A novel protocol for the design of artificial (β/α)8-barrel proteins
Martina, Cristina ; Figueroa Yévenes, Maximiliano ; et al
Poster (2016, March)
Designing de novo proteins of more than 100 amino acids is still challenging. The creation of artificial (β/α)8-barrel proteins had only one successful example in literature, thank to use of internal ... [more ▼]
Designing de novo proteins of more than 100 amino acids is still challenging. The creation of artificial (β/α)8-barrel proteins had only one successful example in literature, thank to use of internal spatial symmetry. Here we present a protocol to design de novo (β/α)8-barrel proteins without symmetry restriction. First, the backbone was created in 4 steps: (I) Rosetta ParametricDesign produced an highly symmetric polyalanine scaffold with no loops; (II) Rosetta Fixed-Backbone Design used the previous output to substitute the alanines in all the position; (III) Loops were constructed with Modeller joining the terminus of the secondary structure elements and (IV) RosettaRelax performed relaxation, creating around 4000 different models. 28 backbone models were selected for the next steps of sequence design. To design the final proteins for experimental validation, 10 cycles of Rosetta Design and Relax were performed. In the first cycle only apolar amino acids were allowed in hydrophobic regions; in the next 6 cycles, amino acids were allowed based on the definition of 3 regions: core, boundaries and surface. All the amino acids were allowed in each position in the last 3 cycles. More than 10000 different sequences were created and analyzed in term of amino acid composition, sequence similarity with natural protein, secondary structure prediction, and molecular dynamics simulations. The 30 best candidate sequences have been selected for experimental verification. [less ▲]Detailed reference viewed: 67 (5 ULg)
A novel protocol for the design of artificial (β/α)8-barrel proteins
Martina, Cristina ; Figueroa Yévenes, Maximiliano ; et al
The design of protein de novo is an emerging field in biochemistry, where artificial proteins are first designed in silico and then validated experimentally. This research, which rests mainly on our ... [more ▼]
The design of protein de novo is an emerging field in biochemistry, where artificial proteins are first designed in silico and then validated experimentally. This research, which rests mainly on our current understanding of protein structure, function, folding, stability and solubility, contributes to expand our knowledge of proteins in general. Our group has a long tradition in the design of artificial (β/α)8 -barrel proteins (called Octarellins). This fold is extremely interesting because it is widespread in nature (10% of the known proteins contain this fold) and in catalysis (it is present in 5/6 classes of enzyme). Here we present a protocol to design de novo (β/α)8-barrels with the more recent and best performing tools: Rosetta and Modeller (modelling softwares), and GROMACS (molecular dynamic simulations). First, 4000 artificial backbone structures were created with the use of modelling packages Rosetta and Modeller. 54 out of them were selected as targets for the following steps of sequence design and energy minimization (10 cycles), in order to find the best sequence to fit each target. More than 10000 different artificial sequences were created. Selection steps were performed in order to reduce the number of candidates for each target and the best ones were subjected to molecular dynamic simulation. Among this, 5 models were finally chosen for gene synthesis and experimental validation, and are currently being tested for expression in E. coli and preliminary purification. [less ▲]Detailed reference viewed: 15 (2 ULg)
Biophysical characterization data of the artificial protein Octarellin V.1 and binding test with its X-ray helpers.
Figueroa Yévenes, Maximiliano ; Vandenameele, Julie ; et al
in Data in Brief (2016), 8
The artificial protein Octarellin V.1 (http://dx.doi.org/10.1016/j.jsb.2016.05.004) was obtained through a direct evolution process over the de novo designed Octarellin V (http://dx.doi.org/10.1016 ... [more ▼]
The artificial protein Octarellin V.1 (http://dx.doi.org/10.1016/j.jsb.2016.05.004) was obtained through a direct evolution process over the de novo designed Octarellin V (http://dx.doi.org/10.1016/S0022-2836(02)01206-8). The protein has been characterized by circular dichroism and fluorescence techniques, in order to obtain data related to its thermo and chemical stability. Moreover, the data for the secondary structure content studied by circular dichroism and infra red techniques is reported for the Octarellin V and V.1. Two crystallization helpers, nanobodies (http://dx.doi.org/10.1038/nprot.2014.039) and alphaRep (http://dx.doi.org/10.1016/j.jmb.2010.09.048), have been used to create stable complexes. Here we present the data obtained of the binding characterization of the Octarellin V.1 with the crystallization helpers by isothermal titration calorimetry. [less ▲]Detailed reference viewed: 10 (0 ULg)
The role of active site flexible loops in catalysis and of zinc in conformational stability of Bacillus cereus 569/H/9 beta-lactamase.
