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Journal articles on the topic 'Disulfide bonds'

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Published: 4 June 2021

Last updated: 27 April 2022

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1

Hogg, Philip J. "Allosteric Disulfide Bonds in Thrombosis and Thrombolysis." Blood 108, no. 11 (November 16, 2006): 4036. http://dx.doi.org/10.1182/blood.v108.11.4036.4036.

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Abstract Allosteric disulfide bonds control protein function by mediating conformational change when they undergo reduction or oxidation. The known allosteric disulfides are characterized by a particular bond geometry, the -RHStaple. A number of thrombosis and thrombolysis proteins contain one or more disulfide bonds of this type. Tissue factor (TF) is the first haemostasis protein shown to be controlled by an allosteric disulfide, the Cys186-Cys209 bond in the membrane-proximal fibronectin type III domain. TF exists in three forms on the cell surface; a cryptic form that is inert, a coagulant form that binds factor VIIa to initiate coagulation, or a signaling form that binds VIIa and cleaves protease activated receptor 2 that functions in inflammation, tumor progression and angiogenesis. Reduction and oxidation of the Cys186-Cys209 bond is central to the transition between the three activities of TF. The redox state of the bond appears to be controlled by protein disulphide isomerase and NO. Plasmin(ogen), vitronectin, glycoprotein 1balpha, integrin beta3 and thrombomodulin also contain -RHStaple disulfides and there is circumstantial evidence that the function of these proteins may involve redox change of these disulfide bonds.

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2

Pijning, Aster E., Joyce Chiu, Reichelle X. Yeo, Jason W. H. Wong, and Philip J. Hogg. "Identification of allosteric disulfides from labile bonds in X-ray structures." Royal Society Open Science 5, no. 2 (February 2018): 171058. http://dx.doi.org/10.1098/rsos.171058.

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Protein disulfide bonds link pairs of cysteine sulfur atoms and are either structural or functional motifs. The allosteric disulfides control the function of the protein in which they reside when cleaved or formed. Here, we identify potential allosteric disulfides in all Protein Data Bank X-ray structures from bonds that are present in some molecules of a protein crystal but absent in others, or present in some structures of a protein but absent in others. We reasoned that the labile nature of these disulfides signifies a propensity for cleavage and so possible allosteric regulation of the protein in which the bond resides. A total of 511 labile disulfide bonds were identified. The labile disulfides are more stressed than the average bond, being characterized by high average torsional strain and stretching of the sulfur–sulfur bond and neighbouring bond angles. This pre-stress likely underpins their susceptibility to cleavage. The coagulation, complement and oxygen-sensing hypoxia inducible factor-1 pathways, which are known or have been suggested to be regulated by allosteric disulfides, are enriched in proteins containing labile disulfides. The identification of labile disulfide bonds will facilitate the study of this post-translational modification.

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3

Schmidt, Bryan, Lorraine Ho, and Philip J. Hogg. "Allosteric Disulfide Bonds†." Biochemistry 45, no. 24 (June 2006): 7429–33. http://dx.doi.org/10.1021/bi0603064.

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4

Glidewell, Christopher, John N. Low, and James L. Wardell. "Conformational preferences and supramolecular aggregation in 2-nitrophenylthiolates: disulfides and thiosulfonates." Acta Crystallographica Section B Structural Science 56, no. 5 (October 1, 2000): 893–905. http://dx.doi.org/10.1107/s0108768100007114.

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In each of the asymmetrically substituted disulfides 2-nitro-4′-methyldiphenyl disulfide, C13H11NO2S2 (1), 2-nitro-4′-chlorodiphenyl disulfide, C12H8ClNO2S2 (2), 2,4-dinitro-4′-methyldiphenyl disulfide, C13H10N2O4S2 (3), and 2,4-dinitrophenyl-2′-methoxycarbonylmethyl disulfide, C9H8N2O6S2 (4), and in both of the symmetrically substituted disulfides bis(2-nitrophenyl) disulfide, C12H8N2O4S2 (5), and bis(2-nitro-4-trifluoromethylphenyl) disulfide, C14H6F6N2O4S2 (6), the 2-nitro groups are essentially coplanar with the adjacent aryl ring and the S atom remote from the nitrated aryl ring is also essentially coplanar and transoid to the nitro group. In S-(2-nitrophenyl) 2-nitrobenzene thiosulfonate, C12H8N2O6S2 (7), which contains three independent molecules in the asymmetric unit, all six of the independent nitro groups are twisted out of the plane of the adjacent aryl rings. The crystal structures of (1)–(3) contain isolated molecules, that of (4) contains centrosymmetric dimers held together by C—H...O hydrogen bonds, while in the structures of (5)—(7), respectively, the C—H...O hydrogen bonds generate one-, two- and three-dimensional arrays. The interplay between molecular conformation and supramolecular aggregation is discussed.

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5

Liu, Tao, Yan Wang, Xiaozhou Luo, Jack Li, Sean A. Reed, Han Xiao, Travis S. Young, and Peter G. Schultz. "Enhancing protein stability with extended disulfide bonds." Proceedings of the National Academy of Sciences 113, no. 21 (May 9, 2016): 5910–15. http://dx.doi.org/10.1073/pnas.1605363113.

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Disulfide bonds play an important role in protein folding and stability. However, the cross-linking of sites within proteins by cysteine disulfides has significant distance and dihedral angle constraints. Here we report the genetic encoding of noncanonical amino acids containing long side-chain thiols that are readily incorporated into both bacterial and mammalian proteins in good yields and with excellent fidelity. These amino acids can pair with cysteines to afford extended disulfide bonds and allow cross-linking of more distant sites and distinct domains of proteins. To demonstrate this notion, we preformed growth-based selection experiments at nonpermissive temperatures using a library of random β-lactamase mutants containing these noncanonical amino acids. A mutant enzyme that is cross-linked by one such extended disulfide bond and is stabilized by ∼9 °C was identified. This result indicates that an expanded set of building blocks beyond the canonical 20 amino acids can lead to proteins with improved properties by unique mechanisms, distinct from those possible through conventional mutagenesis schemes.

