scholarly journals Erratum to "Conformational Dynamics of Sclerostin-LRP6 Complex Analyzed by HDX-MS" [Biomol. Ther. 29 (2021) 527-535]

2022 ◽  
Author(s):  
Yejin Jeong ◽  
Jinuk Kim ◽  
Hee-Jung Choi ◽  
Ka Young Chung
Keyword(s):  
Conformational Dynamics ◽  
Hdx Ms

scholarly journals MinE conformational dynamics regulate membrane binding, MinD interaction, and Min oscillation

2017 ◽  
Vol 114 (29) ◽  
pp. 7497-7504 ◽  
Author(s):  
Kyung-Tae Park ◽  
Maria T. Villar ◽  
Antonio Artigues ◽  
Joe Lutkenhaus
Keyword(s):  
Conformational Dynamics ◽  
Active Form ◽  
Hydrogen Deuterium Exchange ◽  
Conformational Switch ◽  
Form Analysis ◽  
Hydrogen Deuterium ◽  
Z Ring ◽  
Hdx Ms ◽  
Β Sheet ◽  
Rule Out

InEscherichia coliMinE induces MinC/MinD to oscillate between the ends of the cell, contributing to the precise placement of the Z ring at midcell. To do this, MinE undergoes a remarkable conformational change from a latent 6β-stranded form that diffuses in the cytoplasm to an active 4β-stranded form bound to the membrane and MinD. How this conformational switch occurs is not known. Here, using hydrogen–deuterium exchange coupled to mass spectrometry (HDX-MS) we rule out a model in which the two forms are in rapid equilibrium. Furthermore, HDX-MS revealed that a MinE mutant (D45A/V49A), previously shown to produce an aberrant oscillation and unable to assemble a MinE ring, is more rigid than WT MinE. This mutant has a defect in interaction with MinD, suggesting it has difficulty in switching to the active form. Analysis of intragenic suppressors of this mutant suggests it has difficulty in releasing the N-terminal membrane targeting sequences (MTS). These results indicate that the dynamic association of the MTS with the β-sheet is fine-tuned to balance MinE’s need to sense MinD on the membrane with its need to diffuse in the cytoplasm, both of which are necessary for the oscillation. The results lead to models for MinE activation and MinE ring formation.

scholarly journals Conformational dynamics of FERM-mediated autoinhibition in Pyk2 tyrosine kinase

2019 ◽  
Author(s):  
Hanna S. Loving ◽  
Eric S. Underbakke
Keyword(s):  
Tyrosine Kinase ◽  
Conformational Dynamics ◽  
Kinase Domain ◽  
Ferm Domain ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Protein Scaffolding ◽  
Hdx Ms

AbstractPyk2 is a non-receptor tyrosine kinase that evolved from gene duplication of focal adhesion kinase (FAK) and subsequent functional specialization in the brain and hemopoietic cells. Pyk2 shares a domain organization with FAK, with an N-terminal regulatory FERM domain adjoining the kinase domain. FAK regulation involves integrin-mediated membrane clustering to relieve autoinhibitory interactions between FERM and kinase domains. Pyk2 regulation remains cryptic, involving Ca2+ influx and protein scaffolding. While the mechanism of the FAK FERM domain in autoinhibition is well-established, the regulatory role of the Pyk2 FERM is ambiguous. We probed the mechanisms of FERM-mediated autoinhibition of Pyk2 using hydrogen/deuterium exchange mass spectrometry (HDX-MS) and kinase activity profiling. The results reveal FERM-kinase interfaces responsible for autoinhibition. Pyk2 autoinhibition impacts activation loop conformation. In addition, the autoinhibitory FERM-kinase interface exhibits allosteric linkage with the FERM basic patch conserved in both FAK and Pyk2.Table of Contents graphic

scholarly journals Protein Footprinting, Conformational Dynamics and Interface-Adjacent Neutralization ‘Hotspots’ in the SARS-CoV-2 Spike Protein Receptor Binding Domain / Human ACE2 Interaction

2020 ◽  
Author(s):  
Dominic Narang ◽  
Matthew Balmer ◽  
D. Andrew James ◽  
Derek Wilson
Keyword(s):  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Conformational Dynamics ◽  
Binding Domain ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Angiotensin Converting Enzyme 2 ◽  
Additional Information ◽  
Protein Receptor ◽  
Hdx Ms

This study provides an HDX-MS based analysis of the interaction between the SARS-CoV-2 spike protein and the human Angiotensin Converting Enzyme 2. <div><br></div><div>- The data agree exactly with the X-ray co-crystal structure of this complex, but provide additional information based on shifts in dynamics that are observed just outside the interface. </div><div><br></div><div>- These dynamic changes occur specifically in regions that are the primary targets of neutralizing antibodies that target spike protein, suggesting that the neutralization mechanism may result from suppression of dynamic shifts in the spike Receptor Binding Domain (RBD) that are necessary for favorable binding thermodynamics in the spike / ACE2 interaction.</div>

