Publications by authors named "Rainer Rudolph"

53 Publications

New binding mode to TNF-alpha revealed by ubiquitin-based artificial binding protein.

PLoS One 2012 20;7(2):e31298. Epub 2012 Feb 20.

Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.

A variety of approaches have been employed to generate binding proteins from non-antibody scaffolds. Utilizing a beta-sheet of the human ubiquitin for paratope creation we obtained binding proteins against tumor necrosis factor (TNF)-alpha. The bioactive form of this validated pharmacological target protein is a non-covalently linked homo-trimer. This structural feature leads to the observation of a certain heterogeneity concerning the binding mode of TNF-alpha binding molecules, for instance in terms of monomer/trimer specificity. We analyzed a ubiquitin-based TNF-alpha binder, selected by ribosome display, with a particular focus on its mode of interaction. Using enzyme-linked immunosorbent assays, specific binding to TNF-alpha with nanomolar affinity was observed. In isothermal titration calorimetry we obtained comparable results regarding the affinity and detected an exothermic reaction with one ubiquitin-derived binding molecule binding one TNF-alpha trimer. Using NMR spectroscopy and other analytical methods the 1:3 stoichiometry could be confirmed. Detailed binding analysis showed that the interaction is affected by the detergent Tween-20. Previously, this phenomenon was reported only for one other type of alternative scaffold-derived binding proteins--designed ankyrin repeat proteins--without further investigation. As demonstrated by size exclusion chromatography and NMR spectroscopy, the presence of the detergent increases the association rate significantly. Since the special architecture of TNF-alpha is known to be modulated by detergents, the access to the recognized epitope is indicated to be restricted by conformational transitions within the target protein. Our results suggest that the ubiquitin-derived binding protein targets a new epitope on TNF-alpha, which differs from the epitopes recognized by TNF-alpha neutralizing antibodies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031298PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282696PMC
June 2012

Binding specificity of the ectodomain of the parathyroid hormone receptor.

Biophys Chem 2011 Mar 14;154(2-3):66-72. Epub 2011 Jan 14.

Institute of Biochemistry/Biotechnology, Faculty of Science I, Martin-Luther-University Halle-Wittenberg, Germany.

The parathyroid hormone (PTH)1 receptor is a member of the class B G protein-coupled receptor (GPCR) family and regulates bone and mineral metabolism of vertebrates. A truncated highly active parathyroid hormone fragment PTH (1-34) exerts stimulatory effects on the receptor and is used for treatment of osteoporosis. To study the interacting amino acids of the natural peptide ligand PTH (1-84) with the ectodomain of its receptor we used peptide micro arrays on solid cellulose membranes. The amino acids Arg20 and Trp23 within the identified core binding stretch PTH (20-26) were found to be most important for affinity to the ectodomain of PTH1R. Isothermal titration calorimetry and NMR spectroscopy allowed peptide binding studies in solution and verified peptide positions required for high affinity. With this combination of biochemical and biophysical methods we extend former findings on this essential interaction and can now provide a strategy to screen for optimized therapeutic peptides.
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http://dx.doi.org/10.1016/j.bpc.2011.01.002DOI Listing
March 2011

Recombinant expression, in vitro refolding, and biophysical characterization of the human glucagon-like peptide-1 receptor.

Biochemistry 2010 Sep;49(36):7956-65

Institute of Biochemistry and Biotechnology, Martin-Luther-University, Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany.

Activation of the glucagon-like peptide-1 receptor (GLP-1R) upon ligand binding leads to the release of insulin from pancreatic cells. This strictly glucose-dependent process renders the receptor and its ligands useful in the treatment of type II diabetes mellitus. To enable a biophysical characterization in vitro, we expressed the human full-length GLP-1R in the cytosol of Escherichia coli as inclusion bodies. After purification, refolding of the SDS-solubilized receptor was achieved by the exchange of SDS against the detergent Brij78 using an artificial chaperone system. Far-UV circular dichroism spectroscopic studies revealed that the receptor adopts a characteristic alpha-helical structure in Brij78 micelles. Ligand binding of the renatured protein was quantified by fluorescence quenching and surface plasmon resonance spectroscopy. In the presence of Brij micelles, the refolded receptor binds the agonist exendin-4 with an apparent dissociation constant of approximately 100 nM in a reversible one-step mechanism. To demonstrate that the detected ligand binding activity is not only due to an autonomously functional N-terminal domain (nGLP-1R) but also due to additional contacts with the juxtamembrane part, we separately expressed and refolded the extracellular domain relying on identical protocols established for the full-length GLP-1R. In support of the suggested multidomain binding mode, the nGLP-1R binds exendin-4 with a lower affinity (K(app) in the micromolar range) and a different kinetic mechanism. The lower ligand affinity of the nGLP-1R results entirely from a decreased kinetic stability of the receptor-ligand complex, dissociation of which is approximately 40-fold faster in the case of the nGLP-1R compared to the full-length GLP-1R. In summary, a framework was developed to produce functional human full-length GLP-1R by recombinant expression in E. coli as a prerequisite for eventual structure determination and a rigorous biophysical characterization including protein variants.
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http://dx.doi.org/10.1021/bi101159sDOI Listing
September 2010

L-arginine hydrochloride increases the solubility of folded and unfolded recombinant plasminogen activator rPA.

Protein Sci 2010 Sep;19(9):1783-95

Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.

