Czaplewski Cezary, Oldziej Stanislaw, Liwo Adam, Scheraga Harold A
Baker Laboratory of Chemistry, Cornell University, Ithaca, NY 14853-1301, USA.
Protein Eng Des Sel. 2004 Jan;17(1):29-36. doi: 10.1093/protein/gzh003.
The presence of disulfide bonds is essential for maintaining the structure and function of many proteins. The disulfide bonds are usually formed dynamically during folding. This process is not accounted for in present algorithms for protein-structure prediction, which either deduce the possible positions of disulfide bonds only after the structure is formed or assume fixed disulfide bonds during the course of simulated folding. In this work, the conformational space annealing (CSA) method and the UNRES united-residue force field were extended to treat dynamic formation of disulfide bonds. A harmonic potential is imposed on the distance between disulfide-bonded cysteine side-chain centroids to describe the energetics of bond distortion and an energy gain of 5.5 kcal/mol is added for disulfide-bond formation. Formation, breaking and rearrangement of disulfide bonds are included in the CSA search by introducing appropriate operations; the search can also be carried out with a fixed disulfide-bond arrangement. The algorithm was applied to four proteins: 1EI0 (alpha), 1NKL (alpha), 1L1I (beta-helix) and 1ED0 (alpha + beta). For 1EI0, a low-energy structure with correct fold was obtained both in the runs without and with disulfide bonds; however, it was obtained as the lowest in energy only with the native disulfide-bond arrangement. For the other proteins studied, structures with the correct fold were obtained as the lowest (1NKL and 1L1I) or low-energy structures (1ED0) only in runs with disulfide bonds, although the final disulfide-bond arrangement was non-native. The results demonstrate that, by including the possibility of formation of disulfide bonds, the predictive power of the UNRES force field is enhanced, even though the disulfide-bond potential introduced here rarely produces disulfide bonds in native positions. To the best of our knowledge, this is the first algorithm for energy-based prediction of the structure of disulfide-bonded proteins without any assumption as to the positions of native disulfides or human intervention. Directions for improving the potentials and the search method are suggested.
二硫键的存在对于维持许多蛋白质的结构和功能至关重要。二硫键通常在折叠过程中动态形成。目前的蛋白质结构预测算法并未考虑这一过程，这些算法要么仅在结构形成后推断二硫键的可能位置，要么在模拟折叠过程中假定二硫键固定不变。在这项工作中，构象空间退火（CSA）方法和UNRES统一残基力场被扩展以处理二硫键的动态形成。对二硫键连接的半胱氨酸侧链质心之间的距离施加一个谐波势，以描述键畸变的能量学，并为二硫键形成添加5.5千卡/摩尔的能量增益。通过引入适当的操作，二硫键的形成、断裂和重排在CSA搜索中得以包含；搜索也可以在固定的二硫键排列下进行。该算法应用于四种蛋白质：1EI0（α）、1NKL（α）、1L1I（β-螺旋）和1ED0（α + β）。对于1EI0，在有无二硫键的运行中均获得了具有正确折叠的低能量结构；然而，只有在天然二硫键排列的情况下，它才作为能量最低的结构被获得。对于其他研究的蛋白质，只有在有二硫键的运行中，才获得了具有正确折叠的最低能量结构（1NKL和1L1I）或低能量结构（1ED0），尽管最终的二硫键排列是非天然的。结果表明，通过考虑二硫键形成的可能性，UNRES力场的预测能力得到了增强，尽管这里引入的二硫键势很少在天然位置产生二硫键。据我们所知，这是第一种基于能量预测二硫键连接蛋白质结构的算法，无需对天然二硫键的位置进行任何假设或人为干预。文中还提出了改进势和搜索方法的方向。
