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Oxidative Folding of Proteins and Peptides

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Organic Chemistry".

Deadline for manuscript submissions: closed (15 April 2021) | Viewed by 27341

Special Issue Editor

Department of Chemistry, School of Science, Tokai University, Kanagawa, Japan
Interests: selenium chemistry; protein chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since the pioneering work by Dr. Christian Anfinsen—a 1972 Nobel Laureate in Chemistry—in the 1960s, researchers have devoted many efforts to compiling experimental and theoretical outcomes from protein folding studies in the literature. In earlier years, such studies were focused on reproducing the process of protein folding in vitro to observe the transiently generated intermediates. As a result, the major folding pathways were characterized for several disulfide-containing proteins, such as bovine pancreatic trypsin inhibitor (BPTI) and ribonuclease A (RNase A). However, the general principle of protein folding, which can be applied to a variety of proteins, has not yet been elucidated.

On the other hand, oxidative protein folding in vivo has also been studied in depth in the last few decades. While a protein with disulfide bonds slowly gains its native structure in vitro under suitable redox conditions, this spontaneous process is controlled in vivo by various intracellular factors, such as protein disulfide isomerase (PDI) and molecular chaperons, which allow the protein to fold to its native structure in a short time. Proteins fold inside a cellular organelle, called endoplasmic reticulum (ER), but this oxidation process would also generate misfolded polypeptides (or non-natural species with scrambled disulfide bonds) in a certain ratio. The produced toxic misfolded species, however, can be reduced with the aid of other factors and returned to the regular folding process again. The structures and functional mechanisms of these factors remain largely unknown.

Recently, new experimental methodologies have been devised and successfully applied to various disulfide-containing proteins. For example, new folding reagents and artificial model peptides have been developed to elucidate the oxidative folding pathways in vitro in more detail. Structural and functional analyses of the factor proteins, which are involved in the oxidative protein folding in vivo, have been elaborated to promote our understanding of oxidative protein folding. These factors were also found to be relevant to protein misfolding diseases.

In this Special Issue of Molecules, original research articles as well as reviews in related research areas, namely oxidative folding of protein and peptides, are cordially invited.

Prof. Dr. Michio Iwaoka
Guest Editor

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Keywords

  • Disulfide formation and rearrangement
  • Folding mechanisms
  • In-cell folding
  • Protein misfolding
  • Artificial peptides and proteins

Published Papers (8 papers)

