1
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Carugo O. Survey of the Intermolecular Disulfide Bonds Observed in Protein Crystal Structures Deposited in the Protein Data Bank. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070986. [PMID: 35888076 PMCID: PMC9323673 DOI: 10.3390/life12070986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 11/29/2022]
Abstract
About 5% of the disulfide bonds (DBs) observed in the Protein Data Bank bridge two protein chains. Several of their features were comprehensively analyzed, resulting in a structural atlas of the intermolecular DBs. The analysis was performed on a very large set of data extracted from the Protein Data Bank, according to the RaSPDB procedure. It was observed that the two chains tend to have different sequences and belong to the same structural class. Intermolecular DBs tend to be more solvent accessible and less distorted from the most stable conformation than intermolecular DBs while showing similar B-factors. They tend to occur in beta strands and in mainly-beta structures. These and other data should prove useful in protein modelling and design.
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Affiliation(s)
- Oliviero Carugo
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy;
- Italy & Max Perutz Labs, Department of Structural and Computational Biology, University of Vienna, 1010 Wien, Austria
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2
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Touzeau J, Seydou M, Maurel F, Tallet L, Mutschler A, Lavalle P, Barbault F. Theoretical and Experimental Elucidation of the Adsorption Process of a Bioinspired Peptide on Mineral Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11374-11385. [PMID: 34516122 DOI: 10.1021/acs.langmuir.1c01994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Inorganic materials used for biomedical applications such as implants generally induce the adsorption of proteins on their surface. To control this phenomenon, the bioinspired peptidomimetic polymer 1 (PMP1), which aims to reproduce the adhesion of mussel foot proteins, is commonly used to graft specific proteins on various surfaces and to regulate the interfacial mechanism. To date and despite its wide application, the elucidation at the atomic scale of the PMP1 mechanism of adsorption on surfaces is still unknown. The purpose of the present work was thus to unravel this process through experimental and computational investigations of adsorption of PMP1 on gold, TiO2, and SiO2 surfaces. A common mechanism of adsorption is identified for the adsorption of PMP1 which emphasizes the role of electrostatics to approach the peptide onto the surface followed by a full adhesion process where the entropic desolvation step plays a key role. Besides, according to the fact that mussel naturally controls the oxidation states of its proteins, further investigations were performed for two distinct redox states of PMP1, and we conclude that even if both states are able to allow interaction of PMP1 with the surfaces, the oxidation of PMP1 leads to a stronger interaction.
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Affiliation(s)
- J Touzeau
- Université de Paris, ITODYS, CNRS, UMR 7086, 15 rue J-A de Baïf, F-75013 Paris, France
| | - M Seydou
- Université de Paris, ITODYS, CNRS, UMR 7086, 15 rue J-A de Baïf, F-75013 Paris, France
| | - F Maurel
- Université de Paris, ITODYS, CNRS, UMR 7086, 15 rue J-A de Baïf, F-75013 Paris, France
| | - L Tallet
- Institut National de la Santé et de la Recherche Médicale, Inserm UMR_S 1121 Biomaterials and Bioengineering, 11 rue Humann, 67000 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, 67000 Strasbourg, France
| | - A Mutschler
- Institut National de la Santé et de la Recherche Médicale, Inserm UMR_S 1121 Biomaterials and Bioengineering, 11 rue Humann, 67000 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, 67000 Strasbourg, France
| | - P Lavalle
- Institut National de la Santé et de la Recherche Médicale, Inserm UMR_S 1121 Biomaterials and Bioengineering, 11 rue Humann, 67000 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, 67000 Strasbourg, France
| | - F Barbault
- Université de Paris, ITODYS, CNRS, UMR 7086, 15 rue J-A de Baïf, F-75013 Paris, France
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3
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Dopp JL, Reuel NF. Simple, functional, inexpensive cell extract for in vitro prototyping of proteins with disulfide bonds. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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4
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Budisa N, Schneider T. Expanding the DOPA Universe with Genetically Encoded, Mussel-Inspired Bioadhesives for Material Sciences and Medicine. Chembiochem 2019; 20:2163-2190. [PMID: 30830997 DOI: 10.1002/cbic.201900030] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Indexed: 12/21/2022]
Abstract
Catechols are a biologically relevant group of aromatic diols that have attracted much attention as mediators of adhesion of "bio-glue" proteins in mussels of the genus Mytilus. These organisms use catechols in the form of the noncanonical amino acid l-3,4-dihydroxyphenylalanine (DOPA) as a building block for adhesion proteins. The DOPA is generated post-translationally from tyrosine. Herein, we review the properties, natural occurrence, and reactivity of catechols in the design of bioinspired materials. We also provide a basic description of the mussel's attachment apparatus, the interplay between its different molecules that play a crucial role in adhesion, and the role of post-translational modifications (PTMs) of these proteins. Our focus is on the microbial production of mussel foot proteins with the aid of orthogonal translation systems (OTSs) and the use of genetic code engineering to solve some fundamental problems in the bioproduction of these bioadhesives and to expand their chemical space. The major limitation of bacterial expression systems is their intrinsic inability to introduce PTMs. OTSs have the potential to overcome these challenges by replacing canonical amino acids with noncanonical ones. In this way, PTM steps are circumvented while the genetically programmed precision of protein sequences is preserved. In addition, OTSs should enable spatiotemporal control over the complex adhesion process, because the catechol function can be masked by suitable chemical protection. Such caged residues can then be noninvasively unmasked by, for example, UV irradiation or thermal treatment. All of these features make OTSs based on genetic code engineering in reprogrammed microbial strains new and promising tools in bioinspired materials science.
