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Biomolecules
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The Illumination of Biophysical Mechanisms by Hydrogen Exchange: A Themed...
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The Illumination of Biophysical Mechanisms by Hydrogen Exchange: A Themed Issue in Honor of Professor S. Walter Englander

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 5621

Special Issue Editor

Prof. Dr. A. Joshua Wand

E-Mail Website
Guest Editor
Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77845, USA
Interests: protein biophysics; protein thermodynamics; protein dynamics; allostery; protein design & engineering; NMR spectroscopy

Special Issue Information

Dear Colleagues,

I am pleased to announce that Biomolecules will dedicate a Special Issue in honor of Professor Walter Englander in recognition of his seminal contributions to the development of the phenomenon of hydrogen exchange as a tool to investigate protein thermodynamics, dynamics, and function. Entitled “The illumination of biophysical mechanisms by hydrogen exchange,” this themed issue is intended to highlight the powerful capabilities of hydrogen exchange (HX) to reveal fundamental properties of proteins ranging from their stability, folding, dynamics, and function. Contributions are invited that focus on advancing or utilizing hydrogen exchange (HX) techniques in addressing inquiries about biomolecular structure, dynamics, and function. This call for submissions is specifically directed towards the protein biochemistry and biophysics communities. Contributions will be reviewed as usual; publication charges will apply. We ask that you provide your manuscript for review by the end of August 2024.

Prof. Dr. A. Joshua Wand
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • hydrogen exchange chemistry
  • HX–NMR
  • HX-MS
  • protein folding
  • allostery
  • protein binding
  • protein thermodynamics
  • protein biophysics
  • protein function

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Published Papers (3 papers)

