Protein dynamics and conformational changes explored by hydrogen/deuterium exchange mass spectrometry

Zheng, Jie; Strutzenberg, Timothy S.; Pascal, Bruce D.; Griffin, Patrick R.

doi:10.1016/j.sbi.2019.06.007

Cited by 72 publications

(60 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, the protocol for partial denaturation requires optimisation for each complex and can fail for proteins that are resistant to mild denaturants or precipitate easily upon denaturation. Other solution-phase methods exist to study higherorder protein structure by subsequent MS analysis, for example chemical crosslinking, 54 protein footprinting methods including fast photochemical oxidation of proteins (FPOP), 16 and hydrogen-deuterium exchange; [55][56][57][58] however, these are beyond the scope of this perspective. Integration of information from different native and non-native techniques can provide valuable structural insights.…”

Section: Native Mass Spectrometry Of Protein Complexesmentioning

confidence: 99%

Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry

et al. 2020

View full text Add to dashboard Cite

show abstract

Section: Native Mass Spectrometry Of Protein Complexesmentioning

confidence: 99%

Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry

et al. 2020

View full text Add to dashboard Cite

show abstract

“…1A). 63 Using this combination of techniques, we show how the C-terminal extensions confer distinct Tier-0 dynamics to the structural core in a manner specific to their three-dimensional orientation. This arrangement also dictates specific geometrical criteria, crucial for establishing specific ligand interactions, all of which we detail in this work.…”

Section: Introductionmentioning

confidence: 98%

Evolution of structural dynamics in bilobed proteins

Gouridis¹,

Muthahari²,

Boer³

et al. 2020

Preprint

View full text Add to dashboard Cite

Novel biophysical tools allow the structural dynamics of proteins, and the regulation of such dynamics by binding partners, to be explored in unprecedented detail. Although this has provided critical insights into protein function, the means by which structural dynamics direct protein evolution remains poorly understood. Here, we investigated how proteins with a bilobed structure, composed of two related domains from the type-II periplasmic binding protein domain family, have undergone divergent evolution leading to modification of their structural dynamics and function. We performed a structural analysis of ~600 bilobed proteins with a common primordial structural core, which we complemented with biophysical studies to explore the structural dynamics of selected examples by single-molecule Foerster resonance energy transfer and Hydrogen-Deuterium exchange mass spectrometry. We show that evolutionary modifications of the structural core, largely at its termini, enables distinct structural dynamics, allowing the diversification of these proteins into transcription factors, enzymes, and extra-cytoplasmic transport-related proteins. Structural embellishments of the core created new interdomain interactions that stabilized structural states, reshaping the active site geometry, and ultimately, altered substrate specificity. Our findings reveal an as yet unrecognized mechanism for the emergence of functional promiscuity during long periods of protein evolution and are applicable to a large number of domain architectures.

show abstract

“…The structural MS toolbox contains multiple complementary approaches. Next to native MS and top-down MS, a variety of peptide-centric MS methods, such as thermal proteome profiling (TPP), limited proteolysis (LiP), hydrogen/deuterium exchange (HDX) MS and chemical cross-linking MS (XL-MS or CLMS), have emerged and enabled structural studies of a wide range of biomolecules (Feng et al, 2014;Heck, 2008;Leitner et al, 2010;Savitski et al, 2014;Zheng et al, 2019). With recent advances in instrumentation, sample preparation, and data analysis, especially XL-MS has started to fulfill its potential to complement well established structural methods such as X-ray crystallography, nuclear magnetic resonance spectroscopy (NMR), and cryo-electron microscopy (cryo-EM) (Leitner et al, 2016;Matthew Allen Bullock et al, 2016;Rappsilber, 2011).…”

Section: Introductionmentioning

confidence: 99%

Selective cross-linking of coinciding protein assemblies by in-gel cross-linking mass-spectrometry

Hevler

Lukassen

Cabrera‐Orefice

et al. 2020

Preprint

View full text Add to dashboard Cite

Cross-linking mass spectrometry has developed into an important method to study protein structures and interactions. The in-solution cross-linking workflows involve time and sample consuming steps and do not provide sensible solutions for differentiating cross-links obtained from co-occurring protein oligomers, complexes, or conformers. Here we developed a cross-linking workflow combining blue native PAGE with in-gel cross-linking mass spectrometry (IGX-MS). This workflow circumvents steps, such as buffer exchange and cross-linker concentration optimization. Additionally, IGX-MS enables the parallel analysis of co-occurring protein complexes using only small amounts of sample. Another benefit of IGX-MS observed by experiments on GroEL and purified bovine heart mitochondria, is the substantial reduction of artificial over-length cross-links when compared to in-solution cross-linking. We next used IGX-MS to investigate the complement components C5, C6, and their hetero-dimeric C5b6 complex. The obtained cross-links were used to generate a refined structural model of the complement component C6, resembling C6 in its inactivated state. This finding shows that IGX-MS can be used to provide new insights into the initial stages of the terminal complement pathway.

show abstract

Protein dynamics and conformational changes explored by hydrogen/deuterium exchange mass spectrometry

Cited by 72 publications

References 54 publications

Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry

Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry

Evolution of structural dynamics in bilobed proteins

Selective cross-linking of coinciding protein assemblies by in-gel cross-linking mass-spectrometry

Contact Info

Product

Resources

About