L-arginine hydrochloride (L-ArgHCl) was found to be an effective enhancer for in vitro protein refolding more than two decades ago. A detailed understanding of the mechanism of action, by which L-ArgHCl as co-solvent is capable to effectively suppress protein aggregation, while protein stability is preserved, has remained elusive. Concepts for the effects of co-solvents, which have been established over the last decades, were found to be insufficient to completely explain the effects of L-ArgHCl on protein refolding. In this article, we present data, which clearly establish that L-ArgHCl acts on the equilibrium solubility of the native model protein recombinant plasminogen activator (rPA), while for S-carboxymethylated rPA (IAA-rPA) that served as a model protein for denatured protein states, equilibrium solubilities could not be obtained. Solid to solute free transfer energies for native rPA were lowered by up to 14 kJ mol(-1) under the tested conditions. This finding is in marked contrast to a previously proposed model in which L-ArgHCl acts as a neutral crowder which exclusively has an influence on the stability of the transition state of aggregation. The effects on the apparent solubility of IAA-rPA, as well as on the aggregation kinetics of all studied protein species, that were observed in the present work could tentatively be explained within the framework of a nucleation-aggregation scheme, in which L-ArgHCl exerts a strong effect on the pre-equilibria leading to formation of the aggregation seed.
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http://dx.doi.org/10.1002/pro.465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975141PMC
September 2010

Ionic liquids as refolding additives: variation of the anion.

J Biotechnol 2010 Oct 12;150(1):64-72. Epub 2010 Jul 12.

Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany.

Several ionic liquids have been shown to act as suppressors of protein aggregation and to effectively promote the in vitro refolding of denatured proteins. In this work, the influence of the anion of these organic salts on their performance as refolding enhancers was tested, using a series of N-ethyl-N'-methyl imidazolium (EMIM) salts. Variation of the anion had a profound effect on the renaturation of the recombinant plasminogen activator rPA, which served as a model protein. The effect was roughly correlated with the stability of proteins in the tested aqueous ionic liquid solutions. Strongly destabilizing anions with higher alkyl substitutions like, e.g., hexyl sulfate were unable to promote protein refolding. However, the dimethyl and diethyl phosphate salts, which are known to be quite compatible with protein stability, also effectively suppressed renaturation, while alkylated sulfate anions with the same influence on protein stability did promote in vitro refolding. Only ionic liquid co-solvent systems with an intermediate capacity for solubilizing the proteinogenic amino acid tryptophan were found to permit effective renaturation of the model protein rPA. The most effective refolding enhancer among the tested ionic liquids was EMIM chloride.
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http://dx.doi.org/10.1016/j.jbiotec.2010.07.003DOI Listing
October 2010

Recombinant production of bioactive human TNF-alpha by SUMO-fusion system--high yields from shake-flask culture.

Protein Expr Purif 2010 Aug 2;72(2):238-43. Epub 2010 Apr 2.

NWG Künstliche Bindeproteine, Institut für Biochemie und Biotechnologie, Technische Biochemie, Martin-Luther-Universität Halle-Wittenberg, Heinrich-Damerow-Str. 4, 06120 Halle, Germany.

Tumor necrosis factor (TNF-alpha) inhibitors, used for the treatment of common inflammatory diseases, currently belong among the most important biotechnologically produced pharmaceuticals. So far four TNF-alpha antagonists have been approved by regulatory authorities for defined subsets of applications. Furthermore, numerous approaches are being taken to develop new protein-based pharmaceuticals and to broaden their application areas in the treatment of TNF-alpha -related diseases. Both the fundamental understanding of disease-related TNF-alpha activity and the subsequent development of corresponding drug candidates demand the availability of large amounts of TNF-alpha as a bioactive protein. We have therefore established a protocol for the rapid high-level synthesis of recombinant human TNF-alpha in Escherichia coli shake-flask cultures and the subsequent purification of the mature protein. Using the advantages of SUMO-fusion technology we were able to produce protein with an authentic N-terminus in high yield. Two immobilized metal ion-affinity chromatography steps with a protease cleavage step in between and subsequent size-exclusion chromatography were utilized to purify the protein. The protein was obtained from the last chromatography step as a trimer, while purity was at least 96% as estimated by SDS-PAGE. The identity of the protein was confirmed by MALDI-TOF mass spectrometry. Recombinant mature TNF-alpha was correctly folded as assessed by CD spectroscopy and its biological activity was confirmed by an L929 cell assay.
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http://dx.doi.org/10.1016/j.pep.2010.03.022DOI Listing
August 2010

Mammalian G protein-coupled receptor expression in Escherichia coli: II. Refolding and biophysical characterization of mouse cannabinoid receptor 1 and human parathyroid hormone receptor 1.

Anal Biochem 2010 Jun 20;401(1):74-80. Epub 2010 Feb 20.

Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS, and Universités of Marseille, F-13288 Marseille Cedex 09, France.

