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1.
Antioxid Redox Signal ; 31(4): 261-274, 2019 08 01.
Article in English | MEDLINE | ID: mdl-30880408

ABSTRACT

Aims: Efficient oxidative protein folding (OPF) in the endoplasmic reticulum (ER) is a key requirement of the eukaryotic secretory pathway. In particular, protein folding linked to the formation of disulfide bonds, an activity dependent on the enzyme protein disulfide isomerase (PDI), is crucial. For the de novo formation of disulfide bonds, reduced PDI must be reoxidized by an ER-located oxidase (ERO1). Despite some knowledge of this pathway, the kinetic parameters with which these components act and the importance of specific parameters, such as PDI reoxidation by Ero1, for the overall performance of OPF in vivo remain poorly understood. Results: We established an in vitro system using purified yeast (Saccharomyces cerevisiae) PDI (Pdi1p) and ERO1 (Ero1p) to investigate OPF. This necessitated the development of a novel reduction/oxidation processing strategy to generate homogenously oxidized recombinant yeast Ero1p. This new methodology enabled the quantitative assessment of the interaction of Pdi1p and Ero1p in vitro by measuring oxygen consumption and reoxidation of reduced RNase A. The resulting quantitative data were then used to generate a simple model that can describe the oxidizing capacity of Pdi1p and Ero1p in vitro and predict the in vivo effect of modulation of the levels of these proteins. Innovation: We describe a model that can be used to explore the OPF pathway and its control in a quantitative way. Conclusion: Our study informs and provides new insights into how OPF works at a molecular level and provides a platform for the design of more efficient heterologous protein expression systems in yeast.


Subject(s)
Protein Folding , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism
2.
Biochim Biophys Acta Proteins Proteom ; 1865(11 Pt A): 1383-1394, 2017 Nov.
Article in English | MEDLINE | ID: mdl-28844745

ABSTRACT

Protein disulfide isomerase (PDI) has diverse functions in the endoplasmic reticulum as catalyst of redox transfer, disulfide isomerization and oxidative protein folding, as molecular chaperone and in multi-subunit complexes. It interacts with an extraordinarily wide range of substrate and partner proteins, but there is only limited structural information on these interactions. Extensive evidence on the flexibility of PDI in solution is not matched by any detailed picture of the scope of its motion. A new rapid method for simulating the motion of large proteins provides detailed molecular trajectories for PDI demonstrating extensive changes in the relative orientation of its four domains, great variation in the distances between key sites and internal motion within the core ligand-binding domain. The review shows that these simulations are consistent with experimental evidence and provide insight into the functional capabilities conferred by the extensive flexible motion of PDI.


Subject(s)
Endoplasmic Reticulum/enzymology , Molecular Chaperones/chemistry , Molecular Dynamics Simulation , Protein Disulfide-Isomerases/chemistry , Animals , Biocatalysis , Conserved Sequence , Gene Expression , Humans , Molecular Chaperones/genetics , Molecular Chaperones/metabolism , Oxidation-Reduction , Protein Disulfide-Isomerases/genetics , Protein Disulfide-Isomerases/metabolism , Protein Domains , Protein Folding , Protein Structure, Secondary , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae/genetics , Structural Homology, Protein
3.
Proteins ; 84(12): 1776-1785, 2016 12.
Article in English | MEDLINE | ID: mdl-27616289

ABSTRACT

We have studied the mobility of the multidomain folding catalyst, protein disulfide isomerase (PDI), by a coarse-graining approach based on flexibility. We analyze our simulations of yeast PDI (yPDI) using measures of backbone movement, relative positions and orientations of domains, and distances between functional sites. We find that there is interdomain flexibility at every interdomain junction but these show very different characteristics. The extent of interdomain flexibility is such that yPDI's two active sites can approach much more closely than is found in crystal structures-and indeed hinge motion to bring these sites into proximity is the lowest energy normal mode of motion of the protein. The flexibility predicted for yPDI (based on one structure) includes the other known conformation of yPDI and is consistent with (i) the mobility observed experimentally for mammalian PDI and (ii) molecular dynamics. We also observe intradomain flexibility and clear differences between the domains in their propensity for internal motion. Our results suggest that PDI flexibility enables it to interact with many different partner molecules of widely different sizes and shapes, and highlights considerable similarities of yPDI and mammalian PDI. Proteins 2016; 84:1776-1785. © 2016 Wiley Periodicals, Inc.


