Biomolecules & Therapeutics : eISSN 2005-4483 / pISSN 1976-9148

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Fig. 4. Constructing three-dimensional structure of NOEY2 by homology modelling and prediction of the potential key residues in the N-terminal domain of human NOEY2. (A) Four x-ray and NMR structures were used as template structures for homology modelling of NOEY2. A-I, Rap1A (PDB code: 1GUA), A-II, Rap2A (3RAP), A-III, H-Ras (1K8R), A-IV, interleukin 6 (1IL6). In panel A, structures in green are used for the main body of the NOEY2 model, and the orange-coloured structure is a reference for the N-terminal domain. (B) Manually connected initial model of NOEY2. N-terminal domain is shown in cyan, with grey showing the main body. (C) Five different conformations of the N-termini domain were selected from a 50 ps equilibration run for the production run (in salmon colours). The starting structure is green; the blue-coloured N-terminal conformation in the Figure was used for further detailed analysis. (D) Final simulated structure for human NOEY2 protein. N-terminus and the main body of the protein are coloured blue and grey, respectively. This structure was time evolved from one of five conformers (blue colour in panel C). The Figure was generated with PYMOL (http://pymol.sourceforge.net). (E, F) Two different angle views of key residues in the ribbon diagram, main body and N-terminus domain, are shown in grey and blue colour, respectively. Key residues are highlighted as a stick model with element colours. (G) Interaction of backbone oxygen atoms in carboxyl group of Lys15 with the two side chains of Trp57 (3.27 ) and Gln189 (3.14 ). (H) Interaction of side chain Arg16 with the two backbone oxygen atoms of Gly79 (2.80 ) and His82 (2.80 ). Hydrogen bonds are shown as a yellow line. The backbone of the key residues highlighted in golden yellow. Atom colours in stick model: red – oxygen, blue – nitrogen, and green – carbon. INSIGHT II program (Accelrys, Inc., San Diego, CA, USA) was used to produce the Figures.
Biomolecules & Therapeutics 2021;29:506~518 https://doi.org/10.4062/biomolther.2021.121
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