G protein-coupled receptors (GPCRs) represent approximately 3% of the human proteome. They are involved in a large number of diverse processes and, therefore, are the most prominent class of pharmacological targets. Besides rhodopsin, X-ray structures of classical GPCRs have only recently been resolved, including the beta1 and beta2 adrenergic receptors and the A2A adenosine receptor. This lag in obtaining GPCR structures is due to several tedious steps that are required before beginning the first crystallization experiments: protein expression, detergent solubilization, purification, and stabilization. With the aim to obtain active membrane receptors for functional and crystallization studies, we recently reported a screen of expression conditions for approximately 100 GPCRs in Escherichia coli, providing large amounts of inclusion bodies, a prerequisite for the subsequent refolding step. Here, we report a novel artificial chaperone-assisted refolding procedure adapted for the GPCR inclusion body refolding, followed by protein purification and characterization. The refolding of two selected targets, the mouse cannabinoid receptor 1 (muCB1R) and the human parathyroid hormone receptor 1 (huPTH1R), was achieved from solubilized receptors using detergent and cyclodextrin as protein folding assistants. We could demonstrate excellent affinity of both refolded and purified receptors for their respective ligands. In conclusion, this study suggests that the procedure described here can be widely used to refold GPCRs expressed as inclusion bodies in E. coli.
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http://dx.doi.org/10.1016/j.ab.2010.02.017DOI Listing
June 2010

Crystal structure of glucagon-like peptide-1 in complex with the extracellular domain of the glucagon-like peptide-1 receptor.

J Biol Chem 2010 Jan 27;285(1):723-30. Epub 2009 Oct 27.

Department of GLP-1 and Obesity Biology, Novo Nordisk, 2760 Måløv, Denmark.

GLP-1 (glucagon-like peptide-1) is an incretin released from intestinal L-cells in response to food intake. Activation of the GLP-1 receptor potentiates the synthesis and release of insulin from pancreatic beta-cells in a glucose-dependent manner. The GLP-1 receptor belongs to class B of the G-protein-coupled receptors, a subfamily characterized by a large N-terminal extracellular ligand binding domain. Exendin-4 and GLP-1 are 50% identical, and exendin-4 is a full agonist with similar affinity and potency for the GLP-1 receptor. We recently solved the crystal structure of the GLP-1 receptor extracellular domain in complex with the competitive antagonist exendin-4(9-39). Interestingly, the isolated extracellular domain binds exendin-4 with much higher affinity than the endogenous agonist GLP-1. Here, we have solved the crystal structure of the extracellular domain in complex with GLP-1 to 2.1 Aresolution. The structure shows that important hydrophobic ligand-receptor interactions are conserved in agonist- and antagonist-bound forms of the extracellular domain, but certain residues in the ligand-binding site adopt a GLP-1-specific conformation. GLP-1 is a kinked but continuous alpha-helix from Thr(13) to Val(33) when bound to the extracellular domain. We supplemented the crystal structure with site-directed mutagenesis to link the structural information of the isolated extracellular domain with the binding properties of the full-length receptor. The data support the existence of differences in the binding modes of GLP-1 and exendin-4 on the full-length GLP-1 receptor.
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http://dx.doi.org/10.1074/jbc.M109.033829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804221PMC
January 2010

Prokaryotic expression, in vitro folding, and molecular pharmacological characterization of the neuropeptide Y receptor type 2.

Biotechnol Prog 2009 Nov-Dec;25(6):1732-9

Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

G protein-coupled receptors (GPCRs) are a class of membrane proteins that represent a major target for pharmacological developments. However, there is still little knowledge about GPCR structure and dynamics since high-level expression and characterization of active GPCRs in vitro is extremely complicated. Here, we describe the recombinant expression and functional folding of the human Y(2) receptor from inclusion bodies of E. coli cultures. Milligram protein quantities were produced using high density fermentation and isolated in a single step purification with a yield of over 20 mg/L culture. Extensive studies were carried out on in vitro refolding and stabilization of the isolated receptor in detergent solution. The specific binding of the ligand, the 36 residue neuropeptide Y (NPY), to the recombinant Y(2) receptors in micellar form was shown by several radioligand affinity assays. In competition experiments, an IC(50) value in low nanomolar range could be determined. Further, a K(D) value of 1.9 nM was determined from a saturation assay, where NPY was titrated to the recombinant Y(2) receptors.
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http://dx.doi.org/10.1002/btpr.266DOI Listing
April 2010

Identification of a disulfide bridge essential for transport function of the human proton-coupled amino acid transporter hPAT1.

J Biol Chem 2009 Aug 23;284(33):22123-32. Epub 2009 Jun 23.

Institute of Biochemistry/Biotechnology, Faculty of Science I, Biozentrum, Martin-Luther-University Halle-Wittenberg, Halle, Germany.

The proton-coupled amino acid transporter 1 (PAT1, SLC36A1) mediates the uptake of small neutral amino acids at the apical membrane of intestinal epithelial cells after protein digestion. The transporter is currently under intense investigation, because it is a possible vehicle for oral drug delivery. Structural features of the protein such as the number of transmembrane domains, the substrate binding site, or essential amino acids are still unknown. In the present study we use mutagenesis experiments and biochemical approaches to determine the role of the three putative extracellular cysteine residues on transport function and their possible involvement in the formation of a disulfide bridge. As treatment with the reducing reagent dithiothreitol impaired transport function of hPAT1 wild type protein, substitution of putative extracellular cysteine residues Cys-180, Cys-329, and Cys-473 by alanine or serine was performed. Replacement of the two highly conserved cysteine residues Cys-180 and Cys-329 abolished the transport function of hPAT1 in Xenopus laevis oocytes. Studies of wild type and mutant transporters expressed in human retinal pigment epithelial (HRPE) cells suggested that the binding of the substrate was inhibited in these mutants. Substitution of the third putative extracellular nonconserved cysteine residue Cys-473 did not affect transport function. All mutants were expressed at the plasma membrane. Biotinylation of free sulfhydryl groups using maleimide-PEG(11)-biotin and SDS-PAGE analysis under reducing and nonreducing conditions provided direct evidence for the existence of an essential disulfide bond between Cys-180 and Cys-329. This disulfide bridge is very likely involved in forming or stabilizing the substrate binding site.
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http://dx.doi.org/10.1074/jbc.M109.023713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755936PMC
August 2009

Suppression of protein aggregation by L-arginine.

