Peptide conformer acidity analysis of protein flexibility monitored by hydrogen exchange.
Peptide conformer acidity analysis of protein flexibility monitored by hydrogen exchange.
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DOI：
10.1021/bi901219x
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发表时间：
2009-10-06
期刊：
影响因子：
2.9
通讯作者：
Hernandez, Griselda
中科院分区：
文献类型：
--
作者：
LeMaster, David M.;Anderson, Janet S.;Hernandez, Griselda
在高分辨率x射线结构中，泛素、fk506结合蛋白、糜凝胰蛋白酶抑制剂2和红氧还蛋白暴露于溶剂中的酰胺氢在氢氧化物催化下的交换速率跨越了十亿倍的范围，这是通过连续介质方法预测的。为了便于分析瞬时可及酰胺，在接近生理条件下测定了泛素各主酰胺的氢氧化物催化速率常数。使用先前报道的核磁共振抑制泛素分子动力学集合（PDB代码2NR2和2K39）作为玻尔兹曼加权构象分布的表示，几乎所有高暴露酰胺的交换率都比使用高分辨率x射线结构更准确地预测。更引人注目的是，对核磁共振弛豫约束系系中暴露于溶剂的酰胺氢的预测，在该系系中144种蛋白质构象中，有不止一种但不到一半的构象，几乎同样准确。与此形成鲜明对比的是，在残余偶极偶联抑制的泛素集合中，许多类似酰胺的交换率被大大高估了，尤其明显的是赖氨酸44至赖氨酸48段，它构成了参与多泛素化的蛋白酶体靶向酶的主要相互作用位点。对于这两种组合，活性位点区域的“激发态”构象具有显著升高的肽酸，其种群水平比蛋白质构象的玻尔兹曼分布中可能存在的水平高102至103。这些结果表明，酰胺氢交换的化学一致性解释如何能够提供对瞬时蛋白质构象的种群和详细结构的见解。
The amide hydrogens that are exposed to solvent in the high-resolution X-ray structures of ubiquitin, FK506-binding protein, chymotrypsin inhibitor 2, and rubredoxin span a billion-fold range in hydroxide-catalyzed exchange rates which are predictable by continuum dielectric methods. To facilitate analysis of transiently accessible amides, the hydroxide-catalyzed rate constants for every backbone amide of ubiquitin were determined under near physiological conditions. With the previously reported NMR-restrained molecular dynamics ensembles of ubiquitin (PDB codes 2NR2 and 2K39) used as representations of the Boltzmann-weighted conformational distribution, nearly all of the exchange rates for the highly exposed amides were more accurately predicted than by use of the high-resolution X-ray structure. More strikingly, predictions for the amide hydrogens of the NMR relaxation-restrained ensemble that become exposed to solvent in more than one but less than half of the 144 protein conformations in this ensemble were almost as accurate. In marked contrast, the exchange rates for many of the analogous amides in the residual dipolar coupling-restrained ubiquitin ensemble are substantially overestimated, as was particularly evident for the Ile 44 to Lys 48 segment which constitutes the primary interaction site for the proteasome targeting enzymes involved in polyubiquitylation. For both ensembles, “excited state” conformers in this active site region having markedly elevated peptide acidities are represented at a population level that is 102 to 103 above what can exist in the Boltzmann distribution of protein conformations. These results indicate how a chemically consistent interpretation of amide hydrogen exchange can provide insight into both the population and the detailed structure of transient protein conformations.
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影响因子：
2.9
作者：
Antosiewicz, J;McCammon, JA;Gilson, MK
通讯作者：
Gilson, MK
影响因子：
15
作者：
Forsyth, WR;Robertson, AD
通讯作者：
Robertson, AD
DOI：
10.1073/pnas.96.18.10118
发表时间：
1999-08-31
影响因子：
11.1
作者：
Freire, E
通讯作者：
Freire, E
影响因子：
2.9
作者：
Hernandez, Griselda;Anderson, Janet S.;LeMaster, David M.
通讯作者：
LeMaster, David M.
影响因子：
5.6
作者：
DELEPIERRE, M;DOBSON, CM;WEDIN, RE
通讯作者：
WEDIN, RE