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Structural Biology of Proteins and Peptides
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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: closed (31 December 2020) | Viewed by 17023

Special Issue Editors

Prof. Dr. Jya-Wei Cheng

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Guest Editor
Department of Medical Science, Institute of Biotechnology, National Tsing Hua University, Hsinchu 300, Taiwan
Interests: antimicrobial peptides; anticancer peptides; chemokines; drug design; nuclear magnetic resonances; structures of peptides and proteins
Dr. Shih-Che Sue

E-Mail 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

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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

E-Mail 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

E-Mail 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, Collections and Topics 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 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. 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 (6 papers)

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Research

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11 pages, 2537 KiB  
Article
The Effect of Octapeptide Repeats on Prion Folding and Misfolding
by Kun-Hua Yu, Mei-Yu Huang, Yi-Ru Lee, Yu-Kie Lin, Hau-Ren Chen and Cheng-I Lee
Int. J. Mol. Sci. 2021, 22(4), 1800; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22041800 - 11 Feb 2021
Cited by 6 | Viewed by 2029
Abstract
Misfolding of prion protein (PrP) into amyloid aggregates is the central feature of prion diseases. PrP has an amyloidogenic C-terminal domain with three α-helices and a flexible tail in the N-terminal domain in which multiple octapeptide repeats are present in most mammals. The [...] Read more.
Misfolding of prion protein (PrP) into amyloid aggregates is the central feature of prion diseases. PrP has an amyloidogenic C-terminal domain with three α-helices and a flexible tail in the N-terminal domain in which multiple octapeptide repeats are present in most mammals. The role of the octapeptides in prion diseases has previously been underestimated because the octapeptides are not located in the amyloidogenic domain. Correlation between the number of octapeptide repeats and age of onset suggests the critical role of octapeptide repeats in prion diseases. In this study, we have investigated four PrP variants without any octapeptides and with 1, 5 and 8 octapeptide repeats. From the comparison of the protein structure and the thermal stability of these proteins, as well as the characterization of amyloids converted from these PrP variants, we found that octapeptide repeats affect both folding and misfolding of PrP creating amyloid fibrils with distinct structures. Deletion of octapeptides forms fewer twisted fibrils and weakens the cytotoxicity. Insertion of octapeptides enhances the formation of typical silk-like fibrils but it does not increase the cytotoxicity. There might be some threshold effect and increasing the number of peptides beyond a certain limit has no further effect on the cell viability, though the reasons are unclear at this stage. Overall, the results of this study elucidate the molecular mechanism of octapeptides at the onset of prion diseases. Full article
(This article belongs to the Special Issue Structural Biology of Proteins and Peptides)
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14 pages, 3287 KiB  
Article
Structural Insights into the Active Site Formation of DUSP22 in N-loop-containing Protein Tyrosine Phosphatases
by Chih-Hsuan Lai, Co-Chih Chang, Huai-Chia Chuang, Tse-Hua Tan and Ping-Chiang Lyu
Int. J. Mol. Sci. 2020, 21(20), 7515; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21207515 - 12 Oct 2020
Cited by 4 | Viewed by 2352
Abstract
Cysteine-based protein tyrosine phosphatases (Cys-based PTPs) perform dephosphorylation to regulate signaling pathways in cellular responses. The hydrogen bonding network in their active site plays an important conformational role and supports the phosphatase activity. Nearly half of dual-specificity phosphatases (DUSPs) use three conserved residues, [...] Read more.
Cysteine-based protein tyrosine phosphatases (Cys-based PTPs) perform dephosphorylation to regulate signaling pathways in cellular responses. The hydrogen bonding network in their active site plays an important conformational role and supports the phosphatase activity. Nearly half of dual-specificity phosphatases (DUSPs) use three conserved residues, including aspartate in the D-loop, serine in the P-loop, and asparagine in the N-loop, to form the hydrogen bonding network, the D-, P-, N-triloop interaction (DPN–triloop interaction). In this study, DUSP22 is used to investigate the importance of the DPN–triloop interaction in active site formation. Alanine mutations and somatic mutations of the conserved residues, D57, S93, and N128 substantially decrease catalytic efficiency (kcat/KM) by more than 102-fold. Structural studies by NMR and crystallography reveal that each residue can perturb the three loops and induce conformational changes, indicating that the hydrogen bonding network aligns the residues in the correct positions for substrate interaction and catalysis. Studying the DPN–triloop interaction reveals the mechanism maintaining phosphatase activity in N-loop-containing PTPs and provides a foundation for further investigation of active site formation in different members of this protein class. Full article
(This article belongs to the Special Issue Structural Biology of Proteins and Peptides)
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11 pages, 2615 KiB  
Article
Interactions between the Intrinsically Disordered Regions of hnRNP-A2 and TDP-43 Accelerate TDP-43′s Conformational Transition
by Wan-Chin Chiang, Ming-Hsuan Lee, Tsai-Chen Chen and Jie-rong Huang
Int. J. Mol. Sci. 2020, 21(16), 5930; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21165930 - 18 Aug 2020
Cited by 6 | Viewed by 3179
Abstract
Most biological functions involve protein–protein interactions. Our understanding of these interactions is based mainly on those of structured proteins, because encounters between intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) are much less studied, regardless of the fact that more [...] Read more.
Most biological functions involve protein–protein interactions. Our understanding of these interactions is based mainly on those of structured proteins, because encounters between intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) are much less studied, regardless of the fact that more than half eukaryotic proteins contain IDRs. RNA-binding proteins (RBPs) are a large family whose members almost all have IDRs in addition to RNA binding domains. These IDRs, having low sequence similarity, interact, but structural details on these interactions are still lacking. Here, using the IDRs of two RBPs (hnRNA-A2 and TDP-43) as a model, we demonstrate that the rate at which TDP-43′s IDR undergoes the neurodegenerative disease related α-helix-to-β-sheet transition increases in relation to the amount of hnRNP-A2′s IDR that is present. There are more than 1500 RBPs in human cells and most of them have IDRs. RBPs often join the same complexes to regulate genes. In addition to the structured RNA-recognition motifs, our study demonstrates a general mechanism through which RBPs may regulate each other’s functions through their IDRs. Full article
(This article belongs to the Special Issue Structural Biology of Proteins and Peptides)
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16 pages, 2346 KiB  
Article
The Structure of Amyloid Versus the Structure of Globular Proteins
by Piotr Fabian, Mateusz Banach, Katarzyna Stapor, Leszek Konieczny, Magdalena Ptak-Kaczor and Irena Roterman
Int. J. Mol. Sci. 2020, 21(13), 4683; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21134683 - 30 Jun 2020
Cited by 13 | Viewed by 2130
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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25 pages, 3961 KiB  
Article
Impact of the Hereditary P301L Mutation on the Correlated Conformational Dynamics of Human Tau Protein Revealed by the Paramagnetic Relaxation Enhancement NMR Experiments
by Ryosuke Kawasaki and Shin-ichi Tate
Int. J. Mol. Sci. 2020, 21(11), 3920; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21113920 - 30 May 2020
Cited by 9 | Viewed by 3054
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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Review

