Wei Chung-Cheng, Ho Ming-Hsun, Wang Wen-Hung, Sun Ying-Chieh
Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei 116, Taiwan.
J Phys Chem B. 2005 Oct 27;109(42):19980-6. doi: 10.1021/jp052349k.
A molecular dynamics simulation of the folding of conantokin-T (con-T), a short helical peptide with 5 helical turns of 21 amino acids with 10 charged residues, was carried out to examine folding pathways for this peptide and to predict the folding rate. In the 18 trajectories run at 300 K, 16 trajectories folded, with an averaged folding time of approximately 50 ns. Two trajectories did not fold in up to 200 ns simulation. The folded structure in folded trajectories is in good agreement with experimental structure. An analysis of the trajectories showed that, at the beginning of a few nanoseconds, helix formation started from residues 5-9 with assistance of a hydrophobic clustering involving Tyr5, Met8, and Leu9. The peptide formed a U-shape mainly due to charge-charge interactions between charged residues at the N- and C-terminus segments. In the next approximately 10 ns, several nonnative charge-charge interactions were broken and nonnative Gla10-Lys18 (this denotes a salt bridge between Gal10 and Lys18) and/or Gla10-Lys19 interactions appeared more frequently in this folding step and the peptide became a fishhook J-shape. From this structure, the peptide folded to the folded state in 7 of all 16 folded trajectories in approximately 15 ns. Alternatively, in approximately 30 ns, the con-T went to a conformation in an L-shape with 4 helical turns and a kink at the Arg13 and Gla14 segment in the other 9 trajectories. Con-T in the L-shape then required another approximately 15 ns to fold into the folded state. In addition, in overall folding times, the former 7 trajectories folded faster with the total folding times all shorter than 45 ns, while the latter 9 trajectories folded at a time longer than 45 ns, resulting in an average folding time of approximately 50 ns. Two major folding intermediates found in 2 nonfolded trajectories are stabilized by charge clusters of 5 and 6 charged residues, respectively. With inclusion of friction and solvent-solvent interactions, which were ignored in the present GB/SA solvation model, the folding time obtained above should be multiplied by a factor of 1.25-1.7 according to a previous, similar simulation study. This results in a folding time of 65-105 ns, slightly shorter than the folding time of 127 ns for an alanine-based peptide of the same length. This suggests that the energy barrier of folding for this type of peptides with many charged residues is slightly lower than alanine-based helical peptides by less than 1 kcal/mol.
对芋螺毒素 -T（Con-T）进行了分子动力学模拟，Con-T是一种短螺旋肽，由21个氨基酸组成，有5个螺旋圈，含10个带电荷残基，目的是研究该肽的折叠途径并预测折叠速率。在300K下运行的18条轨迹中，16条轨迹发生折叠，平均折叠时间约为50纳秒。两条轨迹在长达200纳秒的模拟中未发生折叠。折叠轨迹中的折叠结构与实验结构高度吻合。对轨迹的分析表明，在最初的几纳秒内，螺旋形成从残基5 - 9开始，在涉及Tyr5、Met8和Leu9的疏水簇的辅助下进行。该肽主要由于N端和C端片段带电荷残基之间的电荷 - 电荷相互作用而形成U形。在接下来的约10纳秒内，一些非天然的电荷 - 电荷相互作用被打破，非天然的Gla10 - Lys18（表示Gla10和Lys18之间的盐桥）和/或Gla10 - Lys19相互作用在这个折叠步骤中更频繁地出现，肽变成鱼钩状J形。从这个结构开始，在所有16条折叠轨迹中的7条中，肽在大约15纳秒内折叠成折叠状态。或者，在大约30纳秒内，Con-T在另外9条轨迹中进入一种L形构象，有4个螺旋圈，在Arg13和Gla14片段处有一个扭结。L形的Con-T然后需要另外约15纳秒折叠成折叠状态。此外，在总折叠时间方面，前7条轨迹折叠得更快，总折叠时间都短于45纳秒，而后9条轨迹折叠时间长于45纳秒，平均折叠时间约为50纳秒。在2条未折叠轨迹中发现的两个主要折叠中间体分别由5个和6个带电荷残基的电荷簇稳定。考虑到在当前GB/SA溶剂化模型中被忽略的摩擦和溶剂 - 溶剂相互作用，根据之前类似的模拟研究，上述获得的折叠时间应乘以1.25 - 1.7的系数。这导致折叠时间为65 - 105纳秒，略短于相同长度的基于丙氨酸的肽的127纳秒折叠时间。这表明这种具有许多带电荷残基的肽的折叠能垒比基于丙氨酸的螺旋肽略低，低不到1千卡/摩尔。