Subject(s)
Molecular Dynamics Simulation , Protein Disulfide-Isomerases/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae/chemistry , Binding Sites , Gene Expression , Pliability , Protein Binding , Protein Folding , Protein Interaction Domains and Motifs , Protein Structure, Secondary , Saccharomyces cerevisiae/enzymology , Structure-Activity Relationship , Thermodynamics
4.
Biophys J ; 108(7): 1739-1746, 2015 Apr 07.
Article in English | MEDLINE | ID: mdl-25863065

ABSTRACT

Determining the folding core of a protein yields information about its folding process and dynamics. The experimental procedures for identifying the amino acids that make up the folding core include hydrogen-deuterium exchange and Φ-value analysis and can be expensive and time consuming. Because of this, there is a desire to improve upon existing methods for determining protein folding cores theoretically. We have obtained HDX data for the complex of cyclophilin A with the immunosuppressant cyclosporin A. We compare these data, as well as literature values for uncomplexed cyclophilin A, to theoretical predictions using a combination of rigidity analysis and coarse-grained simulations of protein motion. We find that in this case, the most specific prediction of folding cores comes from a combined approach that models the rigidity of the protein using the first software suite and the dynamics of the protein using the froda tool.


Subject(s)
Cyclophilin A/chemistry , Cyclosporine/chemistry , Protein Folding , Amino Acid Sequence , Cyclophilin A/metabolism , Cyclosporine/metabolism , Molecular Dynamics Simulation , Molecular Sequence Data , Protein Binding , Protein Structure, Tertiary
5.
Biochim Biophys Acta ; 1853(3): 756-63, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25554517

ABSTRACT

Numerous therapeutic proteins are expressed in Escherichia coli and targeted to the periplasm in order to facilitate purification and enable disulfide bond formation. Export is normally achieved by the Sec pathway, which transports proteins through the plasma membrane in a reduced, unfolded state. The Tat pathway is a promising alternative means of export, because it preferentially exports correctly folded proteins; however, the reducing cytoplasm of standard strains has been predicted to preclude export by Tat of proteins that contain disulfide bonds in the native state because, in the reduced state, they are sensed as misfolded and rejected. Here, we have tested a series of disulfide-bond containing biopharmaceuticals for export by the Tat pathway in CyDisCo strains that do enable disulfide bond formation in the cytoplasm. We show that interferon α2b, human growth hormone (hGH) and two antibody fragments are exported with high efficiency; surprisingly, however, they are efficiently exported even in the absence of cytoplasmic disulfide formation. The exported proteins acquire disulfide bonds in the periplasm, indicating that the normal disulfide oxidation machinery is able to act on the proteins. Tat-dependent export of hGH proceeds even when the disulfide bonds are removed by substitution of the Cys residues involved, suggesting that these substrates adopt tertiary structures that are accepted as fully-folded by the Tat machinery.


Subject(s)
Disulfides/metabolism , Escherichia coli Proteins/physiology , Human Growth Hormone/metabolism , Immunoglobulin Fragments/metabolism , Interferon-alpha/metabolism , Membrane Transport Proteins/physiology , Periplasm/metabolism , Amino Acid Sequence , Antibodies/chemistry , Antibodies/metabolism , Disulfides/chemistry , Escherichia coli/metabolism , Humans , Interferon alpha-2 , Metabolic Networks and Pathways , Molecular Sequence Data , Organisms, Genetically Modified , Oxidation-Reduction , Protein Transport , Recombinant Proteins/metabolism
6.
PLoS One ; 9(1): e82511, 2014.
Article in English | MEDLINE | ID: mdl-24465374

ABSTRACT

In contrast to molecular chaperones that couple protein folding to ATP hydrolysis, protein disulfide-isomerase (PDI) catalyzes protein folding coupled to formation of disulfide bonds (oxidative folding). However, we do not know how PDI distinguishes folded, partly-folded and unfolded protein substrates. As a model intermediate in an oxidative folding pathway, we prepared a two-disulfide mutant of basic pancreatic trypsin inhibitor (BPTI) and showed by NMR that it is partly-folded and highly dynamic. NMR studies show that it binds to PDI at the same site that binds peptide ligands, with rapid binding and dissociation kinetics; surface plasmon resonance shows its interaction with PDI has a Kd of ca. 10(-5) M. For comparison, we characterized the interactions of PDI with native BPTI and fully-unfolded BPTI. Interestingly, PDI does bind native BPTI, but binding is quantitatively weaker than with partly-folded and unfolded BPTI. Hence PDI recognizes and binds substrates via permanently or transiently unfolded regions. This is the first study of PDI's interaction with a partly-folded protein, and the first to analyze this folding catalyst's changing interactions with substrates along an oxidative folding pathway. We have identified key features that make PDI an effective catalyst of oxidative protein folding - differential affinity, rapid ligand exchange and conformational flexibility.