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Research

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11 pages, 2698 KiB  
Article
Ca2+ Regulates ERp57-Calnexin Complex Formation
Molecules 2021, 26(10), 2853; https://doi.org/10.3390/molecules26102853 - 11 May 2021
Cited by 6 | Viewed by 3314
Abstract
ERp57, a member of the protein disulfide isomerase family, is a ubiquitous disulfide catalyst that functions in the oxidative folding of various clients in the mammalian endoplasmic reticulum (ER). In concert with ER lectin-like chaperones calnexin and calreticulin (CNX/CRT), ERp57 functions in virtually [...] Read more.
ERp57, a member of the protein disulfide isomerase family, is a ubiquitous disulfide catalyst that functions in the oxidative folding of various clients in the mammalian endoplasmic reticulum (ER). In concert with ER lectin-like chaperones calnexin and calreticulin (CNX/CRT), ERp57 functions in virtually all folding stages from co-translation to post-translation, and thus plays a critical role in maintaining protein homeostasis, with direct implication for pathology. Here, we present mechanisms by which Ca2+ regulates the formation of the ERp57-calnexin complex. Biochemical and isothermal titration calorimetry analyses revealed that ERp57 strongly interacts with CNX via a non-covalent bond in the absence of Ca2+. The ERp57-CNX complex not only promoted the oxidative folding of human leukocyte antigen heavy chains, but also inhibited client aggregation. These results suggest that this complex performs both enzymatic and chaperoning functions under abnormal physiological conditions, such as Ca2+ depletion, to effectively guide proper oxidative protein folding. The findings shed light on the molecular mechanisms underpinning crosstalk between the chaperone network and Ca2+. Full article
(This article belongs to the Special Issue Oxidative Folding of Proteins and Peptides)
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14 pages, 1471 KiB  
Article
Conjugate of Thiol and Guanidyl Units with Oligoethylene Glycol Linkage for Manipulation of Oxidative Protein Folding
Molecules 2021, 26(4), 879; https://doi.org/10.3390/molecules26040879 - 07 Feb 2021
Cited by 1 | Viewed by 2142
Abstract
Oxidative protein folding is a biological process to obtain a native conformation of a protein through disulfide-bond formation between cysteine residues. In a cell, disulfide-catalysts such as protein disulfide isomerase promote the oxidative protein folding. Inspired by the active sites of the disulfide-catalysts, [...] Read more.
Oxidative protein folding is a biological process to obtain a native conformation of a protein through disulfide-bond formation between cysteine residues. In a cell, disulfide-catalysts such as protein disulfide isomerase promote the oxidative protein folding. Inspired by the active sites of the disulfide-catalysts, synthetic redox-active thiol compounds have been developed, which have shown significant promotion of the folding processes. In our previous study, coupling effects of a thiol group and guanidyl unit on the folding promotion were reported. Herein, we investigated the influences of a spacer between the thiol group and guanidyl unit. A conjugate between thiol and guanidyl units with a diethylene glycol spacer (GdnDEG-SH) showed lower folding promotion effect compared to the thiol–guanidyl conjugate without the spacer (GdnSH). Lower acidity and a more reductive property of the thiol group of GdnDEG-SH compared to those of GdnSH likely resulted in the reduced efficiency of the folding promotion. Thus, the spacer between the thiol and guanidyl groups is critical for the promotion of oxidative protein folding. Full article
(This article belongs to the Special Issue Oxidative Folding of Proteins and Peptides)
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9 pages, 1954 KiB  
Article
Multiple Disulfide-Bonded States of Native Proteins: Estimate of Number Using Probabilities of Disulfide Bond Formation
Molecules 2020, 25(23), 5729; https://doi.org/10.3390/molecules25235729 - 04 Dec 2020
Cited by 6 | Viewed by 2579
Abstract
The polypeptide backbone of proteins is held together by two main types of covalent bonds: the peptide bonds that link the amino acid residues and the disulfide bonds that link pairs of cysteine amino acids. Disulfide bonds form as a protein folds in [...] Read more.
The polypeptide backbone of proteins is held together by two main types of covalent bonds: the peptide bonds that link the amino acid residues and the disulfide bonds that link pairs of cysteine amino acids. Disulfide bonds form as a protein folds in the cell and formation was assumed to be complete when the mature protein emerges. This is not the case for some secreted human blood proteins. The blood clotting protein, fibrinogen, and the protease inhibitor, α2-macroglobulin, exist in multiple disulfide-bonded or covalent states in the circulation. Thousands of different states are predicted assuming no dependencies on disulfide bond formation. In this study, probabilities for disulfide bond formation are employed to estimate numbers of covalent states of a model polypeptide with reference to α2-macroglobulin. When disulfide formation is interdependent in a protein, the number of covalent states is greatly reduced. Theoretical estimates of the number of states will aid the conceptual and experimental challenges of investigating multiple disulfide-bonded states of a protein. Full article
(This article belongs to the Special Issue Oxidative Folding of Proteins and Peptides)
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11 pages, 2060 KiB  
Article
Topological Regulation of the Bioactive Conformation of a Disulfide-Rich Peptide, Heat-Stable Enterotoxin
Molecules 2020, 25(20), 4798; https://doi.org/10.3390/molecules25204798 - 21 Oct 2020
Cited by 5 | Viewed by 2115
Abstract
Heat-stable enterotoxin (STa) produced by enterotoxigenic E. coli causes acute diarrhea and also can be used as a specific probe for colorectal cancer cells. STa contains three intra-molecular disulfide bonds (C1–C4, C2–C5, and C3–C6 connectivity). The chemical synthesis of ST [...] Read more.
Heat-stable enterotoxin (STa) produced by enterotoxigenic E. coli causes acute diarrhea and also can be used as a specific probe for colorectal cancer cells. STa contains three intra-molecular disulfide bonds (C1–C4, C2–C5, and C3–C6 connectivity). The chemical synthesis of STa provided not only the native type of STa but also a topological isomer that had the native disulfide pairings. Interestingly, the activity of the topological isomer was approximately 1/10–1/2 that of the native STa. To further investigate the bioactive conformation of this molecule and the regulation of disulfide-coupled folding during its chemical syntheses, we examined the folding mechanism of STa that occurs during its chemical synthesis. The folding intermediate of STa with two disulfide bonds (C1–C4 and C3–C6) and two Cys(Acm) residues, the precursor peptide, was treated with iodine to produce a third disulfide bond under several conditions. The topological isomer was predominantly produced under all conditions tested, along with trace amounts of the native type of STa. In addition, NMR measurements indicated that the topological isomer has a left-handed spiral structure similar to that of the precursor peptide, while the native type of STa had a right-handed spiral structure. These results indicate that the order of the regioselective formation of disulfide bonds is important for the regulation of the final conformation of disulfide-rich peptides in chemical synthesis. Full article
(This article belongs to the Special Issue Oxidative Folding of Proteins and Peptides)
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Review