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Affiliation(s)
- Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany.,Chair of Chemical Synthetic Biology, Department of Chemistry, University of Manitoba, 144 Dysart Road, R3T 2N2, Winnipeg, MB, Canada
| | - Tobias Schneider
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany
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5
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Landeta C, Boyd D, Beckwith J. Disulfide bond formation in prokaryotes. Nat Microbiol 2018; 3:270-280. [PMID: 29463925 DOI: 10.1038/s41564-017-0106-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 12/21/2017] [Indexed: 12/25/2022]
Abstract
Interest in protein disulfide bond formation has recently increased because of the prominent role of disulfide bonds in bacterial virulence and survival. The first discovered pathway that introduces disulfide bonds into cell envelope proteins consists of Escherichia coli enzymes DsbA and DsbB. Since its discovery, variations on the DsbAB pathway have been found in bacteria and archaea, probably reflecting specific requirements for survival in their ecological niches. One variation found amongst Actinobacteria and Cyanobacteria is the replacement of DsbB by a homologue of human vitamin K epoxide reductase. Many Gram-positive bacteria express enzymes involved in disulfide bond formation that are similar, but non-homologous, to DsbAB. While bacterial pathways promote disulfide bond formation in the bacterial cell envelope, some archaeal extremophiles express proteins with disulfide bonds both in the cytoplasm and in the extra-cytoplasmic space, possibly to stabilize proteins in the face of extreme conditions, such as growth at high temperatures. Here, we summarize the diversity of disulfide-bond-catalysing systems across prokaryotic lineages, discuss examples for understanding the biological basis of such systems, and present perspectives on how such systems are enabling advances in biomedical engineering and drug development.
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Affiliation(s)
- Cristina Landeta
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Dana Boyd
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Jon Beckwith
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
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6
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Zhang F, Xie G, Pan J. Tunable Adsorption and Film Formation of Mussel Adhesive Protein by Potential Control. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8749-8756. [PMID: 28071917 DOI: 10.1021/acs.langmuir.6b04125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Mussel adhesive proteins are of great interest in many applications because of their outstanding adhesive property and film-forming ability. Understanding and controlling the film formation and its performance is crucial for the effective use of such proteins. In this study, we focus on the potential controlled film formation and compaction of one mussel adhesive protein, Mefp-1. The adsorption and film-forming behavior of Mefp-1 on a platinum (Pt) substrate under applied potentials were investigated by cyclic voltammetry, potential-controlled electrochemical impedance spectroscopy (EIS), and quartz crystal microbalance with dissipation monitoring (QCM-D). Moreover, microfriction measurements were performed to evaluate the mechanical properties of the Mefp-1 films formed at selected potentials. The results led to the conclusion that Mefp-1 adsorbs on the Pt substrate through both electrostatic and nonelectrostatic interactions and shows an effective blocking effect for the electroactive sites on the substrate. The properties of the adsorbed Mefp-1 film vary with the applied potential, and the compactness of the adsorbed Mefp-1 film can be reversibly tuned by the applied potential.