Montagner, Caroline ; ; et al
in Journal of Biological Chemistry (2016), 291(31), 16124-16137
Metallo-beta-lactamases catalyse the hydrolysis of most beta-lactam antibiotics and hence represent a major clinical concern. The development of inhibitors for these enzymes is complicated by the ... [more ▼]
Metallo-beta-lactamases catalyse the hydrolysis of most beta-lactam antibiotics and hence represent a major clinical concern. The development of inhibitors for these enzymes is complicated by the diversity and flexibility of their substrate binding sites, motivating research into their structure and function. In this study, we examined the conformational properties of the Bacillus cereus beta-lactamase II in the presence of chemical denaturants using a variety of biochemical and biophysical techniques. The apoenzyme was found to unfold cooperatively, with a Gibbs free energy of stabilization (DeltaG degrees ) of 32 +/- 2 kJ.mol11. For holoBcII, a first non-cooperative transition leads to multiple interconverting native-like states, in which both zinc atoms remain bound in an apparently unaltered active site and the protein displays a well-organized compact hydrophobic core with structural changes confined to the enzyme surface, but with no catalytic activity. 2D NMR data revealed that the loss of activity occurs concomitantly with perturbations in two loops that border the enzyme active site. A second cooperative transition, corresponding to global unfolding, is observed at higher denaturant concentrations, with DeltaG degrees value of 65 +/- 1.4 kJ.mol11. These combined data highlight the importance of the two zinc ions in maintaining structure as well as a relatively well-defined conformation for both active site loops in order to maintain enzymatic activity. [less ▲]Detailed reference viewed: 35 (13 ULg)
The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools.
Figueroa Yévenes, Maximiliano ; ; Vandevenne, Marylène et al
in Journal of structural biology (2016)
Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the ... [more ▼]
Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (alphabetaalpha) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of them predicted a TIM-barrel fold, i.e. the structure we set out to design more than 10years ago. In addition, local software runs that are human operated can sample a structure similar to the experimental one but fail in selecting it, suggesting that the scoring and ranking functions should be improved. We propose that artificial proteins could be used as tools to test the accuracy of protein structure prediction algorithms, because their lack of evolutionary pressure and unique sequences features. [less ▲]Detailed reference viewed: 21 (5 ULg)
The CebE/MsiK Transporter is a Doorway to the Cello-oligosaccharide-mediated Induction of Streptomyces scabies Pathogenicity
Jourdan, Samuel ; ; et al
in Scientific Reports (2016)Detailed reference viewed: 29 (13 ULg)
Unravelling the mechanisms of a protein refolding process based on the association of detergents and co-solvents.
; ; et al
in Journal of peptide science : an official publication of the European Peptide Society (2016)
A new technique associating the detergent Sodium Dodecyl Sulphate (SDS) and an alcohol-type co-solvent has been set up, showing an unexpected efficiency to refold several types of soluble or membrane ... [more ▼]
A new technique associating the detergent Sodium Dodecyl Sulphate (SDS) and an alcohol-type co-solvent has been set up, showing an unexpected efficiency to refold several types of soluble or membrane proteins. The present contribution deepens the fundamental knowledge on the phenomena underlying this process, considering the refolding of two model peptides featuring the main protein secondary structures: alpha-helix and beta-sheet. Their refolding was monitored by fluorescence and circular dichroism, and it turns out that: (i) 100% recovery of the folded structure is observed for both peptides, (ii) the highest the SDS concentration, the more co-solvent to be added to recover the peptides' native structures, (iii) a high alcohol concentration is required to alter the SDS denaturing properties, (iv) the co-solvent performance relies on its specific lipophilic-hydrophilic balanced character, (v) the size of the micelle formed by the detergent does not enter the process critical parameters, and (vi) increasing the salt concentration up to 1 M NaCl has a beneficial impact on the process efficiency. These mechanistic aspects will help us to improve the method and extend its application. Copyright (c) 2016 European Peptide Society and John Wiley & Sons, Ltd. [less ▲]Detailed reference viewed: 27 (5 ULg)
Kinetic Study of Laboratory Mutants of NDM-1 Metallo-beta-Lactamase and the Importance of an Isoleucine at Position 35.
