SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis

Lima, Diogo Borges; Lima, Tatiani B.; Balbuena, Tiago Santana; Neves-Ferreira, Ana Gisele C.; Barbosa, Valmir C.; Gozzo, Fábio C.; Carvalho, Paulo C.

doi:10.1016/j.jprot.2015.01.013

Cited by 88 publications

(64 citation statements)

References 20 publications

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“…Proteins with at least 2 identified peptides along with human IL-8 and HofQ sequences were included into the crosslinked peptide search along with the reversed-sequence counterparts. The search was performed with SIM-XL software 1.2.0.3 [46]. BS3 was defined as the crosslinking agent, and carbamidomethylation of cysteine and oxidation of methionine were defined as the fixed and variable modifications, respectively.…”

Section: Methodsmentioning

confidence: 99%

Interactions between the Aggregatibacter actinomycetemcomitans secretin HofQ and host cytokines indicate a link between natural competence and interleukin-8 uptake

et al. 2018

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Naturally competent bacteria acquire DNA from their surroundings to survive in nutrient-poor environments and incorporate DNA into their genomes as new genes for improved survival. The secretin HofQ from the oral pathogen Aggregatibacter actinomycetemcomitans has been associated with DNA uptake. Cytokine sequestering is a potential virulence mechanism in various bacteria and may modulate both host defense and bacterial physiology. The objective of this study was to elucidate a possible connection between natural competence and cytokine uptake in A. actinomycetemcomitans. The extramembranous domain of HofQ (emHofQ) was shown to interact with various cytokines, of which IL-8 exhibited the strongest interaction. The dissociation constant between emHofQ and IL-8 was 43 nM in static settings and 2.4 μM in dynamic settings. The moderate binding affinity is consistent with the hypothesis that emHofQ recognizes cytokines before transporting them into the cells. The interaction site was identified via crosslinking and mutational analysis. By structural comparison, relateda type I KH domain with a similar interaction site was detected in the Neisseria meningitidis secretin PilQ, which has been shown to participate in IL-8 uptake. Deletion of hofQ from the A. actinomycetemcomitans genome decreased the overall biofilm formation of this organism, abolished the response to cytokines, i.e., decreased eDNA levels in the presence of cytokines, and increased the susceptibility of the biofilm to tested β-lactams. Moreover, we showed that recombinant IL-8 interacted with DNA. These results can be used in further studies on the specific role of cytokine uptake in bacterial virulence without interfering with natural-competence-related DNA uptake.

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Section: Methodsmentioning

confidence: 99%

Interactions between the Aggregatibacter actinomycetemcomitans secretin HofQ and host cytokines indicate a link between natural competence and interleukin-8 uptake

et al. 2018

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“…In another case, assumptions can be made based on the acquired fragment spectra (an MS/MS-level approach). For example, one method requires that evidence of a dead-ended version of a crosslinked individual peptide should be observable (19). This idea is based on the assumption that crosslinking chemistries will always generate a distribution of all product types, with the actual crosslinking event itself occurring with a relatively low abundance.…”

Section: Methodsmentioning

confidence: 99%

“…However, useful informatics routines are essential for gaining access to quality crosslinking information as site identification is not a trivial problem (15). Some noteworthy tools that have emerged in the last few years include xQuest (16), Merox (17), Stavrox (18), Sim-XL (19), pLink (20), XlinkX (21), and XiQ (22). The proliferation of such tools is a strong indication that new XL reagents and methods require dynamic software development to accommodate the needs of challenging structural applications.…”

mentioning

confidence: 99%

High Sensitivity Crosslink Detection Coupled With Integrative Structure Modeling in the Mass Spec Studio

