Non-covalent complexes of the peptide fragment Gly-Asn-Asn-Gln-Gln-Asn-Tyr in the gas-phase. Photodissociative cross-linking, Born–Oppenheimer molecular dynamics, and ab initio computational binding study
Non-covalent complexes of the peptide fragment Gly-Asn-Asn-Gln-Gln-Asn-Tyr in the gas-phase. Photodissociative cross-linking, Born–Oppenheimer molecular dynamics, and ab initio computational binding study
复制标题
气相中肽片段 Gly-Asn-Asn-Gln-Gln-Asn-Tyr 的非共价复合物。
DOI：
10.1039/c8cp06893c
复制
发表时间：
2019
影响因子：
3.3
通讯作者：
Tureček, František
中科院分区：
文献类型：
--
作者：
Huang, Shu R.;Liu, Yang;Tureček, František
短淀粉样肽基序Gly-Asn-Asn-Gln-Gln-Asn-Tyr（GNNQQNY）与在N-末端用二氮丙环标记的肽对应物（*GNNQQNY）的非共价复合物在气相中作为单电荷离子产生。特定的激光光解（UVPD）的气相复合物中的二氮杂环丙烷标签在355 nm处产生的瞬态卡宾中间体进行共价交联的目标GNNQQNY肽。交联产率范围在0.8和4.5%之间，这取决于肽C-末端酰胺和羧酸酯的组合。通过碰撞诱导解离串联质谱（CID-MS 3）分析共价复合物，提供靶肽氨基酸残基处的交联分布。观察到在靶肽Gln-4-Gln-5-Asn-6-Tyr-7区段处交联的一般偏好。采用Born-Oppenheimer分子动力学方法计算了9种最低自由能构象的100 ps轨道，这些构象是通过ω B 97 X-D/6-31+G（d，p）梯度几何优化确定的.分析了初始卡宾原子与靶肽中的X-H键之间的紧密接触的轨迹。紧密接触分析指出Gln-5和Tyr-7残基是最可能的交联位点，与实验CID-MS 3结果一致。通过DFT计算的结构和能量的非共价键合的酰胺复合物进行了评价。虽然反平行排列的GNNQQNY和 *GNNQQNY肽有利于在低能量的气相和溶剂化的复合物，构象和肽-肽界面表面被发现不同的二级结构的干界面在GNNQQNY图案的淀粉样蛋白聚集体。
Non-covalent complexes of the short amyloid peptide motif Gly-Asn-Asn-Gln-Gln-Asn-Tyr (GNNQQNY) with peptide counterparts that were tagged with a diazirine ring at the N-termini (*GNNQQNY) were generated as singly charged ions in the gas phase. Specific laser photodissociation (UVPD) of the diazirine tag in the gas-phase complexes at 355 nm generated transient carbene intermediates that underwent covalent cross-linking with the target GNNQQNY peptide. The crosslinking yields ranged between 0.8 and 4.5%, depending on the combinations of peptide C-terminal amides and carboxylates. The covalent complexes were analyzed by collision-induced dissociation tandem mass spectrometry (CID-MS3), providing distributions of cross-links at the target peptide amino acid residues. A general preference for cross-linking at the target peptide Gln-4-Gln-5-Asn-6-Tyr-7 segment was observed. Born–Oppenheimer molecular dynamics calculations were used to obtain 100 ps trajectories for nine lowest free-energy conformers identified by ωB97X-D/6-31+G(d,p) gradient geometry optimizations. The trajectories were analyzed for close contacts between the incipient carbene atom and the X–H bonds in the target peptide. The close-contact analysis pointed to the Gln-5 and Tyr-7 residues as the most likely sites of cross-linking, consistent with the experimental CID-MS3 results. Non-covalent binding in the amide complexes was evaluated by DFT calculations of structures and energies. Although antiparallel arrangements of the GNNQQNY and *GNNQQNY peptides were favored in low-energy gas-phase and solvated complexes, the conformations and peptide–peptide interface surfaces were found to differ from the secondary structure of the dry interface in GNNQQNY motifs of amyloid aggregates.