Project description:We employ hydrogen-deuterium exchange mass spectrometry (HDX-MS) to investigate the conformational dynamics required to facilitate based Brownian ratchet mechanism for protein secretion (by the SecA-SecYEG complex).
Project description:Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful protein footprinting technique to study protein dynamics and binding; however, HDX-MS data analysis is often challenging and time consuming. Moreover, the HDX community is expanding to investigate multi-protein and highly complex protein systems such as cell lysates which further complicates data analysis. Thus, a simple and easy-to-use open source software package designed to analyze large and highly complex protein systems is needed. In this vein, we have developed The Deuterium Calculator, a Python-based software package for HDX-MS data analysis. The Deuterium Calculator is capable of differential and nondifferential HDX-MS analysis, produces standardized data files according to the recommendations put forth by the International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX) to increase transparency in data analysis, and generates Woods’ plots for statistical analysis and data visualization. This standard output can be used to perform further analysis on HDX such as determination of labeling time dependent deuteration and for the study of protein folding kinetics or differential uptake. Moreover, the Deuterium Calculator is capable of analyzing large HDX-MS datasets (e.g., LC-HDX-MS from complex samples such as cell lysates) to determine the extent of deuteration on individual peptides from numerous proteins, perform differential analysis under varying experimental conditions, and time-dependent deuterium exchange. The Deuterium Calculator is freely available for download at https://github.com/OUWuLab/TheDeuteriumCalculator.git.
Project description:Hydrogen deuterium exchange mass spectrometry of PLIN3 in the presence of three different membrane vesicles to analyze structural changes induced by membrane binding.
Project description:Hydrogen-Deuterium eXchange coupled to Mass Spectrometry (HDX-MS) analysis to investigate the solvent accessibility of the full human 20S proteasome alone or in complex with PA28 regulatory particles. Our work reveals a reciprocal crosstalk between the inner and outer rings of the human 20S proteasome. HDX-MS experiments were performed on a Synapt-G2Si (Waters Scientific, Manchester, UK) coupled to a Twin HTS PAL dispensing and labelling robot (LEAP Technologies, Carborro, NC, USA) via a NanoAcquity system with HDX technology (Waters, Manchester, UK).
Project description:TRAMP is a eukaryotic protein complex with RNA helicase and polyadenylase activity that marks and delivers a variety of RNA substrates to the nuclear exosome for degradation. Prior work has characterized binding of Trf4 and Air2 to the helicase core of Mtr4 and the regulation of both enzymatic activities in TRAMP. Air2 contains a conserved sequence that is predicted to bind the arch domain of Mtr4, though this interface is dispensable for TRAMP formation. To understand the interactions of the Saccharomyces cerevisiae TRAMP complex and its interactions with RNA, we have applied hydrogen-deuterium exchange mass spectrometry. We demonstrate that Air2 simultaneously binds the helicase core and the fist of Mtr4 in solution, constraining the arch to a conformation ready to bind RNA. We characterize the previously unknown interactions of Trf4 and Air2 with RNA and show how interactions with substrates are altered in TRAMP, supporting a mechanistic model for the enhancement of Mtr4 activity in TRAMP.
Project description:We used hydrogen deuterium exchange mass spectrometry (HDX-MS) to define the interface of TRAPPII with three Rab GTPases (Rab1, Rab11, Rab43). These experiments were performed in the presence of EDTA to generate a nucleotide free stabilised Rab-GEF complex. Significant decreases in deuterium incorporation (defined as >4%, >0.4Da, two tailed T-test p value <0.01) were identified in the TRAPPC2L, TRAPPC4, and TRAPPC5 in the presence of Rab GTPases with no other changes in other TRAPP subunits. Here we show that all three Rab GTPases bind at a conserved interface of TRAPPII.
Project description:CRISPR RNA-guided detection and degradation of foreign DNA is a dynamic process. Viruses can interfere with this cellular defense by expressing small proteins called anti-CRISPRs. While structural models of anti-CRISPRs bound to their target complex provide static snapshots that inform mechanism, the dynamics and thermodynamics of these interactions are often overlooked. Here we use hydrogen deuterium exchange-mass spectrometry (HDX-MS) and differential scanning fluorimetry (DSF) experiments to determine how anti-CRISPR binding impacts the conformational landscape of the type IF CRISPR RNA guided surveillance complex (Csy) upon binding of two different anti-CRISPR proteins (AcrIF9 and AcrIF2). The results demonstrate that AcrIF2 binding relies on enthalpic stabilization, whereas AcrIF9 uses an entropy driven reaction to bind the CRISPR RNA-guided surveillance complex. Collectively, this work reveals the thermodynamic basis and mechanistic versatility of anti-CRISPR-mediated immune suppression. More broadly, this work presents a striking example of how allosteric effectors are employed to regulate nucleoprotein complexes.
Project description:SARS-CoV-2 nsp7 and nsp8 are important cofactors of the RTC, as they interact and regulate the activity of RNA-dependent RNA polymerase and other nspsHere we used solution-based structural proteomic techniques, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and crosslinking mass spectrometry (XL-MS), illuminate the dynamics of SARS-CoV-2 full-length nsp7, nsp8, and nsp7:nsp8 proteins and protein complex.
Project description:CD47 is the only 5-transmembrane (5-TM) spanning receptor of the immune system. Its extracellular domain (ECD) is a cell surface ‘marker of self’ that binds SIRPα and inhibits macrophage phagocytosis, and cancer immuno-therapy approaches in clinical trials are focused on blocking CD47/SIRPα interaction. Using hydrogen-deuterium exchange we show that CD47’s ECLR architecture, comprised of two extracellular loops and the SWF loop, creates a molecular environment stabilizing the ECD for presentation on the cell surface.