Sarpe

Rafiei

Hepburn

et al. 2016

Molecular & Cellular Proteomics

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The Mass Spec Studio package was designed to support the extraction of hydrogen-deuterium exchange and covalent labeling data for a range of mass spectrometry (MS)-based workflows, to integrate with restraint-driven protein modeling activities. In this report, we present an extension of the underlying Studio framework and provide a plug-in for crosslink (XL) detection. To accommodate flexibility in XL methods and applications, while maintaining efficient data processing, the plug-in employs a peptide library reduction strategy via a presearch of the tandem-MS data. We demonstrate that prescoring linear unmodified peptide tags using a probabilistic approach substantially reduces search space by requiring both crosslinked peptides to generate sparse data attributable to their linear forms. The method demonstrates highly sensitive crosslink peptide identification with a low false positive rate. Integration with a Haddock plug-in provides a resource that can combine multiple sources of data for protein modeling activities. We generated a structural model of porcine transferrin bound to TbpB, a membranebound receptor essential for iron acquisition in Actinobacillus pleuropneumoniae. Using mutational data and crosslinking restraints, we confirm the mechanism by which TbpB recognizes the iron-loaded form of transferrin, and note the requirement for disparate sources of restraint data for accurate model construction. The software plugin is freely available at www.msstudio. Integrative methods in structural biology use data from disparate sources to generate accurate models of large protein structures and assemblies (1). In this way, the reach of classical structure providers such as x-ray crystallography and NMR can be extended. Biophysical data with an underlying spatial component can be combined with "building block" structures in a molecular modeling framework, to generate high-fidelity models of systems of impressive size and complexity (2-5). Mass spectrometry can provide rich sets of data in support these activities, in the form of topographical footprints (covalent labeling, CL) 1 (6 -8), conformational dynamics (hydrogen/deuterium exchange, HX) (9, 10) and distance restraints (crosslinking, XL) (11-13). We have built informatics routines within the Mass Spec Studio framework to mine restraints from both CL and HX data (14), to support such data-driven molecular modeling activities. In this study, we describe a new plug-in built into the Studio for identifying crosslinks from LC-MS/MS data sets.Advances in instrumentation, methods and cross-linking protocols have generated renewed interest in what is an older technique. However, useful informatics routines are essential for gaining access to quality crosslinking information as site identification is not a trivial problem (15). Some noteworthy tools that have emerged in the last few years include xQuest (16), Merox (17), Stavrox (18), pLink (20), XlinkX (21), and XiQ (22). The proliferation of such tools is a strong indication that new XL reagents and methods re...

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“…Recently, a user-friendly program (SIM-XL) was developed for structural protein characterization by using peptide cross-linking analysis method for tandem mass spectrometric data [18]. In proteomics studies, a GUI program (IPeak) also presented for identification of the peptides data obtained from LC-MS/MS method [19]. To identify TLC (Thin Layer Chromatography) information from MSI (Mass Spectrometry Imaging) data sets, a program (DetectTLC) was developed [20].…”

Section: Background and Theorymentioning

confidence: 99%

Chemical Analysis Program for the Time of Flight Mass Spectrometry System

Kepceoğlu

Kılıç

2016

International Journal of Applied Mathematics, Electronics and Computers

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Abstract:In this work, we present a computer program that reads, manipulates, analyses and stores the mass spectra obtained by using Laser Time of Flight Mass Spectrometry (L-TOF-MS) system described elsewhere. This program allows users to record the characteristic parameters of experimental data such as vacuum pressure, voltages, laser power, sample name etc. both manually and automatically. Also, the obtained mass spectra can be used to investigate chemical substances (NO x , SO x , organic molecules etc.) or can be used to real time identification of the sample differences for given material database (metal oxides, alloys, paintings, healthy and cancerous tissues etc.) by using different mathematical and statistical procedures (PCA, LDA, kNN etc.). We have recently presented a simple chemical analysis procedure by starting from reading raw MS data from oscilloscope using TCP/IP protocol and following data processing steps. We have a great success to reduce the numbers of steps and time duration consumed for the following procedure.

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SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis

Cited by 88 publications

References 20 publications

Interactions between the Aggregatibacter actinomycetemcomitans secretin HofQ and host cytokines indicate a link between natural competence and interleukin-8 uptake

Interactions between the Aggregatibacter actinomycetemcomitans secretin HofQ and host cytokines indicate a link between natural competence and interleukin-8 uptake

High Sensitivity Crosslink Detection Coupled With Integrative Structure Modeling in the Mass Spec Studio

Chemical Analysis Program for the Time of Flight Mass Spectrometry System

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