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6

Onda, Yayoi. "Oxidative Protein-Folding Systems in Plant Cells." International Journal of Cell Biology 2013 (2013): 1–15. http://dx.doi.org/10.1155/2013/585431.

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Plants are unique among eukaryotes in having evolved organelles: the protein storage vacuole, protein body, and chloroplast. Disulfide transfer pathways that function in the endoplasmic reticulum (ER) and chloroplasts of plants play critical roles in the development of protein storage organelles and the biogenesis of chloroplasts, respectively. Disulfide bond formation requires the cooperative function of disulfide-generating enzymes (e.g., ER oxidoreductase 1), which generate disulfide bonds de novo, and disulfide carrier proteins (e.g., protein disulfide isomerase), which transfer disulfides to substrates by means of thiol-disulfide exchange reactions. Selective molecular communication between disulfide-generating enzymes and disulfide carrier proteins, which reflects the molecular and structural diversity of disulfide carrier proteins, is key to the efficient transfer of disulfides to specific sets of substrates. This review focuses on recent advances in our understanding of the mechanisms and functions of the various disulfide transfer pathways involved in oxidative protein folding in the ER, chloroplasts, and mitochondria of plants.

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7

Saunders, Aleister J., Gregory B. Young, and Gary J. Pielak. "Polarity of disulfide bonds." Protein Science 2, no. 7 (July 1993): 1183–84. http://dx.doi.org/10.1002/pro.5560020713.

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8

Robinson, Philip J., Shingo Kanemura, Xiaofei Cao, and Neil J. Bulleid. "Protein secondary structure determines the temporal relationship between folding and disulfide formation." Journal of Biological Chemistry 295, no. 8 (January 17, 2020): 2438–48. http://dx.doi.org/10.1074/jbc.ra119.011983.

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How and when disulfide bonds form in proteins relative to the stage of their folding is a fundamental question in cell biology. Two models describe this relationship: the folded precursor model, in which a nascent structure forms before disulfides do, and the quasi-stochastic model, where disulfides form prior to folding. Here we investigated oxidative folding of three structurally diverse substrates, β2-microglobulin, prolactin, and the disintegrin domain of ADAM metallopeptidase domain 10 (ADAM10), to understand how these mechanisms apply in a cellular context. We used a eukaryotic cell-free translation system in which we could identify disulfide isomers in stalled translation intermediates to characterize the timing of disulfide formation relative to translocation into the endoplasmic reticulum and the presence of non-native disulfides. Our results indicate that in a domain lacking secondary structure, disulfides form before conformational folding through a process prone to nonnative disulfide formation, whereas in proteins with defined secondary structure, native disulfide formation occurs after partial folding. These findings reveal that the nascent protein structure promotes correct disulfide formation during cotranslational folding.

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9

van Anken, Eelco, Rogier W. Sanders, I. Marije Liscaljet, Aafke Land, Ilja Bontjer, Sonja Tillemans, Alexey A. Nabatov, William A. Paxton, Ben Berkhout, and Ineke Braakman. "Only Five of 10 Strictly Conserved Disulfide Bonds Are Essential for Folding and Eight for Function of the HIV-1 Envelope Glycoprotein." Molecular Biology of the Cell 19, no. 10 (October 2008): 4298–309. http://dx.doi.org/10.1091/mbc.e07-12-1282.

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Protein folding in the endoplasmic reticulum goes hand in hand with disulfide bond formation, and disulfide bonds are considered key structural elements for a protein's folding and function. We used the HIV-1 Envelope glycoprotein to examine in detail the importance of its 10 completely conserved disulfide bonds. We systematically mutated the cysteines in its ectodomain, assayed the mutants for oxidative folding, transport, and incorporation into the virus, and tested fitness of mutant viruses. We found that the protein was remarkably tolerant toward manipulation of its disulfide-bonded structure. Five of 10 disulfide bonds were dispensable for folding. Two of these were even expendable for viral replication in cell culture, indicating that the relevance of these disulfide bonds becomes manifest only during natural infection. Our findings refine old paradigms on the importance of disulfide bonds for proteins.

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10

Haworth, Naomi L., and Merridee A. Wouters. "Cross-strand disulfides in the non-hydrogen bonding site of antiparallel β-sheet (aCSDns): poised for biological switching." RSC Advances 5, no. 105 (2015): 86303–21. http://dx.doi.org/10.1039/c5ra10672a.

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aCSDns are forbidden disulfides with protein redox-activity. Within the aCSDn structural motif, a cognate substrate of Trx-like enzymes, the disulfide bonds are strained and metastable, facilitating their role as redox-regulated protein switches.

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11

Wedemeyer, William J., Ervin Welker, Mahesh Narayan, and Harold A. Scheraga. "Disulfide Bonds and Protein Folding†." Biochemistry 39, no. 15 (April 2000): 4207–16. http://dx.doi.org/10.1021/bi992922o.

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12

Wedemeyer, William J., Ervin Welker, Mahesh Narayan, and Harold A. Scheraga. "Disulfide Bonds and Protein Folding." Biochemistry 39, no. 23 (June 2000): 7032. http://dx.doi.org/10.1021/bi005111p.

