Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks DOI Open Access
Clinton Yu,

Eric J. Novitsky,

Xiaorong Wang

et al.

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

Published: Aug. 7, 2024

Cross-linking mass spectrometry (XL-MS) is a powerful technology for mapping protein-protein interactions (PPIs) at the systems-level. By covalently connecting pairs of proximal residues, cross-linking reagents provide distance restraints to infer protein conformations and interaction interfaces. While binary cross-links have been remarkably informative, multimeric can offer enhanced spatial resolution facilitate characterization dynamic heterogeneous complexes. However, identification remains extremely challenging due fragmentation complexity vast expansion database search space. Here, we present novel trioxane-based MS-cleavable homotrifunctional cross-linker TSTO, which target three lysine residues simultaneously. Owing its unique structure MS-cleavability, TSTO enables fast unambiguous cross-linked peptides using LC-MS

Language: Английский

Preserved respiratory chain capacity and physiology in mice with profoundly reduced levels of mitochondrial respirasomes DOI Creative Commons
Dusanka Milenkovic, Jelena Misic, Johannes F. Hevler

et al.

Cell Metabolism, Journal Year: 2023, Volume and Issue: 35(10), P. 1799 - 1813.e7

Published: Aug. 25, 2023

The mammalian respiratory chain complexes I, III

Language: Английский

Citations

38
New advances in cross-linking mass spectrometry toward structural systems biology DOI Open Access
Clinton Yu, Lan Huang

Current Opinion in Chemical Biology, Journal Year: 2023, Volume and Issue: 76, P. 102357 - 102357

Published: July 3, 2023

Language: Английский

Citations

27
Mapping protein–protein interactions by mass spectrometry DOI Creative Commons
Xiaonan Liu, Lawrence Abad,

Lopamudra Chatterjee

et al.

Mass Spectrometry Reviews, Journal Year: 2024, Volume and Issue: unknown

Published: May 14, 2024

Abstract Protein–protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization function of proteome, their perturbation is associated with various diseases, such as cancer, neurodegeneration, infectious diseases. Recent advances mass spectrometry (MS)‐based protein interactomics have significantly expanded our understanding PPIs cells, techniques that continue to improve terms sensitivity, specificity providing new opportunities study diverse systems. These differ depending on type interaction being studied, each approach having its set advantages, disadvantages, applicability. This review highlights recent enrichment methodologies interactomes before MS analysis compares unique features specifications. It emphasizes prospects further improvement potential applications advancing knowledge contexts.

Language: Английский

Citations

10
SHARK‐capture identifies functional motifs in intrinsically disordered protein regions DOI Creative Commons
Chi Fung Willis Chow, Swantje Lenz, Maxim Scheremetjew

et al.

Protein Science, Journal Year: 2025, Volume and Issue: 34(4)

Published: March 18, 2025

Abstract Increasing insights into how sequence motifs in intrinsically disordered regions (IDRs) provide functions underscore the need for systematic motif detection. Contrary to structured where can be readily identified from alignments, rapid evolution of IDRs limits usage alignment‐based tools reliably detecting within. Here, we developed SHARK‐capture, an alignment‐free detection tool designed difficult‐to‐align regions. SHARK‐capture innovates on word‐based methods by flexibly incorporating amino acid physicochemistry assess similarity without requiring rigid definitions equivalency groups. offers consistently strong performance a benchmark, with superior residue‐level performance. known functional across orthologs microtubule‐associated zinc finger protein BuGZ. We also short IDR S. cerevisiae RNA helicase Ded1p, which experimentally verified capable promoting ATPase activity. Our improved allows us systematically calculate 10,889 2695 yeast and it as resource. most precise yet identification conserved is freely available Python package ( https://pypi.org/project/bio-shark/ ) https://git.mpi-cbg.de/tothpetroczylab/shark .

Language: Английский

Citations

1
Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation DOI Creative Commons

Temiloluwa Majekodunmi,

Dustin Britton, Jin Kim Montclare

et al.

