Determination of sequence-specific intrinsic size parameters from cross sections for 162 tripeptides
Determination of sequence-specific intrinsic size parameters from cross sections for 162 tripeptides
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DOI：
10.1021/jp050761u
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发表时间：
2005-06-16
影响因子：
3.3
通讯作者：
Clemmer, DE
中科院分区：
文献类型：
--
作者：
Hilderbrand, AE;Clemmer, DE
离子迁移率和质谱技术已被用来测量162个三肽序列（27个不同的六个序列异构体集）的横截面。异构体的通式为ABC、AC B、BAC、BCA、CA B和CBA，其中A对应于氨基酸Asp、Glu或Gly，B对应于Lys、Arg或Leu，C对应于Phe、Tyr或Ser。从这些数据中，我们推导出一组反映氨基酸在序列中位置的单个氨基酸的大小参数。这些序列特异性内在尺寸参数（SSISP）用于逆转162个测量序列的横截面值，并预测由这些残基组成的所有剩余三肽序列（567个不同序列）的横截面。在几种类型的肽组合物中，氨基酸在序列中的位置对导出的参数具有显著影响。例如，肽的第三位置中的亮氨酸的序列特异性固有大小参数（SSISP（Leu（3）类似于比SSISP（Leu（3））大10%。平均而言，使用SSISP得到的横截面比如前所述（Valentine等，J.Phys.Chem.1999，103，1203）从仅组成的固有尺寸参数得到的横截面提供了更好的实验值表示。最后，分子建模技术被用来获得一些洞察的起源横截面的差异，所产生的序列变异。
Ion mobility and mass spectrometry techniques have been used to measure cross sections for 162 tripeptide sequences (27 different sets of six sequence isomers). The isomers have the general forms ABC, ACB, BAC, BCA, CAB, and CBA, where A corresponds to the amino acids Asp, Glu, or Gly, B corresponds to Lys, Arg, or Leu, and C corresponds to Phe, Tyr, or Ser. From these data, we derive a set of size parameters for individual amino acids that reflect the position of the amino acid in the sequence. These sequence-specific intrinsic size parameters (SSISPs) are used to retrodict cross-section values for the 162 measured sequences and to predict cross sections for all remaining tripeptide sequences (567 different sequences) that are comprised of these residues. In several types of peptide compositions, the position of the amino acid in the sequence has a significant impact on the parameter that is derived. For example, the sequence-specific intrinsic size parameter for leucine in the third position of a peptide (SSISP(Leu(3))) is similar to 10% larger than SSISP(Leu,). On average, cross sections that are derived using SSISPs provide a better representation of the experimental value than those derived from composition only intrinsic size parameters, derived as described previously (Valentine et al. J. Phys. Chem. 1999, 103, 1203). Finally, molecular modeling techniques are used to derive some insight into the origin of cross-section differences that arise from sequence variation.