Modeling Figures

Directions: In this section, post your figures with the associated captions. Be thorough in your caption. Display in a fashion similar to what is below. Criteria are listed below,

Choice of figures included: Are they informative? Are all the figures you should have included presented?
Quality of the figures: Your figures should be polished and professional; you should pay close attention to color, background, font, resolution, contrast, labeling, etc.; Is there extra white space where there shouldn't be, is space properly used within the figure?
Captions: Do the captions give the reader enough context to be able to determine what the figure represents? Are the captions grammatically correct?

Figure A1: (a) Features structure alignment between Thermotaga maritima phosphoglucoisomerase (TmaPGI (PBD: 2Q8N)) in tan and Chlamydia trachomatis phosphoglucoisomerase (CtrPGI (PBD: 6OTU)) in blue crystalized with glucose-6-phosphate (G6P) substrate. The RMSD for the aligned TmaPGI and CtrPGI was 1.001 Å, which implies similarity (b) Features active site alignment between TmaPGI and CtrPGI crystalised with glucose-6-phosphate (G6P) substrate. Alignments were completed utilizing Chrimera. (c) Features TmaPGI, CtPGI, Francisella tularensus (FtuPGI), Mus musculus (MmuPGI), Homo sapiens (HsaPGI), Triticum aestivum (TaePGI), Bdellovibrio bacteriovorus (BbaPGI), Geobacillus stearothermophilus (GstPGI), Bacillus anthracis (BanPGI), Staphylococcus aureus (SauPGI), and Thermus thermophilus (TthPGI). The salmon box highlights the highly conserved K422. The alignment was generated by Espript.

Figure A2: Active site of the wildtype and K422 mutant. (a) Features TmaPGI WT important residues K422 and H310 with docked G6P. The orientation (#34) of G6P was chosen out of 235 options due to the position of the phosphate group with the residue of interest (K422) and a SP-dG of -6.0312. (b) Features the K422H mutation in TmaPGI with docked G6P. The orientation (#122) of G6P was chosen out of 198 options due to the position of the phosphate group with the residue of interest (K422H) and a SP-dG of -5.9680.

Figure A3: Structures of basic amino acids. From left to right the basic amino acids histidine, lysine, and arginine are shown which have pKa values of 6.04, 10.79, and 12.48 respectively. The side chain of each amino acid is outlined in red.

Figure A4. Electrostatic Potential Mapping of TmaPGI: (a) Demonstrates the electrostatic potential in the wild-type TmaPGI active site with G6P and K422. The presence of a blue and white surface implies a positive to neutral active site environment surrounding K422. The orientation (#34) of G6P was chosen out of 235 options due to the position of the phosphate group with the residue of interest (K422) and a SP-dG of -6.0312. (b) Demonstrates the electrostatic potential of the K422H mutant with G6P and K422H. The presence of a red surface implies a negative active site environment surrounding K422H. The orientation (#122) of G6P was chosen out of 198 options due to the position of the phosphate group with the residue of interest (K422H) and a SP-dG of -5.9680.

Figure A5: Docked G6P in the active site to determine H-bonds. (a) Shows the calculated H-bond between K422 and G6P at 2.006 Å. The H-bond is represented by a pink line. The orientation (#34) of G6P was chosen out of 235 options due to the position of the phosphate group with the residue of interest (K422) and a SP-dG of -6.0312. (b) Shows the calculated H-bond between K422H and G6P at 2.212 Å. The H-bond is represented by a pink line. The orientation (#122) of G6P was chosen out of 198 options due to the position of the phosphate group with the residue of interest (K422H) and a SP-dG of -5.9680.

** this assignment would be do around the halfway point in the course, maybe between exam 1 and 2

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