A synthetic CRISPR-Cas nuclease with expanded enzymatic activities DOI Open Access
Ylenia Jabalera, Igor Tascón, Sara Samperio

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 12, 2023

Summary Clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonucleases have revolutionized biotechnology for their potential as programmable genome editors. Yet, most natural nucleases and variants limitations. Here, we report a fully synthetic CRISPR-associated (Cas) nuclease (α-synCas) designed by Ancestral Sequence Reconstruction (ASR) that displays set of robust distinct targeting properties, not found in any other known CRISPR-Cas Class 2 system. We show α-synCas is PAMless able to catalyse RNA-guided, specific cleavage dsDNA, ssDNA ssRNA. The enzyme also capable sequence-nonspecific degradation ssRNA following activation complementary targets. Furthermore, exhibits editing activity human cells bacteria. Cryo-electron microscopy structures ternary quaternary complexes provide framework understand the structural basis its expanded enzymatic activities. capability multimodal virtually nucleic acid sequence distinguishes promising new tool extend current CRISPR-based technologies.

Language: Английский

Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion DOI Creative Commons
Nikolaj G. Koch, Nediljko Budiša

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(16), P. 9580 - 9608

Published: July 2, 2024

Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial methanogenic metabolic pathways, laid foundation burgeoning field genetic code expansion. primary focus is discussion to successfully engineer PylRS recognize new substrates and exhibit higher

Language: Английский

Citations

14
Using BpyAla to generate Copper Artificial Metalloenzymes: a catalytic and structural study DOI Creative Commons

E. Klemencic,

Richard C. Brewster, Hafiz Saqib Ali

et al.

Catalysis Science & Technology, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Artificial metalloenzymes (ArMs) have emerged as a promising avenue in the field of biocatalysis, offering new reactivity. However, their design remains challenging due to limited understanding protein dynamics and how introduced cofactors alter scaffold structure. Here we present structures catalytic activity novel copper ArMs capable (

Language: Английский

Citations

7
Colloidal Protein–Silver Nanoparticle Metalloenzyme as Artificial Redox Biocatalyst DOI Open Access

Glenn Bojanov,

Carla Garcia‐Sanz, José M. Palomo

et al.

Catalysts, Journal Year: 2025, Volume and Issue: 15(1), P. 61 - 61

Published: Jan. 11, 2025

Efficient and sustainable catalytic processes are crucial for advancing green chemical manufacturing. Here, we describe the synthesis of novel silver artificial metalloenzymes in colloidal form aqueous media room temperature. The strategy is based on situ generation nanoparticles by a genetically modified Geobacillus thermocatenulatus lipase (GTL) active site as an inducer scaffold protein, producing enzyme–Ag bioconjugate. Using structural analysis formation XRD UV spectra, found Ag2O species with around 11 nm average diameter size. Gel filtration chromatography demonstrated presence single protein molecules bioconjugates, although were initially formed cysteine coordination but later other parts (five AgNPs per molecules, which concordance size). enzyme structure was altered after nanoparticle Ag-S interaction, observed fluorescence analysis. This new showed reductive activity against p-nitrophenol to p-amino high conversion > 99% reduction acetophenone phenylethanol, enantioselective quite moderate higher water that co-solvents. Finally, oxidase-like evaluated direct oxidation phenylethanol water, obtained at 23% yield ketone 60 h.

Language: Английский

Citations

0
Artificial intelligence driven innovations in biochemistry: A review of emerging research frontiers DOI Creative Commons

Mohammed Abdul Lateef Junaid

Biomolecules and Biomedicine, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 14, 2025

Artificial intelligence (AI) has become a powerful tool in biochemistry, greatly enhancing research capabilities by enabling the analysis of complex datasets, predicting molecular interactions, and accelerating drug discovery. As AI continues to evolve, its applications biochemistry are poised expand, revolutionizing both theoretical applied research. This review explores current potential with focus on data analysis, modeling, enzyme engineering, metabolic pathway studies. Key techniques—such as machine learning algorithms, natural language processing, AI-based modeling—are discussed. The also highlights emerging areas benefiting from AI, including personalized medicine synthetic biology. methodology involves an extensive existing literature, particularly peer-reviewed studies biochemistry. AI-driven tools like AlphaFold, which have significantly advanced protein structure prediction, evaluated alongside AI’s role expediting addresses challenges such quality, model interpretability, ethical considerations. Results indicate that expanded scope biochemical facilitating large-scale simulations, opening new avenues inquiry. However, remain, handling concerns. In conclusion, is transforming driving innovation expanding possibilities. Future advancements interdisciplinary collaboration, integration automated techniques will be crucial fully unlocking advancing

