Artificial enzymes bringing together computational design and directed evolution

Mariz, Beatriz de Pina; Carvalho, Sara; Batalha, Íris L.; Pina, Ana Sofia

doi:10.1039/d0ob02143a

Cited by 23 publications

(14 citation statements)

References 112 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Computational enzyme design and directed evolution are important techniques in enzyme engineering, and a synergy between the two techniques promotes effective de novo enzyme design. − Inert protein scaffolds are conferred initial activity with the creation or modification of active sites during computational enzyme design, and these scaffolds mature to approach natural enzymes during directed evolution, which has been used to realize a variety of enzymatic transformations, such as Kemp elimination, − retro-aldol reactions, − Diels–Alder reactions, − and Morita–Baylis–Hilman reactions. , However, de novo enzymes developed exclusively through computational enzyme design tend to present limited catalytic activity. , This is attributed to the limitations of conformational sampling, energy functions, and conformational dynamics . Directed evolution can compensate for these deficiencies and provide enzymes with improved functions.…”

Section: Introductionmentioning

confidence: 99%

Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes

Wang

Zhang

et al. 2023

J. Chem. Inf. Model.

View full text Add to dashboard Cite

Computational enzyme design has been successfully applied to identify new alternatives to natural enzymes for the biosynthesis of important compounds. However, the moderate catalytic activities of de novo designed enzymes indicate that the modeling accuracy of current computational enzyme design methods should be improved. Here, high-throughput molecular dynamics simulations were used to enhance computational enzyme design, thus allowing the identification of variants with higher activities in silico. Different time schemes of high-throughput molecular dynamics simulations were tested to identify the catalytic features of evolved Kemp eliminases. The 20 × 1 ns molecular dynamics simulation scheme was sufficiently accurate and computationally viable to screen the computationally designed massive variants of Kemp elimination enzymes. The developed hybrid computational strategy was used to redesign the most active Kemp eliminase, HG3.17, and five variants were generated and experimentally confirmed to afford higher catalytic efficiencies than that of HG3.17, with one double variant (D52Q/A53S) exhibiting a 55% increase. The hybrid computational enzyme design strategy is general and computationally economical, with which we anticipate the efficient creation of practical enzymes for industrial biocatalysis.

show abstract

Section: Introductionmentioning

confidence: 99%

Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes

Wang

Zhang

et al. 2023

J. Chem. Inf. Model.

View full text Add to dashboard Cite

show abstract

“…Moreover, computational enzyme design made significant contributions beyond serendipity [2] . And these designed active sites also benefited from directed evolution, showing substantial structural changes in the scaffolds, compared to the initial model, [3] but with increased catalytic activity.…”

Section: Introductionmentioning

confidence: 99%

Catalytic Peptides: the Challenge between Simplicity and Functionality

Carvalho

Reis

Pereira

et al. 2022

Israel Journal of Chemistry

View full text Add to dashboard Cite

Enzymes' machinery has been an inspiration for chemists. Peptides are vital players in the origin of life, being ancestors of complex enzymes. Even short peptides that are simple in terms of the number of residues are reprogrammable and built to encode chemical information for catalysis, substrate recognition, and molecular interactions. The combinatorial search of the sequence space led to identifying peptides with catalytic activities. However, most of these sequences remain unevolved, leading to modest rates in aqueous media. Short peptides present conformational flexibility, which is their primary liability for catalysis. To overcome this, supramolecular motifs and secondary frameworks are used as scaffolds to incorporate catalytic residues and improve their efficiency. This review discusses the strategies used to discover and evolve catalytic function in short peptides beyond the de novo design and the advantages of using these approaches to enhance catalysis.

show abstract

“…However, there are still many potentials to be exploited in this subject [1][2][3][4]. The enzyme market is growing by around 7% a year, relying on new ways of cheapening their use and the well-known advantages of mild reaction conditions, specificity, reduced byproduct formation, product separation, biodegradability, and high efficiency [5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Current Status and Future Perspectives of Supports and Protocols for Enzyme Immobilization

Cavalcante

Sousa

et al. 2021

Catalysts

View full text Add to dashboard Cite

The market for industrial enzymes has witnessed constant growth, which is currently around 7% a year, projected to reach $10.5 billion in 2024. Lipases are hydrolase enzymes naturally responsible for triglyceride hydrolysis. They are the most expansively used industrial biocatalysts, with wide application in a broad range of industries. However, these biocatalytic processes are usually limited by the low stability of the enzyme, the half-life time, and the processes required to solve these problems are complex and lack application feasibility at the industrial scale. Emerging technologies create new materials for enzyme carriers and sophisticate the well-known immobilization principles to produce more robust, eco-friendlier, and cheaper biocatalysts. Therefore, this review discusses the trending studies and industrial applications of the materials and protocols for lipase immobilization, analyzing their advantages and disadvantages. Finally, it summarizes the current challenges and potential alternatives for lipases at the industrial level.

show abstract

Artificial enzymes bringing together computational design and directed evolution

Abstract: This manuscript reviews the combination of computational enzyme design and directed evolution and its advantages in the development of artificial enzymes.

Cited by 23 publications

References 112 publications

Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes

Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes

Catalytic Peptides: the Challenge between Simplicity and Functionality

Current Status and Future Perspectives of Supports and Protocols for Enzyme Immobilization

Contact Info

Product

Resources

About