Difference between revisions of "Part:BBa K3656307:Experience"

(→‎Applications of BBa_K3656307)
(→‎Construction of OT3-CA2-MU-His expression plasmid)
 
(6 intermediate revisions by the same user not shown)
Line 5: Line 5:
  
 
===Applications of BBa_K3656307===
 
===Applications of BBa_K3656307===
 +
====Construction of OT3-CA2-MU-His expression plasmid====
 
By using the software Autodock for molecular docking, we studied the docking conformation of the substrate at the catalytic site, and analyzed the interaction between the residue at the catalytic site and the substrate. Autodock and PyMOL were used to further investigate the effects of secondary and tertiary structures of catalytic sites on catalytic processes. After research and discussion, we set up the mutation site and the alternative residue scheme, carried on the molecular docking of the recombinant enzyme, and then compared the enzyme-substrate docking conformation before and after the reorganization. Finally, suitable mutation sites and alternative residues were selected to simulate the mutation and the catalytic performance was improved theoretically.
 
By using the software Autodock for molecular docking, we studied the docking conformation of the substrate at the catalytic site, and analyzed the interaction between the residue at the catalytic site and the substrate. Autodock and PyMOL were used to further investigate the effects of secondary and tertiary structures of catalytic sites on catalytic processes. After research and discussion, we set up the mutation site and the alternative residue scheme, carried on the molecular docking of the recombinant enzyme, and then compared the enzyme-substrate docking conformation before and after the reorganization. Finally, suitable mutation sites and alternative residues were selected to simulate the mutation and the catalytic performance was improved theoretically.
  
−
Based on the simulation results, we finally determine appropriate mutations are respectively: 122: P and K (proline mutation of lysine) 122, 123, P and K (proline mutation of lysine) 123, 128, P and K (proline mutation of lysine) 128, 132: L - > K (leucine mutation of lysine) 132, 134: L - > K (134th leucine mutation of lysine), and 137 - bit: P→K (leucine at 137 was mutated to lysine), and the mutated OT3-CA (OT3-ca-Mu, BBa_K3656307, Fig.1) was finally obtained, which enhanced its catalytic activity under high temperature conditions.
+
Based on the simulation results, we finally determine appropriate mutations are respectively: 122: P→K (the 122nd proline is mutated to lysine), position 123: P→K (the 123rd proline is mutated to Lysine), position 128: P→K (mutation of the 128th proline  to lysine), position 132: L→K (mutation of 132nd leucine to lysine), position 134: L→K ( Leucine at position 134 was mutated to lysine), and position 137: P→K (leucine at position 137 was mutated to lysine), and finally a mutant OT3-CA (OT3-CA-MU, BBa_K3656307, Fig.9 and 10) to enhance its catalytic activity under high-temperature conditions was obtained (Fig. 1).
  
−
[[File:T--AHUT-ZJU-China--BBaK3656307_1.png|400px|thumb|center|Fig. 1 Structure of Mutant OT3-CA]]
+
[[File:T--AHUT-ZJU-China--BBaK3656307_1.png|500px|thumb|center|Fig. 1 Structure of Mutant OT3-CA]]
−
{| border="1" cellspacing="0" cellpadding="5" align="center"
+
<center>
−
|!Name               ! OT3-CA-WT   ! OT3-CA-MU   |-
+
{|class="wikitable" style="text-align: center;"
−
| Part Number          | BBa_K3656305 | BBa_K3656309 |-
+
|+ ''Table 1. Using Auto Dock software to analyze the docking results of OT3-CA-WT and OT3-CA-MU with carbonic acid respectively.''
−
| binding_energy      | -5.08        | -5.37       |-
+
|-
−
| ligand_efficiency    | -1.27        | -1.34       |-
+
! Name                 !! OT3-CA-WT   !! OT3-CA-MU  
−
| inhib_constant      | 187.83      | 116.58       |-
+
|-
−
| inhib_constant_units | uM          | uM           |-
+
| Part Number          || BBa_K3656305 || BBa_K3656309  
−
| intermol_energy      | -5.68        | -5.96       |-
+
|-
−
| vdw_hb_desolv_energy | -1.76        | -1.92       |-
+
| binding_energy      || -5.08        || -5.37  
−
| electrostatic_energy | -3.92        | -4.04       |-
+
|-
−
| total_intermal      | 0.05        | 0.02         |-
+
| ligand_efficiency    || -1.27        || -1.34  
−
| torsional_energy    | 0.6          | 0.6         |-
+
|-
−
| unbound_energy      | 0.05        | 0.02         |-
+
| inhib_constant      || 187.83      || 116.58
 +
|-
 +
| inhib_constant_units || uM          || uM  
 +
|-
 +
| intermol_energy      || -5.68        || -5.96
 +
|-
 +
| vdw_hb_desolv_energy || -1.76        || -1.92
 +
|-
 +
| electrostatic_energy || -3.92        || -4.04
 +
|-
 +
| total_intermal      || 0.05        || 0.02
 +
|-
 +
| torsional_energy    || 0.6          || 0.6
 +
|-
 +
| unbound_energy      || 0.05        || 0.02
 
