Structural Modelling of the Sm-like Protein Hfq from Escherichia coli.
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.
Arluison
Véronique
V
Institut de Biologie Physico-Chimique, CNRS UPR 9073, 13 rue P. et M. Curie, 75005 Paris, France.
Derreumaux
Philippe
P
Allemand
Frédéric
F
Folichon
Marc
M
Hajnsdorf
Eliane
E
Régnier
Philippe
P
D000595:Amino Acid Sequence; D002352:Carrier Proteins / Q000737:chemistry*; D003198:Computer Simulation; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins; D035001:Host Factor 1 Protein; D006801:Humans; D034982:Integration Host Factors; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry; D016601:RNA-Binding Proteins / Q000737:chemistry*; D017411:Ribonucleoproteins, Small Nuclear / Q000737:chemistry; D017386:Sequence Homology, Amino Acid
D002352:Carrier Proteins; D029968:Escherichia coli Proteins; D035001:Host Factor 1 Protein; D034982:Integration Host Factors; D016601:RNA-Binding Proteins; D017411:Ribonucleoproteins, Small Nuclear; C090866:Sm protein D3; C440502:integration host factor, E coli; D012313:RNA