Computational Design of New Protein Catalysts

Kiss, Gert; Johnson, Scott A.; Nosrati, Geoffrey R.; Çelebi‐Ölçüm, Nihan; Kim, Seonah; Paton, Robert S.; Houk, K. N.

doi:10.1002/9783527636402.ch16

Cited by 1 publication

(1 citation statement)

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“…The total score should not be greater than the total score of the original scaffold protein. The ligand binding energy was less than −10.0 Rosetta energy units (REU) (SR_interface_1_2 < −10.0), the total score of the catalytic residue conforming to the constraint range was less than 1 (all_cst < 1.0), the number of the polar atoms that were unsaturated and buried in the ligand and catalytic residues was no more than two (SR_burunsat_pm ≤ 2), and more than 66% of the ligands’ surface was buried in the protein (SR_dsasa_1_2 > 0.66) [ 39 , 40 ]. The designed enzyme results were sorted according to the total score, and the best-designed results were experimentally characterized.…”

Section: Methodsmentioning

confidence: 99%

A De Novo Designed Esterase with p-Nitrophenyl Acetate Hydrolysis Activity

Zhang

et al. 2020

Molecules

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Esterases are a large family of enzymes with wide applications in the industry. However, all esterases originated from natural sources, limiting their use in harsh environments or newly- emerged reactions. In this study, we designed a new esterase to develop a new protocol to satisfy the needs for better biocatalysts. The ideal spatial conformation of the serine catalytic triad and the oxygen anion hole at the substrate-binding site was constructed by quantum mechanical calculation. The catalytic triad and oxygen anion holes were then embedded in the protein scaffold using the new enzyme protocol in Rosetta 3. The design results were subsequently evaluated, and optimized designs were used for expression and purification. The designed esterase had significant lytic activities towards p-nitrophenyl acetate, which was confirmed by point mutations. Thus, this study developed a new protocol to obtain novel enzymes that may be useful in unforgiving environments or novel reactions.

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Section: Methodsmentioning

confidence: 99%

A De Novo Designed Esterase with p-Nitrophenyl Acetate Hydrolysis Activity

Zhang

et al. 2020

Molecules

View full text Add to dashboard Cite

show abstract

Computational Design of New Protein Catalysts

Cited by 1 publication

References 61 publications

A De Novo Designed Esterase with p-Nitrophenyl Acetate Hydrolysis Activity

A De Novo Designed Esterase with p-Nitrophenyl Acetate Hydrolysis Activity

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