Schwarzinger S, Kroon G J, Foss T R, Chung J, Wright P E, Dyson H J
Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
J Am Chem Soc. 2001 Apr 4;123(13):2970-8. doi: 10.1021/ja003760i.
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 (15)N(H), (1)H(N), and (13)CO resonances of neighboring residues, utilizing complete resonance assignments for a set of five-residue peptides Ac-G-G-X-G-G-NH(2). 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.
在化学位移指数计算中，无规卷曲化学位移常用于检测蛋白质中的二级结构元件。虽然该技术对于折叠蛋白非常可靠，但应用于未折叠蛋白时，某些核的测量值与无规卷曲位移存在显著偏差。虽然其中一些偏差可归因于未折叠蛋白中的残余结构，但其他偏差显然是由局部序列效应引起的。特别是，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。我们利用一组五肽Ac-G-G-X-G-G-NH₂的完整共振归属，对20种天然氨基酸对相邻残基的(¹⁵)N(H)、(¹)H(N)和(¹³)CO共振的无规卷曲位移的影响进行了详细的定量分析。这项工作包括对用于推导无规卷曲化学位移的序列依赖性校正因子的概念进行验证，以及对可应用于给定位置两个残基以内氨基酸的序列依赖性校正因子进行全面列表。这套新的校正因子将在折叠蛋白以及短的无结构肽和未折叠蛋白中具有重要应用。
