Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 23, 2024

Engineering stabilized proteins is a fundamental challenge in the development of industrial and pharmaceutical biotechnologies. We present Stability Oracle: structure-based graph-transformer framework that achieves SOTA performance on accurately identifying thermodynamically stabilizing mutations. Our introduces several innovations to overcome well-known challenges data scarcity bias, generalization, computation time, such as: Thermodynamic Permutations for augmentation, structural amino acid embeddings model mutation with single structure, protein structure-specific attention-bias mechanism makes transformers viable alternative graph neural networks. provide training/test splits mitigate leakage ensure proper evaluation. Furthermore, examine our engineering contributions, we fine-tune ESM2 representations (Prostata-IFML) achieve sequence-based models. Notably, Oracle outperforms Prostata-IFML even though it was pretrained 2000X less has 548X parameters. establishes path fine-tuning virtually any phenotype, necessary task accelerating protein-based

Language: Английский

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A Comprehensive Review on the Enantiomeric Separation of Chiral Drugs Using Metal-Organic Frameworks

Chemosphere, Journal Year: 2024, Volume and Issue: 364, P. 143083 - 143083

Published: Aug. 16, 2024

Language: Английский

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A New Age of Biocatalysis Enabled by Generic Activation Modes

JACS Au, Journal Year: 2024, Volume and Issue: 4(6), P. 2068 - 2080

Published: May 31, 2024

Biocatalysis is currently undergoing a profound transformation. The field moves from relying on nature's chemical logic to discipline that exploits generic activation modes, allowing for novel biocatalytic reactions and, in many instances, entirely new chemistry. Generic modes enable wide range of reaction types and played pivotal role advancing the fields organo- photocatalysis. This perspective aims summarize principal harnessed enzymes develop biocatalysts. Although extensively researched past, highlighted when applied within enzyme active sites, facilitate transformations have largely eluded efficient selective catalysis. advance attributed multiple tunable interactions substrate binding pocket precisely control competing pathways transition states. We will highlight cases synthetic methodologies achieved by engineered provide insights into potential future developments this rapidly evolving field.

Language: Английский

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Directed Evolution and Unusual Protonation Mechanism of Pyridoxal Radical C–C Coupling Enzymes for the Enantiodivergent Photobiocatalytic Synthesis of Noncanonical Amino Acids

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

Visible light-driven pyridoxal radical biocatalysis has emerged as a new strategy for the stereoselective synthesis of valuable noncanonical amino acids in protecting-group-free fashion. In our previously developed dehydroxylative C–C coupling using engineered PLP-dependent tryptophan synthases, an enzyme-controlled unusual α-stereochemistry reversal and pH-controlled enantiopreference were observed. Herein, through high-throughput photobiocatalysis, we evolved set stereochemically complementary PLP enzymes, allowing both l- d-amino with enhanced enantiocontrol across broad pH window. These newly acid synthases permitted use range organoboron substrates, including boronates, trifluoroborates, boronic acids, excellent efficiency. Mechanistic studies unveiled unexpected racemase activity earlier enzyme variants. This promiscuous was abolished shedding light on origin enantiocontrol. Further mechanistic investigations suggest switch proton donor to account stereoinvertive formation highlighting stereoinversion mechanism that is rare conventional two-electron enzymology.

Language: Английский

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Hydrodeuteroalkylation of Unactivated Olefins Using Thianthrenium Salts

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

Published: June 13, 2024

Isotopically labeled alkanes play a crucial role in organic and pharmaceutical chemistry. While some deuterated methylating agents are readily available, the limited accessibility of other deuteroalkyl reagents has hindered synthesis corresponding products. In this study, we introduce nickel-catalyzed system that facilitates various deuterium-labeled through hydrodeuteroalkylation d2-labeled alkyl TT salts with unactivated alkenes. Diverging from traditional reagents, thianthrenium (TT) can effectively selectively deuterium at α position chains using D

Language: Английский

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Threonine Aldolase-Catalyzed Enantioselective α-Alkylation of Amino Acids through Unconventional Photoinduced Radical Initiation

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(32), P. 22476 - 22484

Published: July 4, 2024

Visible light-driven pyridoxal radical biocatalysis has emerged as a promising strategy for the stereoselective synthesis of valuable noncanonical amino acids (ncAAs). Previously, use well-tailored photoredox catalysts represented key to enable efficient phosphate (PLP) enzyme-catalyzed reactions. Here, we report PLP-dependent threonine aldolase-catalyzed asymmetric α-C–H alkylation abundant using Katritzky pyridinium salts alkylating agents. The engineered aldolases allowed this redox-neutral proceed efficiently, giving rise challenging α-trisubstituted and -tetrasubstituted ncAA products in protecting-group-free fashion with excellent enantiocontrol. Mechanistically, enantioselective α-alkylation capitalizes on unique reactivity persistent enzymatic quinonoid intermediate derived from PLP cofactor acid substrate allow novel C–C coupling. Surprisingly, photobiocatalytic process does not require well-established operates through an unconventional photoinduced generation involving PLP-derived aldimine. ability develop reactions without relying classic photocatalysts or photoenzymes opens up new avenues advancing intermolecular that are known either organic chemistry enzymology.

Language: Английский

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Engineering a Photoenzyme to Use Red Light

Published: March 18, 2024

Photoenzymatic catalysis is an emerging platform for asymmetric synthesis. In most of these reactions, the protein templates a charge transfer complex between cofactor and substrate, which absorbs in blue region electromagnetic spectrum. Here, we report engineering photoenzymatic ‘ene’-reductase to utilize red light (620 nm) radical cyclization reaction. Mechanistic studies indicate that ac-tivity achieved by introducing broadly absorbing shoulder off previously identified cyan absorption feature. Molecular dynamics simulations, docking, excited-state calculations suggest 𝜋→ 𝜋* transition from flavin while feature red-shift transition, occurs upon substrate binding. Differences excitation event help disfavor alkylation cofactor, pathway catalyst decomposition observed with but not red.

Language: Английский

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Mechanistic investigation of repurposed photoenzymes with new-to-nature reactivity

Current Opinion in Green and Sustainable Chemistry, Journal Year: 2025, Volume and Issue: 52, P. 101009 - 101009

Published: Feb. 27, 2025

Language: Английский

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Bridging chemistry and biology for light-driven new-to-nature enantioselective photoenzymatic catalysis

Chemical Society Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Merging enzymes with light-driven photocatalysis has given rise to the burgeoning field of photoenzymatic catalysis.

Language: Английский

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A systematic evaluation of the language-of-viral-escape model using multiple machine learning frameworks

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 8, 2024

Abstract Predicting the evolutionary patterns of emerging and endemic viruses is key for mitigating their spread in host populations. In particular, it critical to rapidly identify mutations with potential immune escape or increased disease burden (variants concern). Knowing which circulating are such variants concern can inform treatment mitigation strategies as alternative vaccines targeted social distancing. A recent study proposed that be identified using two quantities extracted from protein language models, grammaticality semantic change. These defined analogy concepts natural processing. Grammaticality intended a measure whether variant viral viable, change escape. Here, we systematically test this hypothesis, taking advantage several high-throughput datasets have become available, also testing additional machine learning models calculating metric. We find viability, though more traditional metric ΔΔ G appears effective. By contrast, do not compelling evidence useful tool identifying mutations.

Language: Английский

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