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(15), P. 9113 - 9135

Published: July 15, 2024

The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire available protein structures chemistries. Through residue-specific incorporation, properties can be globally modified, resulting in creation novel with diverse tailored characteristics. In this review, we highlight recent advancements techniques as well applications engineered materials. Specifically, discuss their utility bio-orthogonal acid tagging (BONCAT), fluorescent (FUNCAT), threonine-derived (THRONCAT), cross-linking, fluorination, enzyme engineering. This review underscores importance a tool for development to meet research industrial needs.

Language: Английский

Citations

7
High throughput methods to study protein-protein interactions during host-pathogen interactions DOI Creative Commons
Giridhar Chandrasekharan, Meera Unnikrishnan

European Journal of Cell Biology, Journal Year: 2024, Volume and Issue: 103(2), P. 151393 - 151393

Published: Jan. 24, 2024

The ability of a pathogen to survive and cause an infection is often determined by specific interactions between the host proteins. Such can be both intra- extracellular may define outcome infection. There are range innovative biochemical, biophysical bioinformatic techniques currently available identify protein-protein (PPI) pathogen. However, complexity diversity host-pathogen PPIs has led development several high throughput (HT) that enable study multiple at once and/or screen samples same time, in unbiased manner. We review here major HT laboratory-based technologies employed for host-bacterial interaction studies.

Language: Английский

Citations

6
Chemical cross-linking and mass spectrometry enabled systems-level structural biology DOI
Luke Botticelli, Anna Bakhtina,

Nathan K. Kaiser

et al.

Current Opinion in Structural Biology, Journal Year: 2024, Volume and Issue: 87, P. 102872 - 102872

Published: June 26, 2024

Language: Английский

Citations

6
FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Data Sets Built on FragPipe DOI
Edgar Manriquez‐Sandoval, J. P. N. Brewer, Gabriela Lule

et al.

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: 23(7), P. 2332 - 2342

Published: May 24, 2024

Here, we present FLiPPR, or FragPipe LiP (limited proteolysis) Processor, a tool that facilitates the analysis of data from limited proteolysis mass spectrometry (LiP-MS) experiments following primary search and quantification in FragPipe. LiP-MS has emerged as method can provide proteome-wide information on protein structure been applied to range biological biophysical questions. Although be carried out with standard laboratory reagents spectrometers, analyzing slow poses unique challenges compared typical quantitative proteomics workflows. To address this, leverage then process its output FLiPPR. FLiPPR formalizes specific imputation heuristic carefully uses missing report most significant structural changes. Moreover, introduces merging scheme protein-centric multiple hypothesis correction scheme, enabling processed sets more robust less redundant. These improvements strengthen statistical trends when previously published are reanalyzed FragPipe/FLiPPR workflow. We hope will lower barrier for users adopt LiP-MS, standardize procedures analysis, systematize facilitate eventual larger-scale integration data.

Language: Английский

Citations

5
DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples DOI
Fenglong Jiao, Clinton Yu,

Andrew Wheat

et al.

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: 23(8), P. 3269 - 3279

Published: Feb. 9, 2024

Protein–protein interactions (PPIs) are fundamental to understanding biological systems as protein complexes the active molecular modules critical for carrying out cellular functions. Dysfunctional PPIs have been associated with various diseases including cancer. Systems-wide PPI analysis not only sheds light on pathological mechanisms, but also represents a paradigm in identifying potential therapeutic targets. In recent years, cross-linking mass spectrometry (XL-MS) has emerged powerful tool defining endogenous of networks. While proteome-wide studies performed cell lysates, intact cells and tissues, applications XL-MS clinical samples reported. this study, we adopted DSBSO-based vivo platform map interaction landscapes from two breast cancer patient-derived xenograft (PDX) models. As result, generated PDX network comprising 2,557 human proteins identified unique subtypes. Interestingly, most observed differences correlated well abundance changes determined by TMT-based proteome quantitation. Collectively, work demonstrated feasibility samples, established an analytical workflow tissue that can be generalized mapping patient future dissect disease-relevant

Language: Английский

Citations

4
Emerging Approaches to Investigating Functional Protein Dynamics in Modular Redox Enzymes: Nitric Oxide Synthase as a Model System DOI Creative Commons
Ting Jiang, Megan C. Thielges, Changjian Feng

et al.

Journal of Biological Chemistry, Journal Year: 2025, Volume and Issue: unknown, P. 108282 - 108282

Published: Feb. 1, 2025

Language: Английский

Citations

0