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Affiliation(s)
- Fan Zhang
- Division of Surface and Corrosion Science, Department of Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology , Drottning Kristinas väg 51, SE-100 44 Stockholm, Sweden
| | - Guoxin Xie
- Division of Surface and Corrosion Science, Department of Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology , Drottning Kristinas väg 51, SE-100 44 Stockholm, Sweden
- State Key Laboratory of Tribology, Tsinghua University , Beijing 100084, China
| | - Jinshan Pan
- Division of Surface and Corrosion Science, Department of Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology , Drottning Kristinas väg 51, SE-100 44 Stockholm, Sweden
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7
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Raimondi D, Orlando G, Messens J, Vranken WF. Investigating the Molecular Mechanisms Behind Uncharacterized Cysteine Losses from Prediction of Their Oxidation State. Hum Mutat 2016; 38:86-94. [PMID: 27667481 DOI: 10.1002/humu.23129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 09/13/2016] [Accepted: 09/20/2016] [Indexed: 01/08/2023]
Abstract
Cysteines are among the rarest amino acids in nature, and are both functionally and structurally very important for proteins. The ability of cysteines to form disulfide bonds is especially relevant, both for constraining the folded state of the protein and for performing enzymatic duties. But how does the variation record of human proteins reflect their functional importance and structural role, especially with regard to deleterious mutations? We created HUMCYS, a manually curated dataset of single amino acid variants that (1) have a known disease/neutral phenotypic outcome and (2) cause the loss of a cysteine, in order to investigate how mutated cysteines relate to structural aspects such as surface accessibility and cysteine oxidation state. We also have developed a sequence-based in silico cysteine oxidation predictor to overcome the scarcity of experimentally derived oxidation annotations, and applied it to extend our analysis to classes of proteins for which the experimental determination of their structure is technically challenging, such as transmembrane proteins. Our investigation shows that we can gain insights into the reason behind the outcome of cysteine losses in otherwise uncharacterized proteins, and we discuss the possible molecular mechanisms leading to deleterious phenotypes, such as the involvement of the mutated cysteine in a structurally or enzymatically relevant disulfide bond.
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Affiliation(s)
- Daniele Raimondi
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center (SBRC), VIB, Brussels, Belgium.,Machine Learning Group, ULB, Brussels, Belgium
| | - Gabriele Orlando
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center (SBRC), VIB, Brussels, Belgium.,Machine Learning Group, ULB, Brussels, Belgium
| | - Joris Messens
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center (SBRC), VIB, Brussels, Belgium
| | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center (SBRC), VIB, Brussels, Belgium
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8
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Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet JF, Jagusztyn-Krynicka EK. Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain. Front Microbiol 2015; 6:1065. [PMID: 26500620 PMCID: PMC4597128 DOI: 10.3389/fmicb.2015.01065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/16/2015] [Indexed: 12/15/2022] Open
Abstract
Helicobacter pylori does not encode the classical DsbA/DsbB oxidoreductases that are crucial for oxidative folding of extracytoplasmic proteins. Instead, this microorganism encodes an untypical two proteins playing a role in disulfide bond formation – periplasmic HP0231, which structure resembles that of EcDsbC/DsbG, and its redox partner, a membrane protein HpDsbI (HP0595) with a β-propeller structure. The aim of presented work was to assess relations between HP0231 structure and function. We showed that HP0231 is most closely related evolutionarily to the catalytic domain of DsbG, even though it possesses a catalytic motif typical for canonical DsbA proteins. Similarly, the highly diverged N-terminal dimerization domain is homologous to the dimerization domain of DsbG. To better understand the functioning of this atypical oxidoreductase, we examined its activity using in vivo and in vitro experiments. We found that HP0231 exhibits oxidizing and chaperone activities but no isomerizing activity, even though H. pylori does not contain a classical DsbC. We also show that HP0231 is not involved in the introduction of disulfide bonds into HcpC (Helicobactercysteine-rich protein C), a protein involved in the modulation of the H. pylori interaction with its host. Additionally, we also constructed a truncated version of HP0231 lacking the dimerization domain, denoted HP0231m, and showed that it acts in Escherichia coli cells in a DsbB-dependent manner. In contrast, HP0231m and classical monomeric EcDsbA (E. coli DsbA protein) were both unable to complement the lack of HP0231 in H. pylori cells, though they exist in oxidized forms. HP0231m is inactive in the insulin reduction assay and possesses high chaperone activity, in contrast to EcDsbA. In conclusion, HP0231 combines oxidative functions characteristic of DsbA proteins and chaperone activity characteristic of DsbC/DsbG, and it lacks isomerization activity.