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13

Depuydt, Matthieu, Joris Messens, and Jean-Francois Collet. "How Proteins Form Disulfide Bonds." Antioxidants & Redox Signaling 15, no. 1 (July 2011): 49–66. http://dx.doi.org/10.1089/ars.2010.3575.

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14

Yang, Hui, Yunhao Bai, Banglu Yu, Zhiqiang Wang, and Xi Zhang. "Supramolecular polymers bearing disulfide bonds." Polym. Chem. 5, no. 22 (2014): 6439–43. http://dx.doi.org/10.1039/c4py01003e.

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15

Raina, S., and D. Missiakas. "MAKING AND BREAKING DISULFIDE BONDS." Annual Review of Microbiology 51, no. 1 (October 1997): 179–202. http://dx.doi.org/10.1146/annurev.micro.51.1.179.

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16

Rabenstein, Dallas L., and Yvon Theriault. "A nuclear magnetic resonance study of the formation and conformational equilibria of symmetrical and mixed disulfides of captopril." Canadian Journal of Chemistry 63, no. 1 (January 1, 1985): 33–39. http://dx.doi.org/10.1139/v85-006.

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The oxidation of captopril (CpSH, 1-(D-3-mercapto-2-methylpropanoyl)-1-proline) by glutathione disulfide (GSSG) via thiol/disulfide exchange to form, in the first step, CpSSG and GSH and, in the second step, CpSSCp and GSH, has been studied in aqueous solution by 1H nmr. Due to slow rotation around the amide bond(s) of CpSH and CpSSCp and of the captopril part of CpSSG, separate resonances are observed for the cis and trans conformations across these bonds. Conformational equilibrium constants were estimated as a function of pH for CpSH, CpSSCp, and CpSSG from the intensities of resonances for the cis and trans isomers. These equilibrium constants were used in the determination of equilibrium constants for the two steps in the oxidation of CpSH by GSSG. The results suggest that CpSH has a greater tendency to reduce disulfide bonds by thiol/disulfide exchange at physiological pH, and thus form mixed disulfides, than do the thiol groups in amino acids. Also, the conformational equilibrium constants indicate that, at physiological pH, approximately two thirds of the captopril, either free or in a disulfide form, has the trans conformation.

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17

Kadokura, Hiroshi, Lorenzo Nichols, and Jon Beckwith. "Mutational Alterations of the Key cis Proline Residue That Cause Accumulation of Enzymatic Reaction Intermediates of DsbA, a Member of the Thioredoxin Superfamily." Journal of Bacteriology 187, no. 4 (February 15, 2005): 1519–22. http://dx.doi.org/10.1128/jb.187.4.1519-1522.2005.

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ABSTRACT The DsbA-DsbB pathway introduces disulfide bonds into newly translocated proteins. Conversion of the conserved cis proline 151 of DsbA to several hydrophilic residues results in accumulation of mixed disulfides between DsbA and its dedicated oxidant, DsbB. However, only a proline-to-threonine change causes accumulation of mixed disulfides of DsbA with its substrates.

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18

Singh, Sneha, Mohammad Suhail Akhter, Johannes Dodt, Amit Sharma, Senthilvelrajan Kaniyappan, Hamideh Yadegari, Vytautas Ivaskevicius, Johannes Oldenburg, and Arijit Biswas. "Disruption of Structural Disulfides of Coagulation FXIII-B Subunit; Functional Implications for a Rare Bleeding Disorder." International Journal of Molecular Sciences 20, no. 8 (April 22, 2019): 1956. http://dx.doi.org/10.3390/ijms20081956.

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Congenital FXIII deficiency is a rare bleeding disorder in which mutations are detected in F13A1 and F13B genes that express the two subunits of coagulation FXIII, the catalytic FXIII-A, and protective FXIII-B. Mutations in FXIII-B subunit are considerably rarer compared to FXIII-A. Three mutations in the F13B gene have been reported on its structural disulfide bonds. In the present study, we investigate the structural and functional importance of all 20 structural disulfide bonds in FXIII-B subunit. All disulfide bonds were ablated by individually mutating one of its contributory cysteine’s, and these variants were transiently expressed in HEK293t cell lines. The expression products were studied for stability, secretion, the effect on oligomeric state, and on FXIII-A activation. The structural flexibility of these disulfide bonds was studied using classical MD simulation performed on a FXIII-B subunit monomer model. All 20 FXIII-B were found to be important for the secretion and stability of the protein since ablation of any of these led to a secretion deficit. However, the degree of effect that the disruption of disulfide bond had on the protein differed between individual disulfide bonds reflecting a functional hierarchy/diversity within these disulfide bonds.

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19

Hogg, Philip J. "Multiple Disulfide-Bonded States of Native Proteins: Estimate of Number Using Probabilities of Disulfide Bond Formation." Molecules 25, no. 23 (December 4, 2020): 5729. http://dx.doi.org/10.3390/molecules25235729.

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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.

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20

Phinney, Brett S., and Dennis T. Brown. "Sindbis Virus Glycoprotein E1 Is Divided into Two Discrete Domains at Amino Acid 129 by Disulfide Bridge Connections." Journal of Virology 74, no. 19 (October 1, 2000): 9313–16. http://dx.doi.org/10.1128/jvi.74.19.9313-9316.2000.

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ABSTRACT The E1 membrane glycoprotein of Sindbis virus contains structural and functional domains, which are conformationally dependent on the presence of intramolecular disulfide bridges (B. A. Abell and D. T. Brown, J. Virol. 67:5496–5501, 1993; R. P. Anthony, A. M. Paredes, and D. T. Brown, Virology 190:330–336, 1992). We have examined the disulfide bonds in E1 and have determined that the E1 membrane glycoprotein contains two separate sets of interconnecting disulfide linkages, which divide the protein into two domains at amino acid 129. These separate sets of disulfides may stabilize and define the structural and functional regions of the E1 protein.

