Arluison Véronique, Derreumaux Philippe, Allemand Frédéric, Folichon Marc, Hajnsdorf Eliane, Régnier Philippe
Institut de Biologie Physico-Chimique, CNRS UPR 9073, 13 rue P. et M. Curie, 75005 Paris, France.
J Mol Biol. 2002 Jul 19;320(4):705-12. doi: 10.1016/s0022-2836(02)00548-x.
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 beta 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 physico-chemical properties of Hfq and highlights amino acid residues that could interact with RNA.
大肠杆菌的Hfq多肽是一种核酸结合蛋白，参与多种蛋白质的表达。推导其三维结构对于我们在分子水平上理解其在基因调控中的作用很重要。在本研究中，我们结合计算分析和生物物理分析来推导Hfq的可能结构。作为确定结构的第一步，我们利用网络上可用的二级结构预测以及蛋白质结构域和折叠识别方法，寻找可能的序列-结构兼容性。尽管最初其置信度远低于阈值，但我们提出了一种本质上为β折叠特征的折叠结构，即小核核糖核蛋白的Sm基序，并通过一系列生物物理和生化研究进一步验证。利用优化的序列比对和分子力学方法，基于人类Sm D3B结构对Hfq六聚体结构进行了建模。该结构解释了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。