Subject(s)
Protein Disulfide-Isomerases/chemistry , Protein Disulfide-Isomerases/metabolism , Proteins/metabolism , Magnetic Resonance Imaging , Magnetic Resonance Spectroscopy , Mass Spectrometry , Oxidation-Reduction , Protein Binding , Protein Folding , Proteins/chemistry , Surface Plasmon Resonance
7.
Biotechnol Prog ; 30(2): 281-90, 2014.
Article in English | MEDLINE | ID: mdl-24376243

ABSTRACT

Numerous high-value therapeutic proteins are produced in Escherichia coli and exported to the periplasm, as this approach simplifies downstream processing and enables disulfide bond formation. Most recombinant proteins are exported by the Sec pathway, which transports substrates across the plasma membrane in an unfolded state. The Tat system also exports proteins to the periplasm, but transports them in a folded state. This system has attracted interest because of its tendency to transport correctly folded proteins, but this trait renders it unable to export proteins containing disulfide bonds since these are normally acquired only in the periplasm; reduced substrates tend to be recognized as incorrectly folded and rejected. In this study we have used a series of novel strains (termed CyDisCo) which oxidise disulfide bonds in the cytoplasm, and we show that these cells efficiently export a range of disulfide-containing proteins when a Tat signal peptide is attached. These test proteins include alkaline phosphatase (PhoA), a phytase containing four disulfide bonds (AppA), an antiinterleukin 1ß scFv and human growth hormone. No export of PhoA or AppA is observed in wild-type cells lacking the CyDisCo factors. The PhoA, AppA and scFv proteins were exported in an active form by Tat in the CyDisCo strain, and mass spectrometry showed that the vast majority of the scFv protein was disulfide-bonded and correctly processed. The evidence indicates that this combination of Tat + CyDisCo offers a novel means of exporting active, correctly folded disulfide bonded proteins to the periplasm.


Subject(s)
Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Membrane Transport Proteins/metabolism , Periplasm/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Cell Engineering , Disulfides , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Fermentation , Membrane Transport Proteins/genetics , Periplasm/chemistry , Protein Folding , Recombinant Proteins/genetics
8.
FEBS J ; 280(16): 3810-21, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23745597

ABSTRACT

The twin-arginine translocation (Tat) system transports folded proteins across the plasma membrane in bacteria, and heterologous proteins can be exported by this pathway if a Tat-type signal peptide is present at the N-terminus. The system thus has potential for biopharmaceutical production in Escherichia coli, where export to the periplasm is often a favoured approach. Previous studies have shown that E. coli cells can export high levels of protein by the Tat pathway, and the protein product accummulates almost exclusively in the periplasm. In this study, we analysed E. coli cells that express the Bacillus subtilis TatAdCd system in place of the native TatABC system. We show that a heterologous model protein, comprising the TorA signal peptide linked to green fluorescent protein (TorA-GFP), is efficiently exported by the TatAdCd system. However, whereas the GFP is exported initially to the periplasm during batch fermentation, the mature protein is increasingly found in the extracellular culture medium. By the end of a 16-h fermentation, ~ 90% of exported GFP is present in the medium as active mature protein. The total protein profiles of the medium and periplasm are essentially identical, confirming that the outer membrane becomes leaky during the fermentation process. The cells are otherwise intact, and there is no large-scale release of cytoplasmic contents. Export levels are relatively high, with ~ 0.35 g GFP·L⁻¹ culture present in the medium. This system thus offers a means of producing recombinant protein in E. coli and harvesting directly from the medium, with potential advantages in terms of ease of purification and downstream processing.


