Sung S S
Research Institute, Cleveland Clinic Foundation, Ohio 44195.
Biophys J. 1994 Jun;66(6):1796-803. doi: 10.1016/S0006-3495(94)80973-7.
Using a solvent-referenced energy calculation, a 16-residue peptide with alanine side chains folded into predominantly alpha-helical conformations during constant temperature (274 K) simulations. From different initial conformations, helical conformations were reached and the multiple energy minima did not become a serious problem. Under the same conditions, the simulation did not indiscriminately fold a sequence such as polyglycine into stable helices. Interesting observations from the simulations relate to the folding mechanism. The electrostatic interactions between the successive amides favored extended conformations (or beta strands) and caused energy barriers to helix folding. beta-bends were observed as intermediates during helix nucleation. The helix propagation toward the C-terminus seemed faster than that toward the N-terminus. In helical conformations, hydrogen bond oscillation between the i,i+ 4 and the i,i+3 patterns was observed. The i,i+3 hydrogen bonds occurred more frequently during helix propagation and deformation near both ends of the helical segment.
使用溶剂参考能量计算方法，在恒温（274K）模拟过程中，一个带有丙氨酸侧链的16残基肽折叠成主要为α-螺旋构象。从不同的初始构象出发，均能达到螺旋构象，且多个能量极小值并未成为严重问题。在相同条件下，模拟并不会随意地将诸如聚甘氨酸这样的序列折叠成稳定的螺旋。模拟中有趣的观察结果与折叠机制有关。连续酰胺之间的静电相互作用有利于伸展构象（或β链），并导致螺旋折叠的能量障碍。在螺旋成核过程中观察到β-转角作为中间体。螺旋向C端的延伸似乎比向N端更快。在螺旋构象中，观察到i,i + 4和i,i + 3模式之间的氢键振荡。在螺旋片段两端附近的螺旋延伸和变形过程中，i,i + 3氢键出现得更为频繁。
