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Anjalikrishna PK, Gadre SR, Suresh CH. Topology of electrostatic potential and electron density reveals a covalent to non-covalent carbon-carbon bond continuum. Phys Chem Chem Phys 2023; 25:25191-25204. [PMID: 37721180 DOI: 10.1039/d3cp03268j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The covalent and non-covalent nature of carbon-carbon (CC) interactions in a wide range of molecular systems can be characterized using various methods, including the analysis of molecular electrostatic potential (MESP), represented as V(r), and the molecular electron density (MED), represented as ρ(r). These techniques provide valuable insights into the bonding between carbon atoms in different molecular environments. By uncovering a fundamental exponential relationship between the distance of the CC bond and the highest eigenvalue (λv1) of V(r) at the bond critical point (BCP), this study establishes the continuum model for all types of CC interactions, including transition states. The continuum model is further delineated into three distinct regions, namely covalent, borderline cases, and non-covalent, based on the gradient, , with the bond distance of the CC interaction. For covalent interactions, this parameter exhibits a more negative value than -5.0 a.u. Å-1, while for non-covalent interactions, it is less negative than -1.0 a.u. Å-1. Borderline cases, which encompass transition state structures, fall within the range of -1.0 to -5.0 a.u. Å-1. Furthermore, this study expands upon Popelier's analysis of the Laplacian of the MED, denoted as ∇2ρ, to encompass the entire spectrum of covalent, non-covalent, and borderline cases of CC interactions. Therefore, the present study presents compelling evidence supporting the concept of a continuum model for CC bonds in chemistry. Additionally, this continuum model is further explored within the context of C-N, C-O, C-S, N-N, O-O, and S-S interactions, albeit with a limited dataset.
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Affiliation(s)
- Puthannur K Anjalikrishna
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, 695019, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shridhar R Gadre
- Departments of Chemistry and Scientific Computing, Modelling & Simulation, Savitribai Phule Pune University, Pune 411007, India
| | - Cherumuttathu H Suresh
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, 695019, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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2
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Sun J, Song C, Ma D, Shen S, Huo S. Expanding the Toolbox for Peptide Disulfide Bond Formation via l-Methionine Selenoxide Oxidation. J Org Chem 2021; 86:4035-4044. [PMID: 33620221 DOI: 10.1021/acs.joc.0c02877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, l-methionine selenoxide (MetSeO) was used as an oxidant for the construction of peptide disulfide bonds. Excellent yields for various disulfide-containing peptides were achieved via the MetSeO oxidation method in different solvents and on a resin. Most importantly, the construction of disulfide bonds can be performed in the trifluoroacetic acid cocktail used for the cleavage of peptides from the resin, which obviates the steps of peptide purification and lyophilization. This facilitates and simplifies the synthesis of disulfide-containing peptides. Kinetic and mechanistic studies of the reaction between MetSeO and dithiothreitol (DTT, a model compound of dicysteine-containing peptide) show that the reaction is first order in both [MetSeO] and [DTT], and a reaction mechanism is proposed that can help us gain insights into the reaction of the oxidative synthesis of disulfide bonds via MetSeO oxidation.
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Affiliation(s)
- Jingjing Sun
- College of Chemistry and Environmental Science, Key Laboratory of Analytical Science and Technology of Hebei Province, and MOE Key Laboratory of Medicinal Chemistry and Molecular Diagnostics, Hebei University, Baoding 071002, Hebei Province, P. R. China
| | - Changying Song
- College of Chemistry and Environmental Science, Key Laboratory of Analytical Science and Technology of Hebei Province, and MOE Key Laboratory of Medicinal Chemistry and Molecular Diagnostics, Hebei University, Baoding 071002, Hebei Province, P. R. China
| | - Dongying Ma
- College of Chemistry and Environmental Science, Key Laboratory of Analytical Science and Technology of Hebei Province, and MOE Key Laboratory of Medicinal Chemistry and Molecular Diagnostics, Hebei University, Baoding 071002, Hebei Province, P. R. China
| | - Shigang Shen
- College of Chemistry and Environmental Science, Key Laboratory of Analytical Science and Technology of Hebei Province, and MOE Key Laboratory of Medicinal Chemistry and Molecular Diagnostics, Hebei University, Baoding 071002, Hebei Province, P. R. China
| | - Shuying Huo
- College of Chemistry and Environmental Science, Key Laboratory of Analytical Science and Technology of Hebei Province, and MOE Key Laboratory of Medicinal Chemistry and Molecular Diagnostics, Hebei University, Baoding 071002, Hebei Province, P. R. China
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Arai K, Iwaoka M. Flexible Folding: Disulfide-Containing Peptides and Proteins Choose the Pathway Depending on the Environments. Molecules 2021; 26:E195. [PMID: 33401729 PMCID: PMC7794709 DOI: 10.3390/molecules26010195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 11/18/2022] Open
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 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.