Subject(s)
Bacillus subtilis/metabolism , Bacterial Proteins/metabolism , Escherichia coli/metabolism , Membrane Transport Proteins/metabolism , Protein Sorting Signals , Recombinant Fusion Proteins/metabolism , Bacterial Proteins/genetics , Batch Cell Culture Techniques , Escherichia coli/growth & development , Escherichia coli/ultrastructure , Fermentation , Green Fluorescent Proteins/biosynthesis , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Kinetics , Membrane Transport Proteins/genetics , Oxidoreductases, N-Demethylating/biosynthesis , Oxidoreductases, N-Demethylating/chemistry , Oxidoreductases, N-Demethylating/genetics , Oxidoreductases, N-Demethylating/metabolism , Recombinant Fusion Proteins/biosynthesis , Recombinant Fusion Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
9.
Biochem J ; 450(2): 321-32, 2013 Mar 01.
Article in English | MEDLINE | ID: mdl-23234573

ABSTRACT

ERp27 (endoplasmic reticulum protein 27.7 kDa) is a homologue of PDI (protein disulfide-isomerase) localized to the endoplasmic reticulum. ERp27 is predicted to consist of two thioredoxin-fold domains homologous with the non-catalytic b and b' domains of PDI. The structure in solution of the N-terminal b-like domain of ERp27 was solved using high-resolution NMR data. The structure confirms that it has the thioredoxin fold and that ERp27 is a member of the PDI family. (15)N-NMR relaxation data were obtained and ModelFree analysis highlighted limited exchange contributions and slow internal motions, and indicated that the domain has an average order parameter S(2) of 0.79. Comparison of the single-domain structure determined in the present study with the equivalent domain within full-length ERp27, determined independently by X-ray diffraction, indicated very close agreement. The domain interface inferred from NMR data in solution was much more extensive than that observed in the X-ray structure, suggesting that the domains flex independently and that crystallization selects one specific interdomain orientation. This led us to apply a new rapid method to simulate the flexibility of the full-length protein, establishing that the domains show considerable freedom to flex (tilt and twist) about the interdomain linker, consistent with the NMR data.


Subject(s)
Endoplasmic Reticulum/metabolism , Nuclear Magnetic Resonance, Biomolecular/methods , Protein Disulfide-Isomerases/chemistry , Binding Sites , Heat-Shock Proteins/chemistry , Heat-Shock Proteins/metabolism , Humans , Models, Molecular , Protein Disulfide-Isomerases/metabolism , Protein Folding , Protein Structure, Tertiary , X-Ray Diffraction
10.
Top Curr Chem ; 328: 1-34, 2013.
Article in English | MEDLINE | ID: mdl-21630134

ABSTRACT

Oxidative folding is the simultaneous process of forming disulphide bonds and native structure in proteins. Pathways of oxidative folding are highly diverse and in eukaryotes are catalysed by protein disulphide isomerases (PDIs). PDI consists of four thioredoxin-like domains, two of which contain active sites responsible for disulphide interchange reactions. The four domains are arranged in a horseshoe shape with the two active sites facing each other at the opening of the horseshoe. An extended hydrophobic surface at the bottom of the horseshoe is responsible for non-covalent, hydrophobic interactions with the folding protein. This binding site is capable of distinguishing between fully-folded and partially- or un-folded proteins. PDI is not only a catalyst of the formation of disulphide bonds, but also catalyses folding steps which involve significant conformational change in the folding protein. This review brings together the latest catalytic and structural data aimed at understanding how this is achieved.


Subject(s)
Oxidative Stress , Protein Folding , Biocatalysis , Humans , Models, Molecular , Protein Disulfide-Isomerases/metabolism
11.
Biochemistry ; 52(3): 497-507, 2013 Jan 22.
Article in English | MEDLINE | ID: mdl-23237426

ABSTRACT

Uricase (Urc) is an oxidoreductase enzyme of both general and commercial interest, the former because of its lack of a cofactor and the latter because of its use in the treatment of hyperuricemic disorders. Results of fluorometry and circular dichroism (CD) spectroscopy indicate that the main phase of thermal Urc inactivation follows an irreversible two-state mechanism, with loss of ~20% of the helical structure, loss of the majority of the tertiary structure, and partial exposure of tryptophan residues to solution being approximately concurrent with activity loss. Results of size exclusion chromatography and 8-anilinonaphthalene-1-sulfonate binding studies confirm that this process results in the formation of aggregated molten globules. In addition to this process, CD studies indicate the presence of a rapid reversible denaturation phase that is not completely coupled to the main phase. Urc inactivation is inhibited by the presence of glycerol and trimethylamine oxide, stabilizers of hydrophobic interactions and backbone structure respectively, confirming that loss of hydrophobic bonding and loss of helical structure are key events in the loss of Urc activity. NaCl, however, destabilizes the enzyme at elevated temperature, emphasizing the importance of ionic interactions to Urc stability. A model is developed in which interfacial disruption, involving local loss of hydrophobic interactions, ionic bonds, and helical structure, leads to Urc inactivation and aggregation. Additional studies of Urc inactivation at a more ambient temperature indicate that the inactivation process followed under such conditions is different from that followed at higher temperatures, highlighting the limitations of high-temperature enzyme stability studies.