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Affiliation(s)
- Katarzyna M Bocian-Ostrzycka
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Anna M Łasica
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology Warsaw, Poland
| | - Stanisław Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology Warsaw, Poland
| | - Magdalena J Grzeszczuk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Karolina Drabik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Aneta M Dobosz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Renata Godlewska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology Warsaw, Poland
| | - Jean-Francois Collet
- de Duve Institute, Université catholique de Louvain (UCL)/Walloon Excellence in Life Sciences and Biotechnology Brussels, Belgium
| | - Elżbieta K Jagusztyn-Krynicka
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
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9
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Affiliation(s)
- Yong Du
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization; Department of Polymer Science and Engineering; Zhejiang University; Hangzhou 310027 P.R. China
| | - Hao-Cheng Yang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization; Department of Polymer Science and Engineering; Zhejiang University; Hangzhou 310027 P.R. China
| | - Xiao-Ling Xu
- Department of Chemistry; Zhejiang University; Hangzhou 310027 P.R. China
| | - Jian Wu
- Department of Chemistry; Zhejiang University; Hangzhou 310027 P.R. China
| | - Zhi-Kang Xu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization; Department of Polymer Science and Engineering; Zhejiang University; Hangzhou 310027 P.R. China
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10
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Yu DJ, Li Y, Hu J, Yang X, Yang JY, Shen HB. Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:611-621. [PMID: 26357272 DOI: 10.1109/tcbb.2014.2359451] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Disulfide connectivity is an important protein structural characteristic. Accurately predicting disulfide connectivity solely from protein sequence helps to improve the intrinsic understanding of protein structure and function, especially in the post-genome era where large volume of sequenced proteins without being functional annotated is quickly accumulated. In this study, a new feature extracted from the predicted protein 3D structural information is proposed and integrated with traditional features to form discriminative features. Based on the extracted features, a random forest regression model is performed to predict protein disulfide connectivity. We compare the proposed method with popular existing predictors by performing both cross-validation and independent validation tests on benchmark datasets. The experimental results demonstrate the superiority of the proposed method over existing predictors. We believe the superiority of the proposed method benefits from both the good discriminative capability of the newly developed features and the powerful modelling capability of the random forest. The web server implementation, called TargetDisulfide, and the benchmark datasets are freely available at: http://csbio.njust.edu.cn/bioinf/TargetDisulfide for academic use.
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11
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Analysis of the isomerase and chaperone-like activities of an amebic PDI (EhPDI). BIOMED RESEARCH INTERNATIONAL 2015; 2015:286972. [PMID: 25695056 PMCID: PMC4324885 DOI: 10.1155/2015/286972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 11/20/2014] [Accepted: 11/24/2014] [Indexed: 12/20/2022]
Abstract
Protein disulfide isomerases (PDI) are eukaryotic oxidoreductases that catalyze the formation and rearrangement of disulfide bonds during folding of substrate proteins. Structurally, PDI enzymes share as a common feature the presence of at least one active thioredoxin-like domain. PDI enzymes are also involved in holding, refolding, and degradation of unfolded or misfolded proteins during stressful conditions. The EhPDI enzyme (a 38 kDa polypeptide with two active thioredoxin-like domains) has been used as a model to gain insights into protein folding and disulfide bond formation in E. histolytica. Here, we performed a functional complementation assay, using a ΔdsbC mutant of E. coli, to test whether EhPDI exhibits isomerase activity in vivo. Our preliminary results showed that EhPDI exhibits isomerase activity; however, further mutagenic analysis revealed significant differences in the functional role of each thioredoxin-like domain. Additional studies confirmed that EhPDI protects heat-labile enzymes against thermal inactivation, extending our knowledge about its chaperone-like activity. The characterization of EhPDI, as an oxidative folding catalyst with chaperone-like function, represents the initial step to dissect the molecular mechanisms involved in protein folding in E. histolytica.
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12
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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: 39] [Impact Index Per Article: 4.3] [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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13
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Raimondi D, Orlando G, Vranken WF. Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements. Bioinformatics 2014; 31:1219-25. [DOI: 10.1093/bioinformatics/btu794] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/18/2014] [Indexed: 12/23/2022] Open
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14
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Yang J, Cohen Stuart MA, Kamperman M. Jack of all trades: versatile catechol crosslinking mechanisms. Chem Soc Rev 2014; 43:8271-98. [PMID: 25231624 DOI: 10.1039/c4cs00185k] [Citation(s) in RCA: 410] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Catechols play an important role in many natural systems. They are known to readily interact with both organic (e.g., amino acids) and inorganic (e.g., metal ions, metal oxides) compounds, thereby providing a powerful system for protein curing. Catechol crosslinked protein networks, such as sclerotized cuticle and byssal threads of the mussel, have been shown to exhibit excellent mechanical properties. A lot of effort has been devoted to mimicking the natural proteins using synthetic catechol-functionalized polymers. Despite the success in developing catechol-functionalized materials, the crosslinking chemistry of catechols is still a subject of debate. To develop materials with controlled and superior properties, a clear understanding of the crosslinking mechanism of catechols is of vital importance. This review describes the crosslinking pathways of catechol and derivatives in both natural and synthetic systems. We discuss existing pathways of catechol crosslinking and parameters that affect the catechol chemistry in detail. This overview will point towards a rational direction for further investigation of the complicated catechol chemistry.