Localization of Conformational Dynamics of Arrestins by HDX-MS

2017 ◽  
pp. 119-132
Author(s):  
Ji Young Park ◽  
Hee Ryung Kim ◽  
Ka Young Chung
Keyword(s):  
Conformational Dynamics ◽  
Hdx Ms

Structural and dynamic insights into the subtype-specific IP3-binding mechanism of the IP3 receptor

2016 ◽  
Vol 473 (20) ◽  
pp. 3533-3543 ◽  
Author(s):  
Su Youn Lee ◽  
Hee-Seop Yoo ◽  
Hye-Seung Choi ◽  
Ka Young Chung ◽  
Min-Duk Seo
Keyword(s):  
Conformational Dynamics ◽  
Titration Calorimetry ◽  
Binding Affinities ◽  
Binding Mechanism ◽  
Ip3 Receptor ◽  
Release Channel ◽  
Thermal Stabilities ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Hdx Ms

There are three subtypes of vertebrate inositol 1,4,5-trisphosphate (IP3) receptor (IP3R), a Ca2+-release channel on the ER membrane — IP3R1, IP3R2, and IP3R3 — each of which has a distinctive role in disease development. To determine the subtype-specific IP3-binding mechanism, we compared the thermodynamics, thermal stability, and conformational dynamics between the N-terminal regions of IP3R1 (IP3R1-NT) and IP3R3 (IP3R3-NT) by performing circular dichroism (CD), isothermal titration calorimetry (ITC), and hydrogen–deuterium exchange mass spectrometry (HDX-MS). Previously determined crystal structures of IP3R1-NT and HDX-MS results from this study revealed that both IP3R1 and IP3R3 adopt a similar IP3-binding mechanism. However, several regions, including the α- and β-interfaces, of IP3R1-NT and IP3R3-NT show significantly different conformational dynamics upon IP3 binding, which may explain the different IP3-binding affinities between the subtypes. The importance of the interfaces for subtype-specific IP3 binding is also supported by the different dynamic conformations of the two subtypes in the apo-states. Furthermore, IP3R1-NT and IP3R3-NT show different IP3-binding affinities and thermal stabilities, but share similar thermodynamic properties for IP3 binding. These results collectively provide new insights into the mechanism underlying IP3 binding to IP3Rs and the subtype-specific regulatory mechanism.

scholarly journals Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9408
Author(s):  
Shanshan Wu ◽  
Tam T.T.N. Nguyen ◽  
Olga V. Moroz ◽  
Johan P. Turkenburg ◽  
Jens E. Nielsen ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Solvent Accessibility ◽  
Conformational Dynamics ◽  
Structural Heterogeneity ◽  
Catalytic Process ◽  
Conformational Heterogeneity ◽  
X Ray ◽  
Exchange Mass Spectrometry ◽  
Bacillus Lentus ◽  
Hdx Ms

Background Several examples have emerged of enzymes where slow conformational changes are of key importance for function and where low populated conformations in the resting enzyme resemble the conformations of intermediate states in the catalytic process. Previous work on the subtilisin protease, Savinase, from Bacillus lentus by NMR spectroscopy suggested that this enzyme undergoes slow conformational dynamics around the substrate binding site. However, the functional importance of such dynamics is unknown. Methods Here we have probed the conformational heterogeneity in Savinase by following the temperature dependent chemical shift changes. In addition, we have measured changes in the local stability of the enzyme when the inhibitor phenylmethylsulfonyl fluoride is bound using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Finally, we have used X-ray crystallography to compare electron densities collected at cryogenic and ambient temperatures and searched for possible low populated alternative conformations in the crystals. Results The NMR temperature titration shows that Savinase is most flexible around the active site, but no distinct alternative states could be identified. The HDX shows that modification of Savinase with inhibitor has very little impact on the stability of hydrogen bonds and solvent accessibility of the backbone. The most pronounced structural heterogeneities detected in the diffraction data are limited to alternative side-chain rotamers and a short peptide segment that has an alternative main-chain conformation in the crystal at cryo conditions. Collectively, our data show that there is very little structural heterogeneity in the resting state of Savinase and hence that Savinase does not rely on conformational selection to drive the catalytic process.

scholarly journals HDX-MS reveals nucleotide-regulated, anti-correlated opening and closure of SecA and SecY channels of the bacterial translocon

2019 ◽  
Author(s):  
Zainab Ahdash ◽  
Euan Pyle ◽  
William J. Allen ◽  
Robin A. Corey ◽  
Ian Collinson ◽  
...  
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Protein Transport ◽  
Atp Hydrolysis ◽  
Protein Translocation ◽  
Conformational Dynamics ◽  
Brownian Ratchet ◽  
Exchange Mass Spectrometry ◽  
Dependent Transport ◽  
Hdx Ms