Curr Pharm Biotechnol 2009 Jun;10(4):408-14

Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Saale, Germany.

L-Arginine is one of the most commonly used and most generally applicable suppressors of protein aggregation. Its effect as enhancer of in vitro protein refolding was serendipitously discovered two decades ago. This article aims at giving a brief overview about the discovery of the arginine effect, the range of its applications that have been explored over the past two decades, and of the current state of the discussion regarding the mechanisms responsible for the action of L-arginine as suppressor of aggregation.
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http://dx.doi.org/10.2174/138920109788488851DOI Listing
June 2009

Affilin molecules selected against the human papillomavirus E7 protein inhibit the proliferation of target cells.

J Mol Biol 2009 Jul 21;390(4):710-21. Epub 2009 May 21.

Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.

Intracellular binding proteins can be applied as research tools for target validation and study of protein function in cells and potentially as therapeutics. The success of intracellular binding reagents depends on their affinity and specificity for target molecules, although their stability and functionality in the intracellular environment actually determine their usefulness for such application. Alternative binding proteins derived from scaffolds devoid of disulfide bonds are well suited for intracellular use, as their folding and stability are usually not impaired under reducing conditions. Here, we describe the generation of intracellular binding reagents called Affilin, based on the human gammaB-crystallin scaffold. The target was human papillomavirus E7 protein implicated in the development of cervical cancer. E7 binders were selected from the combinatorial gammaB-crystallin library by conventional phage display technique. Affilin variants specifically bound the E7 protein with affinities in the nanomolar range. Intracellular expression of Affilin molecules in E7-positive cells led to inhibition of cellular proliferation. The effect was specific, as the growth of E7-negative cells or cells expressing the wild-type gammaB-crystallin scaffold remained unaffected. These results demonstrate that the gammaB-crystallin scaffold allows the de novo generation of alternative binding proteins, which are suitable for intracellular applications as they retain their functionality in the reducing environment of mammalian cells.
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http://dx.doi.org/10.1016/j.jmb.2009.05.027DOI Listing
July 2009

Passing the baton in class B GPCRs: peptide hormone activation via helix induction?

Trends Biochem Sci 2009 Jun 14;34(6):303-10. Epub 2009 May 14.

Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.

G-protein-coupled receptors (GPCRs) represent the largest constellation of validated drug targets. Crystal structures of class A GPCRs have facilitated major advances in understanding the principles underlying GPCR activation. By contrast, relatively little is known about class B GPCRs, a family of receptors for a variety of therapeutically relevant peptide hormones. Encouraging progress has recently been made through the structural elucidation of several extracellular hormone-binding domains of class B GPCRs in complex with their natural ligands or synthetic analogues. The structures reveal similar modes of ligand binding, with concomitant alpha-helical structuring of the ligand. The latter suggests an attractive mechanical model for class B GPCR activation.
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http://dx.doi.org/10.1016/j.tibs.2009.02.004DOI Listing
June 2009

Enhancing the fluorescence of tyr-59 in ubiquitin by blocking proton transfer.

Phys Chem Chem Phys 2009 May 3;11(18):3580-3. Epub 2009 Mar 3.

Departamento de Química, Instituto Superior Técnico, Universidade Técnica de Lisboa, 1049-001, Lisboa, Portugal.

Two highly fluorescent mutants of ubiquitin (E51Q and E51A) were produced by mutation of a single amino acid, demonstrating that excited-state proton transfer from the tyrosine residue to the carboxylate group of Glu-51 in ubiquitin is responsible for the reduced fluorescence of wild-type ubiquitin (wt-UBQ) at pH 5. E51A shows a Tm=59 degrees C at pH 1.5 and a Tm>80 degrees C at pH 5 similar to wt-UBQ, which shows that the mutation has not altered the protein structure significantly. The high and constant fluorescence from pH 1.5 to pH 7 allows for the study of the folding/unfolding over a wide range of pHs which would otherwise be impossible with wt-UBQ.
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http://dx.doi.org/10.1039/b819365gDOI Listing
May 2009

The role of N-glycosylation in transport function and surface targeting of the human solute carrier PAT1.

FEBS Lett 2009 May 3;583(10):1631-6. Epub 2009 May 3.

Institute of Biochemistry/Biotechnology, Faculty of Science I, Martin-Luther-University Halle-Wittenberg, Halle, Germany.

In the present study we show in the Xenopus laevis expression system that the proton-coupled amino acid transporter 1 (PAT1, SLC36A1) is glycosylated at asparagine residues N174, N183 and N470. To determine the functional role of N-glycosylation, glycosylation-deficient mutants were analyzed by two-electrode voltage-clamp measurements after expression in X. laevis oocytes. Single replacements of asparagine residues had no effect on transport activity. However, multiple substitutions resulted in a decreased transport rate, leaving K(t) unchanged. Immunofluorescence localisation revealed a diminished plasma membrane expression of glycosylation-defective mutants. This indicates that N-glycans are not required for transport function, but are important for membrane targeting.
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http://dx.doi.org/10.1016/j.febslet.2009.04.037DOI Listing
May 2009

Mammalian G-protein-coupled receptor expression in Escherichia coli: I. High-throughput large-scale production as inclusion bodies.