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Affiliation(s)
- Juan Yang
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703HB Wageningen, The Netherlands.
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15
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Araújo DGB, Nakao L, Gozzo P, Souza CDA, Balderrama V, Gugelmin ES, Kuczynski AP, Olandoski M, de Noronha L. Expression level of quiescin sulfhydryl oxidase 1 (QSOX1) in neuroblastomas. Eur J Histochem 2014; 58:2228. [PMID: 24704990 PMCID: PMC3980203 DOI: 10.4081/ejh.2014.2228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 11/23/2022] Open
Abstract
Neuroblastoma is the most common extracranial solid malignant tumor observed during childhood. Although these tumors can sometimes regress spontaneously or respond well to treatment in infants, genetic alterations that influence apoptosis can, in some cases, confer resistance to chemotherapy or result in relapses and adversely affect prognosis for these patients. The aim of this study was to correlate immunohistochemical expression of the protein quiescin sulfhydryl oxidase 1 (QSOX1) in samples obtained from untreated neuroblastomas with the patients’ clinical and pathological prognostic factors and clinical course. Neuroblastoma samples (n=23) obtained from histology blocks were arrayed into tissue microarrays and analysed by immunohistochemistry. The cases were classified according to the following clinical and pathological prognostic factors: age at diagnosis greater or less than/equal to 18 months; location of the lesion at diagnosis (abdominal or extra-abdominal); presence or absence of bone-marrow infiltration; tumor differentiation (well or poorly differentiated); Shimada histopathologic classification (favourable or unfavourable); state of the tumor extracellular matrix (Schwannian-stroma rich or poor); amplification of the MYCN oncogene; and clinical course (dead or alive with or without relapses/residual lesions). Twelve of the cases were female, 9 children were over 18 months old, 9 cases presented with extra-abdominal tumors and 9 cases exhibited tumors with unfavourable histologies. Fifteen patients underwent bone-marrow biopsy, and 4 of these were positive for metastasis. Nine patients died. The higher immunohistochemical expression of QSOX1 was more common in well-differentiated samples (P=0.029), in stroma-rich samples (P=0.029) and in samples from patients with a high prevalence of relapses/residual disease. The functions of QSOX1 include extracellular matrix maturation and the induction of apoptosis. Therefore, QSOX1 may be involved in neuroblastoma differentiation and regression and may thus function as a biomarker for identifying risk groups for this neoplasm.
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16
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17
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Walden PM, McMahon RM, Archbold JK. Membrane Protein Structures for Rational Antimicrobial Drug Design. Aust J Chem 2014. [DOI: 10.1071/ch14333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Antibiotic resistance is a major global health threat. Bacteria have developed novel resistance mechanisms to many of the latest generations of antibiotics and there is an urgent need to develop new therapies to combat these infections. Infections that are caused by multi-drug resistant Gram-negative bacteria result in poor prognosis, prolonged illness, and greater costs for health care. Recent research has pointed to several key bacterial membrane proteins as potential targets for drug and vaccine development. However, determination of the structures of these membrane proteins is not a trivial task. Here we review recent breakthroughs of the structural determination of bacterial membrane proteins and their potential for the future rational design of novel antimicrobial therapies.
