Sessions R B, Gibbs N, Dempsey C E
Biochemistry Department and Centre for Molecular Recognition, Bristol University, School of Medical Sciences, United Kingdom.
Biophys J. 1998 Jan;74(1):138-52. doi: 10.1016/S0006-3495(98)77775-6.
Molecular dynamics simulations of ion channel peptides alamethicin and melittin, solvated in methanol at 27 degrees C, were run with either regular alpha-helical starting structures (alamethicin, 1 ns; melittin 500 ps either with or without chloride counterions), or with the x-ray crystal coordinates of alamethicin as a starting structure (1 ns). The hydrogen bond patterns and stabilities were characterized by analysis of the dynamics trajectories with specified hydrogen bond angle and distance criteria, and were compared with hydrogen bond patterns and stabilities previously determined from high-resolution NMR structural analysis and amide hydrogen exchange measurements in methanol. The two alamethicin simulations rapidly converged to a persistent hydrogen bond pattern with a high level of 3(10) hydrogen bonding involving the amide NH's of residues 3, 4, 9, 15, and 18. The 3(10) hydrogen bonds stabilizing amide NH's of residues C-terminal to P2 and P14 were previously proposed to explain their high amide exchange stabilities. The absence, or low levels of 3(10) hydrogen bonds at the N-terminus or for A15 NH, respectively, in the melittin simulations, is also consistent with interpretations from amide exchange analysis. Perturbation of helical hydrogen bonding in the residues before P14 (Aib10-P14, alamethicin; T11-P14, melittin) was characterized in both peptides by variable hydrogen bond patterns that included pi and gamma hydrogen bonds. The general agreement in hydrogen bond patterns determined in the simulations and from spectroscopic analysis indicates that with suitable conditions (including solvent composition and counterions where required), local hydrogen-bonded secondary structure in helical peptides may be predicted from dynamics simulations from alpha-helical starting structures. Each peptide, particularly alamethicin, underwent some large amplitude structural fluctuations in which several hydrogen bonds were cooperatively broken. The recovery of the persistent hydrogen bonding patterns after these fluctuations demonstrates the stability of intramolecular hydrogen-bonded secondary structure in methanol (consistent with spectroscopic observations), and is promising for simulations on extended timescales to characterize the nature of the backbone fluctuations that underlie amide exchange from isolated helical polypeptides.
对在27摄氏度的甲醇中溶剂化的离子通道肽短杆菌肽和蜂毒素进行了分子动力学模拟，模拟时采用规则的α-螺旋起始结构（短杆菌肽，1纳秒；蜂毒素，500皮秒，有无氯离子抗衡离子），或采用短杆菌肽的X射线晶体坐标作为起始结构（1纳秒）。通过用指定的氢键角度和距离标准分析动力学轨迹来表征氢键模式和稳定性，并与先前从高分辨率NMR结构分析和甲醇中的酰胺氢交换测量确定的氢键模式和稳定性进行比较。两次短杆菌肽模拟迅速收敛到一种持久的氢键模式，其中涉及残基3、4、9、15和18的酰胺NH的3(10)氢键水平较高。先前曾提出3(10)氢键稳定P2和P14 C端残基的酰胺NH，以解释它们高的酰胺交换稳定性。蜂毒素模拟中N端或A15 NH分别不存在或3(10)氢键水平较低，这也与酰胺交换分析的解释一致。两种肽中P14之前的残基（短杆菌肽中的Aib10 - P14；蜂毒素中的T11 - P14）的螺旋氢键扰动通过包括π和γ氢键的可变氢键模式来表征。模拟中确定的氢键模式与光谱分析的总体一致性表明，在合适的条件下（包括所需的溶剂组成和抗衡离子），螺旋肽中的局部氢键二级结构可以从α-螺旋起始结构的动力学模拟中预测出来。每种肽，特别是短杆菌肽，都经历了一些大幅度的结构波动，其中几个氢键协同断裂。这些波动后持久氢键模式的恢复证明了甲醇中分子内氢键二级结构的稳定性（与光谱观察一致），并且有望在更长的时间尺度上进行模拟，以表征孤立螺旋多肽酰胺交换背后的主链波动性质。