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21

Shabanpoor, Fazel, Mohammed Akhter Hossain, Feng Lin, and John D. Wade. "ChemInform Abstract: Sequential Formation of Regioselective Disulfide Bonds in Synthetic Peptides with Multiple Disulfide Bonds." ChemInform 46, no. 20 (April 27, 2015): no. http://dx.doi.org/10.1002/chin.201520319.

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22

Markgren, Joel, Mikael Hedenqvist, Faiza Rasheed, Marie Skepö, and Eva Johansson. "Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo Simulations." Biomolecules 10, no. 8 (July 23, 2020): 1095. http://dx.doi.org/10.3390/biom10081095.

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Gluten protein crosslinking is a predetermined process where specific intra- and intermolecular disulfide bonds differ depending on the protein and cysteine motif. In this article, all-atom Monte Carlo simulations were used to understand the formation of disulfide bonds in gliadins and low molecular weight glutenin subunits (LMW-GS). The two intrinsically disordered proteins appeared to contain mostly turns and loops and showed “self-avoiding walk” behavior in water. Cysteine residues involved in intramolecular disulfide bonds were located next to hydrophobic peptide sections in the primary sequence. Hydrophobicity of neighboring peptide sections, synthesis chronology, and amino acid chain flexibility were identified as important factors in securing the specificity of intramolecular disulfide bonds formed directly after synthesis. The two LMW-GS cysteine residues that form intermolecular disulfide bonds were positioned next to peptide sections of lower hydrophobicity, and these cysteine residues are more exposed to the cytosolic conditions, which influence the crosslinking behavior. In addition, coarse-grained Monte Carlo simulations revealed that the protein folding is independent of ionic strength. The potential molecular behavior associated with disulfide bonds, as reported here, increases the biological understanding of seed storage protein function and provides opportunities to tailor their functional properties for different applications.

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23

Li, Jun Sheng, Wei Jing, Liu Juan Yan, and Li Na Li. "Preparation of Water-Soluble Soy Protein-Based Surfactants by Oxidizing Disulfide Bonds." Advanced Materials Research 236-238 (May 2011): 63–66. http://dx.doi.org/10.4028/www.scientific.net/amr.236-238.63.

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In this paper, the correlations between the cleavage degree of disulfide bonds and soy protein surface activity had been studied in order to show the surface activity of soy protein. The disulfide bonds of soy protein were oxidized to sulfonic groups by performic acid. The distribution of polar and nonpolar groups, and the molecular structure of soy protein were changed because of the oxidation damage of disulfide bonds, and these changes led to changes in surface activity of soy protein. The results showed that the emulsifying property of soy protein was improved by oxidizing the disulfide bonds of protein compared with that of natural soy protein. The change of soy protein emulsifying property is closely related with the degree of the disulfide bond oxidation damage,and that was also an effective way to prepare the protein-based surfactant.

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24

Go, Eden P., Albert Cupo, Rajesh Ringe, Pavel Pugach, John P. Moore, and Heather Desaire. "Native Conformation and Canonical Disulfide Bond Formation Are Interlinked Properties of HIV-1 Env Glycoproteins." Journal of Virology 90, no. 6 (December 30, 2015): 2884–94. http://dx.doi.org/10.1128/jvi.01953-15.

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ABSTRACTWe investigated whether there is any association between a native-like conformation and the presence of only the canonical (i.e., native) disulfide bonds in the gp120 subunits of a soluble recombinant human immunodeficiency virus type 1 (HIV-1) envelope (Env) glycoprotein. We used a mass spectrometry (MS)-based method to map the disulfide bonds present in nonnative uncleaved gp140 proteins and native-like SOSIP.664 trimers based on the BG505envgene. Our results show that uncleaved gp140 proteins were not homogeneous, in that substantial subpopulations (20 to 80%) contained aberrant disulfide bonds. In contrast, the gp120 subunits of the native-like SOSIP.664 trimer almost exclusively retained the canonical disulfide bond pattern. We also observed that the purification method could influence the proportion of an Env protein population that contained aberrant disulfide bonds. We infer that gp140 proteins may always contain a variable but substantial proportion of aberrant disulfide bonds but that the impact of this problem can be minimized via design and/or purification strategies that yield native-like trimers. The same factors may also be relevant to the production and purification of monomeric gp120 proteins that are free of aberrant disulfide bonds.IMPORTANCEIt is widely thought that a successful HIV-1 vaccine will include a recombinant form of the Env protein, a trimer located on the virion surface. To increase yield and simplify purification, Env proteins are often made in truncated, soluble forms. A consequence, however, can be the loss of the native conformation concomitant with the virion-associated trimer. Moreover, some soluble recombinant Env proteins contain aberrant disulfide bonds that are not expected to be present in the native trimer. To assess whether these observations are linked, to determine the extent of disulfide bond scrambling, and to understand why scrambling occurs, we determined the disulfide bond profiles of two soluble Env proteins with different designs that are being assessed as vaccine candidates. We found that uncleaved gp140 forms heterogeneous mixtures in which aberrant disulfide bonds abound. In contrast, BG505 SOSIP.664 trimers are more homogeneous, native-like entities that contain predominantly the native disulfide bond profile.

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25

Butera, Diego, Kristina M. Cook, Joyce Chiu, Jason W. H. Wong, and Philip J. Hogg. "Control of blood proteins by functional disulfide bonds." Blood 123, no. 13 (March 27, 2014): 2000–2007. http://dx.doi.org/10.1182/blood-2014-01-549816.