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Affiliation(s)
| | - Michio Iwaoka
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan;
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Iwaoka M, Mitsuji T, Shinozaki R. Oxidative folding pathways of bovine milk β-lactoglobulin with odd cysteine residues. FEBS Open Bio 2019; 9:1379-1391. [PMID: 31087497 PMCID: PMC6668375 DOI: 10.1002/2211-5463.12656] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/13/2019] [Indexed: 01/06/2023] Open
Abstract
Bovine β‐lactoglobulin (BLG) is a major whey protein with unique structural characteristics: it possesses a free Cys thiol (SH) and two disulfide (SS) bonds and consists of a β‐barrel core surrounded by one long and several short α helices. Although SS‐intact conformational folding has been studied in depth, the oxidative folding pathways and accompanying SS formation/rearrangement are poorly understood. In this study, we used trans‐3,4‐dihydroxyselenolane oxide, a water‐soluble selenoxide reagent which undergoes rapid and quantitative SS formation, to determine the oxidative folding pathways of BLG variant A (BLGA) at pH 8.0 and 25 °C. This was done by characterizing two key one‐SS intermediates, a particular folding intermediate having a Cys66–Cys160 SS bond (I‐1) and a particular folding intermediate having a Cys106–Cys119 SS bond (I‐2), which have a native Cys66–Cys160 and Cys106–Cys119 SS bond, respectively. In the major folding pathway, the reduced protein (R) with abundant α helices was oxidized to I‐1, which was then transformed to I‐2 through SS rearrangement. The native protein (N) was formed by oxidation of I‐2. The redundant Cys121 thiol facilitates SS rearrangement. N is also generated from an ensemble of folding intermediates having two SS bonds (2SS) intermediates with scrambled SS bonds through SS rearrangement, but this minor pathway is deteriorative due to aggregation or overoxidation of 2SS. During oxidative folding of BLGA, α→β conformational transition occurred as previously observed in SS‐intact folding. These findings are informative not only for elucidating oxidative folding pathways of other members of the β‐lactoglobulin family, but also for understanding the roles of a redundant Cys thiol in the oxidative folding process of a protein with odd Cys residues.
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Affiliation(s)
- Michio Iwaoka
- Department of Chemistry, School of Science, Tokai University, Hiratsuka-shi, Kanagawa, Japan
| | - Takumi Mitsuji
- Department of Chemistry, School of Science, Tokai University, Hiratsuka-shi, Kanagawa, Japan
| | - Reina Shinozaki
- Department of Chemistry, School of Science, Tokai University, Hiratsuka-shi, Kanagawa, Japan
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Abstract
trans-3,4-Dihydroxyselenolane oxide (DHSox), a water-soluble cyclic selenoxide reagent, is useful for rapid and quantitative formation of disulphide (SS) bonds in a reduced state of SS-containing proteins because the selenoxide is a strong but selective oxidant for thiol substrates (RSH) in a wide range of pH. Due to this advantage over common disulphide reagents, such as oxidized dithiothreitol (DTTox) and glutathione (GSSG), DHSox enables clear characterization of oxidative folding pathways of proteins. DHSox is also useful for facile diagnosis of weakly folded structure, or reactivity (i.e., pKa) of the thiols, present in a reduced polypeptide chain and the partially oxidized folding intermediates, identification of the key SS intermediates that can be oxidized directly to the native state, and preparation of SS-scrambled misfolded protein species. In this chapter, these diverse utilities of DHSox in protein folding study are demonstrated.
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Affiliation(s)
- Kenta Arai
- Department of Chemistry, School of Science, Tokai University, Hiratsuka-shi, Kanagawa, Japan
| | - Michio Iwaoka
- Department of Chemistry, School of Science, Tokai University, Hiratsuka-shi, Kanagawa, Japan.
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Characterization and optimization of two-chain folding pathways of insulin via native chain assembly. Commun Chem 2018. [DOI: 10.1038/s42004-018-0024-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Shinozaki R, Iwaoka M. Effects of Metal Ions, Temperature, and a Denaturant on the Oxidative Folding Pathways of Bovine α-Lactalbumin. Int J Mol Sci 2017; 18:ijms18091996. [PMID: 28926961 PMCID: PMC5618645 DOI: 10.3390/ijms18091996] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/02/2022] Open
Abstract
Bovine α-lactalbumin (αLA) has four disulfide (SS) bonds in the native form (N). On the oxidative folding pathways of this protein, two specific SS folding intermediates, i.e., (61–77, 73–91) and des[6–120], which have two and three native SS bonds, respectively, accumulate predominantly in the presence of Ca2+. In this study, we reinvestigated the pathways using a water-soluble cyclic selenoxide reagent, trans-3,4-dihydroxyselenolane oxide (DHSox), as a strong and quantitative oxidant to oxidize the fully reduced form (R). In the presence of ethylenediaminetetraacetic acid (EDTA) (under a metal-free condition), SS formation randomly proceeded, and N did not regenerate. On the other hand, two specific SS intermediates transiently generated in the presence of Ca2+. These intermediates could be assigned to (61–77, 73–91) and des[6–120] having two common SS bonds, i.e., Cys61-Cys77 and Cys73-Cys91, near the calcium binding pocket of the β-sheet domain. Much faster folding to N was observed in the presence of Mn2+, whereas Na+, K+, Mg2+, and Zn2+ did not affect the pathways. The two key intermediates were susceptible to temperature and a denaturant. The oxidative folding pathways revealed were significantly different from those of hen egg white lysozyme, which has the same SS-bonding pattern as αLA, suggesting that the folding pathways of SS-containing proteins can alter depending on the amino acid sequence and other factors, even when the SS-bond topologies are similar to each other.
