Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry

Lau, Andy M.; Ahdash, Zainab; Martens, Chloé; Politis, Argyris

doi:10.1093/bioinformatics/btz022

Cited by 63 publications

(60 citation statements)

References 11 publications

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“…All HDX-MS peptide data can be found in Supporting Data Table 2. ( b ) ΔHDX extent for (AcrB WT +CIP+PAβN) – AcrB WT is coloured onto the L-state monomer of AcrB (PDB:2HRT) using Deuteros 34 . Connecting-loop from adjacent monomer is included.…”

Section: Resultsmentioning

confidence: 99%

“…Confidence intervals for differential HDX-MS (ΔHDX) measurements of any individual time point were then determined according to Houde et al . 46 using Deuteros software 34 . There was no correlation found between ΔHDX values and their standard deviations (R 2 = 0.09).…”

Section: Methodsmentioning

confidence: 99%

“…Only peptides which satisfied a ΔHDX confidence interval of 98 % were considered significant. All ΔHDX AcrB structure figures were generated from the data using Deuteros in-house source code/software 34 and Pymol 47 . All data and meta-data are reported in Supporting Data Tables 1-2.…”

Section: Methodsmentioning

confidence: 99%

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Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB

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Ahdash

Fais

et al. 2020

Preprint

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Resistance-nodulation-division (RND) efflux pumps play a key role in inherent and evolved multidrug-resistance (MDR) in bacteria. AcrB is the prototypical member of the RND family and acts to recognise and export a wide range of chemically distinct molecules out of bacteria, conferring resistance to a variety of antibiotics. Although high resolution structures exist for AcrB, its conformational fluctuations and their putative role in function are largely unknown, preventing a complete mechanistic understanding of efflux and inhibition. Here, we determine these structural dynamics in the presence of AcrB substrates using hydrogen/deuterium exchange mass spectrometry, complemented by molecular modelling, drug binding and bacterial susceptibility studies. We show that the well-studied efflux pump inhibitor phenylalanine-arginine-β-naphthylamide (PAβN) potentiates antibiotic activity by restraining drug-binding pocket dynamics, rather than preventing antibiotic binding. We also reveal that a drug-binding pocket substitution discovered within an MDR clinical isolate, AcrBG288D, modifies the plasticity of the transport pathway, which could explain its altered substrate specificity. Our results provide molecular insight into drug export and inhibition of a major MDR-conferring efflux pump and the important directive role of its dynamics.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB

Reading

Ahdash

Fais

et al. 2020

Preprint

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“…The relative fractional uptake (RFU) was calculated from RFU a = [Y a,t / (MaxUptake a x D)], where Y is the deuterium uptake for peptide a at incubation time t, and D is the percentage of deuterium in the sample after mixing the protein with the labeling solution. 99% Confidence intervals were calculated using Deuteros (Lau et al, 2019) and were found to be of 0.7 Da or smaller for the sum of RFU over all time points.…”

Section: Data Evaluation and Statistical Analysismentioning

confidence: 99%

A Topological Switch Enables Misfolding of the Cystic Fibrosis Transmembrane Conductance Regulator

Scholl

Sigoillot

Overtus

et al. 2020

Preprint

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Cystic Fibrosis (CF) is a common lethal genetic disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) anion channel. Misfolding and degradation of CFTR are the hallmarks of the predominant mutation, F508del, located in the first nucleotide binding domain (NBD1). While the mutation is known to affect the thermal stability of NBD1 and assembly of CFTR domains, the molecular events that lead to misfolding of F508del-CFTR remain elusive. Here, we demonstrate that NBD1 of CFTR can adopt an alternative conformation that departs from the canonical NBD fold previously observed for CFTR and other ATP-binding cassette (ABC) transporter proteins. Crystallography studies reveal that this conformation involves a topological reorganization of the β-subdomain of NBD1. This alternative state is adopted by wild-type CFTR in cells and enhances channel activity. Single-molecule fluorescence resonance energy transfer microscopy shows that the equilibrium between the conformations is regulated by ATP binding. Under destabilizing conditions, however, this conformational flexibility enables unfolding of the β-subdomain. Our data indicate that in wild-type CFTR switching to this topologically-swapped conformation of NBD1 regulates channel function, but, in the presence of the F508del mutation, it allows domain misfolding and subsequent protein degradation. Our work provides a framework to design conformation-specific therapeutics to prevent noxious transitions.

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“…Results generated by HDX-MS are complex and demanding in terms of analysis, interpretation and visual presentation. While there are many open-source and free to use software packages addressing the challenges of HDX-MS data analysis ( Hourdel et al, 2016 ; Kavan and Man, 2011 ; Lau et al, 2019 ; Lumpkin and Komives, 2019 ), HaDeX aims to cover post-processing workflow, where results of the experiment are analyzed and presented in a publication-friendly format (for comparison of mentioned tools see Supplementary Information SI1). It forces HDX-MS users to rely on several pieces of software, thus making the already laborious process even more time-consuming.…”

Section: Introductionmentioning

confidence: 99%

HaDeX: an R package and web-server for analysis of data from hydrogen–deuterium exchange mass spectrometry experiments

et al. 2020

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Motivation Hydrogen-deuterium mass spectrometry (HDX-MS) is a rapidly developing technique for monitoring dynamics and interactions of proteins. The development of new devices has to be followed with new software suites adressing emerging standards in data analysis. Results We propose HaDeX, a novel tool for processing, analysis and vizualisation of HDX-MS experiments. HaDeX supports a reproducible analytical process, including data exploration, quality control and generation of publication-quality figures. Availability HaDeX is available primarily as a web-server (http://mslab-ibb.pl/shiny/HaDeX/), but its all functionalities are also accessible as the R package (https://CRAN.R-project.org/package=HaDeX) and standalone software (https://sourceforge.net/projects/HaDeX/). Supplementary information Supplementary data are available at Bioinformatics online.

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Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry

Cited by 63 publications

References 11 publications

Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB

Perturbed structural dynamics underlie inhibition and altered specificity of the multidrug efflux pump AcrB

A Topological Switch Enables Misfolding of the Cystic Fibrosis Transmembrane Conductance Regulator

HaDeX: an R package and web-server for analysis of data from hydrogen–deuterium exchange mass spectrometry experiments

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