Primary Citation PubMed: 23302862
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Published in 2014
Differential HDX data were analyzed using software developed in-house ( 12 ); the percentage differences in the uptake of heavy water between apo and holo IR-ECDs were mapped to the three-dimensional ... tructures (Protein Data Bank [PDB] identifiers: 2DTG and 3W11, respectively).
Publication Year: 2014
Flexibility in the insulin receptor ectodomain enables docking of insulin in crystallographic conformation observed in a hormone-bound microreceptor.
(2014) Membranes (Basel) 4
PubMed: 25309993 | PubMedCentral: PMC4289863 | DOI: 10.3390/membranes4040730
Importantly, alignment (based upon the L1 domain) of the apo-ectodomain structure (PDB code 3LOH) with a hormone-bound receptor structure (PDB code 3W11) unambiguously reveals the displacement of ... 3b1; CT ( Figure 2 b), and implies the detachment of the flexible C-terminus of insulin B-chain because α CT (in hormone-bound structure) occupies the position of this structural motif in free hormone ( Figure 2 c).
MDFF Fitting In Figure 4 , we show the root-mean-squared-deviation (RMSD) evolution of C α -atoms of L1/insulin/ α CT relative to the crystal conformation (PDB code 3W11) during MDFF fitting.
The trace of C α -RMSD vs. simulation time (ns) for L1/insulin/ α CT with respect to their final conformation in the crystal structure (PDB code 3W11) is shown.
The contacts at Site 1 between insulin and IR are also similar ( Figure 5 b) to the crystal structure (PDB code 3W11), while at site 2 ( Figure 5 c,d) we observe insulin residues (i) A12, A13, A14, A15, A17 in the vicinity of F1 residues R554, G555, L556, K557, and Y562; (ii) A10 and B18 near residues Y507 and K484 (F1), respectively; and (iii) B10 and B13 in the vicinity of S596, L599, D620, and P621 (F2).
( a ) Alignment of insulin-bound structure of IR fragment (PDB code 3W11) with the apo-IR ectodomain (PDB code 3LOH).
( a ) Insulin conformation from our previous [ 61 ] structural model of insulin/IR∆ β (brighter tubes) is overlayed on the insulin conformation in the hormone-bound crystal structure (darker tubes, PDB code 3W11).
Specifically, we created individual as well as combined density maps (at ∼ 4 Å resolution and with a grid-spacing of 1 Å) of the L1 domain, insulin, and α CT using complex A (PDB code 3W11) of Menting et al. [ 58 ].
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