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Molecular docking study of L-Asparaginase I from Vibrio campbellii in the treatment of acute lymphoblastic leukemia (ALL)

Abdul Khader Sultan Mohideen
Abdul Khader Sultan Mohideen
   | 18 janv. 2020
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Article Category: Research article
Publié en ligne: 18 janv. 2020
Pages: 8 - 16
DOI: https://doi.org/10.2478/ebtj-2020-0002
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© 2020 Abdul Khader Sultan Mohideen, published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Figure 1

Schematic representation of the reaction mechanism between L-Asparaginase and L-asparagine. The enzyme catalyzes the hydrolysis of L-asparagine into aspartic acid and ammonia depriving the tumour cells to utilize this amino acid and inhibiting tumour growth.
Schematic representation of the reaction mechanism between L-Asparaginase and L-asparagine. The enzyme catalyzes the hydrolysis of L-asparagine into aspartic acid and ammonia depriving the tumour cells to utilize this amino acid and inhibiting tumour growth.

Figure 2

Crystal structure of L-asparagine (L-Asn) amino acid molecule. The L-Asn contains a central α-carbon atom to which both the amino (blue) and carboxyl groups (red) are attached. The other two bonds of the α-carbon atom are satisfied by the hydrogen (white) atom and the R group- side chain (Retrieved from Library of 3D Molecular Structures).
Crystal structure of L-asparagine (L-Asn) amino acid molecule. The L-Asn contains a central α-carbon atom to which both the amino (blue) and carboxyl groups (red) are attached. The other two bonds of the α-carbon atom are satisfied by the hydrogen (white) atom and the R group- side chain (Retrieved from Library of 3D Molecular Structures).

Figure 3

Modeled dimeric structure of L- Asparaginase I from V. campbellii. The two monomers (large and small) are shown in blue and green respectively. The larger and smaller monomers comprising of N-terminal and C-terminal regions.
Modeled dimeric structure of L- Asparaginase I from V. campbellii. The two monomers (large and small) are shown in blue and green respectively. The larger and smaller monomers comprising of N-terminal and C-terminal regions.

Figure 4

Topology of the L-Asparaginase I from V. campbellii with large arrows showing β-sheets, cylinders representing α-helices and small arrows indicating β-turns on both the N-terminal and C-terminal regions of the dimeric enzyme. The two monomers are connected together by a linker region comprising of coil proteins (cartoon representation using Pro-origami).
Topology of the L-Asparaginase I from V. campbellii with large arrows showing β-sheets, cylinders representing α-helices and small arrows indicating β-turns on both the N-terminal and C-terminal regions of the dimeric enzyme. The two monomers are connected together by a linker region comprising of coil proteins (cartoon representation using Pro-origami).

Figure 5

The Ramachandran map for L-Asparaginase I of V. campbellii shows the phi-psi torsion angles for all residues. The shading on the plot represents different regions. The red color corresponds to the core regions representing the most favourable combinations of phi-psi values.
The Ramachandran map for L-Asparaginase I of V. campbellii shows the phi-psi torsion angles for all residues. The shading on the plot represents different regions. The red color corresponds to the core regions representing the most favourable combinations of phi-psi values.

Figure 6

ProSA-web z-scores of all protein chains in PDB determined by X-ray crystallography (light blue) or NMR spectroscopy (dark blue) with respect to their length. The plot shows only chains with less than 1000 residues and a z-score ≤ 10. The z-scores of L-ASP I and 2OCD_A are highlighted as large dots.
ProSA-web z-scores of all protein chains in PDB determined by X-ray crystallography (light blue) or NMR spectroscopy (dark blue) with respect to their length. The plot shows only chains with less than 1000 residues and a z-score ≤ 10. The z-scores of L-ASP I and 2OCD_A are highlighted as large dots.

Figure 7

Molecular docking result of L-Asparaginase I and L-asparagine obtained from Argus Lab v.4.0, showing the ligand substrate binding with the enzyme. The ligand substrate is bound to the active site of the larger N-terminal domain of the enzyme.
Molecular docking result of L-Asparaginase I and L-asparagine obtained from Argus Lab v.4.0, showing the ligand substrate binding with the enzyme. The ligand substrate is bound to the active site of the larger N-terminal domain of the enzyme.

Figure 8

LigPlot showing the docked complex of ligand substrate L-asparagine and enzyme L-Asparaginase. The ligand L-asparagine (Asn) is bound to the enzyme within the sphere of the radius 8 Å. The enzyme residues are close to L-Asn (central residue) along the N and C direction contribute to short and medium range interaction.
LigPlot showing the docked complex of ligand substrate L-asparagine and enzyme L-Asparaginase. The ligand L-asparagine (Asn) is bound to the enzyme within the sphere of the radius 8 Å. The enzyme residues are close to L-Asn (central residue) along the N and C direction contribute to short and medium range interaction.

Figure 9

Molecular interactions between L-asparaginase I and ligand substrate L-Asn substrate showing the active site of L-asparaginase I dimer. The side chain carboxyl group of the L-Asn (Central residue) is in close contact with the hydroxyl groups of both candidate nucleophiles, T14 and T91.
Molecular interactions between L-asparaginase I and ligand substrate L-Asn substrate showing the active site of L-asparaginase I dimer. The side chain carboxyl group of the L-Asn (Central residue) is in close contact with the hydroxyl groups of both candidate nucleophiles, T14 and T91.

Figure 10

The enzyme L-asparaginase I showing a catalytic triad containing residues (red) in its active site. The triad comprising of residues threonine (nucleophile), serine (base) and aspartic acid (acid). The L-asparagine substrate (black) is bound to the enzyme.
The enzyme L-asparaginase I showing a catalytic triad containing residues (red) in its active site. The triad comprising of residues threonine (nucleophile), serine (base) and aspartic acid (acid). The L-asparagine substrate (black) is bound to the enzyme.

Blastp report of amino acid sequences producing significant alignments with L-ASP I of V. campbellii

PDB IDQuery coverage (%)Max Identity (%)E valueGap (%)Positive (%)
2OCD_A100858e-168091
2P2D_A99734e-139084
2HIM_A99732e-138084
3NTX_A99702e-132082

Molecular interactions between ligand substrate L-Asn and L-ASP I of V. campbellii.

S.No.LigandResidue and atomLigand atomBond length (A°)
1L-AsnT14 & OG1OC2HD22.42.6
2S60 & OGO3.5
3T91 & OG1OD11H1.72.8
4D92 & OD11H2.4
5S 117 & O2HD22.3
6Q118 & O1HD22.3
7N170 & ND2OD12.4
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