Cross-linking/mass spectrometry at the crossroads

Piersimoni, Lolita; Sinz, Andrea

doi:10.1007/s00216-020-02700-x

Cited by 40 publications

(39 citation statements)

References 32 publications

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“…Magenta lines indicate that these cross-linking constraints are satisfied by over 50% of the structures within each cluster. The calculated C α -C α distance of each pair of amino acids satisfies the cross-linking constraint if it is smaller than a certain threshold: ABAS < 17 Å 76 , EDC < 10 Å 26 , SDA < 15 Å 26 , TATA < 15 Å 77 , CBDPS < 28 Å 78 , BS 3 < 30 Å 79 .…”

Section: Resultsmentioning

confidence: 99%

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

Chen

Zaer

Drori

et al. 2020

Preprint

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The intrinsically disordered protein, α-synuclein, implicated in synaptic vesicle homeostasis and neurotransmitter release, is also associated with several neurodegenerative diseases. The different roles of α-synuclein are characterized by distinct structural states (membrane-bound, dimer, tetramer, oligomer, and fibril), which are originated from its various monomeric conformations. The pathological states, determined by the ensemble of α-synuclein monomer conformations and dynamic pathways of interconversion between dominant states, remain elusive due to their transient nature. Here, we use inter-dye distance distributions from bulk time-resolved Förster resonance energy transfer as restraints in discrete molecular dynamics simulations to map the conformational space of the α-synuclein monomer. We further confirm the generated conformational ensemble in orthogonal experiments utilizing far-UV circular dichroism and cross-linking mass spectrometry. Single-molecule protein-induced fluorescence enhancement measurements show that within this conformational ensemble, some of the conformations of α-synuclein are surprisingly stable, exhibiting conformational transitions slower than milliseconds. Our comprehensive analysis of the conformational ensemble reveals essential structural properties and potential conformations that promote its various functions in membrane interaction or oligomer and fibril formation.

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Section: Resultsmentioning

confidence: 99%

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

Chen

Zaer

Drori

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…Targeting the lysine residues is desirable due to their relatively high prevalence (~6% of all residues), their distribution across solvent-accessible protein surfaces, and the specificity of primary amine-targeting chemistries. Because it can be difficult to characterize the proteins with few or no lysine residues using these amine-reactive agents, other residues, like serine, threonines, and tyrosines, are also targeted for cross-linking [ 71 , 80 ]. The majority of recent studies have made use of non-cleavable cross-linkers and, thus, the DSS and BS3 have become the reagents of choice.…”

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

“… The generic workflow of cross-linking mass spectrometry (CLMS) experiments. ( a ) A wide range of samples (from purified proteins to intact tissues and organs) applicable to perform CLMS experiments [ 11 , 80 ]. ( b ) In a representative CLMS workflow, a selected linker is applied to the sample and the cross-linking reaction is carried out.…”

Section: Figurementioning

confidence: 99%

“…The cross-links can be also visualized by integrative modeling techniques. CLMS techniques convey the structural information in the form of distance restraints on single protein, protein complexes and allows to portray protein networks [ 11 , 80 , 81 , 82 ]. In this figure the structures of protein or peptides were prepared using BIOVIA Discovery Studio (Dassault Systèmes, BIOVIA Corp., San Diego, CA, USA) visualizer tool.…”

Section: Figurementioning

confidence: 99%

“… In addition to tools presented in this table other programs such as; XLSearch, ECL 2.0, MaxQuant, xTract, Protein Prospector, pQuant, mMass, CLMSVault, xVis, XlinkX, Mango, CLPM, Crux, DXMSMS, FINDX etc., can also be used for identification of cross-linked peptides [ 11 , 80 , 105 ]. …”

Section: Figurementioning

confidence: 99%

See 2 more Smart Citations

Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

et al. 2021

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The fundamentals of how protein–protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein–protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.

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Direct Observation of “Elongated” Conformational States in α‐Synuclein upon Liquid‐Liquid Phase Separation

et al. 2022

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α-Synuclein (α-syn) is an intrinsically disordered protein (IDP) that undergoes liquid-liquid phase separation (LLPS), fibrillation, and forms insoluble intracellular Lewy bodies in neurons, which are the hallmark of Parkinson's Disease (PD). Neurotoxicity precedes the formation of aggregates and might be related to α-syn LLPS. The molecular mechanisms underlying the early stages of LLPS are still elusive. To obtain structural insights into α-syn upon LLPS, we take advantage of cross-linking/mass spectrometry (XL-MS) and introduce an innovative approach, termed COM-PASS (COMPetitive PAiring StatisticS). In this work, we show that the conformational ensemble of α-syn shifts from a "hairpin-like" structure towards more "elongated" conformational states upon LLPS. We obtain insights into the critical initial stages of LLPS and establish a novel mass spectrometry-based approach that will aid to solve open questions in LLPS structural biology.

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Cross-linking/mass spectrometry at the crossroads

Cited by 40 publications

References 32 publications

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds

Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

Direct Observation of “Elongated” Conformational States in α‐Synuclein upon Liquid‐Liquid Phase Separation

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