Subject(s)
Candida/enzymology , Excipients/chemistry , Excipients/metabolism , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Urate Oxidase/chemistry , Urate Oxidase/metabolism , Anilino Naphthalenesulfonates/chemistry , Anilino Naphthalenesulfonates/metabolism , Chromatography, Gel , Circular Dichroism , Enzyme Stability/drug effects , Fluorometry , Fungal Proteins/genetics , Glycerol/chemistry , Glycerol/metabolism , Hot Temperature , Hydrophobic and Hydrophilic Interactions , Kinetics , Methylamines/chemistry , Methylamines/metabolism , Protein Binding , Protein Denaturation/drug effects , Protein Structure, Secondary , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Urate Oxidase/genetics
12.
Biotechnol Bioeng ; 109(10): 2533-42, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22539025

ABSTRACT

Numerous high-value recombinant proteins that are produced in bacteria are exported to the periplasm as this approach offers relatively easy downstream processing and purification. Most recombinant proteins are exported by the Sec pathway, which transports them across the plasma membrane in an unfolded state. The twin-arginine translocation (Tat) system operates in parallel with the Sec pathway but transports substrate proteins in a folded state; it therefore has potential to export proteins that are difficult to produce using the Sec pathway. In this study, we have produced a heterologous protein (green fluorescent protein; GFP) in Escherichia coli and have used batch and fed-batch fermentation systems to test the ability of the newly engineered Tat system to export this protein into the periplasm under industrial-type production conditions. GFP cannot be exported by the Sec pathway in an active form. We first tested the ability of five different Tat signal peptides to export GFP, and showed that the TorA signal peptide directed most efficient export. Under batch fermentation conditions, it was found that TorA-GFP was exported efficiently in wild type cells, but a twofold increase in periplasmic GFP was obtained when the TatABC components were co-expressed. In both cases, periplasmic GFP peaked at about the 12 h point during fermentation but decreased thereafter, suggesting that proteolysis was occurring. Typical yields were 60 mg periplasmic GFP per liter culture. The cells over-expressed the tat operon throughout the fermentation process and the Tat system was shown to be highly active over a 48 h induction period. Fed-batch fermentation generated much greater yields: using glycerol feed rates of 0.4, 0.8, and 1.2 mL h(-1), the cultures reached OD(600) values of 180 and periplasmic GFP levels of 0.4, 0.85, and 1.1 g L(-1) culture, respectively. Most or all of the periplasmic GFP was shown to be active. These export values are in line with those obtained in industrial production processes using Sec-dependent export approaches.


Subject(s)
Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Membrane Transport Proteins/metabolism , Metabolic Engineering/methods , Periplasm/metabolism , Recombinant Proteins/metabolism , Biotechnology/methods , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Genes, Reporter , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Membrane Transport Proteins/genetics , Protein Transport , Recombinant Proteins/genetics
13.
Biotechnol Bioeng ; 109(4): 983-91, 2012 Apr.
Article in English | MEDLINE | ID: mdl-22125050