; ; et al
in Antimicrobial agents and chemotherapy (2016), 60(4), 2366-72
Two laboratory mutants of NDM-1 were generated by replacing the isoleucine at position 35 with threonine and serine residues: the NDM-1(I35T)and NDM-1(I35S)enzymes. These mutants were well characterized ... [more ▼]
Two laboratory mutants of NDM-1 were generated by replacing the isoleucine at position 35 with threonine and serine residues: the NDM-1(I35T)and NDM-1(I35S)enzymes. These mutants were well characterized, and their kinetic parameters were compared with those of the NDM-1 wild type. Thekcat,Km, andkcat/Kmvalues calculated for the two mutants were slightly different from those of the wild-type enzyme. Interestingly, thekcat/Kmof NDM-1(I35S)for loracarbef was about 14-fold higher than that of NDM-1. Far-UV circular dichroism (CD) spectra of NDM-1 and NDM-1(I35T)and NDM-1(I35S)enzymes suggest local structural rearrangements in the secondary structure with a marked reduction of alpha-helix content in the mutants. [less ▲]Detailed reference viewed: 22 (7 ULg)
Influence of substrate nature and β-lactoglobulin on cleanability after soiling by suspension spraying and drying
Toure, Yetioman ; Sindic, Marianne ; et al
in Chemical Engineering Science (2015), 134
Glass and stainless steel (StSteel, AISI304-2R), previously cleaned with ethanol (-Eth) or with ethanol and UV–Ozone treatment (-UVO), were soiled with quartz suspensions in water and in a β-lactoglobulin ... [more ▼]
Glass and stainless steel (StSteel, AISI304-2R), previously cleaned with ethanol (-Eth) or with ethanol and UV–Ozone treatment (-UVO), were soiled with quartz suspensions in water and in a β-lactoglobulin (β-LGB) solution, and dried. The cleanability (ease of quartz particle detachment) in water was evaluated using a radial-flow cell. The soiling suspension containing β-LGB was used as such or after heating for 4h at 75°C, which provoked coagulation of about 75% of β-LGB. The substrate–solution interfaces were characterized by X-ray photoelectron spectroscopy (XPS) analysis of conditioned substrates and by contact angle measurements. The substrate surfaces are covered by a layer of organic contaminants which are not removed by pre-cleaning or are adsorbed from the surroundings. The presence of β-LGB in the soiling suspension leads to protein adsorption, but a significant amount of contaminants remains at the surface. For three of the substrates tested (Glass-Eth, Glass-UVO, StSteel-UVO) the increase of cleanability when the soiling suspension contained β-LGB may be explained by lower capillary forces acting upon drying. Capillary forces are proportional to the liquid surface tension and depend in a less important way on substrate contact angle. However the order of cleanability observed for the substrates soiled with a suspension of quartz particles in water (Glass-Eth≅Glass-UVO<StSteel-UVO<StSteel-Eth) and the influence of β-LGB on the cleanability of StSteel-Eth may not be explained only by computed capillary forces. The contact angle may exert a direct influence on droplet spreading and particle–substrate contact. The organic contaminants present on the surfaces, which are often neglected by supposing model solid surfaces, may have a significant influence on cleanability through physico-chemical processes which remain to be appreciated. [less ▲]Detailed reference viewed: 119 (12 ULg)
A novel form of ficin from Ficus carica latex: Purification and characterization
; Matagne, André ; et al
in Phytochemistry (2015), 117
A novel ficin form, named ficin E, was purified from fig tree latex by a combination of cation-exchange chromatography on SP-Sepharose Fast Flow, Thiopropyl Sepharose 4B and fplc-gel filtration ... [more ▼]