Language: Английский

Citations

0
An artificial metal-free peroxidase designed using a ferritin cage DOI Creative Commons
Jiaxin Tian, Basudev Maity, Tadaomi Furuta

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 12, 2025

Abstract Developing artificial enzymes is challenging because it requires precise design of active sites with well-arranged amino acid residues. Histidine-rich oligopeptides have been recently shown to exhibit peroxidase-mimetic activities, but their catalytic function relies on maintaining unique supramolecular structures. This work demonstrates the a specific array histidine residues internal surface ferritin cage as an center for catalysis. The crystal structures mutants revealed histidine-histidine interactions, forming well-defined clusters (His-clusters). These activities by oxidizing 3,3’,5, 5’-tetramethylbenzidine (TMB) in presence hydrogen peroxide. Molecular dynamics simulations further highlight co-localization TMB and peroxide at histidine-rich clusters, indicating that confined environment enhances interactions. study presents simple yet effective approach cofactor-free enzymes, paving way innovations bioinspired

Language: Английский

Citations

0
A De Novo Design Strategy to Convert FAcD from Dimer to Active Monomer DOI Creative Commons
Ke-Wei Chen, Cuizhen Wang,

Hsu-Nan Huang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 14, 2025

Abstract Enzymes largely exist in various oligomeric states, but monomeric enzymes are more conducive to industrial applications. Converting an enzyme into active monomer is a significant challenge. In this study, we present de novo design strategy convert fluoroacetate dehalogenase (FAcD) from its native dimeric form monomer. Using the AI-based method ProteinMPNN, identified critical protein-protein interaction (PPI) sites at dimer interface. ArDCA, another AI tool, was employed pinpoint catalytic hotspots. Six mutants, Mu1-Mu6 , were designed. Molecular dynamics (MD) simulations, coupled with mass spectrometry, confirmed that these mutants stable monomers. The pre-reaction state (PRS) model predicted three of exhibited activity. particular, Mu5 11 mutations wild-type, have high activity, and subsequently by kinetics experiment, k cat 672.2 min -1 T 50 30 > 100 °C, comparable wild-type ( = 676.3 84 °C). Notably, Y149M mutation increased activity nearly forty-fold, demonstrating effectiveness our strategy.

Language: Английский

Citations

0
Enzymes and Natural Products DOI

Bryan Hanley

Published: Jan. 1, 2025

Language: Английский

Citations

0
New Glycosalen–Manganese(III) Complexes and RCA120 Hybrid Systems as Superoxide Dismutase/Catalase Mimetics DOI Creative Commons
Valeria Lanza, Graziella Vecchio

Biomimetics, Journal Year: 2023, Volume and Issue: 8(5), P. 447 - 447

Published: Sept. 21, 2023

Reactive oxygen species are implicated in several human diseases, including neurodegenerative disorders, cardiovascular dysfunction, inflammation, hereditary and ageing. Mn

Language: Английский

Citations

4
Reliability Issues and Challenges in Biosensor Development DOI
Pedro Victor Valadares Romanholo, João Vitor Fernandes PAIVA, Lívia F. Sgobbi

et al.

Published: Jan. 1, 2024

This chapter addresses the main issues related to reliability and challenges in development of biosensors by scientific community, limitations going beyond frontiers laboratory bench reaching market. We discuss concern biological recognition element, obstacles be overcome matter involving transduction superficiality analytical evaluation their commercialization.

Language: Английский

Citations

1
A thiopyridine-bound mirror-image copper center in an artificial non-heme metalloenzyme DOI
Yoshitsugu Morita,

Hiroki Kubo,

Ryusei Matsumoto

et al.

Journal of Inorganic Biochemistry, Journal Year: 2024, Volume and Issue: 260, P. 112694 - 112694

Published: Aug. 13, 2024

Language: Английский

Citations

1