Anal Biochem 2009 Mar 24;386(2):147-55. Epub 2008 Dec 24.

Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS, and Universités of Marseille, Case 932, 163 Ave de Luminy, F-13288 Marseille Cedex 09, France.

G-protein-coupled receptors (GPCRs) represent approximately 3% of human proteome and the most prominent class of pharmacological targets. Despite their important role in many functions, only the X-ray structures of rhodopsin, and more recently of the beta(1)- and beta(2)-adrenergic receptors, have been resolved. Structural studies of GPCRs require that several tedious preliminary steps be fulfilled before setting up the first crystallization experiments: protein expression, detergent solubilization, purification, and stabilization. Here we report on screening expression conditions of approximately 100 GPCRs in Escherichia coli with a view to obtain large amounts of inclusion bodies, a prerequisite to the subsequent refolding step. A set of optimal conditions, including appropriate vectors (Gateway pDEST17oi), strain (C43), and fermentation at high optical density, define the best first instance choice. Beyond this minimal setting, however, the rate of success increases significantly with the number of conditions tested. In contrast with experiments based on a single GPCR expression, our approach provides statistically significant results and indicates that up to 40% of GPCRs can be expressed as inclusion bodies in quantities sufficient for subsequent refolding, solubilization, and purification.
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http://dx.doi.org/10.1016/j.ab.2008.12.016DOI Listing
March 2009

Dissecting NGF interactions with TrkA and p75 receptors by structural and functional studies of an anti-NGF neutralizing antibody.

J Mol Biol 2008 Sep 10;381(4):881-96. Epub 2008 Jun 10.

Lay Line Genomics SpA, via di Castel Romano 100, I-00128 Rome, Italy.

The anti-nerve growth factor (NGF) monoclonal antibody alphaD11 is a potent antagonist that neutralizes the biological functions of its antigen in vivo. NGF antagonism is expected to be a highly effective and safe therapeutic approach in many pain states. A comprehensive functional and structural analysis of alphaD11 monoclonal antibody was carried out, showing its ability to neutralize NGF binding to either tropomyosine receptor kinase A (TrkA) or p75 receptors. The 3-D structure of the alphaD11 Fab fragment was solved at 1.7 A resolution. A computational docking model of the alphaD11 Fab-NGF complex, based on epitope mapping using a pool of 44 NGF mutants and experimentally validated by small-angle X-ray scattering, provided the structural basis for identifying the residues involved in alphaD11 Fab binding. The present study pinpoints loop II of NGF to be an important structural determinant for NGF biological activity mediated by TrkA receptor.
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http://dx.doi.org/10.1016/j.jmb.2008.06.008DOI Listing
September 2008

Ionic liquids and proteases: a clean alliance for semisynthesis.

Chembiochem 2008 Jun;9(9):1493-9

Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany.

Herein we present the first report on protease-catalysed ligation of cleavage-sensitive peptide and protein fragments in ionic-liquid-containing solvent systems. By applying the newly established [MMIM][Me2PO4]/buffer mixture as a reaction medium, significant advantages over purely aqueous or conventional organic solvent-containing media could be identified, including in particular the use of active wild-type proteases as biocatalysts, the suppression of any competitive proteolytic side reactions, the high turnover rates compared to classical organic solvents and the high stability of chemically labile reactants.
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http://dx.doi.org/10.1002/cbic.200800025DOI Listing
June 2008

The NMR solution structure of the artificial protein M7 matches the computationally designed model.

Proteins 2008 Aug;72(3):1104-7

Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, D-06099 Halle, Saale, Germany.

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http://dx.doi.org/10.1002/prot.22107DOI Listing
August 2008

In vitro-refolding of a single-chain Fv fragment in the presence of heteroaromatic thiols.

J Biotechnol 2008 Apr 18;134(3-4):218-21. Epub 2008 Jan 18.

Institut für Biotechnologie, Martin-Luther-Universität Halle/Wittenberg, Kurt-Mothes-Str.3, 06120 Halle (Saale), Germany.

The aim of the present work was to explore the use of heteroaromatic thiol compounds, namely derivatives of pyridine and pyrimidine, as redox reagents for the in vitro-refolding of a recombinantly expressed single-chain Fv fragment (scFvOx). The mixed disulfide of scFvOx with glutathione was used as a starting material, while reduced glutathione, 4-mercaptopyridine, 2-mercaptopyrimidine, 2-mercaptopyridine N-oxide, and the mercaptobenzene derivative thiosalicylic acid, respectively, served as catalysts for the formation of native disulfide bonds during renaturation. In contrast to thiosalicylic acid, and despite their significantly lower thiol pKa values, none of the heteroaromatic thiol compounds accelerated the apparent kinetics of in vitro-refolding compared to the naturally occurring peptide glutathione. However, significantly improved renaturation yields were observed in the presence of 4-mercaptopyridine and 2-mercaptopyrimidine, demonstrating the usefulness of aromatic thiol compounds as reagents for the in vitro-refolding of antibody fragments.
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http://dx.doi.org/10.1016/j.jbiotec.2008.01.009DOI Listing
April 2008

Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain.

