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Special Issue "Structural Biology of Proteins and Peptides"

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

Deadline for manuscript submissions: 31 December 2020.

Special Issue Editors

Prof. Jya-Wei Cheng
Website
Guest Editor
Institute of Biotechnology, National Tsing Hua University, Taiwan
Interests: Antimicrobial peptides; chemokines; anti-infectious drug design; anti-cancer drug design; Nuclear Magnetic Resonance; structural biology of proteins and peptides
Dr. Shih-Che Sue
Website
Guest Editor
Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
Interests: Structural biology of chemokines and chemokin-binding receptors; protein engineering and enzyme mechanism; NMR spectroscopy
Dr. Kuen-Phon Wu
Website
Guest Editor
Institute of Biological Chemistry,Academia Sinica, Taiwan
Interests: Structure biology of protein ubiquitination; protein misfolding and degradation; X-ray crystallography; Cryo-electron microscopy
Dr. Hui-Chun Cheng
Website
Guest Editor
Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
Interests: Structural biology of AAA ATPases; protein phase separation; regulation of microtubules; X-ray crystallography
Dr. Shang-Te (Danny) Hsu
Website
Guest Editor
Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
Interests: protein dynamics; structural biology; DNA/RNA quadruplexes; NMR spectroscopy; biophysical chemistry
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

Proteins and peptides fold into specific three-dimensional structures to carry out their biological functions. These biological functions can be regulated by interactions with other biological ligands, and/or post-translational modifications. The conformational and chemical spaces of polypeptides can be further expanded by the introduction of non-natural amino acids, leading to novel functions that can be exploited in biotechnology and biomedicine. Understanding the molecular basis of structure–function relationships forms the foundation of structural biology, which has benefitted from contemporary method developments that increase the spatial and temporal resolutions pertinent to the understanding of biological functions. This Special Issue invites contributions describing advances in our understanding of protein structures and functions, and folding and misfolding using experimental and theoretical approaches. Original research articles and reviews are both welcome.

Prof. Jya-Wei Cheng
Dr. Shih-Che Sue
Dr. Kuen-Phon Wu
Dr. Hui-Chun Cheng
Dr. Shang-Te Hsu
Guest Editors

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 structures
  • Protein folding
  • X-ray crystallography
  • NMR spectroscopy
  • Cryo-electron microscopy
  • Expanding genetic codes
  • Peptide-based chemical probes
  • Antimicrobial peptides
  • Protein engineering
  • Protein dynamics
  • Protein modification
  • Ubiquitination
  • Ubiquitylation
  • Enzyme mechanis

Published Papers (2 papers)

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Research

Open AccessArticle
The Structure of Amyloid Versus the Structure of Globular Proteins
Int. J. Mol. Sci. 2020, 21(13), 4683; https://doi.org/10.3390/ijms21134683 - 30 Jun 2020
Abstract
The issue of changing the structure of globular proteins into an amyloid form is in the focus of researchers' attention. Numerous experimental studies are carried out, and mathematical models to define the essence of amyloid transformation are sought. The present work focuses on [...] Read more.
The issue of changing the structure of globular proteins into an amyloid form is in the focus of researchers' attention. Numerous experimental studies are carried out, and mathematical models to define the essence of amyloid transformation are sought. The present work focuses on the issue of the hydrophobic core structure in amyloids. The form of ordering the hydrophobic core in globular proteins is described by a 3D Gaussian distribution analog to the distribution of hydrophobicity in a spherical micelle. Amyloid fibril is a ribbon-like micelle made up of numerous individual chains, each representing a flat structure. The distribution of hydrophobicity within a single chain included in the fibril describes the 2D Gaussian distribution. Such a description expresses the location of polar residues on a circle with a center with a high level of hydrophobicity. The presence of this type of order in the amyloid forms available in Preotin Data Bank (PDB) (both in proto- and superfibrils) is demonstrated in the present work. In this system, it can be assumed that the amyloid transformation is a chain transition from 3D Gauss ordering to 2D Gauss ordering. This means changing the globular structure to a ribbon-like structure. This observation can provide a simple mathematical model for simulating the amyloid transformation of proteins. Full article
(This article belongs to the Special Issue Structural Biology of Proteins and Peptides)
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Open AccessArticle
Impact of the Hereditary P301L Mutation on the Correlated Conformational Dynamics of Human Tau Protein Revealed by the Paramagnetic Relaxation Enhancement NMR Experiments
Int. J. Mol. Sci. 2020, 21(11), 3920; https://doi.org/10.3390/ijms21113920 - 30 May 2020
Abstract
Tau forms intracellular insoluble aggregates as a neuropathological hallmark of Alzheimer’s disease. Tau is largely unstructured, which complicates the characterization of the tau aggregation process. Recent studies have demonstrated that tau samples two distinct conformational ensembles, each of which contains the soluble and [...] Read more.
Tau forms intracellular insoluble aggregates as a neuropathological hallmark of Alzheimer’s disease. Tau is largely unstructured, which complicates the characterization of the tau aggregation process. Recent studies have demonstrated that tau samples two distinct conformational ensembles, each of which contains the soluble and aggregation-prone states of tau. A shift to populate the aggregation-prone ensemble may promote tau fibrillization. However, the mechanism of this ensemble transition remains elusive. In this study, we explored the conformational dynamics of a tau fragment by using paramagnetic relaxation enhancement (PRE) and interference (PRI) NMR experiments. The PRE correlation map showed that tau is composed of segments consisting of residues in correlated motions. Intriguingly, residues forming the β-structures in the heparin-induced tau filament coincide with residues in these segments, suggesting that each segment behaves as a structural unit in fibrillization. PRI data demonstrated that the P301L mutation exclusively alters the transiently formed tau structures by changing the short- and long-range correlated motions among residues. The transient conformations of P301L tau expose the amyloid motif PHF6 to promote tau self-aggregation. We propose the correlated motions among residues within tau determine the population sizes of the conformational ensembles, and perturbing the correlated motions populates the aggregation-prone form. Full article
(This article belongs to the Special Issue Structural Biology of Proteins and Peptides)
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