Page 42 - GPD-2-3

Gene & Protein in Disease Effect of phytochemicals in diabetes

backbone confirmation, and Ramachandran Z score The active site, surface features, and functional region
(−3 to +3) supporting good quality protein backbone of the target protein were identified by CASTp, an online
confirmation (Table 4). AMPK1 (Template-4rer.1.A) and tool, and it shows the occurrence of basic, acidic, and
AMPK2 (Template-7myj.2.A) have > 95% highly preferred neutral types of amino acids in the active site. From the
region and the Z-score value lies between −3.6 and −2.1. catalytic site amino acids, residues Arg199 for AMPK1 and
Hence, it was predicted that the selected target protein has Glu264 for AMPK2 were selected based on lesser binding
a good backbone. QMEAN scores (represents the degree of energy among 5 random selections.
nativeness of protein) for AMPK1 are 0.68 ± 0.05 and for
AMPK2 0.73 ± 0.05 (Table 5). Greater than 0.6 QMEAN 3.2. Examination of ligand library and lead
scores for the model protein indicated good quality/more identification
nativeness of protein, thus, the selected target can be used From the PubChem database , the SDF file containing
[50]
for model preparation. the structure and details of C. roseus alkaloids and related

Table 1. Physiochemical property of target proteins (UniProt and ProtParam value)
Protein UniProt/PubMed ID Length Molecular pI Instability Aliphatic GRAVY Extinction coefficients T 1/2
(AA) weight index index (AI) (M cm , at 280 nm)
‑1
‑1
AMPK1 AAPK1_HUMAN/Q13131 559 AA 64 kDa 8.32 49.44 84.03 −0.461 60,905 30 h
AMPK2 AAPK2_HUMAN/P54646 552 AA 62 kDa 7.65 49.20 85.11 −0.295 53,290 30 h
Abbreviations: AA: Amino acid; pI: Isoelectric point; GRAVY: Grand average of hydropathicity; T : Estimated half-life (mammalian reticulocytes, in vitro)
1/2

Table 2. Secondary structure detail of target protein (SOPMA result)
Proteins Length α‑helix 310 helix π‑helix β‑bridge Extended β‑turn Bend Random Ambiguous Other
(AA) (Hh) (Gg) (Ii) (Bb) strand (Ee) (Tt) region (Ss) coil (Cc) states states
AMPK1 559 AA 30.95% 0.00% 0.00% 0.00% 17.35% 6.80% 0.00% 44.90% 0.00% 0.00%
AMPK2 552 AA 27.72% 0.00% 0.00% 0.00% 17.39% 8.15% 0.00% 46.74% 0.00% 0.00%
Abbreviation: SOPMA: Self-optimized prediction method

Table 3. Nature of target protein based on SOSUI prediction
Receptor Protein nature No Region Transmembrane sequence Type
AMPK1 Soluble protein
AMPK2 Membrane Protein 1 6–28 KVLLGLLGAAALVTIITVPVVLL Primary

Table 4. Ramachandran Z‑score and Ramachandran plot of target proteins
S. No. Receptor Ramachandran Ramachandran plot
Z‑score
1 AMPK1 −3.583 Highly preferred observations (Green Crosses) 463 (95.859%)
(Template: 4rer. 1.A) Preferred observations (Brown Triangles) 16 (3.313%)
Questionable observations (Red Circles) 4 (0.828%)

2 AMPK2 −2.135 Highly preferred observations (Green Crosses) 464 (96.667%)
(Template: 7myj. 2.A) Preferred observations (Brown Triangles) 12 (2.500%)
Questionable observations (Red Circles) 4 (0.833%)

Note: The Ramachandran Z-score showed how normal a model is as compared to the reference, a score of±3 indicated good protein backbone
confirmation.

Volume 2 Issue 3 (2023) 4 https://doi.org/10.36922/gpd.0927