A novel ficin form, named ficin E, was purified from fig tree latex by a combination of cation-exchange chromatography on SP-Sepharose Fast Flow, Thiopropyl Sepharose 4B and fplc-gel filtration chromatography. The new ficin appeared not to be sensitive to thiol derivatization by a polyethylene glycol derivative, allowing its purification. The protease is homogeneous according to PAGE, SDS–PAGE, mass spectrometry, N-terminal micro-sequencing analyses and E-64 active site titration. N-terminal sequencing of the first ten residues has shown high identity with the other known ficin (iso)forms. The molecular weight was found to be (24,294 ± 10) Da by mass spectrometry, a lower value than the apparent molecular weight observed on SDS–PAGE, around 27 kDa. Far-UV CD data revealed a secondary structure content of 22% a-helix and 26% b-sheet. The protein is not glycosylated as shown by carbohydrate analysis. pH and temperature measurements indicated maxima activity at pH 6.0 and 50 °C, respectively. Preliminary pH stability analyses have shown that the protease conserved its compact structure in slightly acidic, neutral and alkaline media but at acidic pH (<3), the formation of some relaxed or molten state was evidenced by 8-anilino-1-naphtalenesulfonic acid binding characteristics. Comparison with the known ficins A, B, C, D1 and D2 (iso)forms revealed that ficin E showed activity profile that looked like ficin A against two chromogenic substrates while it resembled ficins D1 and D2 against three fluorogenic substrates. Enzymatic activity of ficin E was not affected by Mg2+, Ca2+ and Mn2+ at a concentration up to 10 mM. However, the activity was completely suppressed by Zn2+ at a concentration of 1 mM. Inhibitory activity measurements clearly identified the enzyme as a cysteine protease, being unaffected by synthetic (Pefabloc SC, benzamidine) and by natural proteinaceous (aprotinin) serine proteases inhibitors, by aspartic proteases inhibitors (pepstatin A) and by metallo-proteases inhibitors (EDTA, EGTA). Surprisingly, it was well affected by the metallo-protease inhibitor o-phenanthroline. The enzymatic activity was however completely blocked by cysteine proteases inhibitors (E-64, iodoacetamide), by thiol-blocking compounds (HgCl2) and by cysteine/serine proteases inhibitors (TLCK and TPCK). This is a novel ficin form according to peptide mass fingerprint analysis, specific amidase activity, SDS–PAGE and PAGE electrophoretic mobility, N-terminal sequencing and unproneness to thiol pegylation. [less ▲]Detailed reference viewed: 61 (5 ULg)
Positive cooperativity between acceptor and donor sites of the peptidoglycan glycosyltransferase.
; Dahmane, Ismahene ; Derouaux, Adeline et al
in Biochemical pharmacology (2015), 93(2), 141-50
The glycosyltransferases of family 51 (GT51) catalyze the polymerization of lipid II to form linear glycan chains, which, after cross linking by the transpeptidases, form the net-like peptidoglycan ... [more ▼]
The glycosyltransferases of family 51 (GT51) catalyze the polymerization of lipid II to form linear glycan chains, which, after cross linking by the transpeptidases, form the net-like peptidoglycan macromolecule. The essential function of the GT makes it an attractive antimicrobial target; therefore a better understanding of its function and its mechanism of interaction with substrates could help in the design and the development of new antibiotics. In this work, we have used a surface plasmon resonance Biacore((R)) biosensor, based on an amine derivative of moenomycin A immobilized on a sensor chip surface, to investigate the mechanism of binding of substrate analogous inhibitors to the GT. Addition of increasing concentrations of moenomycin A to the Staphylococcus aureus MtgA led to reduced binding of the protein to the sensor chip as expected. Remarkably, in the presence of low concentrations of the most active disaccharide inhibitors, binding of MtgA to immobilized moenomycin A was found to increase; in contrast competition with moenomycin A occurred only at high concentrations. This finding suggests that at low concentrations, the lipid II analogs bind to the acceptor site and induce a cooperative binding of moenomycin A to the donor site. Our results constitute the first indication of the existence of a positive cooperativity between the acceptor and the donor sites of peptidoglycan GTs. In addition, our study indicates that a modification of two residues (L119N and F120S) within the hydrophobic region of MtgA can yield monodisperse forms of the protein with apparently no change in its secondary structure content, but this is at the expense of the enzyme function. [less ▲]Detailed reference viewed: 89 (17 ULg)
Determination of kinetics and the crystal structure of a novel type 2 isopentenyl diphosphate: dimethylallyl diphosphate isomerase from Streptococcus pneumoniae.