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Pinto RD, Moreira AR, Pereira PJB, dos Santos NMS. Two thioredoxin-superfamily members from sea bass (Dicentrarchus labrax, L.): characterization of PDI (PDIA1) and ERp57 (PDIA3). FISH & SHELLFISH IMMUNOLOGY 2013; 35:1163-1175. [PMID: 23880452 DOI: 10.1016/j.fsi.2013.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 07/03/2013] [Accepted: 07/14/2013] [Indexed: 06/02/2023]
Abstract
PDI (PDIA1) and ERp57 (PDIA3), members of the PDI family and of the thioredoxin (Trx) superfamily, are multifunctional proteins with wide physiological roles and have been implicated in several pathologies. Importantly, they are both involved in the MHC class I antigen presentation pathway. This paper reports the isolation and characterization of full cDNA and genomic clones from sea bass (Dicentrarchus labrax, L.) PDI (Dila-PDI) and ERp57 (Dila-ERp57). The genes are ~12.4 and ~7.1 kb long, originating 2155 and 2173 bp transcripts and encoding 497 and 484 amino acids mature proteins, for Dila-PDI and -ERp57, respectively. The PDI gene consists of eleven exons and ERp57 of thirteen. As described in other species, both molecules are composed of four Trx-like domains (abb'a') followed by a C-terminal tail, retaining two CGHC active sites and an ER-signalling sequence, suggestive of a conserved function. Additionally, three-dimensional homology models further support Dila-PDI and Dila-ERp57 as orthologs of mammalian PDI and ERp57, respectively. Finally, high similarity is observed to their vertebrate counterparts (>69% identity), especially among the few ones from closely related teleosts (>79% identity). Hence, these results provide relevant primary data and will enable further studies to clarify the roles of PDI and ERp57 in European sea bass immunity.
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Affiliation(s)
- Rute D Pinto
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.
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Tang M, Nesbitt AE, Sperling LJ, Berthold DA, Schwieters CD, Gennis RB, Rienstra CM. Structure of the disulfide bond generating membrane protein DsbB in the lipid bilayer. J Mol Biol 2013; 425:1670-82. [PMID: 23416557 PMCID: PMC3670690 DOI: 10.1016/j.jmb.2013.02.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/11/2013] [Accepted: 02/08/2013] [Indexed: 12/16/2022]
Abstract
The integral membrane protein DsbB in Escherichia coli is responsible for oxidizing the periplasmic protein DsbA, which forms disulfide bonds in substrate proteins. We have developed a high-resolution structural model by combining experimental X-ray and solid-state NMR with molecular dynamics (MD) simulations. We embedded the high-resolution DsbB structure, derived from the joint calculation with X-ray reflections and solid-state NMR restraints, into the lipid bilayer and performed MD simulations to provide a mechanistic view of DsbB function in the membrane. Further, we revealed the membrane topology of DsbB by selective proton spin diffusion experiments, which directly probe the correlations of DsbB with water and lipid acyl chains. NMR data also support the model of a flexible periplasmic loop and an interhelical hydrogen bond between Glu26 and Tyr153.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Anna E. Nesbitt
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Lindsay J. Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Charles D. Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert B. Gennis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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Savojardo C, Fariselli P, Martelli PL, Casadio R. Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations. BMC Bioinformatics 2013; 14 Suppl 1:S10. [PMID: 23368835 PMCID: PMC3548674 DOI: 10.1186/1471-2105-14-s1-s10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Recently, information derived by correlated mutations in proteins has regained relevance for predicting protein contacts. This is due to new forms of mutual information analysis that have been proven to be more suitable to highlight direct coupling between pairs of residues in protein structures and to the large number of protein chains that are currently available for statistical validation. It was previously discussed that disulfide bond topology in proteins is also constrained by correlated mutations. Results In this paper we exploit information derived from a corrected mutual information analysis and from the inverse of the covariance matrix to address the problem of the prediction of the topology of disulfide bonds in Eukaryotes. Recently, we have shown that Support Vector Regression (SVR) can improve the prediction for the disulfide connectivity patterns. Here we show that the inclusion of the correlated mutation information increases of 5 percentage points the SVR performance (from 54% to 59%). When this approach is used in combination with a method previously developed by us and scoring at the state of art in predicting both location and topology of disulfide bonds in Eukaryotes (DisLocate), the per-protein accuracy is 38%, 2 percentage points higher than that previously obtained. Conclusions In this paper we show that the inclusion of information derived from correlated mutations can improve the performance of the state of the art methods for predicting disulfide connectivity patterns in Eukaryotic proteins. Our analysis also provides support to the notion that improving methods to extract evolutionary information from multiple sequence alignments greatly contributes to the scoring performance of predictors suited to detect relevant features from protein chains.