AbstractThe bacterial Sec translocon is a multi-component protein complex responsible for translocating diverse proteins across the plasma membrane. For post-translational protein translocation, the Sec-channel – SecYEG – associates with the motor protein SecA to mediate the ATP-dependent transport of unfolded pre-proteins across the membrane. Based on the structure of the machinery, combined with ensemble and single molecule analysis, a diffusional based Brownian ratchet mechanism for protein secretion has been proposed [Allen et al. eLife 2016;5:e15598]. However, the conformational dynamics required to facilitate this mechanism have not yet been fully resolved. Here, we employ hydrogen-deuterium exchange mass spectrometry (HDX-MS) to reveal striking nucleotide-dependent conformational changes in the Sec protein-channel. In addition to the ATP-dependent opening of SecY, reported previously, we observe a counteracting, also ATP-dependent, constriction of SecA around the mature regions of the pre-protein. Thus, ATP binding causes SecY to open and SecA to close, while ATP hydrolysis has the opposite effect. This alternating behaviour could help impose the directionality of the Brownian ratchet for protein transport through the Sec machinery, and possibly in translocation systems elsewhere. The results highlight the power of HDX-MS for interrogating the dynamic mechanisms of diverse membrane proteins; including their interactions with small molecules such as nucleotides (ATPases and GTPases) and inhibitors (e.g. antibiotics).

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

2019 ◽  
Vol 35 (17) ◽  
pp. 3171-3173 ◽  
Author(s):  
Andy M C Lau ◽  
Zainab Ahdash ◽  
Chloe Martens ◽  
Argyris Politis
Keyword(s):  
Mass Spectrometry ◽  
Conformational Dynamics ◽  
Rapid Analysis ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Visualization Of Data ◽  
Hdx Ms

Abstract Summary Hydrogen deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful technique for interrogating the conformational dynamics of proteins and their complexes. Currently, analysis of HDX-MS data remains a laborious procedure, mainly due to the lack of streamlined software to process the large datasets. We present Deuteros which is a standalone software designed to be coupled with Waters DynamX HDX data analysis software, allowing the rapid analysis and visualization of data from differential HDX-MS. Availability and implementation Deuteros is open-source and can be downloaded from https://github.com/andymlau/Deuteros, under the Apache 2.0 license. Written in MATLAB and supported on both Windows and MacOS. Requires the MATLAB runtime library. According to the Wellcome Trust and UK research councils' Common Principles on Data Policy on data, software and materials management and sharing, all data supporting this study will be openly available from the software repository.

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

2018 ◽  
Author(s):  
Andy M. C. Lau ◽  
Zainab Ahdash ◽  
Chloe Martens ◽  
Argyris Politis
Keyword(s):  
Mass Spectrometry ◽  
Conformational Dynamics ◽  
Rapid Analysis ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Visualization Of Data ◽  
Hdx Ms

AbstractSummaryHydrogen deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful technique for interrogating the conformational dynamics of proteins and their complexes. Currently, analysis of HDX-MS data remains a laborious procedure, mainly due to the lack of streamlined software to process the large datasets. We present Deuteros which is a standalone software designed to be coupled with Waters DynamX HDX data analysis software, allowing the rapid analysis and visualization of data from differential HDX-MS.AvailabilityDeuteros is open-source and can be downloaded from https://github.com/andymlau/Deuteros, under the Apache 2.0 license.Implementationwritten in MATLAB and supported on both Windows and MacOS. Requires the MATLAB runtime [email protected]

scholarly journals PyHDX: Derivation and visualization of protection factors from Hydrogen-Deuterium Exchange Mass Spectrometry at near residue resolution

2020 ◽  
Author(s):  
Jochem H. Smit ◽  
Srinath Krishnamurthy ◽  
Bindu Y. Srinivasu ◽  
Spyridoula Karamanou ◽  
Anastassios Economou
Keyword(s):  
Mass Spectrometry ◽  
Local Equilibrium ◽  
Conformational Dynamics ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Free Energies ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Hdx Ms

AbstractHydrogen Deuterium Exchange Mass Spectrometry (HDX-MS) is a powerful technique to monitor the intrinsic and conformational dynamics of proteins. Most HDX-MS experiments compare protein states (e.g. apoprotein vs liganded) and provide detailed information on differential dynamics between them obtained from multiple overlapping peptides. However, differential dynamics are difficult to compare across protein derivatives, oligomeric assemblies, homologues and samples treated under different buffer and protease conditions. A main reason is that peptide-based D-uptake differences do not inform on absolute intrinsic dynamics at the level of single aminoacyl residues. Such information is offered by protection factors, i.e. the position of the local equilibrium between the D-exchange-competent ‘open’ state and the non-exchanging ‘closed’ state. We present PyHDX, a software tool to calculate protection factors and Gibbs free energies typically within minutes from HDX-MS-derived peptide lists. PyHDX provides intrinsic information on the thermodynamics of protein dynamics at single-residue level. An interactive web interface further streamlines the process of transforming peptide lists to either coloured linear sequence maps or 3D structures of Gibbs free energies/protection factors.AvailabilityPyHDX source code is released under the MIT license and can be accessed at the project’s GitHub page.

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