J Biol Chem 2008 Apr 20;283(17):11340-7. Epub 2008 Feb 20.

Department of Structure and Biophysical Chemistry, Novo Nordisk, 2760 Måløv, Denmark.

The glucagon-like peptide-1 receptor (GLP-1R) belongs to Family B1 of the seven-transmembrane G protein-coupled receptors, and its natural agonist ligand is the peptide hormone glucagon-like peptide-1 (GLP-1). GLP-1 is involved in glucose homeostasis, and activation of GLP-1R in the plasma membrane of pancreatic beta-cells potentiates glucose-dependent insulin secretion. The N-terminal extracellular domain (nGLP-1R) is an important ligand binding domain that binds GLP-1 and the homologous peptide Exendin-4 with differential affinity. Exendin-4 has a C-terminal extension of nine amino acid residues known as the "Trp cage", which is absent in GLP-1. The Trp cage was believed to interact with nGLP-1R and thereby explain the superior affinity of Exendin-4. However, the molecular details that govern ligand binding and specificity of nGLP-1R remain undefined. Here we report the crystal structure of human nGLP-1R in complex with the antagonist Exendin-4(9-39) solved by the multiwavelength anomalous dispersion method to 2.2A resolution. The structure reveals that Exendin-4(9-39) is an amphipathic alpha-helix forming both hydrophobic and hydrophilic interactions with nGLP-1R. The Trp cage of Exendin-4 is not involved in binding to nGLP-1R. The hydrophobic binding site of nGLP-1R is defined by discontinuous segments including primarily a well defined alpha-helix in the N terminus of nGLP-1R and a loop between two antiparallel beta-strands. The structure provides for the first time detailed molecular insight into ligand binding of the human GLP-1 receptor, an established target for treatment of type 2 diabetes.
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http://dx.doi.org/10.1074/jbc.M708740200DOI Listing
April 2008

High yield production of recombinant native and modified peptides exemplified by ligands for G-protein coupled receptors.

Protein Expr Purif 2008 Mar;58(1):114-21

Institut für Biochemie und Biotechnologie, Technische Biochemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle, Germany.

G-protein coupled receptors (GPCRs) comprise a large family of membrane proteins and attract pharmaceutical interest as therapeutic targets. Two examples of class B GPCRs that are involved in metabolic diseases are the Parathyroid hormone receptor 1 (PTHR1) and the Glucagon-like-peptide-1 receptor (GLP-1R) which play central roles in osteoporosis and diabetes mellitus type II, respectively. Class B GPCRs are characterised by a large extracellular N-terminal domain with a typical disulfide bridge pattern. This domain is responsible for the binding of peptide hormone ligands. Here we report the recombinant expression of these ligands in natural and several modified forms for their use in functional assays, NMR analyses or affinity purification of receptor/ligand complexes for crystallisation. Applying the SUMO system, low cost expression of soluble fusion-proteins is achieved. Moreover, via the SUMO cleavage site, the authentic N-terminal sequence which is essential for ligand-receptor interactions can be obtained. Purification of the peptide by RP-HPLC results in >98% pure preparations. The strategy can also be adopted for many other purposes, especially if small peptides are needed at either large amounts or with specific features like isotope, affinity or fluorescent labels. Furthermore, for the growing demand for therapeutic peptides, this method could represent a straightforward production process.
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http://dx.doi.org/10.1016/j.pep.2007.10.012DOI Listing
March 2008

Crystal structure of the incretin-bound extracellular domain of a G protein-coupled receptor.

Proc Natl Acad Sci U S A 2007 Aug 21;104(35):13942-7. Epub 2007 Aug 21.

Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany.

Incretins, endogenous polypeptide hormones released in response to food intake, potentiate insulin secretion from pancreatic beta cells after oral glucose ingestion (the incretin effect). This response is signaled by the two peptide hormones glucose-dependent insulinotropic polypeptide (GIP) (also known as gastric inhibitory polypeptide) and glucagon-like peptide 1 through binding and activation of their cognate class 2 G protein-coupled receptors (GPCRs). Because the incretin effect is lost or significantly reduced in patients with type 2 diabetes mellitus, glucagon-like peptide 1 and GIP have attracted considerable attention for their potential in antidiabetic therapy. A paucity of structural information precludes a detailed understanding of the processes of hormone binding and receptor activation, hampering efforts to develop novel pharmaceuticals. Here we report the crystal structure of the complex of human GIP receptor extracellular domain (ECD) with its agonist, the incretin GIP(1-42). The hormone binds in an alpha-helical conformation in a surface groove of the ECD largely through hydrophobic interactions. The N-terminal ligand residues would remain free to interact with other parts of the receptor. Thermodynamic data suggest that binding is concomitant with structural organization of the hormone, resulting in a complex mode of receptor-ligand recognition. The presentation of a well structured, alpha-helical ligand by the ECD is expected to be conserved among other hormone receptors of this class.
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http://dx.doi.org/10.1073/pnas.0706404104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1955799PMC
August 2007

Oxidative folding of nerve growth factor can be mediated by the pro-peptide of neurotrophin-3.

FEBS Lett 2007 Sep 6;581(22):4159-64. Epub 2007 Aug 6.

Institut für Biotechnologie der Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle, Germany.