|}
 
|}
−
 
+
</center>
−
*Table 1. Using Auto Dock software to analyze the docking results of OT3-CA-WT and OT3-CA-MU with carbonic acid respectively.*
+
  
 
Secondly, we also use SnapGene design software to simulate and construct OT3-CA-MU-His recombinant vector (Fig. 2 with pET-28a (+) as the carrier.
 
Secondly, we also use SnapGene design software to simulate and construct OT3-CA-MU-His recombinant vector (Fig. 2 with pET-28a (+) as the carrier.
  
−
[[File:T--AHUT-ZJU-China--BBaK3656307_2.png|400px|thumb|center|Fig. 2 Map of OT3-CA-MU-His recombinant vector]]
+
[[File:T--AHUT-ZJU-China--BBaK3656307_2.png|500px|thumb|center|Fig. 2 Map of OT3-CA-MU-His recombinant vector]]
  
 
===User Reviews===
 
===User Reviews===

Latest revision as of 18:34, 27 October 2020


This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Applications of BBa_K3656307

Construction of OT3-CA2-MU-His expression plasmid

By using the software Autodock for molecular docking, we studied the docking conformation of the substrate at the catalytic site, and analyzed the interaction between the residue at the catalytic site and the substrate. Autodock and PyMOL were used to further investigate the effects of secondary and tertiary structures of catalytic sites on catalytic processes. After research and discussion, we set up the mutation site and the alternative residue scheme, carried on the molecular docking of the recombinant enzyme, and then compared the enzyme-substrate docking conformation before and after the reorganization. Finally, suitable mutation sites and alternative residues were selected to simulate the mutation and the catalytic performance was improved theoretically.

Based on the simulation results, we finally determine appropriate mutations are respectively: 122: P→K (the 122nd proline is mutated to lysine), position 123: P→K (the 123rd proline is mutated to Lysine), position 128: P→K (mutation of the 128th proline to lysine), position 132: L→K (mutation of 132nd leucine to lysine), position 134: L→K ( Leucine at position 134 was mutated to lysine), and position 137: P→K (leucine at position 137 was mutated to lysine), and finally a mutant OT3-CA (OT3-CA-MU, BBa_K3656307, Fig.9 and 10) to enhance its catalytic activity under high-temperature conditions was obtained (Fig. 1).

Fig. 1 Structure of Mutant OT3-CA
Table 1. Using Auto Dock software to analyze the docking results of OT3-CA-WT and OT3-CA-MU with carbonic acid respectively.
Name OT3-CA-WT OT3-CA-MU
Part Number BBa_K3656305 BBa_K3656309
binding_energy -5.08 -5.37
ligand_efficiency -1.27 -1.34
inhib_constant 187.83 116.58
inhib_constant_units uM uM
intermol_energy -5.68 -5.96
vdw_hb_desolv_energy -1.76 -1.92
electrostatic_energy -3.92 -4.04
total_intermal 0.05 0.02
torsional_energy 0.6 0.6
unbound_energy 0.05 0.02

Secondly, we also use SnapGene design software to simulate and construct OT3-CA-MU-His recombinant vector (Fig. 2 with pET-28a (+) as the carrier.

Fig. 2 Map of OT3-CA-MU-His recombinant vector

User Reviews

UNIQ7bbcf49f30e4351c-partinfo-00000000-QINU UNIQ7bbcf49f30e4351c-partinfo-00000001-QINU