Insights into Subunit Interactions in the Heterotetrameric Structure of Potato ADP- Glucose Pyrophosphorylase Aytug Tuncel, Ibrahim Halil Kavakli, Ozlem.

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Presentation transcript:

Insights into Subunit Interactions in the Heterotetrameric Structure of Potato ADP- Glucose Pyrophosphorylase Aytug Tuncel, Ibrahim Halil Kavakli, Ozlem Keskin Biophysical Journal Volume 95, Issue 8, Pages 3628-3639 (October 2008) DOI: 10.1529/biophysj.107.123042 Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 1 Crystal structure of homotetrameric SS composed of four identical chains in different color shades, chains a–d. Biophysical Journal 2008 95, 3628-3639DOI: (10.1529/biophysj.107.123042) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 2 Schematic presentation of (a) the crystal structure of homotetrameric SS and (b–d) proposed models. For construction of the models each large and small subunits were superimposed with the corresponding chain in the crystal structure and the original SS chains were than deleted. (b–d) Correspond to Model-1, Model-2, and Model-3, respectively. (e–j) Schematic presentation of dimeric interactions between the subunits that constitute the heterotetrameric models. LS and SS are composed of 441 and 442 residues respectively. Set 1 contains the D1, D2, D3, and set 2 contains the D4, D5, D6. Biophysical Journal 2008 95, 3628-3639DOI: (10.1529/biophysj.107.123042) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 3 Three-dimensional structures of (a) LS, (b) SS, and (c) their superimposed images. See Materials and Methods for details about the missing regions in SS. Biophysical Journal 2008 95, 3628-3639DOI: (10.1529/biophysj.107.123042) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 4 Yeast two-hybrid analysis of potato AGPase subunit interactions (a) SSWT:SSWT; (b) SSWT:LSWT; (c) SSWT:LSR28A; and (d) SSWT:empty GBT vector. AH109 yeast cells expressing the designated plasmids are selected on a synthetic growth medium without Leu and Trp. Selections for interactions were carried out in the absence of Leu, Trp, and His. Biophysical Journal 2008 95, 3628-3639DOI: (10.1529/biophysj.107.123042) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 5 (a) LSR28 makes several hydrogen bonds (dashed lines) with SSE124 and LSE431 throughout the simulation. In this snapshot it forms total of four H-bonds with SSE124 and LSE431. Note that LSE431 is found in C-terminal β-helix domain and LSR28 is found in the N-terminus. The H-bonds formed by LSR28 makes a significant contrbution to LS-SS interaction by connecting the LS C-terminal β-helix domain and the SS.(b) Modeled structure of the heterotetrameric potato AGPase; subunits LS (cyan) and SS (yellow). The model was generated from the final snapshots of the D2 and D5 simulations. Schematic presentation of the model can also be seen in Fig. 2 c. (c) Snapshot showing the highly conserved residues (red), Thr303, Pro310 in LS, and Thr304, Pro310, Pro311 in SS in Dimer 2 interface. LS is cyan and SS is yellow. Biophysical Journal 2008 95, 3628-3639DOI: (10.1529/biophysj.107.123042) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 6 Order of assembly formation. First LS and SS associate to form a side-by-side dimer. Up-down complexation then takes place. Biophysical Journal 2008 95, 3628-3639DOI: (10.1529/biophysj.107.123042) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 7 Interface residues (shaded) in Model-2. Residues that show >1Å2 change in their solvent accessible surface area on complexation and hold this condition for at least 50% (200 snapshots) of the last 8ns of the simulations were taken as interface residues. Conserved residues were obtained from CONSURF (59). As representatives, alignments were carried out by picking up large and small subunit primary amino acid sequences from different plants. OS, Oryaza sativa; Hv, Hordeum vulgare; Pv, Phaseolus vulgaris; St, Solanum tuberosum, At, Arabidopsis thaliana; and Zm, Zea mays. Biophysical Journal 2008 95, 3628-3639DOI: (10.1529/biophysj.107.123042) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 8 Root mean-square fluctuations (Rmsf) of backbone atoms (C, CA, and N) versus residue number for Dimer 2 and Dimer 5 subunits. Biophysical Journal 2008 95, 3628-3639DOI: (10.1529/biophysj.107.123042) Copyright © 2008 The Biophysical Society Terms and Conditions