Learning from Protein Engineering by Deconvolution of Multi‐Mutational Variants

Angewandte Chemie International Edition, Journal Year: 2024, Volume and Issue: 63(36)

Published: June 17, 2024

Abstract This review analyzes a development in biochemistry, enzymology and biotechnology that originally came as surprise. Following the establishment of directed evolution stereoselective enzymes organic chemistry, concept partial or complete deconvolution selective multi‐mutational variants was introduced. Early experiments led to finding mutations can interact cooperatively antagonistically with one another, not just additively. During past decade, this phenomenon shown be general. In some studies, molecular dynamics (MD) quantum mechanics/molecular mechanics (QM/MM) computations were performed order shed light on origin non‐additivity at all stages an evolutionary upward climb. Data used construct unique multi‐dimensional rugged fitness pathway landscapes, which provide mechanistic insights different from traditional landscapes. Along related line, biochemists have long tested result introducing two point enzyme for reasons, followed by comparison respective double mutant so‐called cycles, showed only additive effects, but more recently also uncovered cooperative antagonistic non‐additive effects. We conclude suggestions future work, call unified overall picture epistasis.

Language: Английский

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SubTuner leverages physics-based modeling to complement AI in enzyme engineering toward non-native substrates

Chem Catalysis, Journal Year: 2025, Volume and Issue: unknown, P. 101334 - 101334

Published: March 1, 2025

Language: Английский

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Organophosphorus S-adenosyl-L-methionine mimetics: synthesis, stability, and substrate properties

Frontiers in Chemistry, Journal Year: 2024, Volume and Issue: 12

Published: Aug. 1, 2024

S-Adenosyl-l-methionine (SAM)-mediated methylation of biomolecules controls their function and regulates numerous vital intracellular processes. Analogs SAM with a reporter group in place the S-methyl are widely used to study these However, many analogs chemically unstable that largely limits practical application. We have developed new compound, SAM-PH , which contains an H-phosphinic (-P(O)(H)OH) instead carboxylic group. SAM-P H is significantly more stable than SAM, retains functional activity catechol-O-methyltransferase methyltransferase WBSCR27 reactions. The last associated Williams-Beuren syndrome. Rac-SAM-P was synthesized chemically, while (R,S)-SAM-P its were prepared enzymatically either from methionine (Met-PH) or analog S-adenosyl-l-homocysteine (SAH-P ) using adenosyltransferase 2A halide methyltransferases, respectively. SAH-P undergoes glycoside bond cleavage presence methylthioadenosine nucleosidase like natural SAH. Thus, promising tools for investigating methyltransferases incorporating groups into substrates.

Language: Английский

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Enzymatic Reactions of S-Adenosyl-L-Methionine: Synthesis and Applications

Biochemistry (Moscow), Journal Year: 2025, Volume and Issue: 90(S1), P. S105 - S134

Published: Feb. 1, 2025

Language: Английский

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Lernen aus Protein‐Engineering durch Dekonvolution von Multi‐Mutationalen Enzymvarianten**

Angewandte Chemie, Journal Year: 2024, Volume and Issue: 136(36)

Published: June 17, 2024

Abstract Diese Übersicht analysiert eine Entwicklung in der Biochemie, Enzymologie und Biotechnologie, die ursprünglich als Überraschung betrachtet wurde. Nach Etablierung gerichteten Evolution stereoselektiver Enzyme organischen Chemie wurde das Konzept partiellen oder vollständigen Dekonvolution selektiver multi‐mutationaler Varianten eingeführt. Frühe Dekonvolutionsexperimente von stereoselektiven Enzymvarianten führten zu Erkenntnis, dass Mutationen kooperativ antagonistisch miteinander interagieren können, nicht nur additiv. Im letzten Jahrzehnt dieses Phänomen allgemeingültig nachgewiesen. In einigen Studien wurden molekulardynamische (MD) quantenmechanische/ molekülmechanische (QM/MM) Berechnungen durchgeführt, um Licht auf den Ursprung Nicht‐Additivität allen Phasen eines evolutionären Aufstiegs werfen. Daten können verwendet werden, einzigartige mehrdimensionale, zerklüftete („rugged“) Fitness‐Pfad‐Landschaften experimentell konstruieren. Sie bieten mechanistische Einblicke, sich traditionellen Fitnesslandschaften erheblich unterscheiden. einem verwandten Bereich haben Biochemiker lange Ergebnis Einführung zwei Punktmutationen Enzym aus mechanistischen Gründen getestet, gefolgt Vergleich mit entsprechenden Doppelmutante sogenannten Doppelmutanten‐Zyklen, additive Effekte zeigten. jüngerer Zeit auch hier kooperative antagonistische nicht‐additive aufgedeckt. Wir schließen Vorschlägen für zukünftige Arbeiten fordern ein einheitliches Gesamtbild Epistasis.

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Directed evolution of C-methyltransferase PsmD for enantioselective pyrroloindole derivative production

Catalysis Science & Technology, Journal Year: 2024, Volume and Issue: 14(21), P. 6298 - 6306

Published: Jan. 1, 2024

The engineering of stereoselective C-methyltransferase PsmD through saturation mutagenesis led to improved activity for larger substrates. An automated process was designed and successfully applied the mutant library production screening.

Language: Английский

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Enzymatic synthesis of S-adenosyl-l-homocysteine and its nucleoside analogs from racemic homocysteine thiolactone

Chemical Science, Journal Year: 2024, Volume and Issue: 15(38), P. 15900 - 15906

Published: Jan. 1, 2024

One-pot enzyme-catalyzed synthesis of S -adenosyl homocysteine and derivatives thereof from racemic thiolactone adenosine or other nucleosides provides simple scalable access to cofactors for methyltransferase biocatalysis.

Language: Английский

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Biocatalytic Amino Acid Functionalisation

ChemMedChem, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 14, 2024

The success of new therapeutic modalities relies on advancements in synthetic chemistry to produce compounds for evaluation throughout the drug discovery process. use non-canonical amino acids (ncAAs) allows properties peptide drugs be modified and optimised beyond defined characteristics 20 proteogenic acids. Synthesis ncAAs can either through a bespoke chemical synthesis, or directly from parent compound - using traditional reagents enzymes achieve desired modification. This review will highlight recent enzymatic functionalisation variety ncAAs.

Language: Английский

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