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Affiliation(s)
- Castrense Savojardo
- Department of Computer Science and Engineering, University of Bologna, Via Mura Anteo Zamboni 7, 41029 Bologna, Italy
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21
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Zheng W, Zhang W, Hu W, Zhang C, Yang Y. Exploring the smallest active fragment of HsQSOX1b and finding a highly efficient oxidative engine. PLoS One 2012; 7:e40935. [PMID: 22911720 PMCID: PMC3401233 DOI: 10.1371/journal.pone.0040935] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 06/15/2012] [Indexed: 11/19/2022] Open
Abstract
Human quiescin-sulfhydryl oxidase 1 isoform b (HsQSOX1b) is a highly efficient, multiple-domain enzyme that directly inserts disulfide bonds into client protein. However, previous studies have focused mainly on the catalytic activity of the whole protein rather than its domain structure. In this research, we dissected the structure and function of HsQSOX1b and explored its mechanism as a highly efficient sulfhydryl oxidase by analyzing the truncated variants. The results showed that the first HsQSOX1b thioredoxin domain was essential for thiol oxidase activity. The smallest active fragment (SAQ) was identified to consist of a helix-rich region (HRR) and an essential for respiration and viability/augmenter of liver regeneration (ERV/ALR) domain, which remained highly active to oxidize an artificial non-thiol substrate but not small molecular and protein thiols. Our study clearly demonstrated that SAQ is a highly efficient oxidative engine, which shows high efficiency in the de novo disulfide formation and oxygen reduction and that this more efficient oxidative engine is necessary for the highly efficient catalysis of QSOXs compared to Erv1 and Erv2. This study will help address the roles of different HsQSOX1b domains in de novo disulfide formation and encourage the engineering of more efficient QSOX variants for the in vitro folding of disulfide-containing proteins.
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Affiliation(s)
- Wenyun Zheng
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Wenyao Zhang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Wei Hu
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Chao Zhang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- * E-mail:
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22
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Sato Y, Inaba K. Disulfide bond formation network in the three biological kingdoms, bacteria, fungi and mammals. FEBS J 2012; 279:2262-71. [DOI: 10.1111/j.1742-4658.2012.08593.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Abstract
SIGNIFICANCE Disulfide bond formation is an essential reaction involved in the folding and maturation of many secreted and membrane proteins. Both prokaryotic and eukaryotic cells utilize various disulfide oxidoreductases and redox-active cofactors to accelerate this oxidative reaction, and higher eukaryotes have diversified and refined these disulfide-introducing cascades over the course of evolution. RECENT ADVANCES In the past decade, atomic resolution structures have been solved for an increasing number of disulfide oxidoreductases, thereby revealing the structural and mechanistic basis of cellular disulfide bond formation systems. CRITICAL ISSUES In this review, we focus on the evolution, structure, and regulatory mechanisms of endoplasmic reticulum oxidoreductin 1 (Ero1) family enzymes, the primary disulfide bond-generating catalysts in the endoplasmic reticulum (ER). Detailed comparison of Ero1 with other oxidoreductases, such as Prx4, QSOX, Erv1/2, and disulfide bond protein B (DsbB), provides important insight into how this ER-resident flavoenzyme acts in a regulated and specific manner to maintain redox and protein homeostasis in eukaryotic cells. FUTURE DIRECTIONS Currently, it is presumed that multiple pathways in addition to that mediated by Ero1 cooperate to achieve oxidative folding of many secretory and membrane proteins in mammalian cells. The important open question is how each oxidative pathway works distinctly or redundantly in response to various cellular conditions.
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Affiliation(s)
- Kazutaka Araki
- Laboratory of Molecular and Cellular Biology, Kyoto Sangyo University, Kyoto, Japan
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24
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Berkmen M. Production of disulfide-bonded proteins in Escherichia coli. Protein Expr Purif 2012; 82:240-51. [DOI: 10.1016/j.pep.2011.10.009] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 10/24/2011] [Accepted: 10/27/2011] [Indexed: 10/15/2022]
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Abstract
3, 4-Dihydroxyphenylanine (Dopa)-containing proteins are key to wet adhesion in mussels and possibly other sessile organisms also. However, Dopa-mediated adhesive bonding is a hard act to follow in that, at least in mussels, bonding depends on Dopa in both reduced and oxidized forms, for adhesion and cohesion, respectively. Given the vulnerability of Dopa to spontaneous oxidation, the most significant challenge to using it in practical adhesion is controlling Dopa redox in a temporally- and spatially defined manner. Mussels appear to achieve such control in their byssal attachment plaques, and factors involved in redox control can be measured with precision using redox probes such as the diphenylpicryl hydrazyl (DPPH) free radical. Understanding the specifics of natural redox control may provide fundamentally important insights for adhesive polymer engineering and antifouling strategies.