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Affiliation(s)
- Reina Shinozaki
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan.
| | - Michio Iwaoka
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan.
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Synthesis, characterization, and structure of trans-3,4-dihydroxy-1-selenolane {DHS(OH)2} substituted derivatives. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Patil NA, Tailhades J, Hughes RA, Separovic F, Wade JD, Hossain MA. Cellular disulfide bond formation in bioactive peptides and proteins. Int J Mol Sci 2015; 16:1791-805. [PMID: 25594871 PMCID: PMC4307334 DOI: 10.3390/ijms16011791] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/02/2015] [Indexed: 11/16/2022] Open
Abstract
Bioactive peptides play important roles in metabolic regulation and modulation and many are used as therapeutics. These peptides often possess disulfide bonds, which are important for their structure, function and stability. A systematic network of enzymes--a disulfide bond generating enzyme, a disulfide bond donor enzyme and a redox cofactor--that function inside the cell dictates the formation and maintenance of disulfide bonds. The main pathways that catalyze disulfide bond formation in peptides and proteins in prokaryotes and eukaryotes are remarkably similar and share several mechanistic features. This review summarizes the formation of disulfide bonds in peptides and proteins by cellular and recombinant machinery.
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Affiliation(s)
- Nitin A Patil
- Florey Institute of Neuroscience and Mental Health, the University of Melbourne, Victoria 3010, Australia.
| | - Julien Tailhades
- Florey Institute of Neuroscience and Mental Health, the University of Melbourne, Victoria 3010, Australia.
| | - Richard Anthony Hughes
- Department of Pharmacology and Therapeutics, the University of Melbourne, Victoria 3010, Australia.
| | - Frances Separovic
- School of Chemistry, the University of Melbourne, Victoria 3010, Australia.
| | - John D Wade
- Florey Institute of Neuroscience and Mental Health, the University of Melbourne, Victoria 3010, Australia.
| | - Mohammed Akhter Hossain
- Florey Institute of Neuroscience and Mental Health, the University of Melbourne, Victoria 3010, Australia.
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Arai K, Moriai K, Ogawa A, Iwaoka M. An Amphiphilic Selenide Catalyst Behaves Like a Hybrid Mimic of Protein Disulfide Isomerase and Glutathione Peroxidase 7. Chem Asian J 2014; 9:3464-71. [DOI: 10.1002/asia.201402726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Indexed: 01/17/2023]
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12
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Reinvestigation of the oxidative folding pathways of hen egg white lysozyme: switching of the major pathways by temperature control. Int J Mol Sci 2013; 14:13194-212. [PMID: 23803654 PMCID: PMC3742182 DOI: 10.3390/ijms140713194] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/04/2013] [Accepted: 06/04/2013] [Indexed: 11/16/2022] Open
Abstract
It has been well established that in the oxidative folding of hen egg white lysozyme (HEL), which has four SS linkages in the native state (N), three des intermediates, i.e., des[76-94], des[64-80], and des [6-127], are populated at 20 °C and N is dominantly formed by the oxidation of des[64-80] and des[6-127]. To elucidate the temperature effects, the oxidative folding pathways of HEL were reinvestigated at 5-45 °C in the presence of 2 M urea at pH 8.0 by using a selenoxide reagent, DHSox. When reduced HEL was reacted with 1-4 equivalents of DHSox, 1S, 2S, 3S, and 4S intermediate ensembles with 1-4 SS linkages, respectively, were produced within 1 min. After the oxidation, 3S was slowly converted to the des intermediates with formation of the native structures through SS rearrangement. At 5 °C, des[76-94] was populated in the largest amount, but the oxidation to N was slower than that of des[64-80] and des[6-127]. At 35 °C, on the other hand, des[64-80] and des[6-127] were no longer stable, and only des[76-94] was populated. The results suggested that the major folding pathways of HEL can be switched from one to the other by temperature control.
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