Sequence-dependent correction of random coil NMR chemical shifts
Sequence-dependent correction of random coil NMR chemical shifts
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DOI：
10.1021/ja003760i
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发表时间：
2001-04-04
影响因子：
15
通讯作者：
Dyson, HJ
中科院分区：
文献类型：
--
作者：
Schwarzinger, S;Kroon, GJA;Dyson, HJ
在化学位移指数计算中，无规卷曲化学位移通常用于检测蛋白质中的二级结构元素。虽然这种技术是非常可靠的折叠的蛋白质，应用到未折叠的蛋白质显示显着偏差，从测量的随机卷曲移位某些核。虽然其中一些偏差可以归因于未折叠蛋白质中的残留结构，但其他偏差显然是由局部序列效应引起的。特别地，酰胺氮、酰胺质子和羰基碳化学位移对局部氨基酸序列高度敏感。我们提出了一个详细的，定量分析的影响，20种天然存在的氨基酸的N-15（H），H-1（N），和（CO）-C-13共振相邻残基的无规卷曲位移，利用一组五个残基的肽Ac-G-G-X-G-G-NH 2的完整的共振分配。这项工作包括一个验证的概念，用于获得序列依赖的校正因子的随机卷曲化学位移，和一个全面的列表序列依赖的校正因子，可以应用于氨基酸从一个给定的位置多达两个残基。这组新的校正因子将对折叠蛋白质以及短的非结构化肽和未折叠蛋白质具有重要的应用。
Random coil chemical shifts are commonly used to detect secondary structure elements in proteins in chemical shift index calculations. While this technique is very reliable for folded proteins, application to unfolded proteins reveals significant deviations from measured random coil shifts for certain nuclei. While some of these deviations can be ascribed to residual structure in the unfolded protein, others are clearly caused by local sequence effects. In particular, the amide nitrogen, amide proton, and carbonyl carbon chemical shifts are highly sensitive to the local amino acid sequence. We present a detailed, quantitative analysis of the effect of the 20 naturally occurring amino acids on the random coil shifts of N-15(H), H-1(N), and (CO)-C-13 resonances of neighboring residues, utilizing complete resonance assignments for a set of five-residue peptides Ac-G-G-X-G-G-NH2. The work includes a validation of the concepts used to derive sequence-dependent correction factors for random coil chemical shifts, and a comprehensive tabulation of sequence-dependent correction factors that can be applied for amino acids up to two residues from a given position. This new set of correction factors will have important applications to folded proteins as well as to short, unstructured peptides and unfolded proteins.