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Biomedicines
Special Issues
Protein (Re)Folding and Aggregation
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Protein (Re)Folding and Aggregation

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Cell Biology and Pathology".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 17049

Special Issue Editors

Dr. Anne Skaja Robinson

E-Mail Website
Guest Editor
Department Head Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
Interests: protein (re)folding; aggregation; aggregation-related disease; G-protein coupled receptors; antibodies
Prof. Dr. Christopher J. Roberts

E-Mail Website
Co-Guest Editor
Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
Interests: protein aggregation and stability; protein phase behavior; protein-protein interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With this Special Issue, we intend to collect all contributions related to protein folding, refolding, and aggregation, with a special emphasis on those related to non-native aggregation associated with disease, such as Alzheimer’s disease and type II diabetes. In addition, non-native aggregation is important in pharmaceutical biotechnology, and control during refolding or storage is also of interest. Of particular interest will be articles or reviews focusing on a mechanistic understanding of events that contribute to or reduce aggregation both in vitro and in vivo.

Dr. Anne Skaja Robinson
Guest Editor
Prof. Christopher J. Roberts
Co-Guest Editor

Manuscript Submission Information

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Keywords

  • amyloid
  • human protein
  • neurodegeneration
  • misfolding
  • cross-beta sheet
  • nucleation
  • oligomer

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Published Papers (6 papers)