We have previously shown that the pro-peptide of human nerve growth factor (NGF) facilitates oxidative folding of the mature part. For the analysis of functional specificities of the pro-peptides of NGF and the related neurotrophin-3 (NT-3) with respect to structure formation, chimeric proteins with swapped pro-peptides were generated. Neither the structure nor the stability of the mature domains was influenced by the heterologous pro-peptides. For the pro-peptide of NT-3 fused to the mature part of NGF, stabilization of the pro-peptide moiety by the NGF part was observed. Folding kinetics and renaturation yields of this chimeric protein were comparable to those of proNGF. Our results demonstrate functional interchangeability between the pro-peptides of NGF and NT-3 with respect to their role in assisting oxidative folding of the mature part.
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http://dx.doi.org/10.1016/j.febslet.2007.07.063DOI Listing
September 2007

Affilin-novel binding molecules based on human gamma-B-crystallin, an all beta-sheet protein.

J Mol Biol 2007 Sep 22;372(1):172-85. Epub 2007 Jun 22.

Scil Proteins GmbH, Heinrich Damerow Str. 1, 06120 Halle (Saale), Germany.

The concept of novel binding proteins as an alternative to antibodies has undergone rapid development and is now ready for practical use in a wide range of applications. Alternative binding proteins, based on suitable scaffolds with desirable properties, are selected from combinatorial libraries in vitro. Here, we describe an approach using a beta-sheet of human gamma-B-crystallin to generate a universal binding site through randomization of eight solvent-exposed amino acid residues selected according to structural and sequence analyses. Specific variants, so-called Affilin, have been isolated from a phage display library against a variety of targets that differ considerably in size and structure. The isolated Affilin variants can be produced in Escherichia coli as soluble proteins and have a high level of thermodynamic stability. The crystal structures of the human wild-type gamma-B-crystallin and a selected Affilin variant have been determined to 1.7 A and 2.0 A resolution, respectively. Comparison of the two molecules indicates that the human gamma-B-crystallin tolerates amino acid exchanges with no major structural change. We conclude that the intrinsically stable and easily expressed gamma-B-crystallin provides a suitable framework for the generation of novel binding molecules.
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http://dx.doi.org/10.1016/j.jmb.2007.06.045DOI Listing
September 2007

A tetrapeptide fragment-based design method results in highly stable artificial proteins.

Proteins 2007 Sep;68(4):839-49

Institut für Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle, Saale, Germany.

Computational protein design has progressed rapidly over the last years. A number of design methods have been proposed and tested. In this paper, we report the successful application of a fragment-based method for protein design. The method uses statistical information on tetrapeptide backbone conformations. The previously published artificial fold of TOP 7 (Kuhlman et al., Science, 2003; 302:1364-1368) was chosen as template. A series of polypeptide sequences were created that were predicted to fold into this target structure. Two of the designed proteins, M5 and M7, were expressed and characterized by fluorescence spectroscopy, circular dichroism and NMR. They showed the hallmarks of well-ordered tertiary structure as well as cooperative folding/unfolding transitions. Furthermore, the two novel proteins were found to be highly stable against temperature and denaturant-induced unfolding.
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http://dx.doi.org/10.1002/prot.21493DOI Listing
September 2007

Periplasmic production of native human proinsulin as a fusion to E. coli ecotin.

Protein Expr Purif 2007 Sep 14;55(1):100-11. Epub 2007 Apr 14.

Institute for Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str 3, D-06120 Halle (Saale), Germany.

Native proinsulin belongs to the class of the difficult-to-express proteins in Escherichia coli. Problems mainly arise due to its small size, a high proteolytic decay, and the necessity to form a native disulfide pattern. In the present study, human proinsulin was produced in the periplasm of E. coli as a fusion to ecotin, which is a small periplasmic protein of 16 kDa encoded by the host, containing one disulfide bond. The fusion protein was secreted to the periplasm and native proinsulin was determined by ELISA. Cultivation parameters were studied in parallel batch mode fermentations using E. coli BL21(DE3)Gold as a host. After improvement of fed-batch high density fermentation conditions, 153 mg fusion protein corresponding to 51.5mg native proinsulin was obtained per L. Proteins were extracted from the periplasm by osmotic shock treatment. The fusion protein was purified in one step by ecotin affinity chromatography on immobilized trypsinogen. After thrombin cleavage of the fusion protein, the products were separated by Ni-NTA chromatography. Proinsulin was quantified by ELISA and characterized by mass spectrometry. To evaluate the influence of periplasmic proteases, the amount of ecotin-proinsulin was determined in E. coli BL21(DE3)Gold and in a periplasmic protease deficient strain, E. coli SF120.
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http://dx.doi.org/10.1016/j.pep.2007.04.006DOI Listing
September 2007

Differential structural properties of GLP-1 and exendin-4 determine their relative affinity for the GLP-1 receptor N-terminal extracellular domain.

Biochemistry 2007 May 20;46(19):5830-40. Epub 2007 Apr 20.

Department of Structure and Biophysical Chemistry, Novo Nordisk, DK-2880 Bagsvaerd, Denmark.