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Abstract Most proteins in nature are chemically modified after they are made to control how, when, and where they function. The 3 core features of proteins are posttranslationally modified: amino acid side chains can be modified, peptide bonds can be cleaved or isomerized, and disulfide bonds can be cleaved. Cleavage of peptide bonds is a major mechanism of protein control in the circulation, as exemplified by activation of the blood coagulation and complement zymogens. Cleavage of disulfide bonds is emerging as another important mechanism of protein control in the circulation. Recent advances in our understanding of control of soluble blood proteins and blood cell receptors by functional disulfide bonds is discussed as is how these bonds are being identified and studied.

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26

Qin, Meng, Wei Wang, and D. Thirumalai. "Protein folding guides disulfide bond formation." Proceedings of the National Academy of Sciences 112, no. 36 (August 21, 2015): 11241–46. http://dx.doi.org/10.1073/pnas.1503909112.

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The Anfinsen principle that the protein sequence uniquely determines its structure is based on experiments on oxidative refolding of a protein with disulfide bonds. The problem of how protein folding drives disulfide bond formation is poorly understood. Here, we have solved this long-standing problem by creating a general method for implementing the chemistry of disulfide bond formation and rupture in coarse-grained molecular simulations. As a case study, we investigate the oxidative folding of bovine pancreatic trypsin inhibitor (BPTI). After confirming the experimental findings that the multiple routes to the folded state contain a network of states dominated by native disulfides, we show that the entropically unfavorable native single disulfide [14–38] between Cys14 and Cys38 forms only after polypeptide chain collapse and complete structuring of the central core of the protein containing an antiparallel β-sheet. Subsequent assembly, resulting in native two-disulfide bonds and the folded state, involves substantial unfolding of the protein and transient population of nonnative structures. The rate of [14–38] formation increases as the β-sheet stability increases. The flux to the native state, through a network of kinetically connected native-like intermediates, changes dramatically by altering the redox conditions. Disulfide bond formation between Cys residues not present in the native state are relevant only on the time scale of collapse of BPTI. The finding that formation of specific collapsed native-like structures guides efficient folding is applicable to a broad class of single-domain proteins, including enzyme-catalyzed disulfide proteins.

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27

Asakawa, Daiki, Hidenori Takahashi, Shinichi Iwamoto, and Koichi Tanaka. "Hydrogen attachment dissociation of peptides containing disulfide bonds." Physical Chemistry Chemical Physics 21, no. 47 (2019): 26049–57. http://dx.doi.org/10.1039/c9cp03923f.

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Because both disulfide and peptide backbone bonds were cleaved by a single hydrogen attachment event, a tandem mass spectrometry with hydrogen attachment dissociation allows the sequencing of peptides containing disulfide bonds.

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28

Duan, Lei, Weihua Kong, Wen Yan, Cheng-Hui Li, Zhong Jin, and Jing-Lin Zuo. "Improving the capacity and cycling-stability of Lithium–sulfur batteries using self-healing binders containing dynamic disulfide bonds." Sustainable Energy & Fuels 4, no. 6 (2020): 2760–67. http://dx.doi.org/10.1039/d0se00309c.

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A self-healing poly(dimethylsiloxane) polymer containing disulfide bonds is synthesized for application in lithium–sulfur batteries. The reversible breakage/formation of the disulfide bonds can capture polysulfides and accelerate their conversion.

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29

Messens, Joris, and Jean-François Collet. "Thiol–Disulfide Exchange in Signaling: Disulfide Bonds As a Switch." Antioxidants & Redox Signaling 18, no. 13 (May 2013): 1594–96. http://dx.doi.org/10.1089/ars.2012.5156.

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30

Maruyama, Kazunori, Hiromichi Nagasawa, and Akinori Suzuki. "2,2′-Bispyridyl disulfide rapidly induces intramolecular disulfide bonds in peptides." Peptides 20, no. 7 (August 1999): 881–84. http://dx.doi.org/10.1016/s0196-9781(99)00076-5.

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31

Wagner, DD, SO Lawrence, BM Ohlsson-Wilhelm, PJ Fay, and VJ Marder. "Topology and order of formation of interchain disulfide bonds in von Willebrand factor." Blood 69, no. 1 (January 1, 1987): 27–32. http://dx.doi.org/10.1182/blood.v69.1.27.27.

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Abstract Interchain disulfide bonds between the subunits in von Willebrand factor (vWf) dimers and in vWf multimers have been studied using some unique features of the cultured human umbilical vein endothelial cell system. Ammonium chloride inhibition of multimerization of vWf allowed selective examination of vWf dimeric molecules, and monoclonal antibody against the vWf propolypeptide was used to separate pro-vWf dimers from mature dimers. After cleavage of dimers and multimers with Staphylococcus aureus V-8 protease, the location of interchain disulfide bonds in amino (N)-terminal or carboxyl (C)-terminal fragments was determined by gel electrophoresis under reduced and nonreduced conditions. The first interchain disulfide bonds formed during dimerization are in the C-terminal region of the subunits, whereas interdimer disulfide bonds are located in the N-terminal portion. These data confirm recent electron microscopic projections of disulfide bond locations and provide support to the hypothetical role of the propolypeptide in the multimerization process.

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32

Wagner, DD, SO Lawrence, BM Ohlsson-Wilhelm, PJ Fay, and VJ Marder. "Topology and order of formation of interchain disulfide bonds in von Willebrand factor." Blood 69, no. 1 (January 1, 1987): 27–32. http://dx.doi.org/10.1182/blood.v69.1.27.bloodjournal69127.

