Ester Production Using the Lipid Composition of Coffee Ground Oil (Coffea arabica): A Theoretical Study of Eversa® Transform 2.0 Lipase as an Enzymatic Biocatalyst
Abstract
:1. Introduction
2. Materials and Methods
2.1. Homology Modeling
2.1.1. Identification and selection of protein-fold
2.1.2. Alignment of Target and Mold Sequences
2.1.3. Model Construction and Optimization
2.1.4. Protein Validation
2.2. Protein Preparation
2.3. Obtaining the Ligand
2.4. Molecular Docking and Visualization of Calculations
2.5. Molecular Dynamic
- Potential energy (kcal/mol) [45];
- Protein–ligand interaction energy (kcal/mol);
- The root mean square deviation of the atomic positions of proteins, binders, and the distances between them (RMSD, Å), and the root mean square deviation of the atomic positions of proteins, ligands, and the distances between them (RMSD, Å);
- Hydrogen bonds were evaluated using Visual Molecular Dynamics (VMD) [46];
- The mean square fluctuation of the minimum distances between proteins and ligands was observed in MD (RMSF, Å) [47]. The plots were generated using the Qtrace program.
- In this study, MD simulations were used to evaluate the stability of a viral protease enzyme with various ligands containing different amounts of α-helix and β-sheets [48]. The long-range interactions were calculated using the SPME method and a Langevin thermal bath at 310 K. The conformational changes of the protein during the MD simulations were described using root mean square deviations (RMSD).
MM/GBSA Calculations
3. Results and Discussion
3.1. Immobilization Locations
3.2. Protein Modeling
3.3. Interaction between Substrate and Lipase
3.4. Molecular Dynamics
3.4.1. RMSD Analysis
3.4.2. RMSF Analysis
3.4.3. H-bonds Analysis
3.4.4. SASA Calculations
3.4.5. MM/GBSA Calculations
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample | Energy (kcal/mol) |
---|---|
CID985 hexadecanoic acid | −5.6 |
CID8181 methyl hexadecanoate | −5.4 |
CID8201 methyl octadecanoate | −5.6 |
CID13584 methyl docosanoate | −5.4 |
CID14259 methyl eicosanoate | −5.7 |
CID5284421 6,9-methyl octadienoate | −6.1 |
CID5364509 methyl octadecenoate | −5.7 |
Sample | Residue | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Tyr 29 | Tyr 92 | Ile 94 | His 152 | Ser 153 | Leu 263 | Phe 265 | His 268 | Val 269 | Trp 270 | His 274 | Leu 283 | Leu 285 | |
CID985 | 3.99 (HI) | 5.38 (HI) | 2.27 (HB) | 5.02 (HI) | 4.41 (HI) 4.72 (HI) 4.97 (HI) | 5.16 (HI) | 4.27 (HI) | ||||||
CID8181 | 5.50 (HI) | 4.33 (HI) 4.07 (HI) | 5.42 (HI) 5.45 (HI) | 4.82 (HI) 4.18 (HI) 4.67 (HI) | 5.34 (HI) | 4.16 (HI) | |||||||
CID8201 | 3.75(CH) | 4.54 (HI) 5.05 (HI) | 3.72 (CH) | 4.85 (HI) 4.92 (HI) | 4.64(HI) 5.14(HI) | 3.96 (HI) 5.31 (HI) | 3.78 4.45 | ||||||
CID13584 | 5.40 (HI) | 4.15 (HI) 4.55 (HI) 5.08 (HI) | 4.63 (HI) 4.55 (HI) 5.19 (HI) | 5.31(HI) | 3.55(CH) | 3.71 (PA) 4.83 (HI) 4.89 (HI) 4.98 (HI) 5.04 (HI) | 4.73 (HI) | 4.32 (HI) | 4.19 (HI) 4.56 (HI) | ||||
CID14259 | 3.44 | 5.32 | 3.74 4.96 5.16 5.31 | 3.73 | 4.89 | ||||||||
CID5284421 | 3.29 | 3.65 | 4.83 5.34 5.18 | 3.54 | 4.94 5.18 | 3.97 4.38 5.28 5.50 | |||||||
CID5364509 | 5.30 | 3.96 | 5.09 | 4.53 4.73 4.88 | 3.79 | 4.75 |
Complex | ∆Eele + ∆Gsol | ∆Evdw | ∆Gbind (kcal/mol) | Standard Deviation |
---|---|---|---|---|
(kcal/mol) | (kcal/mol) | |||
hexadecanoic acid/Eversa | 18.43 | −29.14 | −13.27 | +/− 0.052 |
methyl hexadecanoate/Eversa | 17.67 | −33.93 | −16.26 | +/− 0.023 |
methyl octadecanoate/Eversa | 10.33 | −37.19 | −26.86 | +/− 0.027 |
methyl docosanoate/Eversa | 20.76 | −39.79 | −19.03 | +/− 0.024 |
methyl eicosanoate/Eversa | 13.75 | −37.37 | −23.62 | +/− 0.027 |
6,9-methyl octadienoate/Eversa | 11.97 | −35.38 | −23.41 | +/− 0.026 |
methyl octadecenoate/Eversa | 19.56 | −35.03 | −15.47 | +/− 0.026 |
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Nobre, M.M.R.; Silva, A.F.d.; Menezes, A.M.; Silva, F.L.B.d.; Lima, I.M.; Colares, R.P.; Souza, M.C.M.d.; Marinho, E.S.; Melo, R.L.F.; Santos, J.C.S.d.; et al. Ester Production Using the Lipid Composition of Coffee Ground Oil (Coffea arabica): A Theoretical Study of Eversa® Transform 2.0 Lipase as an Enzymatic Biocatalyst. Compounds 2023, 3, 411-429. https://doi.org/10.3390/compounds3030031
Nobre MMR, Silva AFd, Menezes AM, Silva FLBd, Lima IM, Colares RP, Souza MCMd, Marinho ES, Melo RLF, Santos JCSd, et al. Ester Production Using the Lipid Composition of Coffee Ground Oil (Coffea arabica): A Theoretical Study of Eversa® Transform 2.0 Lipase as an Enzymatic Biocatalyst. Compounds. 2023; 3(3):411-429. https://doi.org/10.3390/compounds3030031
Chicago/Turabian StyleNobre, Millena Mara Rabelo, Ananias Freire da Silva, Amanda Maria Menezes, Francisco Lennon Barbosa da Silva, Iesa Matos Lima, Regilany Paulo Colares, Maria Cristiane Martins de Souza, Emmanuel Silva Marinho, Rafael Leandro Fernandes Melo, José Cleiton Sousa dos Santos, and et al. 2023. "Ester Production Using the Lipid Composition of Coffee Ground Oil (Coffea arabica): A Theoretical Study of Eversa® Transform 2.0 Lipase as an Enzymatic Biocatalyst" Compounds 3, no. 3: 411-429. https://doi.org/10.3390/compounds3030031