; ; et al
in Chembiochem : a European journal of chemical biology (2014), 15(10), 1452-1458
Isopentenyl diphosphate isomerase (IDI) is a key enzyme in the isoprenoid biosynthetic pathway and is required for all organisms that synthesize isoprenoid metabolites from mevalonate. Type 1 IDI (IDI-1 ... [more ▼]
Isopentenyl diphosphate isomerase (IDI) is a key enzyme in the isoprenoid biosynthetic pathway and is required for all organisms that synthesize isoprenoid metabolites from mevalonate. Type 1 IDI (IDI-1) is a metalloprotein that is found in eukaryotes, whereas the type 2 isoform (IDI-2) is a flavoenzyme found in bacteria that is completely absent from human. IDI-2 from the pathogenic bacterium Streptococcus pneumoniae was recombinantly expressed in Escherichia coli. Steady-state kinetic studies of the enzyme indicated that FMNH2 (KM =0.3 muM) bound before isopentenyl diphosphate (KM =40 muM) in an ordered binding mechanism. An X-ray crystal structure at 1.4 A resolution was obtained for the holoenzyme in the closed conformation with a reduced flavin cofactor and two sulfate ions in the active site. These results helped to further approach the enzymatic mechanism of IDI-2 and, thus, open new possibilities for the rational design of antibacterial compounds against sequence-similar and structure-related pathogens such as Enterococcus faecalis or Staphylococcus aureus. [less ▲]Detailed reference viewed: 18 (4 ULg)
Influence of sample and mobile phase composition on peptide retention behaviour and sensitivity in reversed-phase liquid chromatography/mass spectrometry
Houbart, Virginie ; Rozet, Eric ; Matagne, André et al
in Journal of Chromatography. A (2013), 1314Detailed reference viewed: 26 (13 ULg)
Class A β -Lactamases as Versatile Scaffolds to Create Hybrid Enzymes: Applications from Basic Research to Medicine
Huynen, Céline ; ; Matagne, André et al
in BioMed Research International (2013), 2013
Designing hybrid proteins is a major aspect of protein engineering and covers a very wide range of applications frombasic research to medical applications. This review focuses on the use of class A 𝛽 ... [more ▼]
Designing hybrid proteins is a major aspect of protein engineering and covers a very wide range of applications frombasic research to medical applications. This review focuses on the use of class A 𝛽-lactamases as versatile scaffolds to design hybrid enzymes (referred to as 𝛽-lactamase hybrid proteins, BHPs) in which an exogenous peptide, protein or fragment thereof is inserted at various permissive positions.We discuss how BHPs can be specifically designed to create bifunctional proteins, to produce and to characterize proteins that are otherwise difficult to express, to determine the epitope of specific antibodies, to generate antibodies against nonimmunogenic epitopes, and to better understand the structure/function relationship of proteins. [less ▲]Detailed reference viewed: 63 (13 ULg)
The proline-rich motif of the proDer p 3 allergen propeptide is crucial for protease-protease interaction.
Dumez, Marie-Eve ; ; Campisi, Vincenzo et al
in PloS one (2013), 8(9), 68014
The majority of proteases are synthesized in an inactive form, termed zymogen, which consists of a propeptide and a protease domain. The propeptide is commonly involved in the correct folding and specific ... [more ▼]
The majority of proteases are synthesized in an inactive form, termed zymogen, which consists of a propeptide and a protease domain. The propeptide is commonly involved in the correct folding and specific inhibition of the enzyme. The propeptide of the house dust mite allergen Der p 3, NPILPASPNAT, contains a proline-rich motif (PRM), which is unusual for a trypsin-like protease. By truncating the propeptide or replacing one or all of the prolines in the non-glycosylated zymogen with alanine(s), we demonstrated that the full-length propeptide is not required for correct folding and thermal stability and that the PRM is important for the resistance of proDer p 3 to undesired proteolysis when the protein is expressed in Pichia pastoris. Additionally, we followed the maturation time course of proDer p 3 by coupling a quenched-flow assay to mass spectrometry analysis. This approach allowed to monitor the evolution of the different species and to determine the steady-state kinetic parameters for activation of the zymogen by the major allergen Der p 1. This experiment demonstrated that prolines 5 and 8 are crucial for proDer p 3-Der p 1 interaction and for activation of the zymogen. [less ▲]Detailed reference viewed: 53 (20 ULg)
Energetics of protein stability at extreme environmental temperatures in bacterial trigger factors
Struvay, Caroline ; ; Matagne, André et al
in Biochemistry (2013), 52Detailed reference viewed: 56 (16 ULg)
A Nanobody Binding to Non-amyloidogenic Regions of the Protein Human Lysozyme Enhances Partial Unfolding but Inhibits Amyloid Fibril Formation.