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Interchain disulfide bonds between the subunits in von Willebrand factor (vWf) dimers and in vWf multimers have been studied using some unique features of the cultured human umbilical vein endothelial cell system. Ammonium chloride inhibition of multimerization of vWf allowed selective examination of vWf dimeric molecules, and monoclonal antibody against the vWf propolypeptide was used to separate pro-vWf dimers from mature dimers. After cleavage of dimers and multimers with Staphylococcus aureus V-8 protease, the location of interchain disulfide bonds in amino (N)-terminal or carboxyl (C)-terminal fragments was determined by gel electrophoresis under reduced and nonreduced conditions. The first interchain disulfide bonds formed during dimerization are in the C-terminal region of the subunits, whereas interdimer disulfide bonds are located in the N-terminal portion. These data confirm recent electron microscopic projections of disulfide bond locations and provide support to the hypothetical role of the propolypeptide in the multimerization process.

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33

Marques, José R. F., Rute R. da Fonseca, Brett Drury, and André Melo. "Amino Acid Patterns around Disulfide Bonds." International Journal of Molecular Sciences 11, no. 11 (November 18, 2010): 4673–86. http://dx.doi.org/10.3390/ijms11114673.

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34

Hagihara, Yoshihisa, and Dirk Saerens. "Engineering disulfide bonds within an antibody." Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1844, no. 11 (November 2014): 2016–23. http://dx.doi.org/10.1016/j.bbapap.2014.07.005.

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35

Feyertag, Felix, and David Alvarez-Ponce. "Disulfide Bonds Enable Accelerated Protein Evolution." Molecular Biology and Evolution 34, no. 8 (April 18, 2017): 1833–37. http://dx.doi.org/10.1093/molbev/msx135.

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36

Carles, S., F. Lecomte, J. P. Schermann, C. Desfrançois, S. Xu, J. M. Nilles, K. H. Bowen, J. Bergès, and C. Houée-Levin. "Nondissociative Electron Capture by Disulfide Bonds†." Journal of Physical Chemistry A 105, no. 23 (June 2001): 5622–26. http://dx.doi.org/10.1021/jp0040603.

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Welker, Ervin, Lynne D. Raymond, Harold A. Scheraga, and Byron Caughey. "IntramolecularVersusIntermolecular Disulfide Bonds in Prion Proteins." Journal of Biological Chemistry 277, no. 36 (June 24, 2002): 33477–81. http://dx.doi.org/10.1074/jbc.m204273200.

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Li, Jianghong, Ten-Yang Yen, M. Laura Allende, Rajesh K. Joshi, Jian Cai, William M. Pierce, Ewa Jaskiewicz, Douglas S. Darling, Bruce A. Macher, and William W. Young. "Disulfide Bonds of GM2 Synthase Homodimers." Journal of Biological Chemistry 275, no. 52 (October 3, 2000): 41476–86. http://dx.doi.org/10.1074/jbc.m007480200.

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39

Muttathukattil Narayanan, Aswathy. "Disulfide Bonds Modulate Lysozyme Folding Pathways." Biophysical Journal 116, no. 3 (February 2019): 191a. http://dx.doi.org/10.1016/j.bpj.2018.11.1058.

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40

Wetzel, Ronald. "Harnessing disulfide bonds using protein engineering." Trends in Biochemical Sciences 12 (January 1987): 478–82. http://dx.doi.org/10.1016/0968-0004(87)90234-9.

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41

Schuurman, Janine, Gerrard J. Perdok, Annelies D. Gorter, and Rob C. Aalberse. "The inter-heavy chain disulfide bonds of IgG4 are in equilibrium with intra-chain disulfide bonds." Molecular Immunology 38, no. 1 (January 2001): 1–8. http://dx.doi.org/10.1016/s0161-5890(01)00050-5.

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42

Li, Wenyan, Shengchang Lu, Mengchan Zhao, Xinxing Lin, Min Zhang, He Xiao, Kai Liu, et al. "Self-Healing Cellulose Nanocrystals-Containing Gels via Reshuffling of Thiuram Disulfide Bonds." Polymers 10, no. 12 (December 15, 2018): 1392. http://dx.doi.org/10.3390/polym10121392.

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Self-healing gels based on reshuffling disulfide bonds have attracted great attention due to their ability to restore structure and mechanical properties after damage. In this work, self-healing gels with different cellulose nanocrystals (CNC) contents were prepared by embedding the thiuram disulfide bonds into gels via polyaddition. By the reshuffling of thiuram disulfide bonds, the CNC-containing gels repair the crack and recover mechanical properties rapidly under visible light in air. The thiuram disulfide-functionalized gels with a CNC content of 2.2% are highly stretchable and can be stretched approximately 42.6 times of their original length. Our results provide useful approaches for the preparation of dynamic CNC-containing gels with implications in many related engineering applications.

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43

Huang, Sheng-Yu, Tin-Yu Wei, Bing-Shin Liu, Min-Han Lin, Sheng-Kuo Chiang, Sung-Fang Chen, and Wang-Chou Sung. "Monitoring the Disulfide Bonds of Folding Isomers of Synthetic CTX A3 Polypeptide Using MS-Based Technology." Toxins 11, no. 1 (January 17, 2019): 52. http://dx.doi.org/10.3390/toxins11010052.

