Ion mobility-mass spectrometry of intact protein–ligand complexes for pharmaceutical drug discovery and development

Niu, Shuai; Rabuck, Jessica N.; Ruotolo, Brandon T.

doi:10.1016/j.cbpa.2013.06.019

Cited by 71 publications

(76 citation statements)

References 89 publications

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“…Coupling of ion mobility (IM) to mass spectrometry (MS) enables measuring the stoichiometry of protein-ligand interactions (Yin et al, 2008) and probing interaction-mediated conformational changes (Niu et al, 2013). The latter is deduced from collisional cross section (CCS) values for complexes and individual interacting partners upon their surface- or collision-induced dissociation.…”

Section: Resultsmentioning

confidence: 99%

Human Defensins Facilitate Local Unfolding of Thermodynamically Unstable Regions of Bacterial Protein Toxins

et al. 2014

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SUMMARY Defensins are short cationic, amphiphilic, cysteine-rich peptides that constitute the front line immune defense against various pathogens. In addition to exerting direct antibacterial activities, defensins inactivate several classes of unrelated bacterial exotoxins. To date, no coherent mechanism has been proposed that would explain defensins’ enigmatic efficiency towards various toxins. We showed that binding of neutrophil α-defensin HNP1 to affected bacterial toxins caused their local unfolding, potentiated their thermal melting and precipitation, exposed new regions for proteolysis, and increased susceptibility to collisional quenchers, without causing similar affects on tested mammalian structural and enzymatic proteins. Enteric α-defensin HD5 and β-defensin hBD2 shared similar toxin-unfolding effects with HNP1, albeit to different degrees. We propose that protein susceptibility to inactivation by defensins is contingent to their thermolability and conformational plasticity and that the defensin-induced unfolding is a key element in the general mechanism of toxin inactivation by human defensins.

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Section: Resultsmentioning

confidence: 99%

Human Defensins Facilitate Local Unfolding of Thermodynamically Unstable Regions of Bacterial Protein Toxins

et al. 2014

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“…In addition, screening formats such as small-molecule microarrays 23 that facilitate the interrogation of transcription factor binding in the presence of endogenous competing factors enable specificity to be assessed much earlier in the discovery process 24 . Looking toward the future, ion mobility mass spectrometry may be especially effective in a high-throughput capacity as it allows small molecule–induced changes in conformation to be readily detected 25 . There is still significant untapped potential in the broader network of transcription factor interactions as the field continues to define these critical connections.…”

Section: Discussionmentioning

confidence: 99%

Targeting transcription is no longer a quixotic quest

2015

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“…20 Generally, these experiments involve sequentially increasing the kinetic energy of ions as they enter a pressurized ion trap, and thereby collisionally heating them. Subsequent analysis of IM drift time distributions for ion populations post-activation generally reveal increases in ion collision cross sections as in a manner correlated with their increased internal energies.…”

Section: Introductionmentioning

confidence: 99%

Chemical Probes and Engineered Constructs Reveal a Detailed Unfolding Mechanism for a Solvent-Free Multidomain Protein

2016

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Despite the growing application of gas-phase measurements in structural biology and drug discovery, the factors that govern protein stabilities and structures in a solvent-free environment are still poorly understood. Here, we examine the solvent-free unfolding pathway for a group of homologous serum albumins. Utilizing a combination of chemical probes and non-covalent reconstructions, we draw new specific conclusions regarding the unfolding of albumins in the gas-phase, as well as more-general inferences regarding the sensitivity of collision induced unfolding to changes in protein primary and tertiary structure. Our findings suggest that the general unfolding pathway of low charge state albumin ions is largely unaffected by changes in primary structure; however, the stabilities of intermediates along these pathways vary widely as sequences diverge. Additionally, we find that human albumin follows a domain associated unfolding pathway, and are able to assign each unfolded form observed in our gas-phase dataset to the disruption of specific domains within the protein. The totality of our data informs the first detailed mechanism for multi-domain protein unfolding in the gas phase, and highlights key similarities and differences from the known the solution-phase pathway.

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Ion mobility-mass spectrometry of intact protein–ligand complexes for pharmaceutical drug discovery and development

Cited by 71 publications

References 89 publications

Human Defensins Facilitate Local Unfolding of Thermodynamically Unstable Regions of Bacterial Protein Toxins

Human Defensins Facilitate Local Unfolding of Thermodynamically Unstable Regions of Bacterial Protein Toxins

Targeting transcription is no longer a quixotic quest

Chemical Probes and Engineered Constructs Reveal a Detailed Unfolding Mechanism for a Solvent-Free Multidomain Protein

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