Bioorthogonal chemistry: Bridging chemistry, biology, and medicine

Chem, Год журнала: 2023, Номер 9(8), С. 2095 - 2109

Опубликована: Июнь 5, 2023

Язык: Английский

---

Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июль 18, 2024

Abstract While photo-cross-linking (PXL) with alkyl diazirines can provide stringent distance restraints and offer insights into protein structures, unambiguous identification of cross-linked residues hinders data interpretation to the same level that has been achieved chemical cross-linking (CXL). We address this challenge by developing an in-line system systematic modulation light intensity irradiation time, which allows for a quantitative evaluation diazirine photolysis photo-reaction mechanism. Our results reveal two-step pathway mainly sequential generation diazo carbene intermediates. Diazo intermediate preferentially targets buried polar residues, many are inaccessible known CXL probes their limited reactivity. Moreover, we demonstrate tuning duration enhances selectivity towards biasing diazo-mediated reactions over ones. This mechanistic dissection unlocks full potential PXL, paving way accurate mapping against structures ultimately, unveiling dynamic behaviors.

Язык: Английский

---

Cu-Catalyzed Azide–Alkyne–Thiol Reaction Forms Ubiquitous Background in Chemical Proteomic Studies

Journal of the American Chemical Society, Год журнала: 2024, Номер 146(3), С. 2151 - 2159

Опубликована: Янв. 12, 2024

We report here a Cu-catalyzed azide–alkyne–thiol reaction forming thiotriazoles as the major byproduct under widely used bio-orthogonal protein labeling "click" conditions. The development of Cu(I)-catalyzed azide–alkyne cycloaddition (CuAAC) had tremendous impact on many biological discoveries. However, considered chemoselectivity CuAAC is hampered by high reactivity cysteine free thiols, yielding thiotriazole conjugates. byproducts generate false-positive hits in functional proteomic studies. reported detail investigation conjugates between chemical probes containing terminal alkynes, azide tags, and cell lysates reveals formation thiotriazoles, which can be readily detected in-gel fluorescence scanning or after peptide enrichment mass spectrometry-based proteomics. In level identification quantification experiments, produced fluorescent bands enriched proteins may not result from important enzymatically driven falsely assigned hits. This study provides complete list most common background proteins. knowledge this previously overlooked now leads to introduction modified conditions, avoids undesired product formation, diminishes background, hence improves signal-to-noise ratio.

Язык: Английский

---

Cell-selective bioorthogonal labeling

Cell chemical biology, Год журнала: 2023, Номер 31(3), С. 409 - 427

Опубликована: Окт. 13, 2023

Язык: Английский

---

Structure-Based Deep Learning Framework for Modeling Human–Gut Bacterial Protein Interactions

Proteomes, Год журнала: 2025, Номер 13(1), С. 10 - 10

Опубликована: Фев. 17, 2025

Background: The interaction network between the human host proteins and of gut bacteria is essential for establishment health, its dysregulation directly contributes to disease development. Despite great importance, experimental data on protein-protein interactions (PPIs) these species are sparse due limitations. Methods: This study presents a deep learning-based framework predicting PPIs bacterial using structural data. leverages graph-based protein representations variational autoencoders (VAEs) extract embeddings from graphs, which then fused through Bi-directional Cross-Attention module predict interactions. model addresses common challenges in PPI datasets, such as class imbalance, focal loss emphasize harder-to-classify samples. Results: results demonstrated that this exhibits robust performance, with high precision recall across validation test underscoring generalizability. By incorporating proteoforms analysis, accounts complexity within proteomes, making predictions biologically relevant. Conclusions: These findings offer scalable tool investigating microbiota, potentially yielding new treatment targets diagnostics disorders linked microbiome.