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58 pages, 13602 KiB  
Review
Discussions of Fluorescence in Selenium Chemistry: Recently Reported Probes, Particles, and a Clearer Biological Knowledge
Molecules 2021, 26(3), 692; https://doi.org/10.3390/molecules26030692 - 28 Jan 2021
Cited by 30 | Viewed by 4390
Abstract
In this review from literature appearing over about the past 5 years, we focus on selected selenide reports and related chemistry; we aimed for a digestible, relevant, review intended to be usefully interconnected within the realm of fluorescence and selenium chemistry. Tellurium is [...] Read more.
In this review from literature appearing over about the past 5 years, we focus on selected selenide reports and related chemistry; we aimed for a digestible, relevant, review intended to be usefully interconnected within the realm of fluorescence and selenium chemistry. Tellurium is mentioned where relevant. Topics include selenium in physics and surfaces, nanoscience, sensing and fluorescence, quantum dots and nanoparticles, Au and oxide nanoparticles quantum dot based, coatings and catalyst poisons, thin film, and aspects of solar energy conversion. Chemosensing is covered, whether small molecule or nanoparticle based, relating to metal ion analytes, H2S, as well as analyte sulfane (biothiols—including glutathione). We cover recent reports of probing and fluorescence when they deal with redox biology aspects. Selenium in therapeutics, medicinal chemistry and skeleton cores is covered. Selenium serves as a constituent for some small molecule sensors and probes. Typically, the selenium is part of the reactive, or active site of the probe; in other cases, it is featured as the analyte, either as a reduced or oxidized form of selenium. Free radicals and ROS are also mentioned; aggregation strategies are treated in some places. Also, the relationship between reduced selenium and oxidized selenium is developed. Full article
(This article belongs to the Special Issue Oxidative Folding of Proteins and Peptides)
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19 pages, 7603 KiB  
Review
Flexible Folding: Disulfide-Containing Peptides and Proteins Choose the Pathway Depending on the Environments
Molecules 2021, 26(1), 195; https://doi.org/10.3390/molecules26010195 - 02 Jan 2021
Cited by 12 | Viewed by 2324
Abstract
In the last few decades, development of novel experimental techniques, such as new types of disulfide (SS)-forming reagents and genetic and chemical technologies for synthesizing designed artificial proteins, is opening a new realm of the oxidative folding study where peptides and proteins can [...] Read more.
In the last few decades, development of novel experimental techniques, such as new types of disulfide (SS)-forming reagents and genetic and chemical technologies for synthesizing designed artificial proteins, is opening a new realm of the oxidative folding study where peptides and proteins can be folded under physiologically more relevant conditions. In this review, after a brief overview of the historical and physicochemical background of oxidative protein folding study, recently revealed folding pathways of several representative peptides and proteins are summarized, including those having two, three, or four SS bonds in the native state, as well as those with odd Cys residues or consisting of two peptide chains. Comparison of the updated pathways with those reported in the early years has revealed the flexible nature of the protein folding pathways. The significantly different pathways characterized for hen-egg white lysozyme and bovine milk α-lactalbumin, which belong to the same protein superfamily, suggest that the information of protein folding pathways, not only the native folded structure, is encoded in the amino acid sequence. The application of the flexible pathways of peptides and proteins to the engineering of folded three-dimensional structures is an interesting and important issue in the new realm of the current oxidative protein folding study. Full article
(This article belongs to the Special Issue Oxidative Folding of Proteins and Peptides)
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19 pages, 2325 KiB  
Review
PDI-Regulated Disulfide Bond Formation in Protein Folding and Biomolecular Assembly
