Mapping the Ca2+ induced structural change in calreticulin

Boelt, Sanne Grundvad; Norn, Christoffer; Rasmussen, Morten; André, Ingemar; Čiplys, Evaldas; Slibinskas, Rimantas; Højrup, Peter

doi:10.1016/j.jprot.2016.05.015

Cited by 36 publications

(36 citation statements)

References 48 publications

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“…Cross‐linking analyzed by mass spectrometry has become an important actor in this proces. This is illustrated by the plentitude of published studies in which cross‐linking was used to analyse protein complexes such as the study of the interaction partners and dynamics of the cannabinoid receptors, the investigation of the interaction network of human protein kinase D2, analysis of Ca 2+ ‐induced changes in calreticulin, unravelling of the architecture of the human polycomb respressive complex 2, and many others.…”

Section: Discussionmentioning

confidence: 99%

Cross‐linked peptide identification: A computational forest of algorithms

Yılmaz

Shiferaw

Rayó

et al. 2018

Mass Spectrometry Reviews

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Chemical cross-linking analyzed by mass spectrometry (XL-MS) has become an important tool in unravelling protein structure, dynamics, and complex formation. Because the analysis of cross-linked proteins with mass spectrometry results in specific computational challenges, many computational tools have been developed to identify cross-linked peptides from mass spectra and subsequently interpret the identified cross-links within their structural context. In this review, we will provide an overview of the different tools that are currently available to tackle the computational part of an XL-MS experiment. First, we give an introduction on the computational challenges encountered when processing data from a cross-linking experiment. We then discuss available tools to identify peptides that are linked by intact or MS-cleavable cross-linkers, and we provide an overview of tools to interpret cross-linked peptides in the context of protein structure. Finally, we give an outlook on data management and dissemination challenges and opportunities for cross-linking experiments.

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Section: Discussionmentioning

confidence: 99%

Cross‐linked peptide identification: A computational forest of algorithms

Yılmaz

Shiferaw

Rayó

et al. 2018

Mass Spectrometry Reviews

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“…Since then, efforts have been made to automate this approach with XiQ 45 , xTract 48 and incorporation into MaxQuant . Other applications of this technology have shown large conformational rearrangements that occur in the proteasome during particle assembly 50 , the regulation of enzymes 48,51,52 and the regulation of protein interactions 53,54 .…”

Section: Quantitative Clms For Comparative Studiesmentioning

confidence: 99%

Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology

O’Reilly

Rappsilber

2018

Nat Struct Mol Biol

280

252

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Over the last decade, cross-linking/mass spectrometry (CLMS) has developed into a robust and flexible tool that provides medium-resolution structural information on previously intractable protein complexes and and their interactions. CLMS data describes the proximity of amino acid residues and therefore information on the fold of proteins, and the topology of their complexes. Here, we describe notable successes of this technique and common pipelines. Novel CLMS applications such as in-cell cross-linking, probing conformational changes and tertiary structure determination are beginning to make large contributions to molecular biology and the emerging fields of structural systems biology and interactomics.

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“…Based on the crystallografic analysis of a construct containing the N-domain (residues 18–204) and the N-terminal half of the C-domain (residues 299–368) of human CALR connected by a GSG tripeptide but lacking the entire P-domain and C-terminal tail of the C-domain (see below), MoRF1 and MoRF4 are integral parts of the core region of CALR and unlikely to change conformation unless the entire core region is rearranged. Although, the core retains its overall structure both in the presence and absence of Ca 2+ (Boelt et al, 2016 ), this possibility is theoretically possible and deserves to be further investigated. Since MoRF2 is located in a region that serves as a switch between the closed and open conformation [at least in the CALR from two distinct parasites, Trypanosoma cruzi (TcCALR) and Entamoeba histolytica (EhCALR; Moreau et al, 2016 )], this molecular recognition feature clearly deserves further analysis.…”

Section: Structural Features Of Normal Human Calrmentioning

confidence: 99%

Calreticulin: Challenges Posed by the Intrinsically Disordered Nature of Calreticulin to the Study of Its Function

Varricchio

Falchi

Dall’Ora

et al. 2017

Front. Cell Dev. Biol.

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Calreticulin is a Ca2+-binding chaperone protein, which resides mainly in the endoplasmic reticulum but also found in other cellular compartments including the plasma membrane. In addition to Ca2+, calreticulin binds and regulates almost all proteins and most of the mRNAs deciding their intracellular fate. The potential functions of calreticulin are so numerous that identification of all of them is becoming a nightmare. Still the recent discovery that patients affected by the Philadelphia-negative myeloproliferative disorders essential thrombocytemia or primary myelofibrosis not harboring JAK2 mutations carry instead calreticulin mutations disrupting its C-terminal domain has highlighted the clinical need to gain a deeper understanding of the biological activity of this protein. However, by contrast with other proteins, such as enzymes or transcription factors, the biological functions of which are strictly defined by a stable spatial structure imprinted by their amino acid sequence, calreticulin contains intrinsically disordered regions, the structure of which represents a highly dynamic conformational ensemble characterized by constant changes between several metastable conformations in response to a variety of environmental cues. This article will illustrate the Theory of calreticulin as an intrinsically disordered protein and discuss the Hypothesis that the dynamic conformational changes to which calreticulin may be subjected by environmental cues, by promoting or restricting the exposure of its active sites, may affect its function under normal and pathological conditions.

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Mapping the Ca2+ induced structural change in calreticulin

Cited by 36 publications

References 48 publications

Cross‐linked peptide identification: A computational forest of algorithms

Cross‐linked peptide identification: A computational forest of algorithms

Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology

Calreticulin: Challenges Posed by the Intrinsically Disordered Nature of Calreticulin to the Study of Its Function

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