Structural modelling of the Sm-like protein Hfq from Escherichia coli
Structural modelling of the Sm-like protein Hfq from Escherichia coli
复制标题
DOI：
10.1016/s0022-2836(02)00548-x
复制
发表时间：
2002-07-19
影响因子：
5.6
通讯作者：
Régnier, P
中科院分区：
文献类型：
--
作者：
Arluison, V;Derreumaux, P;Régnier, P
大肠杆菌的Hfq多肽是参与许多蛋白质表达的核酸结合蛋白。其三维结构的推导对于我们理解其在分子水平上的基因调控作用是重要的。在这项研究中，我们结合计算和生物物理分析，推导出Hfq的可能结构。作为确定结构的第一步，我们使用二级结构预测以及WEB上提供的蛋白质结构域和折叠识别方法来搜索可能的序列-结构相容性。一个折叠，基本上是P片的字符，小核核糖核蛋白的Sm基序，即使它最初远远低于置信阈值，提出并进一步验证了一系列的生物物理和生物化学研究。使用优化的序列比对和分子力学方法，在人Sm D3 B结构上模拟Hfq六聚体结构。这种结构解释了Hfq的物理化学性质，并突出了可能与RNA相互作用的氨基酸残基。(C)2002爱思唯尔科技有限公司。保留所有权利。
The Hfq polypeptide of Escherichia coli is a nucleic acid-binding protein involved in the expression of many proteins. Derivation of its three-dimensional structure is important for our understanding of its role in gene regulation at the molecular level. In this study, we combined computational and biophysical analysis to derive a possible structure for Hfq. As a first step towards determining the structure, we searched for possible, sequence-structure compatibility, using secondary structure prediction, and protein domain and fold-recognition methods available on the WEB., One fold, essentially P sheet in character, the Sm motif of small nuclear ribonucleoproteins, even though it initially fell well below the confidence thresholds, was proposed and further validated by a series of biophysical and biochemical studies. The Hfq hexamer structure was modelled on the human Sm D3B structure using optimised sequence alignments and molecular mechanics methods. This structure accounts for the physicochemical properties of Hfq and highlights amino acid residues that could interact with RNA. (C) 2002 Elsevier Science Ltd. All rights reserved.