Molecules 2021, 26(1), 171; https://doi.org/10.3390/molecules26010171 - 31 Dec 2020
Cited by 38 | Viewed by 6039
Abstract
Disulfide bonds play a pivotal role in maintaining the natural structures of proteins to ensure their performance of normal biological functions. Moreover, biological molecular assembly, such as the gluten network, is also largely dependent on the intermolecular crosslinking via disulfide bonds. In eukaryotes, [...] Read more.
Disulfide bonds play a pivotal role in maintaining the natural structures of proteins to ensure their performance of normal biological functions. Moreover, biological molecular assembly, such as the gluten network, is also largely dependent on the intermolecular crosslinking via disulfide bonds. In eukaryotes, the formation and rearrangement of most intra- and intermolecular disulfide bonds in the endoplasmic reticulum (ER) are mediated by protein disulfide isomerases (PDIs), which consist of multiple thioredoxin-like domains. These domains assist correct folding of proteins, as well as effectively prevent the aggregation of misfolded ones. Protein misfolding often leads to the formation of pathological protein aggregations that cause many diseases. On the other hand, glutenin aggregation and subsequent crosslinking are required for the formation of a rheologically dominating gluten network. Herein, the mechanism of PDI-regulated disulfide bond formation is important for understanding not only protein folding and associated diseases, but also the formation of functional biomolecular assembly. This review systematically illustrated the process of human protein disulfide isomerase (hPDI) mediated disulfide bond formation and complemented this with the current mechanism of wheat protein disulfide isomerase (wPDI) catalyzed formation of gluten networks. Full article
(This article belongs to the Special Issue Oxidative Folding of Proteins and Peptides)
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19 pages, 2286 KiB  
Review
Revisiting the Formation of a Native Disulfide Bond: Consequences for Protein Regeneration and Beyond
Molecules 2020, 25(22), 5337; https://doi.org/10.3390/molecules25225337 - 16 Nov 2020
Cited by 12 | Viewed by 3325
Abstract
Oxidative protein folding involves the formation of disulfide bonds and the regeneration of native structure (N) from the fully reduced and unfolded protein (R). Oxidative protein folding studies have provided a wealth of information on underlying physico-chemical reactions by which disulfide-bond-containing proteins acquire [...] Read more.
Oxidative protein folding involves the formation of disulfide bonds and the regeneration of native structure (N) from the fully reduced and unfolded protein (R). Oxidative protein folding studies have provided a wealth of information on underlying physico-chemical reactions by which disulfide-bond-containing proteins acquire their catalytically active form. Initially, we review key events underlying oxidative protein folding using bovine pancreatic ribonuclease A (RNase A), bovine pancreatic trypsin inhibitor (BPTI) and hen-egg white lysozyme (HEWL) as model disulfide bond-containing folders and discuss consequential outcomes with regard to their folding trajectories. We re-examine the findings from the same studies to underscore the importance of forming native disulfide bonds and generating a “native-like” structure early on in the oxidative folding pathway. The impact of both these features on the regeneration landscape are highlighted by comparing ideal, albeit hypothetical, regeneration scenarios with those wherein a native-like structure is formed relatively “late” in the R→N trajectory. A special case where the desired characteristics of oxidative folding trajectories can, nevertheless, stall folding is also discussed. The importance of these data from oxidative protein folding studies is projected onto outcomes, including their impact on the regeneration rate, yield, misfolding, misfolded-flux trafficking from the endoplasmic reticulum (ER) to the cytoplasm, and the onset of neurodegenerative disorders. Full article
(This article belongs to the Special Issue Oxidative Folding of Proteins and Peptides)
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