Advances in protein complex analysis by chemical cross-linking coupled with mass spectrometry (CXMS) and bioinformatics

Tran, Bao; Goodlett, David R.; Goo, Young Ah

doi:10.1016/j.bbapap.2015.05.015

Cited by 34 publications

(34 citation statements)

References 81 publications

(132 reference statements)

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“…This was not surprising since RPA alone (23), and probably the Cdc45–RPA complex as well, are highly flexible. Other MS methods can theoretically also provide information about the mutual binding sites (64). We identified four peptides of Cdc45 that might reveal a contact interface with RPA, situated in domain I (Figure 6A, Supplementary Figure S6B), and one peptide placed in the DBD_A subdomain of RPA70 potentially involved in interaction with Cdc45 (Figure 6A, Supplementary Figure S6B).…”

Section: Resultsmentioning

confidence: 99%

Cdc45-induced loading of human RPA onto single-stranded DNA

et al. 2017

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Cell division cycle protein 45 (Cdc45) is an essential component of the eukaryotic replicative DNA helicase. We found that human Cdc45 forms a complex with the single-stranded DNA (ssDNA) binding protein RPA. Moreover, it actively loads RPA onto nascent ssDNA. Pull-down assays and surface plasmon resonance studies revealed that Cdc45-bound RPA complexed with ssDNA in the 8–10 nucleotide binding mode, but dissociated when RPA covered a 30-mer. Real-time analysis of RPA-ssDNA binding demonstrated that Cdc45 catalytically loaded RPA onto ssDNA. This placement reaction required physical contacts of Cdc45 with the RPA70A subdomain. Our results imply that Cdc45 controlled stabilization of the 8-nt RPA binding mode, the subsequent RPA transition into 30-mer mode and facilitated an ordered binding to ssDNA. We propose that a Cdc45-mediated loading guarantees a seamless deposition of RPA on newly emerging ssDNA at the nascent replication fork.

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Section: Resultsmentioning

confidence: 99%

Cdc45-induced loading of human RPA onto single-stranded DNA

et al. 2017

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“…Another chemical modification procedure that provides structural information is chemical cross-linking (CX-MS) introduced by Rappsilber, Siniossoglou, Hurt, and Mann (2000) and Young et al (2000), and recently reviewed in Petrotchenko and Borchers (2010), Rappsilber (2011), Leitner et al (2014, Ramisetty andWashburn (2011), Sinz, Arlt, Chorev, and and Tran, Goodlett, and Goo (2015). In this method, two amino acids are connected to each other through a reagent with two (or more) reactive side groups.…”

Section: Falick and Komivesmentioning

confidence: 99%

“…Time series at which proteins become labelled in vivo (SILAC) or at which isolated protein samples are labelled by in vitro methods (see Section 2.3) may detect temporary interactions in multiplexed tandem MS analyses (Ramisetty & Washburn, 2011). These interactions can be 'frozen' by in vivo or in vitro cross-linking (Tran et al, 2015). The detailed inspection of crosslinked peptides permits the pinpointing of contact sides between the different proteins.…”

Section: The Far From Complete Picture Of Interaction Partners Andmentioning

confidence: 99%

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Bacterial Electron Transfer Chains Primed by Proteomics

Wessels¹,

Almeida²,

Kartal³

et al. 2016

Advances in Bacterial Electron Transport Systems and Their Regulation

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Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.

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“…To gain insight into the structure and interactions of YjbH with Spx we have in this study applied structural modeling combined with chemical crosslinking and mass spectrometry (CXMS), the combination of the three forming a powerful and complementary tool that can provide information about native protein structure and the topology of protein complexes, without the need to raise crystals and with a requirement of only low amounts of protein. In this study, proteins were treated with bifunctional crosslinking reagents that create a covalent link between proximal lysine residues, digested with trypsin, analyzed by mass spectrometry and crosslinks identified.…”

Section: Introductionmentioning

confidence: 99%

Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry

et al. 2016

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Adaptor proteins assist proteases in degrading specific proteins under appropriate conditions. The adaptor protein YjbH promotes the degradation of an important global transcriptional regulator Spx, which controls the expression of hundreds of genes and operons in response to thiol-specific oxidative stress in Bacillus subtilis. Under normal growth conditions, the transcription factor is bound to the adaptor protein and therefore degraded by the AAA+ protease ClpXP. If this binding is alleviated during stress, the transcription factor accumulates and turns on genes encoding stress-alleviating proteins. The adaptor protein YjbH is thus a key player involved in these interactions but its structure is unknown. To gain insight into its structure and interactions we have used chemical crosslinking mass spectrometry. Distance constraints obtained from the crosslinked monomer were used to select and validate a structure model of YjbH and then to probe its interactions with other proteins. The core structure of YjbH is reminiscent of DsbA family proteins. One lysine residue in YjbH (K177), located in one of the α-helices outside the thioredoxin fold, crosslinked to both Spx K99 and Spx K117, thereby suggesting one side of the YjbH for the interaction with Spx. Another lysine residue that crosslinked to Spx was YjbH K5, located in the long and presumably very flexible N-terminal arm of YjbH. Our crosslinking data lend support to a model proposed based on site-directed mutagenesis where the YjbH interaction with Spx can stabilize and present the C-terminal region of Spx for protease recognition and proteolysis. Proteins 2016; 84:1234-1245. © 2016 Wiley Periodicals, Inc.

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Advances in protein complex analysis by chemical cross-linking coupled with mass spectrometry (CXMS) and bioinformatics

Cited by 34 publications

References 81 publications

Cdc45-induced loading of human RPA onto single-stranded DNA

Cdc45-induced loading of human RPA onto single-stranded DNA

Bacterial Electron Transfer Chains Primed by Proteomics

Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry

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