; ; et al
in Journal of Physical Chemistry B (2013)Detailed reference viewed: 31 (7 ULg)
Octarellin VI: using rosetta to design a putative artificial (beta/alpha)8 protein.
Figueroa Yévenes, Maximiliano ; ; et al
in PloS one (2013), 8(8), 71858
The computational protein design protocol Rosetta has been applied successfully to a wide variety of protein engineering problems. Here the aim was to test its ability to design de novo a protein adopting ... [more ▼]
The computational protein design protocol Rosetta has been applied successfully to a wide variety of protein engineering problems. Here the aim was to test its ability to design de novo a protein adopting the TIM-barrel fold, whose formation requires about twice as many residues as in the largest proteins successfully designed de novo to date. The designed protein, Octarellin VI, contains 216 residues. Its amino acid composition is similar to that of natural TIM-barrel proteins. When produced and purified, it showed a far-UV circular dichroism spectrum characteristic of folded proteins, with alpha-helical and beta-sheet secondary structure. Its stable tertiary structure was confirmed by both tryptophan fluorescence and circular dichroism in the near UV. It proved heat stable up to 70 degrees C. Dynamic light scattering experiments revealed a unique population of particles averaging 4 nm in diameter, in good agreement with our model. Although these data suggest the successful creation of an artificial alpha/beta protein of more than 200 amino acids, Octarellin VI shows an apparent noncooperative chemical unfolding and low solubility. [less ▲]Detailed reference viewed: 28 (2 ULg)
The dynamics of lysozyme from bacteriophage lambda in solution probed by NMR and MD simulations.
; ; et al
in Chembiochem : a European journal of chemical biology (2013), 14(14), 1780-8
(15) N NMR relaxation studies, analyses of NMR data to include chemical shifts, residual dipolar couplings (RDC), NOEs and H(N) -H(alpha) coupling constants, and molecular dynamics (MD) simulations have ... [more ▼]
(15) N NMR relaxation studies, analyses of NMR data to include chemical shifts, residual dipolar couplings (RDC), NOEs and H(N) -H(alpha) coupling constants, and molecular dynamics (MD) simulations have been used to characterise the behaviour of lysozyme from bacteriophage lambda (lambda lysozyme) in solution. The lower and upper lip regions in lambda lysozyme (residues 51-60 and 128-141, respectively) show reduced (1) H-(15) N order parameters indicating mobility on a picosecond timescale. In addition, residues in the lower and upper lips also show exchange contributions to T2 indicative of slower timescale motions. The chemical shift, RDC, coupling constant and NOE data for lambda lysozyme indicate that two fluctuating beta-strands (beta3 and beta4) are populated in the lower lip region while the N terminus of helix alpha6 (residues 136-139) forms dynamic helical turns in the upper lip region. This behaviour is confirmed by MD simulations that show hydrogen bonds, indicative of the beta-sheet and helical secondary structure in the lip regions, with populations of 40-60 %. Thus in solution lambda lysozyme adopts a conformational ensemble that will contain both the open and closed forms observed in the crystal structures of the protein. [less ▲]Detailed reference viewed: 31 (5 ULg)
Efficient refolding of a recombinant abzyme : Structural and catalytic characterizations.
; ; et al
in Applied Microbiology & Biotechnology (2013), 97(17), 7721-31
Catalytic antibodies are currently being investigated in order to understand their role under physio-pathological situations. To this end, the knowledge of structure-function relationships is of great ... [more ▼]
Catalytic antibodies are currently being investigated in order to understand their role under physio-pathological situations. To this end, the knowledge of structure-function relationships is of great interest. Recombinant scFv fragments are smaller and easier to genetically manipulate than whole antibodies, making them well suited for this kind of study. Nevertheless they are often described as proteins being laborious to produce. This paper describes a highly efficient method to produce large quantities of refolded soluble catalytic scFv. For the first time, the functionality of a refolded catalytic scFv displaying a beta-lactamase activity has been validated by three approaches: (1) use of circular dichroism to ensure that the refolded had secondary structure consistent with a native scFv fold, (2) development of enzyme-linked immunosorbant assay and surface plasmon resonance (SPR) approaches for testing that the binding characteristics of an inhibitory peptide have been retained, and (3) proof of the subtle catalytic properties conservation through the development of a new sensitive catalytic assay using a fluorogenic substrate. [less ▲]Detailed reference viewed: 83 (1 ULg)