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22 pages, 2554 KiB  
Review
Evolution of Protein Structure and Stability in Global Warming
by Sailen Barik
Int. J. Mol. Sci. 2020, 21(24), 9662; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21249662 - 18 Dec 2020
Cited by 10 | Viewed by 3689
Abstract
This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopulate the planet and continue [...] Read more.
This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopulate the planet and continue life in general, but perhaps with different kinds of flora and fauna. Our focus is on molecular mechanisms, whereby known examples of thermoresistance and their physicochemical characteristics were noted. A comparison of interactions of diverse residues in proteins from thermophilic and mesophilic organisms, as well as reverse genetic studies, revealed a set of imprecise molecular signatures that pointed to major roles of hydrophobicity, solvent accessibility, disulfide bonds, hydrogen bonds, ionic and π-electron interactions, and an overall condensed packing of the higher-order structure, especially in the hydrophobic regions. Regardless of mutations, specialized protein chaperones may play a cardinal role. In evolutionary terms, thermoresistance to global warming will likely occur in stepwise mutational changes, conforming to the molecular signatures, such that each “intermediate” fits a temporary niche through punctuated equilibrium, while maintaining protein functionality. Finally, the population response of different species to global warming may vary substantially, and, as such, some may evolve while others will undergo catastrophic mass extinction. Full article
(This article belongs to the Special Issue Structural Biology of Proteins and Peptides)
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