Sung S S
Research Institute, Cleveland Clinic Foundation, Ohio 44195, USA.
Biophys J. 1995 Mar;68(3):826-34. doi: 10.1016/S0006-3495(95)80259-6.
The folding of short alanine-based peptides with different numbers of lysine residues is simulated at constant temperature (274 K) using the rigid-element Monte Carlo method. The solvent-referenced potential has prevented the multiple-minima problem in helix folding. From various initial structures, the peptides with three lysine residues fold into helix-dominated conformations with the calculated average helicity in the range of 60-80%. The peptide with six lysine residues shows only 8-14% helicity. These results agree well with experimental observations. The intramolecular electrostatic interaction of the charged lysine side chains and their electrostatic hydration destabilize the helical conformations of the peptide with six lysine residues, whereas these effects on the peptides with three lysine residues are small. The simulations provide insight into the helix-folding mechanism, including the beta-bend intermediate in helix initiation, the (i, i + 3) hydrogen bonds, the asymmetrical helix propagation, and the asymmetrical helicities in the N- and C-terminal regions. These findings are consistent with previous studies.
使用刚性元素蒙特卡罗方法在恒温（274 K）下模拟了具有不同赖氨酸残基数量的短丙氨酸基肽的折叠。溶剂参考势避免了螺旋折叠中的多极小值问题。从各种初始结构开始，具有三个赖氨酸残基的肽折叠成以螺旋为主的构象，计算出的平均螺旋度在60%-80%范围内。具有六个赖氨酸残基的肽仅显示8%-14%的螺旋度。这些结果与实验观察结果非常吻合。带电荷的赖氨酸侧链的分子内静电相互作用及其静电水合作用使具有六个赖氨酸残基的肽的螺旋构象不稳定，而对具有三个赖氨酸残基的肽的这些影响较小。模拟为螺旋折叠机制提供了见解，包括螺旋起始中的β-转角中间体、（i，i + 3）氢键、不对称螺旋传播以及N端和C端区域的不对称螺旋度。这些发现与先前的研究一致。