ABSTRACT

The twin arginine translocation (Tat) pathway occurs naturally in E. coli and has the distinct ability to translocate folded proteins across the inner membrane of the cell. It has the potential to export commercially useful proteins that cannot be exported by the ubiquitous Sec pathway. To better understand the bioprocess potential of the Tat pathway, this article addresses the fermentation and downstream processing performances of E. coli strains with a wild-type Tat system exporting the over-expressed substrate protein FhuD. These were compared to strains cell-engineered to over-express the Tat pathway, since the native export capacity of the Tat pathway is low. This low capacity makes the pathway susceptible to saturation by over-expressed substrate proteins, and can result in compromised cell integrity. However, there is concern in the literature that over-expression of membrane proteins, like those of the Tat pathway, can impact negatively upon membrane integrity itself. Under controlled fermentation conditions E. coli cells with a wild-type Tat pathway showed poor protein accumulation, reaching a periplasmic maximum of only 0.5 mg L⁻¹ of growth medium. Cells over-expressing the Tat pathway showed a 25% improvement in growth rate, avoided pathway saturation, and showed 40-fold higher periplasmic accumulation of FhuD. Moreover, this was achieved whilst conserving the integrity of cells for downstream processing: experimentation comparing the robustness of cells to increasing levels of shear showed no detrimental effect from pathway over-expression. Further experimentation on spheroplasts generated by the lysozyme/osmotic shock method--a scaleable way to release periplasmic protein--showed similar robustness between strains. A scale-down mimic of continuous disk-stack centrifugation predicted clarifications in excess of 90% for both intact cells and spheroplasts. Cells over-expressing the Tat pathway performed comparably to cells with the wild-type system. Overall, engineering E. coli cells to over-express the Tat pathway allowed for greater periplasmic yields of FhuD at the fermentation scale without compromising downstream processing performance.


Subject(s)
Batch Cell Culture Techniques/methods , Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Industrial Microbiology/methods , Membrane Transport Proteins/metabolism , Periplasmic Binding Proteins/metabolism , Amino Acid Sequence , Bacterial Translocation , Bacteriological Techniques , Biological Transport, Active , Cell Membrane/metabolism , Centrifugation , Escherichia coli Proteins/genetics , Escherichia coli Proteins/isolation & purification , Fermentation , Membrane Transport Proteins/genetics , Membrane Transport Proteins/isolation & purification , Molecular Sequence Data , Periplasm/metabolism , Periplasmic Binding Proteins/genetics , Periplasmic Binding Proteins/isolation & purification , Protein Sorting Signals/physiology , Protein Transport , Recombinant Fusion Proteins/isolation & purification , Recombinant Fusion Proteins/metabolism , Spheroplasts/metabolism , Viscosity
14.
Enzyme Microb Technol ; 49(1): 79-87, 2011 Jun 10.
Article in English | MEDLINE | ID: mdl-22112275

ABSTRACT

Glucose oxidase (GOx) from Penicillium amagasakiense has a higher specific activity than the more commonly studied Aspergillus niger enzyme, and may therefore be preferred in many medical and industrial applications. The enzyme rapidly inactivates on storage at pH 7.0-7.6 at temperatures between 30 and 40°C. Results of fluorimetry and circular dichroism spectroscopy indicate that GOx inactivation under these conditions is associated with release of the cofactor FAD and molten globule formation, indicated by major loss of tertiary structure but almost complete retention of secondary structure. Inactivation of GOx at pH<7 leads to precipitation, but at pH ≥ 7 it leads to non-specific formation of small soluble aggregates detectable by PAGE and size-exclusion chromatography (SEC). Inactivation of P. amagasakiense GOx differs from that of A. niger GOx in displaying complete rather than partial retention of secondary structure and in being promoted rather than prevented by NaCl. The contrasting salt effects may reflect differences in the nature of the interface between subunits in the native dimers and/or the quantity of secondary structure loss upon inactivation.


Subject(s)
Glucose Oxidase/antagonists & inhibitors , Penicillium/enzymology , Aspergillus niger/enzymology , Enzyme Stability , Flavin-Adenine Dinucleotide/metabolism , Fungal Proteins/antagonists & inhibitors , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Glucose Oxidase/chemistry , Glucose Oxidase/metabolism , Kinetics , Osmolar Concentration , Protein Multimerization , Protein Structure, Secondary , Protein Structure, Tertiary
15.
J Biol Chem ; 285(35): 26788-26797, 2010 Aug 27.
Article in English | MEDLINE | ID: mdl-20516074