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Research

13 pages, 3619 KiB  
Article
Local Flexibility of a New Single-Ring Chaperonin Encoded by Bacteriophage AR9 Bacillus subtilis
by Olga S. Sokolova, Evgeny B. Pichkur, Ekaterina S. Maslova, Lidia P. Kurochkina, Pavel I. Semenyuk, Petr V. Konarev, Valeriya R. Samygina and Tatiana B. Stanishneva-Konovalova
Biomedicines 2022, 10(10), 2347; https://doi.org/10.3390/biomedicines10102347 - 21 Sep 2022
Cited by 1 | Viewed by 2095
Abstract
Chaperonins, a family of molecular chaperones, assist protein folding in all domains of life. They are classified into two groups: bacterial variants and those present in endosymbiotic organelles of eukaryotes belong to group I, while group II includes chaperonins from the cytosol of [...] Read more.
Chaperonins, a family of molecular chaperones, assist protein folding in all domains of life. They are classified into two groups: bacterial variants and those present in endosymbiotic organelles of eukaryotes belong to group I, while group II includes chaperonins from the cytosol of archaea and eukaryotes. Recently, chaperonins of a prospective new group were discovered in giant bacteriophages; however, structures have been determined for only two of them. Here, using cryo-EM, we resolved a structure of a new chaperonin encoded by gene 228 of phage AR9 B. subtilis. This structure has similarities and differences with members of both groups, as well as with other known phage chaperonins, which further proves their diversity. Full article
(This article belongs to the Special Issue Protein (Re)Folding and Aggregation)
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13 pages, 3291 KiB  
Article
Modulating the Fibrillization of Parathyroid-Hormone (PTH) Peptides: Azo-Switches as Reversible and Catalytic Entities
by André Paschold, Bruno Voigt, Gerd Hause, Tim Kohlmann, Sven Rothemund and Wolfgang H. Binder
Biomedicines 2022, 10(7), 1512; https://doi.org/10.3390/biomedicines10071512 - 26 Jun 2022
Cited by 5 | Viewed by 2202
Abstract
We here report a novel strategy to control the bioavailability of the fibrillizing parathyroid hormone (PTH)-derived peptides, where the concentration of the bioactive form is controlled by an reversible, photoswitchable peptide. PTH1–84, a human hormone secreted by the parathyroid glands, is [...] Read more.
We here report a novel strategy to control the bioavailability of the fibrillizing parathyroid hormone (PTH)-derived peptides, where the concentration of the bioactive form is controlled by an reversible, photoswitchable peptide. PTH1–84, a human hormone secreted by the parathyroid glands, is important for the maintenance of extracellular fluid calcium and phosphorus homeostasis. Controlling fibrillization of PTH1–84 represents an important approach for in vivo applications, in view of the pharmaceutical applications for this protein. We embed the azobenzene derivate 3-{[(4-aminomethyl)phenyl]diazenyl}benzoic acid (3,4′-AMPB) into the PTH-derived peptide PTH25–37 to generate the artificial peptide AzoPTH25–37 via solid-phase synthesis. AzoPTH25–37 shows excellent photostability (more than 20 h in the dark) and can be reversibly photoswitched between its cis/trans forms. As investigated by ThT-monitored fibrillization assays, the trans-form of AzoPTH25–37 fibrillizes similar to PTH25–37, while the cis-form of AzoPTH25–37 generates only amorphous aggregates. Additionally, cis-AzoPTH25–37 catalytically inhibits the fibrillization of PTH25–37 in ratios of up to one-fifth. The approach reported here is designed to control the concentration of PTH-peptides, where the bioactive form can be catalytically controlled by an added photoswitchable peptide. Full article
(This article belongs to the Special Issue Protein (Re)Folding and Aggregation)
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12 pages, 2020 KiB  
Article
Structural and Computational Study of the GroEL–Prion Protein Complex
by Aleksandra A. Mamchur, Andrei V. Moiseenko, Irina S. Panina, Igor A. Yaroshevich, Sofia S. Kudryavtseva, Evgeny B. Pichkur, Olga S. Sokolova, Vladimir I. Muronetz and Tatiana B. Stanishneva-Konovalova
Biomedicines 2021, 9(11), 1649; https://doi.org/10.3390/biomedicines9111649 - 9 Nov 2021
Cited by 6 | Viewed by 2670
Abstract
The molecular chaperone GroEL is designed to promote protein folding and prevent aggregation. However, the interaction between GroEL and the prion protein, PrPC, could lead to pathogenic transformation of the latter to the aggregation-prone PrPSc form. Here, the molecular basis [...] Read more.
The molecular chaperone GroEL is designed to promote protein folding and prevent aggregation. However, the interaction between GroEL and the prion protein, PrPC, could lead to pathogenic transformation of the latter to the aggregation-prone PrPSc form. Here, the molecular basis of the interactions in the GroEL–PrP complex is studied with cryo-EM and molecular dynamics approaches. The obtained cryo-EM structure shows PrP to be bound to several subunits of GroEL at the level of their apical domains. According to MD simulations, the disordered N-domain of PrP forms much more intermolecular contacts with GroEL. Upon binding to the GroEL, the N-domain of PrP begins to form short helices, while the C-domain of PrP exhibits a tendency to unfold its α2-helix. In the absence of the nucleotides in the system, these processes are manifested at the hundred nanoseconds to microsecond timescale. Full article
(This article belongs to the Special Issue Protein (Re)Folding and Aggregation)
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19 pages, 2703 KiB  
Article
ATP and Tri-Polyphosphate (TPP) Suppress Protein Aggregate Growth by a Supercharging Mechanism
by Jordan Bye, Kiah Murray and Robin Curtis
Biomedicines 2021, 9(11), 1646; https://doi.org/10.3390/biomedicines9111646 - 9 Nov 2021
Cited by 5 | Viewed by 3085
Abstract
