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Figure 3.
Figure 3. The generated Hfq model. The SWISS-MODEL
server[49] was used to generate the structure of the Hfq
monomeric form. Since automated construction requires 30%
identity between the query and target sequences, the determined
X-ray structure of human Sm D3-B (PDB entry 1D3B) [16] was used
with its amino acid sequences mutated according to the
alignments ( Figure 2(b)). The model was then the subject of
EEF1 energy minimisation. [50] The EEF1 energy model combines
the CHARMM19 polar hydrogen potential energy function and a
simple Gaussian model for the solvation free energy. [50] The
resulting structure was used as a template for generating the
complex following the symmetry operations of the human Sm 1D3B
crystal. The hexamer was minimised for 1500 steps using the EEF1
energy model and the resulting structure satisfied all PROCHECK
stereochemical verifications. [51] (a) Structure of the E. coli
Hfq hexamer. The molecules are shown as ribbons of different
colours showing a helix and b strand. (b) Dimer contacts in the
Hfq hexamer: the b4 strand in one monomer interacts with the b5
strand of a neighbouring subunit. (c) Left, the Hfq putative
base-binding pocket with the conserved residues Phe42 and Lys56;
right, X-ray structure of the base-binding pocket within the
RNA-Af-Sm1 complex.[26] The Figures were produced with the
RASMOL software package. [52] (d) Electrostatic surface charge
potential showing the two faces of the six ring-shaped
structure. The left picture corresponding to the top view shown
in (a) emphasises the positively charged cavity of the ring as
indicated by the blue colour. The right picture points to the
continuously positive surface potential of the other side. The
Figure was produced by GRASP. [53]
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