The SymROP design carries that simplicity and regularity even further.
经验表明，（利用已知蛋白质结构的骨架进行的）蛋白质重新设计比真正的从头设计更有可能产生结构有序、类似天然的结构。因此，为了设计一个由相同短螺旋组成的四螺旋束，我们在此通过对ROP蛋白进行广泛的重新设计来开展工作。通过对理想几何形状的侧链（包括氢原子）进行建模，同时使用Reduce和Probe程序计算全原子接触表面以维持侧链堆积的“拟合优度”，从而从ROP中选择了一个完全对称的SymROP序列。为了估计主链移动和侧链灵活性的可能程度，对候选序列和对照进行了受限分子动力学模拟，包括用Abu取代所有或一半的核心Ala残基。最终得到的17个残基的设计序列与ROP中的相关区域有41%的同源性。SymROP旨在通过模板组装合成蛋白方法构建，以控制束拓扑结构，使用短螺旋，并允许封闭的末端和非天然氨基酸。由于ROP蛋白在一个足够大以拥有真正疏水核心的结构中具有简单性和规则性，它一直是研究螺旋蛋白结构的一个有价值的系统。SymROP设计进一步延续了这种简单性和规则性。