ABSTRACT

Protein disulfide isomerase (PDI), which consists of multiple domains arranged as abb'xa'c, is a key enzyme responsible for oxidative folding in the endoplasmic reticulum. In this work we focus on the conformational plasticity of this enzyme. Proteolysis of native human PDI (hPDI) by several proteases consistently targets sites in the C-terminal half of the molecule (x-linker and a' domain) leaving large fragments in which the N terminus is intact. Fluorescence studies on the W111F/W390F mutant of full-length PDI show that its fluorescence is dominated by Trp-347 in the x-linker which acts as an intrinsic reporter and indicates that this linker can move between "capped" and "uncapped" conformations in which it either occupies or exposes the major ligand binding site on the b' domain of hPDI. Studies with a range of constructs and mutants using intrinsic fluorescence, collision quenching, and extrinsic probe fluorescence (1-anilino-8-naphthalene sulfonate) show that the presence of the a' domain in full-length hPDI moderates the ability of the x-linker to generate the capped conformation (compared with shorter fragments) but does not abolish it. Hence, unlike yeast PDI, the major conformational plasticity of full-length hPDI concerns the mobility of the a' domain "arm" relative to the bb' "trunk" mediated by the x-linker. The chaperone and enzymatic activities of these constructs and mutants are consistent with the interpretation that the reversible interaction of the x-linker with the ligand binding site mediates access of protein substrates to this site.


Subject(s)
Protein Disulfide-Isomerases/chemistry , Protein Folding , Amino Acid Substitution , Anilino Naphthalenesulfonates/chemistry , Binding Sites , Endoplasmic Reticulum/chemistry , Endoplasmic Reticulum/enzymology , Endoplasmic Reticulum/genetics , Humans , Ligands , Mutation, Missense , Protein Disulfide-Isomerases/genetics , Protein Disulfide-Isomerases/metabolism , Protein Structure, Tertiary
16.
Protein Sci ; 18(12): 2569-77, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19844948

ABSTRACT

Purified preparations of the recombinant b'x domain fragment of human protein-disulphide isomerase (PDI), which are homogeneous by mass spectrometry and sodium dodecyl sulfate polyacrylamide gel electrophoresis, comprise more than one species when analyzed by ion-exchange chromatography and nondenaturing polyacrylamide gel electrophoresis. These species were resolved and shown to be monomer and dimer by analytical ultracentrifugation and analytical size-exclusion chromatography. Spectroscopic properties indicate that the monomeric species corresponds to the "capped" conformation observed in the x-ray structure of the I272A mutant of b'x (Nguyen, Wallis, Howard, Haapalainen, Salo, Saaranen, Sidhu, Wierenga, Freedman, Ruddock, and Williamson, J Mol Biol 2008;383:1144-1155) in which the x region binds to a hydrophobic patch on the surface of the b' domain; conversely, the dimeric species has an "open" or "uncapped" conformation in which the x region does not bind to this surface. The larger bb'x fragment of human PDI shows very similar behavior to b'x and can be resolved into a capped monomeric species and an uncapped dimer. Preparations of recombinant b' domain of human PDI and of the bb' domain pair are found exclusively as dimers. Full-length PDI is known to comprise a mixture of monomeric and dimeric species, whereas the isolated a, b, and a' domains of PDI are found exclusively as monomers. These results show that the b' domain of human PDI tends to form homodimers--both in isolation and in other contexts--and that this tendency is moderated by the adjacent x region, which can bind to a surface patch on the b' domain.


Subject(s)
Protein Disulfide-Isomerases/chemistry , Humans , Ligands , Protein Multimerization , Protein Structure, Tertiary
17.
Biochem J ; 423(2): 209-17, 2009 Sep 25.
Article in English | MEDLINE | ID: mdl-19604149

ABSTRACT

PDI (protein disulfide-isomerase) catalyses the formation of native disulfide bonds of secretory proteins in the endoplasmic reticulum. PDI consists of four thioredoxin-like domains, of which two contain redox-active catalytic sites (a and a'), and two do not (b and b'). The b' domain is primarily responsible for substrate binding, although the nature and specificity of the substrate-binding site is still poorly understood. In the present study, we show that the b' domain of human PDI is in conformational exchange, but that its structure is stabilized by the addition of peptide ligands or by binding the x-linker region. The location of the ligand-binding site in b' was mapped by NMR chemical shift perturbation and found to consist primarily of residues from the core beta-sheet and alpha-helices 1 and 3. This site is where the x-linker region binds in the X-ray structure of b'x and we show that peptide ligands can compete with x binding at this site. The finding that x binds in the principal ligand-binding site of b' further supports the hypothesis that x functions to gate access to this site and so modulates PDI activity.