Glucagon-like peptide-1 (GLP-1) and exendin-4 (Ex4) are homologous peptides with established potential for treatment of type 2 diabetes. They bind and activate the pancreatic GLP-1 receptor (GLP-1R) with similar affinity and potency and thereby promote insulin secretion in a glucose-dependent manner. GLP-1R belongs to family B of the seven transmembrane G-protein coupled receptors. The N-terminal extracellular domain (nGLP-1R) is a ligand binding domain with differential affinity for Ex4 and GLP-1: low affinity for GLP-1 and high affinity for exendin-4. The superior affinity of nGLP-1R for Ex4 was previously explained by an additional interaction between nGLP-1R and the C-terminal Trp-cage of Ex4. In this study we have combined biophysical and pharmacological approaches thus relating structural properties of the ligands in solution to their relative binding affinity for nGLP-1R. We used both a tracer competition assay and ligand-induced thermal stabilization of nGLP-1R to measure the relative affinity of full length, truncated, and chimeric ligands for soluble refolded nGLP-1R. The ligands in solution and the conformational consequences of ligand binding to nGLP-1R were characterized by circular dichroism and fluorescence spectroscopy. We found a correlation between the helical content of the free ligands and their relative binding affinity for nGLP-1R, supporting the hypothesis that the ligands are helical at least in the segment that binds to nGLP-1R. The Trp-cage of Ex4 was not necessary to maintain a superior helicity of Ex4 compared to GLP-1. The results suggest that the differential affinity of nGLP-1R is explained almost entirely by divergent residues in the central part of the ligands: Leu10-Gly30 of Ex4 and Val16-Arg36 of GLP-1. In view of our results it appears that the Trp-cage plays only a minor role for the interaction between Ex4 and nGLP-1R and for the differential affinity of nGLP-1R for GLP-1 and Ex4.
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http://dx.doi.org/10.1021/bi062309mDOI Listing
May 2007

The pro-peptide of proNGF: structure formation and intramolecular association with NGF.

Protein Sci 2007 Mar 22;16(3):411-9. Epub 2007 Jan 22.

Martin-Luther-Universität Halle-Wittenberg, Institut für Biotechnologie, 06120 Halle, Germany.

The pro-peptide of human nerve growth factor (NGF) functions as an intramolecular chaperone during oxidative renaturation of proNGF in vitro and interacts intramolecularly with the mature part of native proNGF. Here, we analyzed the structure formation and stability of the pro-peptide in the context of proNGF and its intramolecular interaction with the native mature part. Folding and unfolding of the NGF-coupled pro-peptide, as analyzed by fluorescence, were biphasic reactions with both phases depending on the interaction with the mature part. This interaction was characterized by an overall stability of DeltaG = 20.9 kJ/mol that was subdivided into two reactions, native <--> intermediate state (14.8 kJ/mol) and intermediate <--> unfolded state (6.1 kJ/mol). An additional very fast unfolding reaction was observed using circular dichroism (CD), indicating the presence of at least two kinetically populated intermediates in the unfolding of proNGF. The part of the pro-peptide involved in the intramolecular association with mature NGF comprised the peptide Trp(-83)-Ala(-63) as determined by H/D exchange experiments. Spectroscopic analyses revealed that on the NGF side, a surface area around Trp(21) interacted with the pro-peptide. Trp(21) also participates in binding to TrkA and p75 receptors. These overlapping binding sites of the pro-peptide and the NGF receptors might explain the previously observed lower affinity of proNGF to its receptors as compared to NGF.
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http://dx.doi.org/10.1110/ps.062376207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203323PMC
March 2007

Recombinant human hyaluronidase Hyal-1: insect cells versus Escherichia coli as expression system and identification of low molecular weight inhibitors.

Glycobiology 2007 Apr 16;17(4):444-53. Epub 2007 Jan 16.

Lehrstuhl für Pharmazeutische und Medizinische Chemie II, Institut für Pharmazie, Universität Regensburg, D-93053 Regensburg, Germany.

The human hyaluronidase Hyal-1, one of six human hyaluronidase subtypes, preferentially degrades hyaluronic acid present in the extracellular matrix of somatic tissues. Modulations of Hyal-1 expression have been observed in a number of malignant tumors. However, its role in disease progression is discussed controversially due to limited information on enzyme properties as well as the lack of specific inhibitors. Therefore, we expressed human Hyal-1 in a prokaryotic and in an insect cell system to produce larger amounts of the purified enzyme. In Escherichia coli, Hyal-1 formed inclusion bodies and was refolded in vitro after purification by metal ion affinity chromatography. However, the enzyme was produced with extremely low folding yields (0.5%) and exhibited a low specific activity (0.1 U/mg). Alternatively, Hyal-1 was secreted into the medium of stably transfected Drosophila Schneider-2 (DS-2) cells. After several purification steps, highly pure enzyme with a specific activity of 8.6 U/mg (consistent with the reported activity of human Hyal-1 from plasma) was obtained. Both Hyal-1 enzymes showed pH profiles similar to the hyaluronidase of human plasma with an activity maximum at pH 3.5-4.0. Deglycosylation of Hyal-1, expressed in DS-2 cells, resulted in a decrease in the enzymatic activity determined by a colorimetric hyaluronidase activity assay. Purified Hyal-1 from DS-2 cells was used for the investigation of the inhibitory activity of new ascorbic acid derivatives. Within this series, l-ascorbic acid tridecanoate was identified as the most potent inhibitor with an IC(50) of 50 +/- 4 microM comparable with glycyrrhizic acid.
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http://dx.doi.org/10.1093/glycob/cwm003DOI Listing
April 2007