A common strategy to increase aggregation resistance is through rational mutagenesis to supercharge proteins, which leads to high colloidal stability, but often has the undesirable effect of lowering conformational stability. We show this trade-off can be overcome by using small multivalent polyphosphate ions, [...] Read more.
A common strategy to increase aggregation resistance is through rational mutagenesis to supercharge proteins, which leads to high colloidal stability, but often has the undesirable effect of lowering conformational stability. We show this trade-off can be overcome by using small multivalent polyphosphate ions, adenosine triphosphate (ATP) and tripolyphosphate (TPP) as excipients. These ions are equally effective at suppressing aggregation of ovalbumin and bovine serum albumin (BSA) upon thermal stress as monitored by dynamic and static light scattering. Monomer loss kinetic studies, combined with measurements of native state protein–protein interactions and ζ-potentials, indicate the ions reduce aggregate growth by increasing the protein colloidal stability through binding and overcharging the protein. Out of three additional proteins studied, ribonuclease A (RNaseA), α-chymotrypsinogen (α-Cgn), and lysozyme, we only observed a reduction in aggregate growth for RNaseA, although overcharging by the poly-phosphate ions still occurs for lysozyme and α-Cgn. Because the salts do not alter protein conformational stability, using them as excipients could be a promising strategy for stabilizing biopharmaceuticals once the protein structural factors that determine whether multivalent ion binding will increase colloidal stability are better elucidated. Our findings also have biological implications. Recently, it has been proposed that ATP also plays an important role in maintaining intracellular biological condensates and preventing protein aggregation in densely packed cellular environments. We expect electrostatic interactions are a significant factor in determining the stabilizing ability of ATP towards maintaining proteins in non-dispersed states in vivo. Full article
(This article belongs to the Special Issue Protein (Re)Folding and Aggregation)
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12 pages, 5889 KiB  
Article
The Human NUP58 Nucleoporin Can Form Amyloids In Vitro and In Vivo
by Lavrentii G. Danilov, Svetlana E. Moskalenko, Andrew G. Matveenko, Xenia V. Sukhanova, Mikhail V. Belousov, Galina A. Zhouravleva and Stanislav A. Bondarev
Biomedicines 2021, 9(10), 1451; https://doi.org/10.3390/biomedicines9101451 - 13 Oct 2021
Cited by 7 | Viewed by 2651
Abstract
Amyloids are fibrillar protein aggregates with a cross-β structure and unusual features, including high resistance to detergent or protease treatment. More than two hundred different proteins with amyloid or amyloid-like properties are already known. Several examples of nucleoporins (e.g., yeast Nup49, Nup100, Nup116, [...] Read more.
Amyloids are fibrillar protein aggregates with a cross-β structure and unusual features, including high resistance to detergent or protease treatment. More than two hundred different proteins with amyloid or amyloid-like properties are already known. Several examples of nucleoporins (e.g., yeast Nup49, Nup100, Nup116, and human NUP153) are supposed to form amyloid fibrils. In this study, we demonstrated an ability of the human NUP58 nucleoporin to form amyloid aggregates in vivo and in vitro. Moreover, we found two forms of NUP58 aggregates: oligomers and polymers stabilized by disulfide bonds. Bioinformatic analysis revealed that all known orthologs of this protein are potential amyloids which possess several regions with conserved ability to aggregation. The biological role of nucleoporin amyloid formation is debatable. We suggest that it is a rather abnormal process, which is characteristic for many proteins implicated in phase separation. Full article
(This article belongs to the Special Issue Protein (Re)Folding and Aggregation)
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16 pages, 1373 KiB  
Article
Protein Unfolding: Denaturant vs. Force
by Colleen Kelly and Matthew J. Gage
Biomedicines 2021, 9(10), 1395; https://doi.org/10.3390/biomedicines9101395 - 5 Oct 2021
Cited by 8 | Viewed by 3233
Abstract
While protein refolding has been studied for over 50 years since the pioneering work of Christian Anfinsen, there have been a limited number of studies correlating results between chemical, thermal, and mechanical unfolding. The limited knowledge of the relationship between these processes makes [...] Read more.
While protein refolding has been studied for over 50 years since the pioneering work of Christian Anfinsen, there have been a limited number of studies correlating results between chemical, thermal, and mechanical unfolding. The limited knowledge of the relationship between these processes makes it challenging to compare results between studies if different refolding methods were applied. Our current work compares the energetic barriers and folding rates derived from chemical, thermal, and mechanical experiments using an immunoglobulin-like domain from the muscle protein titin as a model system. This domain, I83, has high solubility and low stability relative to other Ig domains in titin, though its stability can be modulated by calcium. Our experiments demonstrated that the free energy of refolding was equivalent with all three techniques, but the refolding rates exhibited differences, with mechanical refolding having slightly faster rates. This suggests that results from equilibrium-based measurements can be compared directly but care should be given comparing refolding kinetics derived from refolding experiments that used different unfolding methods. Full article
(This article belongs to the Special Issue Protein (Re)Folding and Aggregation)
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