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Structural Modelling of the Sm-like Protein Hfq from Escherichia coli
Authors:Arluison Véronique  Derreumaux Philippe  Allemand Frédéric  Folichon Marc  Hajnsdorf Eliane  Régnier Philippe
Institution:Institut de Biologie Physico-Chimique, CNRS UPR 9073, 13 rue P. et M. Curie, 75005 Paris, France.
Abstract: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.
Keywords:Hfq  RNA-binding protein  Sm-like protein (Lsm)  β barrel topology  protein domain and fold recognition modelling
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