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Native disulfide formation is crucial to the process of disulfide-rich protein folding in vitro. As such, analysis of the disulfide bonds can be used to track the process of the folding reaction; however, the diverse structural isomers interfere with characterization due to the non-native disulfide linkages. Previously, a mass spectrometry (MS) based platform coupled with peptide demethylation and an automatic disulfide bond searching engine demonstrated the potential to screen disulfide-linked peptides for the unambiguous assignment of paired cysteine residues of toxin components in cobra venom. The developed MS-based platform was evaluated to analyze the disulfide bonds of structural isomers during the folding reaction of synthetic cardiotoxin A3 polypeptide (syn-CTX A3), an important medical component in cobra venom. Through application of this work flow, a total of 13 disulfide-linked peptides were repeatedly identified across the folding reaction, and two of them were found to contain cysteine pairings, like those found in native CTX A3. Quantitative analysis of these disulfide-linked peptides showed the occurrence of a progressive disulfide rearrangement that generates a native disulfide bond pattern on syn-CTX A3 folded protein. The formation of these syn-CTX A3 folded protein reaches a steady level in the late stage of the folding reaction. Biophysical and cell-based assays showed that the collected syn-CTX A3 folded protein have a β-sheet secondary structure and cytotoxic activity similar to that of native CTX A3. In addition, the immunization of the syn-CTX A3 folded proteins could induce neutralization antibodies against the cytotoxic activity of native CTX A3. In contrast, these structure activities were poorly observed in the other folded isomers with non-native disulfide bonds. The study highlights the ability of the developed MS platform to assay isomers with heterogeneous disulfide bonds, providing insight into the folding mechanism of the bioactive protein generation.

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Chiu, Joyce, Noppacharn Uaprasert, Oscar Eriksson, Lin Lin, Shihui Guo, Philip Hogg, and Robert Flaumenhaft. "PDI Cleavage of Disulfide Bonds within the TP Receptor Inhibits Signaling through Gα 13." Blood 138, Supplement 1 (November 5, 2021): 579. http://dx.doi.org/10.1182/blood-2021-151753.

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Abstract G-protein coupled receptors (GPCRs) are the most abundant superfamily of cell surface receptors. Approximately 35% of approved drugs target GPCRs and class A GPCRs account for ~85% of this superfamily. Class A GPCRs are characterized in part by two highly conserved disulfides in their extracellular domains that are thought to stabilize protein structure. Whether these disulfides can be enzymatically modified to influence G-protein signaling is not known. We and others have previously shown that disulfide bond modification by thiol isomerases such as protein disulfide isomerase (PDI) represent a previously unrecognized level of control of thrombus formation. We therefore evaluated the ability of recombinant PDI (rPDI) to modulate signaling through modification of the canonical disulfides within platelet GPCRs. Exposure of platelets to rPDI had no effect on stimulation through PAR1, PAR4, or the α 2A-adrenergic receptor. In contrast, rPDI exposure dramatically decreased platelet activation induced by the TP receptor agonists U46619 or arachidonic acid, implicating rPDI-mediated modulation of TP receptor signaling. Consistent with this finding, rPDI blocked U46619-mediated activation of α IIbβ 3, α-granule release, and dense granule release. Conversely, inhibition of endogenous PDI using either inhibitory antibodies or PDI-targeted small molecules enhanced TP receptor-mediated platelet aggregation and granule release, indicating that endogenous platelet PDI influences TP receptor signaling. Inhibition of TP receptor-mediated signaling required PDI active site cysteines since rPDI mutants lacking these cysteines lost inhibitory activity. Evaluation of the inhibitory activity of different PDI fragments showed that the PDI substrate binding domain is also critical for inhibitory activity. The ability to inhibit signaling through the TP receptor was specific for rPDI since incubation with other recombinant thiol isomerases including ERp57, ERp5, and ERp72 had no effect. To determine the specific modifications to TP receptor canonical disulfides induced by PDI, HEK cells were transfected with TP receptor and exposed to rPDI. TP receptor was subsequently immunopreciptated and disulfide-linked peptide analysis was performed using mass spectrometry. Compared to untreated controls, TP receptor exposed to rPDI demonstrated cleavage of Cys11-Cys102 and Cys105-Cys183 bonds and the generation of a new Cys102-Cys183 bond. To determine how modification of the disulfide bonding pattern affected signaling through the TP receptor, we evaluated signaling through specific Gα subunits in platelets. The platelet TP receptor signals through Gα q (which couples to phospholipase and increases calcium flux) and Gα 13 (which couples to RhoA and myosin light chain kinase). PDI-mediated cleavage of the platelet TP receptor resulted in biased signaling, with substantial inhibition of G α13-mediated RhoA-GTP activation and myosin light chain phosphorylation and little effect on Gα q-mediated calcium flux. These results show how PDI can modify platelet signaling and represent the first demonstration that a thiol isomerase can modulate the function of a GPCR via rearrangement of canonical disulfide bonds. Disclosures No relevant conflicts of interest to declare.

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Matsumura, M., W. J. Becktel, M. Levitt, and B. W. Matthews. "Stabilization of phage T4 lysozyme by engineered disulfide bonds." Proceedings of the National Academy of Sciences 86, no. 17 (September 1989): 6562–66. http://dx.doi.org/10.1073/pnas.86.17.6562.

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Four different disulfide bridges (linking positions 9-164, 21-142, 90-122, and 127-154) were introduced into a cysteine-free phage T4 lysozyme at sites suggested by theoretical calculations and computer modeling. The new cysteines spontaneously formed disulfide bonds on exposure to air in vitro. In all cases the oxidized (crosslinked) lysozyme was more stable than the corresponding reduced (noncrosslinked) enzyme toward thermal denaturation. Relative to wild-type lysozyme, the melting temperatures of the 9-164 and 21-142 disulfide mutants were increased by 6.4 degrees C and 11.0 degrees C, whereas the other two mutants were either less stable or equally stable. Measurement of the equilibrium constants for the reduction of the engineered disulfide bonds by dithiothreitol indicates that the less thermostable mutants tend to have a less favorable crosslink in the native structure. The two disulfide bridges that are most effective in increasing the stability of T4 lysozyme have, in common, a large loop size and a location that includes a flexible part of the molecule. The results suggest that stabilization due to the effect of the crosslink on the entropy of the unfolded polypeptide is offset by the strain energy associated with formation of the disulfide bond in the folded protein. The design of disulfide bridges is discussed in terms of protein flexibility.

