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Special Issue "Protein Structure Dynamics and Function"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 31 August 2021.

Special Issue Editor

Prof. Dr. Shin-ichi Tate
Website1 Website2
Guest Editor
1. Department of Mathematical and Life Sciences, School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan;
2. Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
Interests: protein structure; protein structural dynamics; intrinsically disordered protein; protein aggregation; nuclear magnetic resonance spectroscopy
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Special Issue Information

Dear Colleagues,

Protein structural dynamics is intimately related to protein functions. Structure biology demands high-resolution structures primarily coming from X-ray crystallography. However, the crystal structure does not always give a comprehensive understanding of the functional mechanism. This inability is often ascribed to a lack of insight into the time-dependent spatial rearrangement of the regulatory residues, domains, and subunits in proteins, which emphasizes the importance in exploring how structural dynamics engages in functional regulation in proteins. Progress in the experimental and theoretical approaches has improved our understanding of protein structural dynamics and has updated the protein structure and function relationships by adding the roles of structural dynamics. The technical advances have also expanded the research targets from folded proteins to intrinsically disordered proteins that travel much wider conformational spaces over the folded proteins. Intrinsically disordered proteins with liquid–liquid phase separation properties have become focused, which unveils the other remarkable roles of structural dynamics in regulating the phase transition of the protein solution.

The Special Issue “Protein Structure Dynamics and Function” is a continuation of the successful 2018 and 2019 issue “Protein Structural Dynamics.” This issue also aims to present contemporary research on protein structural dynamics, which may include original articles covering technical development, experimental reports on some particular proteins, and theoretical research, as well as review papers relating to the topic.

Prof. Dr. Shin-ichi Tate
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 papers will be 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • Protein strutural dynamics
  • Enzyme functions
  • Intrinsically disordered proteins
  • NMR
  • Single molecular FRET (fluorecense resonance energy transfer)
  • Molecular dynamics simulation
  • Coarse grained molecular dynamics simulation

Published Papers (2 papers)

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Research

Open AccessArticle
The Finite Size Effects and Two-State Paradigm of Protein Folding
Int. J. Mol. Sci. 2021, 22(4), 2184; https://doi.org/10.3390/ijms22042184 - 22 Feb 2021
Abstract
The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size extends the transition interval [...] Read more.
The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size extends the transition interval of the coil-globule phase transition. Based on the pedantic derivation of the two-state model, we introduce the number of amino acid residues of a polypeptide chain as a parameter in the expressions for two cooperativity measures and reveal their physical significance. We conclude that the k2 measure, defined as the ratio of van ’t Hoff and calorimetric enthalpy is related to the degeneracy of the denatured state and describes the number of cooperative units involved in the transition; additionally, it is found that the widely discussed k2=1 is just the necessary condition to classify the protein as the two-state folder. We also find that Ωc, a quantity not limited from above and growing with system size, is simply proportional to the square of the transition interval. This fact allows us to perform the classical size scaling analysis of the coil-globule phase transition. Moreover, these two measures are shown to describe different characteristics of protein folding. Full article
(This article belongs to the Special Issue Protein Structure Dynamics and Function)
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Open AccessArticle
Interferon Beta Activity Is Modulated via Binding of Specific S100 Proteins
Int. J. Mol. Sci. 2020, 21(24), 9473; https://doi.org/10.3390/ijms21249473 - 13 Dec 2020
Abstract
Interferon-β (IFN-β) is a pleiotropic cytokine used for therapy of multiple sclerosis, which is also effective in suppression of viral and bacterial infections and cancer. Recently, we reported a highly specific interaction between IFN-β and S100P lowering IFN-β cytotoxicity to cancer cells (Int [...] Read more.
Interferon-β (IFN-β) is a pleiotropic cytokine used for therapy of multiple sclerosis, which is also effective in suppression of viral and bacterial infections and cancer. Recently, we reported a highly specific interaction between IFN-β and S100P lowering IFN-β cytotoxicity to cancer cells (Int J Biol Macromol. 2020; 143: 633–639). S100P is a member of large family of multifunctional Ca2+-binding proteins with cytokine-like activities. To probe selectivity of IFN-β—S100 interaction with respect to S100 proteins, we used surface plasmon resonance spectroscopy, chemical crosslinking, and crystal violet assay. Among the thirteen S100 proteins studied S100A1, S100A4, and S100A6 proteins exhibit strictly Ca2+-dependent binding to IFN-β with equilibrium dissociation constants, Kd, of 0.04–1.5 µM for their Ca2+-bound homodimeric forms. Calcium depletion abolishes the S100—IFN-β interactions. Monomerization of S100A1/A4/A6 decreases Kd values down to 0.11–1.0 nM. Interferon-α is unable of binding to the S100 proteins studied. S100A1/A4 proteins inhibit IFN-β-induced suppression of MCF-7 cells viability. The revealed direct influence of specific S100 proteins on IFN-β activity uncovers a novel regulatory role of particular S100 proteins, and opens up novel approaches to enhancement of therapeutic efficacy of IFN-β. Full article
(This article belongs to the Special Issue Protein Structure Dynamics and Function)
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