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Research

25 pages, 5663 KiB  
Article
Exploring the CNOT1(800–999) HEAT Domain and Its Interactions with Tristetraprolin (TTP) as Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry
by Maja K. Cieplak-Rotowska, Michał Dadlez and Anna Niedzwiecka
Biomolecules 2025, 15(3), 403; https://doi.org/10.3390/biom15030403 - 11 Mar 2025
Viewed by 564
Abstract
CNOT1, a key scaffold in the CCR4-NOT complex, plays a critical role in mRNA decay, particularly in the regulation of inflammatory responses through its interaction with tristetraprolin. A fragment of the middle part of CNOT1 (residues 800–999) is an example of an α-helical [...] Read more.
CNOT1, a key scaffold in the CCR4-NOT complex, plays a critical role in mRNA decay, particularly in the regulation of inflammatory responses through its interaction with tristetraprolin. A fragment of the middle part of CNOT1 (residues 800–999) is an example of an α-helical HEAT-like repeat domain. The HEAT motif is an evolutionarily conserved motif present in scaffolding and transport proteins across a wide range of organisms. Using hydrogen/deuterium exchange mass spectrometry (HDX MS), a method that has not been widely explored in the context of HEAT repeats, we analysed the structural dynamics of wild-type CNOT1(800–999) and its two double point mutants (E893A/Y900A, E893Q/Y900H) to find the individual contributions of these CNOT1 residues to the molecular recognition of tristetraprolin (TTP). Our results show that the differences in the interactions of CNOT1(800–999) variants with the TTP peptide fragment are due to the absence of the critical residues resulting from point mutations and not due to the perturbation of the protein structure. Nevertheless, the HDX MS was able to detect slight local changes in structural dynamics induced by protein point mutations, which are usually neglected in studies of intermolecular interactions. Full article
(This article belongs to the Special Issue The Illumination of Biophysical Mechanisms by Hydrogen Exchange: A Themed Issue in Honor of Professor S. Walter Englander)
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16 pages, 2676 KiB  
Article
Cooperative Substructure and Energetics of Allosteric Regulation of the Catalytic Core of the E3 Ubiquitin Ligase Parkin by Phosphorylated Ubiquitin
by Xiang Ye, Sravya Kotaru, Rosana Lopes, Shannen Cravens, Mauricio Lasagna and A. Joshua Wand
Biomolecules 2024, 14(10), 1338; https://doi.org/10.3390/biom14101338 - 21 Oct 2024
Cited by 1 | Viewed by 1562
Abstract
Mutations in the parkin gene product Parkin give rise to autosomal recessive juvenile parkinsonism. Parkin is an E3 ubiquitin ligase that is a critical participant in the process of mitophagy. Parkin has a complex structure that integrates several allosteric signals to maintain precise [...] Read more.
Mutations in the parkin gene product Parkin give rise to autosomal recessive juvenile parkinsonism. Parkin is an E3 ubiquitin ligase that is a critical participant in the process of mitophagy. Parkin has a complex structure that integrates several allosteric signals to maintain precise control of its catalytic activity. Though its allosterically controlled structural reorganization has been extensively characterized by crystallography, the energetics and mechanisms of allosteric regulation of Parkin are much less well understood. Allostery is fundamentally linked to the energetics of the cooperative (sub)structure of the protein. Herein, we examine the mechanism of allosteric activation by phosphorylated ubiquitin binding to the enzymatic core of Parkin, which lacks the antagonistic Ubl domain. In this way, the allosteric effects of the agonist phosphorylated ubiquitin can be isolated. Using native-state hydrogen exchange monitored by mass spectrometry, we find that the five structural domains of the core of Parkin are energetically distinct. Nevertheless, association of phosphorylated ubiquitin destabilizes structural elements that bind the ubiquitin-like domain antagonist while promoting the dissociation of the catalytic domain and energetically poises the protein for transition to the fully activated structure. Full article
(This article belongs to the Special Issue The Illumination of Biophysical Mechanisms by Hydrogen Exchange: A Themed Issue in Honor of Professor S. Walter Englander)
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14 pages, 2983 KiB  
Article
Epitope Mapping of Japanese Encephalitis Virus Neutralizing Antibodies by Native Mass Spectrometry and Hydrogen/Deuterium Exchange
by Jagat Adhikari, James Heffernan, Melissa Edeling, Estefania Fernandez, Prashant N. Jethva, Michael S. Diamond, Daved H. Fremont and Michael L. Gross
Biomolecules 2024, 14(3), 374; https://doi.org/10.3390/biom14030374 - 20 Mar 2024
Viewed by 2841
Abstract
Japanese encephalitis virus (JEV) remains a global public health concern due to its epidemiological distribution and the existence of multiple strains. Neutralizing antibodies against this infection have shown efficacy in in vivo studies. Thus, elucidation of the epitopes of neutralizing antibodies can aid [...] Read more.
Japanese encephalitis virus (JEV) remains a global public health concern due to its epidemiological distribution and the existence of multiple strains. Neutralizing antibodies against this infection have shown efficacy in in vivo studies. Thus, elucidation of the epitopes of neutralizing antibodies can aid in the design and development of effective vaccines against different strains of JEV. Here, we describe a combination of native mass spectrometry (native-MS) and hydrogen/deuterium exchange mass spectrometry (HDX-MS) to complete screening of eight mouse monoclonal antibodies (MAbs) against JEV E-DIII to identify epitope regions. Native-MS was used as a first pass to identify the antibodies that formed a complex with the target antigen, and it revealed that seven of the eight monoclonal antibodies underwent binding. Native mass spectra of a MAb (JEV-27) known to be non-binding showed broad native-MS peaks and poor signal, suggesting the protein is a mixture or that there are impurities in the sample. We followed native-MS with HDX-MS to locate the binding sites for several of the complex-forming antibodies. This combination of two mass spectrometry-based approaches should be generally applicable and particularly suitable for screening of antigen–antibody and other protein–protein interactions when other traditional approaches give unclear results or are difficult, unavailable, or need to be validated. Full article
(This article belongs to the Special Issue The Illumination of Biophysical Mechanisms by Hydrogen Exchange: A Themed Issue in Honor of Professor S. Walter Englander)
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