Chemical cross-linking of the urease complex from Helicobacter pylori and analysis by Fourier transform ion cyclotron resonance mass spectrometry and molecular modeling

Carlsohn, Elisabet; Ångström, Jonas; Emmett, Mark R.; Marshall, Alan G.; Nilsson, Carol L.

doi:10.1016/j.ijms.2004.02.021

Cited by 10 publications

(7 citation statements)

References 46 publications

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“…With its ultrahigh resolution and mass accuracy FTICR-MS offers the possibility of unambiguously identifying cross-linked species based only on accurate mass measurements (Carlsohn et al, 2004;Schulz et al, 2004). With the newest Q-TOF instruments, however, which offer mass accuracies that begin to approach those of FTICR mass spectrometers, it might be feasible to analyze cross-linked products with similar mass accuracy.…”

Section: Bottom-up and Top-down Analysis By Esi-fticr-msmentioning

confidence: 99%

Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Sinz

2006

Mass Spectrometry Reviews

608

597

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Closely related to studying the function of a protein is the analysis of its three-dimensional structure and the identification of interaction sites with its binding partners. An alternative approach to the high-resolution methods for three-dimensional protein structure analysis, such as X-ray crystallography and NMR spectroscopy, consists of covalently connecting two functional groups of the protein(s) under investigation. The location of the created cross-links imposes a distance constraint on the location of the respective side chains and allows one to draw conclusions on the three-dimensional structure of the protein or a protein complex. Recently, chemical cross-linking of proteins has been combined with a mass spectrometric analysis of the created cross-linked products. This review article describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the different available strategies that employ chemical cross-linking and different mass spectrometric techniques. The challenges for mass spectrometry caused by the enormous complexity of the cross-linking reaction mixtures are emphasized. The various approaches described in the literature to facilitate the mass spectrometric detection of cross-linked products as well as computer software for data analyses are reviewed.

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Section: Bottom-up and Top-down Analysis By Esi-fticr-msmentioning

confidence: 99%

Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Sinz

2006

Mass Spectrometry Reviews

608

597

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“…Different approaches have been explored to take advantage of probing information. Cross‐linking data have been successfully used in the study of complex assemblies to guide docking experiments in which high‐resolution structures were available for the individual subunits and their interaction surfaces were modeled according to intersubunit constraints 181–184. More frequently, however, probing information is used directly to support the generation of actual models, or indirectly to guide the selection of the most representative structure among a library of plausible models.…”

Section: Utilization Of Spatial Constraints From Probing Datamentioning

confidence: 99%

“…Utilizing solved high‐resolution subunits to assemble full‐fledged structures through docking or simulated annealing is rapidly emerging as one of the strategies of choice for maximizing the benefits of structural probing 181–184. This strategy is capable of producing results that are comparable with those obtained by established structural methods, as demonstrated by the elucidation of the Ffh–FtsY complexes of Escherichia coli and Thermophilus aquaticus , which were tackled by using the amine‐specific cross‐linkers DSS and bis(sulfosuccinimidyl)adipate (BSSA) (Fig.…”

Section: The Rewards Of Structural Probingmentioning

confidence: 99%

Elucidating the higher‐order structure of biopolymers by structural probing and mass spectrometry: MS3D

Fabris

2010

J. Mass Spectrom.

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Chemical probing represents a very versatile alternative for studying the structure and dynamics of substrates that are intractable by established high-resolution techniques. The implementation of MS-based strategies for the characterization of probing products has not only extended the range of applicability to virtually all types of biopolymers, but has also paved the way for the introduction of new reagents that would not have been viable with traditional analytical platforms. As the availability of probing data is steadily increasing on the wings of the development of dedicated interpretation aids, powerful computational approaches have been explored to enable the effective utilization of such information to generate valid molecular models. This combination of factors has contributed to making the possibility of obtaining actual 3D structures by MS-based technologies (MS3D) a reality. Although approaches for achieving structure determination of unknown substrates or assessing the dynamics of known structures may share similar reagents and development trajectories, they clearly involve distinctive experimental strategies, analytical concerns, and interpretation paradigms. This Perspective offers a commentary on methods aimed at obtaining distance constraints for the modeling of full-fledged structures, while highlighting common elements, salient distinctions, and complementary capabilities exhibited by methods employed in dynamics studies. We discuss critical factors to be addressed for completing effective structural determinations and expose possible pitfalls of chemical methods. We survey programs developed for facilitating the interpretation of experimental data and discuss possible computational strategies for translating sparse spatial constraints into all-atom models. Examples are provided to illustrate how the concerted application of very diverse probing techniques can lead to the solution of actual biological substrates.

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“…Since then, the developments in MS have greatly promoted the application of crosslinking in structural biology 7–9. Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) has been shown to be a powerful tool for analyzing crosslinking in reaction mixtures, owing to its high sensitivity, high mass accuracy, high resolving power, and the availability of multiple fragmentation techniques 10–15. The combination of chemical crosslinking with FTICR MS not only yields information about protein–protein interactions but also reveals which residues within protein complexes are close to one another in space.…”

Section: Introductionmentioning

confidence: 99%

Protein flexibility is key to cisplatin crosslinking in calmodulin

Wells

Jimenez‐Roldan

et al. 2012

Protein Science

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Chemical crosslinking in combination with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) has significant potential for studying protein structures and protein-protein interactions. Previously, cisplatin has been shown to be a crosslinker and crosslinks multiple methionine (Met) residues in apo-calmodulin (apo-CaM). However, the interresidue distances obtained from nuclear magnetic resonance structures are inconsistent with the measured distance constraints by crosslinking. Met residues lie too far apart to be crosslinked by cisplatin. Here, by combining FTICR MS with a novel computational flexibility analysis, the flexible nature of the CaM structure is found to be key to cisplatin crosslinking in CaM. It is found that the side chains of Met residues can be brought together by flexible motions in both apo-CaM and calcium-bound CaM (Ca 4 -CaM). The possibility of cisplatin crosslinking Ca 4 -CaM is then confirmed by MS data. Therefore, flexibility analysis as a fast and low-cost computational method can be a useful tool for predicting crosslinking pairs in protein crosslinking analysis and facilitating MS data analysis. Finally, flexibility analysis also indicates that the crosslinking of platinum to pairs of Met residues will effectively close the nonpolar groove and thus will likely interfere with the binding of CaM to its protein targets, as was proved by comparing assays for cisplatin-modified/unmodified CaM binding to melittin. Collectively, these results suggest that cisplatin crosslinking of apo-CaM or Ca 4 -CaM can inhibit the ability of CaM to recognize its target proteins, which may have important implications for understanding the mechanism of tumor resistance to platinum anticancer drugs.

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Chemical cross-linking of the urease complex from Helicobacter pylori and analysis by Fourier transform ion cyclotron resonance mass spectrometry and molecular modeling

Cited by 10 publications

References 46 publications

Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Elucidating the higher‐order structure of biopolymers by structural probing and mass spectrometry: MS3D

Protein flexibility is key to cisplatin crosslinking in calmodulin

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