University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham Street, Victoria, British Columbia V8Z7X8, Canada.
Department of Biochemistry and Biophysics, University of North Carolina, Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
Sci Adv. 2017 Jul 7;3(7):e1700479. doi: 10.1126/sciadv.1700479. eCollection 2017 Jul.
We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein-models for α helix-rich and β sheet-rich proteins, respectively-and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures.
我们提出了一种综合的实验和计算方法，用于从头确定蛋白质结构，其中将短程交联数据作为约束条件纳入快速离散分子动力学（DMD）模拟中，从而缩小构象空间并在实际时间尺度上实现正确的蛋白质折叠。我们在肌红蛋白和 FK506 结合蛋白模型上测试了我们的方法，分别针对富含α螺旋和富含β片层的蛋白质，发现得到的最低能量结构与晶体结构、氢氘交换、表面修饰和长程交联验证数据一致。我们的方法易于应用于其他未知结构的蛋白质。