Subject(s)
Peptide Fragments/metabolism , Protein Disulfide-Isomerases/chemistry , Protein Disulfide-Isomerases/metabolism , Protein Interaction Mapping , Binding Sites , Humans , Ligands , Models, Molecular , Peptide Fragments/chemistry , Peptide Fragments/isolation & purification , Protein Disulfide-Isomerases/isolation & purification , Protein Structure, Secondary , Protein Structure, Tertiary/physiology , Somatostatin/chemistry , Somatostatin/metabolism
19.
J Biol Chem ; 284(1): 199-206, 2009 Jan 02.
Article in English | MEDLINE | ID: mdl-19001419

ABSTRACT

Protein-disulfide isomerase (PDI), a critical enzyme responsible for oxidative protein folding in the eukaryotic endoplasmic reticulum, is composed of four thioredoxin domains a, b, b', a', and a linker x between b' and a'. Ero1-Lalpha, an oxidase for human PDI (hPDI), has been determined to have one molecular flavin adenine dinucleotide (FAD) as its prosthetic group. Oxygen consumption assays with purified recombinant Ero1-Lalpha revealed that it utilizes oxygen as a terminal electron acceptor producing one disulfide bond and one molecule of hydrogen peroxide per dioxygen molecule consumed. Exogenous FAD is not required for recombinant Ero1-Lalpha activity. By monitoring the reactivation of denatured and reduced RNase A, we reconstituted the Ero1-Lalpha/hPDI oxidative folding system in vitro and determined the enzymatic activities of hPDI in this system. Mutagenesis studies suggested that the a' domain of hPDI is much more active than the a domain in Ero1-Lalpha-mediated oxidative folding. A domain swapping study revealed that one catalytic thioredoxin domain to the C-terminal of bb'x, whether a or a', is essential in Ero1-Lalpha-mediated oxidative folding. These data, combined with a pull-down assay and isothermal titration calorimetry measurements, enabled the minimal element for binding with Ero1-Lalpha to be mapped to the b'xa' fragment of hPDI.


Subject(s)
Flavin-Adenine Dinucleotide/chemistry , Hydrogen Peroxide/chemistry , Membrane Glycoproteins/chemistry , Oxidoreductases/chemistry , Oxygen/chemistry , Protein Disulfide-Isomerases/chemistry , Protein Folding , Flavin-Adenine Dinucleotide/genetics , Humans , Membrane Glycoproteins/genetics , Oxidation-Reduction , Oxidoreductases/genetics , Protein Disulfide-Isomerases/genetics , Protein Structure, Tertiary/physiology , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Ribonuclease, Pancreatic/chemistry , Ribonuclease, Pancreatic/genetics
20.
J Mol Biol ; 383(5): 1144-55, 2008 Nov 28.
Article in English | MEDLINE | ID: mdl-18801374

ABSTRACT

Protein disulphide isomerase (PDI) is a key multi-domain protein folding catalyst in the endoplasmic reticulum. The b' domain of PDI is essential for the non-covalent binding of incompletely folded protein substrates. Earlier, we defined the substrate binding site in the b' domain of human PDI by modelling and mutagenesis studies. Here, we show by fluorescence and NMR that recombinant human PDI b'x (comprising the b' domain and the subsequent x linker region) can assume at least two different conformations in solution. We have screened mutants in the b'x region to identify mutations that favour one of these conformers in recombinant b'x, and isolated and characterised examples of both types. We have crystallised one mutant of b'x (I272A mutation) in which one conformer is stabilized, and determined its crystal structure to a resolution of 2.2 A. This structure shows that the b' domain has the typical thioredoxin fold and that the x region can interact with the b' domain by "capping" a hydrophobic site on the b' domain. This site is most likely the substrate binding site and hence such capping will inhibit substrate binding. All of the mutations we previously reported to inhibit substrate binding shift the equilibrium towards the capped conformer. Hence, these mutations act by altering the natural equilibrium and decreasing the accessibility of the substrate binding site. Furthermore, we have confirmed that the corresponding structural transition occurs in the wild type full-length PDI. A cross-comparison of our data with that for other PDI-family members, Pdi1p and ERp44, suggests that the x region of PDI can adopt alternative conformations during the functional cycle of PDI action and that these are linked to the ability of PDI to interact with folding substrates.


Subject(s)
Protein Disulfide-Isomerases/chemistry , Amino Acid Sequence , Crystallography, X-Ray , Humans , Magnetic Resonance Spectroscopy , Models, Molecular , Molecular Sequence Data , Mutant Proteins/chemistry , Mutation/genetics , Protein Structure, Secondary , Protein Structure, Tertiary , Recombinant Proteins/chemistry , Spectrometry, Fluorescence , Substrate Specificity , Tryptophan
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