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Fu, Jiahui, Jihui Gao, Zhongxin Liang, and Dong Yang. "PDI-Regulated Disulfide Bond Formation in Protein Folding and Biomolecular Assembly." Molecules 26, no. 1 (December 31, 2020): 171. http://dx.doi.org/10.3390/molecules26010171.

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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.

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Sun, Yuling, and Yanbin Huang. "Disulfide-crosslinked albumin hydrogels." Journal of Materials Chemistry B 4, no. 16 (2016): 2768–75. http://dx.doi.org/10.1039/c6tb00247a.

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48

Butturini, Elena, Giovanni Gotte, Daniele Dell'Orco, Giulia Chiavegato, Valerio Marino, Diana Canetti, Flora Cozzolino, Maria Monti, Piero Pucci, and Sofia Mariotto. "Intermolecular disulfide bond influences unphosphorylated STAT3 dimerization and function." Biochemical Journal 473, no. 19 (September 27, 2016): 3205–19. http://dx.doi.org/10.1042/bcj20160294.

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Signal transducer and activator of transcription 3 (STAT3) is a transcription factor activated by the phosphorylation of tyrosine 705 in response to many cytokines and growth factors. Recently, the roles for unphosphorylated STAT3 (U-STAT3) have been described in response to cytokine stimulation, in cancers, and in the maintenance of heterochromatin stability. It has been reported that U-STAT3 dimerizes, shuttles between the cytoplasm and nucleus, and binds to DNA, thereby driving genes transcription. Although many reports describe the active role of U-STAT3 in oncogenesis in addition to phosphorylated STAT3, the U-STAT3 functional pathway remains elusive. In this report, we describe the molecular mechanism of U-STAT3 dimerization, and we identify the presence of two intermolecular disulfide bridges between Cys367 and Cys542 and Cys418 and Cys426, respectively. Recently, we reported that the same cysteines contribute to the redox regulation of STAT3 signaling pathway both in vitro and in vivo. The presence of these disulfides is here demonstrated to largely contribute to the structure and the stability of U-STAT3 dimer as the dimeric form rapidly dissociates upon reduction in the S–S bonds. In particular, the Cys367–Cys542 disulfide bridge is shown to be critical for U-STAT3 DNA-binding activity. Mutation of the two Cys residues completely abolishes the DNA-binding capability of U-STAT3. Spectroscopic investigations confirm that the noncovalent interactions are sufficient for proper folding and dimer formation, but that the interchain disulfide bonds are crucial to preserve the functional dimer. Finally, we propose a reaction scheme of U-STAT3 dimerization with a first common step followed by stabilization through the formation of interchain disulfide bonds.

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Kim, Sunghwan, Dionisia P. Sideris, Carolyn S. Sevier, and Chris A. Kaiser. "Balanced Ero1 activation and inactivation establishes ER redox homeostasis." Journal of Cell Biology 196, no. 6 (March 12, 2012): 713–25. http://dx.doi.org/10.1083/jcb.201110090.

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The endoplasmic reticulum (ER) provides an environment optimized for oxidative protein folding through the action of Ero1p, which generates disulfide bonds, and Pdi1p, which receives disulfide bonds from Ero1p and transfers them to substrate proteins. Feedback regulation of Ero1p through reduction and oxidation of regulatory bonds within Ero1p is essential for maintaining the proper redox balance in the ER. In this paper, we show that Pdi1p is the key regulator of Ero1p activity. Reduced Pdi1p resulted in the activation of Ero1p by direct reduction of Ero1p regulatory bonds. Conversely, upon depletion of thiol substrates and accumulation of oxidized Pdi1p, Ero1p was inactivated by both autonomous oxidation and Pdi1p-mediated oxidation of Ero1p regulatory bonds. Pdi1p responded to the availability of free thiols and the relative levels of reduced and oxidized glutathione in the ER to control Ero1p activity and ensure that cells generate the minimum number of disulfide bonds needed for efficient oxidative protein folding.

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50

Koritzinsky, Marianne, Fiana Levitin, Twan van den Beucken, Ryan A. Rumantir, Nicholas J. Harding, Kenneth C. Chu, Paul C. Boutros, Ineke Braakman, and Bradly G. Wouters. "Two phases of disulfide bond formation have differing requirements for oxygen." Journal of Cell Biology 203, no. 4 (November 18, 2013): 615–27. http://dx.doi.org/10.1083/jcb.201307185.

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Most proteins destined for the extracellular space require disulfide bonds for folding and stability. Disulfide bonds are introduced co- and post-translationally in endoplasmic reticulum (ER) cargo in a redox relay that requires a terminal electron acceptor. Oxygen can serve as the electron acceptor in vitro, but its role in vivo remains unknown. Hypoxia causes ER stress, suggesting a role for oxygen in protein folding. Here we demonstrate the existence of two phases of disulfide bond formation in living mammalian cells, with differential requirements for oxygen. Disulfide bonds introduced rapidly during protein synthesis can occur without oxygen, whereas those introduced during post-translational folding or isomerization are oxygen dependent. Other protein maturation processes in the secretory pathway, including ER-localized N-linked glycosylation, glycan trimming, Golgi-localized complex glycosylation, and protein transport, occur independently of oxygen availability. These results suggest that an alternative electron acceptor is available transiently during an initial phase of disulfide bond formation and that post-translational oxygen-dependent disulfide bond formation causes hypoxia-induced ER stress.

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