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Shigeri Y, Inazumi S, Hagihara Y, Yasuda A, Kawasaki H, Arakawa R, Nakata M. Desorption/Ionization Efficiency of Peptides Containing Disulfide Bonds in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. ANAL SCI 2012; 28:295-9. [DOI: 10.2116/analsci.28.295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yasushi Shigeri
- Health Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka, Japan.
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27
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Yu J, Wei W, Danner E, Ashley RK, Israelachvili JN, Waite JH. Mussel protein adhesion depends on interprotein thiol-mediated redox modulation. Nat Chem Biol 2011; 7:588-90. [PMID: 21804534 PMCID: PMC3158268 DOI: 10.1038/nchembio.630] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 05/21/2011] [Indexed: 01/12/2023]
Abstract
Mussel adhesion is mediated by foot proteins (mfp) rich in a catecholic amino acid, 3, 4-dihydroxyphenylalanine (dopa), capable of forming strong bidentate interactions with a variety of surfaces. A facile tendency toward auto-oxidation, however, often renders dopa unreliable for adhesion. Mussels limit dopa oxidation during adhesive plaque formation by imposing an acidic, reducing regime based on thiol-rich mfp-6, which restores dopa by coupling the oxidation of thiols to dopaquinone reduction.
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Affiliation(s)
- Jing Yu
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California, USA
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Savojardo C, Fariselli P, Alhamdoosh M, Martelli PL, Pierleoni A, Casadio R. Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization. ACTA ACUST UNITED AC 2011; 27:2224-30. [PMID: 21715467 DOI: 10.1093/bioinformatics/btr387] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
MOTIVATION Disulfide bonds stabilize protein structures and play relevant roles in their functions. Their formation requires an oxidizing environment and their stability is consequently depending on the redox ambient potential, which may differ according to the subcellular compartment. Several methods are available to predict cysteine-bonding state and connectivity patterns. However, none of them takes into consideration the relevance of protein subcellular localization. RESULTS Here we develop DISLOCATE, a two-step method based on machine learning models for predicting both the bonding state and the connectivity patterns of cysteine residues in a protein chain. We find that the inclusion of protein subcellular localization improves the performance of these predictive steps by 3 and 2 percentage points, respectively. When compared with previously developed methods for predicting disulfide bonds from sequence, DISLOCATE improves the overall performance by more than 10 percentage points. AVAILABILITY The method and the dataset are available at the Web page http://www.biocomp.unibo.it/savojard/Dislocate.html. GRHCRF code is available at http://www.biocomp.unibo.it/savojard/biocrf.html. CONTACT piero.fariselli@unibo.it.
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Affiliation(s)
- Castrense Savojardo
- Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9/2, Bologna, Italy
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29
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Masui S, Vavassori S, Fagioli C, Sitia R, Inaba K. Molecular bases of cyclic and specific disulfide interchange between human ERO1alpha protein and protein-disulfide isomerase (PDI). J Biol Chem 2011; 286:16261-71. [PMID: 21398518 DOI: 10.1074/jbc.m111.231357] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the endoplasmic reticulum (ER) of human cells, ERO1α and protein-disulfide isomerase (PDI) constitute one of the major electron flow pathways that catalyze oxidative folding of secretory proteins. Specific and limited PDI oxidation by ERO1α is essential to avoid ER hyperoxidation. To investigate how ERO1α oxidizes PDI selectively among more than 20 ER-resident PDI family member proteins, we performed docking simulations and systematic biochemical analyses. Our findings reveal that a protruding β-hairpin of ERO1α specifically interacts with the hydrophobic pocket present in the redox-inactive PDI b'-domain through the stacks between their aromatic residues, leading to preferred oxidation of the C-terminal PDI a'-domain. ERO1α associated preferentially with reduced PDI, explaining the stepwise disulfide shuttle mechanism, first from ERO1α to PDI and then from oxidized PDI to an unfolded polypeptide bound to its hydrophobic pocket. The interaction of ERO1α with ERp44, another PDI family member protein, was also analyzed. Notably, ERO1α-dependent PDI oxidation was inhibited by a hyperactive ERp44 mutant that lacks the C-terminal tail concealing the substrate-binding hydrophobic regions. The potential ability of ERp44 to inhibit ERO1α activity may suggest its physiological role in ER redox and protein homeostasis.
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Affiliation(s)
- Shoji Masui
- Division of Protein Chemistry, Post-Genome Science Center, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
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