Design of helices that are stable in vacuo
Design of helices that are stable in vacuo
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DOI：
10.1021/ja983021q
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发表时间：
1998-12-16
影响因子：
15
通讯作者：
Jarrold, MF
中科院分区：
文献类型：
--
作者：
Hudgins, RR;Ratner, MA;Jarrold, MF
R-螺旋是蛋白质中最常见的短程结构基序，1了解其性质是理解蛋白质折叠和酶功能的核心。3种氨基酸具有不同的螺旋倾向。2，4，5丙氨酸具有最高的螺旋倾向，富含丙氨酸的多肽在溶液中得到了广泛的研究。然而，造成不同螺旋倾向的因素当然包括溶剂的影响。6-8原则上，在没有溶剂相互作用的情况下，本征螺旋倾向可以通过气相测量获得。在这里，我们报告了在无溶剂环境中对丙氨酸多肽的研究。含有多达20个残基的质子化聚丙氨酸在真空中不会形成延伸的螺旋。然而，在C末端添加一个单一的赖氨酸(得到Ac-Alan-lysh+)会导致形成非常稳定的单体聚丙氨酸螺旋。Ac-Alan-lysh+肽的设计优化了带电赖氨酸与C-末端骨架羰基的氢键，以及电荷与螺旋偶极的相互作用。观察到Ac-Alan-lysh+多肽只有8个残基的螺旋，这比在溶液中发现的最短螺旋多肽要短得多。最近，各种实验技术被用来研究蛋白质和多肽的气相构象。9-17在这里报告的工作中，我们使用了高分辨率的离子迁移率测量。迁移率是衡量离子在弱电场影响下通过惰性缓冲气体的速度。迁移率取决于离子与缓冲气体的碰撞截面。结构信息是通过比较测量的截面和从分子动力学(MD)模拟得到的构象的方向平均截面计算得出的。12我们的实验装置由一个电喷雾源、一个63厘米长的含有氦缓冲气体的漂移管和一个四极质谱仪组成。这项实验技术的细节已在最近的一份出版物中进行了描述。在CHARMM力场21下，使用21.3参数集、联合原子近似和SHAKE22约束对所有显式键进行了20个分子动力学模拟。在300K下对每个多肽进行0.25-1.0 ns的多次模拟。用轨迹法23计算横截面，并以规则的时间间隔对来自MD模拟的50个结构进行平均。图1a显示了通过在甲酸中电喷雾未纯化的Ac-Ala19-Lys溶液而获得的质谱图。对应于Ac-Alan-lysh+，n(14-19)的质荷比(m/z)的峰值是明显的。多肽大小的分布是由于固相Fmoc合成过程中偶联效率低造成的(AnaSpec Inc.，圣何塞，加利福尼亚州)。图1b显示了用设置为传输Ac-Ala19-lysh+的质谱仪测量的漂移时间分布。有两个主峰：漂移时间为∼170ms的峰归属于Ac-Ala19-lysh+单体，而位于∼155ms的峰归属于m/z相同的(Ac-Al19-Lysh)22+二聚体。25在这项工作中，我们将使用Ωav-14.50n给出的相对横截面比例，其中Ωav(测量的横截面)是？2，14.50？2是计算的理想聚丙氨酸R-螺旋的每个残基的平均横截面，扭转角固定在φ)-57和ψ)-47。在这个尺度下，螺旋构象具有与丙氨酸残基数量无关的相对横截面，而其他…
The R-helix is the most common short-range structural motif in proteins, 1 and understanding its properties is central to understanding protein folding2 and enzyme function. 3 Different amino acids have different helix propensities. 2, 4, 5 Alanine has one of the highest helix propensities, and alanine-rich peptides have been widely studied in solution. However, the factors responsible for the different helix propensities certainly include the effects of the solvent. 6-8 In principle, intrinsic helix propensities can be obtained from gas-phase measurements where solvent interactions are absent. Here we report studies of alanine-based peptides in a solvent-free environment. Protonated polyalanines with up to 20 residues do not form extended helices in a vacuum. However, the addition of a single lysine at the C terminus (to give Ac-Alan-LysH+) results in the formation of very stable, monomeric, polyalanine helices. The design of the Ac-Alan-LysH+ peptide optimizes hydrogen bonding of the charged lysine with the C-terminal backbone carbonyl groups, and the interaction of the charge with the helix dipole. Helices are observed for Ac-Alan-LysH+ peptides with as few as eight residues, which is significantly shorter than the shortest helical peptides found in solution. A variety of experimental techniques have recently been used to examine the gas-phase conformations of proteins and peptides. 9-17 In the work reported here we have used high-resolution ion mobility measurements. 18, 19 The mobility is a measure of how rapidly an ion moves through an inert buffer gas under the influence of a weak electric field. The mobility depends on the ion’s collision cross section with the buffer gas. Structural information is deduced by comparing measured cross sections to orientationally averaged cross sections calculated for conformations derived from molecular dynamics (MD) simulations. 12 Our experimental apparatus consists of an electrospray source, a 63-cm long drift tube containing helium buffer gas, and a quadrupole mass spectrometer. Details of the experimental technique are described in a recent publication. 20 MD simulations were performed with the CHARMM force field21 using the 21.3 parameter set, the united atom approximation, and SHAKE22 constraints on all explicit bonds. Multiple simulations of 0.25-1.0 ns were performed at 300 K for each peptide. Cross sections were calculated by a trajectory method23 and averaged over 50 structures taken from an MD simulation at regular time intervals. Figure 1a shows a mass spectrum obtained by electrospraying a solution of unpurified Ac-Ala19-Lys in formic acid. A progression of peaks at mass to charge (m/z) ratios corresponding to Ac-Alan-LysH+, n) 14-19, is apparent. The distribution of peptide sizes results from inefficient coupling during solid-phase Fmoc synthesis (Anaspec Inc., San Jose, CA). Figure 1b shows a drift time distribution measured with the mass spectrometer set to transmit Ac-Ala19-LysH+. There are two main peaks; the peak at a drift time of∼ 170 ms is assigned to the Ac-Ala19-LysH+ monomer while the one at∼ 155 ms is assigned to the (Ac-Ala19-LysH) 2 2+ dimer, which occurs at the same m/z. 24 The measured drift times are converted into average collision cross sections. 25 In this work we will use a relative cross section scale given by Ωav-14.50n where Ωav (the measured cross section) is in Å2 and 14.50 Å2 is the calculated average cross section per residue for an ideal polyalanine R-helix with the torsion angles fixed at φ)-57 and ψ)-47. With this scale, helical conformations have relative cross sections that are independent of the number of alanine residues, whereas other …