Язык: Английский

---

Structure-Based Modeling of the Gut Bacteria–Host Interactome Through Statistical Analysis of Domain–Domain Associations Using Machine Learning

BioTech, Год журнала: 2025, Номер 14(1), С. 13 - 13

Опубликована: Фев. 25, 2025

The gut microbiome, a complex ecosystem of microorganisms, plays pivotal role in human health and disease. microbiome's influence extends beyond the digestive system to various organs, its imbalance is linked wide range diseases, including cancer neurodevelopmental, inflammatory, metabolic, cardiovascular, autoimmune, psychiatric diseases. Despite significance, interactions between bacteria proteins remain understudied, with less than 20,000 experimentally validated protein host any species. This study addresses this knowledge gap by predicting protein-protein interaction network bacterial proteins. Using statistical associations Pfam domains, comprehensive dataset over one million pan-bacterial-human interactions, as well inter- intra-species from organisms, were used for development machine learning-based prediction method uncover key regulatory molecules dynamic system. study's findings contribute understanding intricate microbiome-host relationship pave way future experimental validation therapeutic strategies targeting microbiome interplay.

Язык: Английский

---

Experimental Approaches to Visualize Effector Protein Translocation During Host‐Pathogen Interactions

BioEssays, Год журнала: 2025, Номер unknown

Опубликована: Март 13, 2025

ABSTRACT Bacterial pathogens deliver effector proteins into host cells by deploying sophisticated secretion systems. This translocation during host‐pathogen interactions is a prerequisite for the manipulation of and organisms important pathogenesis. Analyses dynamics kinetics translocation, subcellular localization, cellular targets lead to understanding mode action function in interplay. review provides an overview biochemical genetic tools that have been developed study protein qualitatively or quantitatively. After introducing challenges analyses interaction, we describe various methods ranging from static visualization fixed dynamic live‐cell imaging translocation. We show main findings enabled approaches, emphasize advantages limitations methods, recent approaches allow real‐time tracking living on single molecule level, highlight open questions field be addressed application new methods.

Язык: Английский

---

Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome

Chemical Reviews, Год журнала: 2025, Номер unknown

Опубликована: Апрель 3, 2025

The cell surface proteome, or surfaceome, is the hub for cells to interact and communicate with outside world. Many disease-associated changes are hard-wired within yet approved drugs target less than 50 proteins. In past decade, proteomics community has made significant strides in developing new technologies tailored studying surfaceome all its complexity. this review, we first dive into unique characteristics functions of emphasizing necessity specialized labeling, enrichment, proteomic approaches. An overview surfaceomics methods provided, detailing techniques measure protein expression how leads novel discovery. Next, highlight advances proximity labeling (PLP), showcasing various enzymatic photoaffinity can map protein-protein interactions membrane complexes on surface. We then review role extracellular post-translational modifications, focusing glycosylation, proteolytic remodeling, secretome. Finally, discuss identifying tumor-specific peptide MHC they have shaped therapeutic development. This emerging field neo-protein epitopes constantly evolving, where targets identified at proteome level encompass defined PTMs, complexes, dysregulated cellular tissue locations. Given functional importance biology therapy, view as a critical piece quest neo-epitope

Язык: Английский

---

Residue-Specific Incorporation of Noncanonical Amino Acids in Auxotrophic Hosts: Quo Vadis?

Chemical Reviews, Год журнала: 2025, Номер unknown

Опубликована: Май 16, 2025

The residue-specific incorporation of noncanonical amino acids in auxotrophic hosts allows the global exchange a canonical acid with its analog. Noncanonical are not encoded by standard genetic code, but they carry unique side chain chemistries, e.g., to perform bioorthogonal conjugation reactions or manipulate physicochemical properties protein such as folding and stability. method was introduced nearly 70 years ago is still widespread use because simplicity robustness. In our study, we review trends field during last two decades. We give an overview application for artificial post-translational modifications selective functionalization directed immobilization proteins. highlight analysis nascent proteomes engineering enzymes biomaterials, progress biosynthesis analogs. also discuss challenges scale-up technique.

Язык: Английский

---

Chemical proteomics for a comprehensive understanding of functional activity and the interactome

Chemical Society Reviews, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Chemoproteomics enables proteome-wide mapping of protein engagements and their functional characteristics depending on the chemical probes.

Язык: Английский

---