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Grattieri M, Babanova S, Santoro C, Guerrini E, Trasatti SPM, Cristiani P, Bestetti M, Atanassov P. Enzymatic Oxygen Microsensor Based on Bilirubin Oxidase Applied to Microbial Fuel Cells Analysis. ELECTROANAL 2015. [DOI: 10.1002/elan.201400543] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Matteo Grattieri
- Department of Chemistry, Materials and Chemical‐Engineering, Politecnico di Milano, Piazza Leonardo Da Vinci, 32, 20133 Milan, Italy
- Department of Chemistry , Università degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Sofia Babanova
- Center for Emerging Energy Technologies, Department of Chemical & Nuclear Engineering, Center for Emerging Energy Technologies, University of New Mexico, Albuquerque, NM 87131, USA
| | - Carlo Santoro
- Center for Emerging Energy Technologies, Department of Chemical & Nuclear Engineering, Center for Emerging Energy Technologies, University of New Mexico, Albuquerque, NM 87131, USA
| | - Edoardo Guerrini
- Department of Chemistry , Università degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Stefano PM Trasatti
- Department of Chemistry , Università degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Pierangela Cristiani
- RSE – Ricerca sul Sistema Energetico S.p.A., Sustainable Development and Energy Sources Department, 20133 Milan, Italy
| | - Massimiliano Bestetti
- Department of Chemistry, Materials and Chemical‐Engineering, Politecnico di Milano, Piazza Leonardo Da Vinci, 32, 20133 Milan, Italy
| | - Plamen Atanassov
- Center for Emerging Energy Technologies, Department of Chemical & Nuclear Engineering, Center for Emerging Energy Technologies, University of New Mexico, Albuquerque, NM 87131, USA
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The tertiary origin of the allosteric activation of E. coli glucosamine-6-phosphate deaminase studied by sol-gel nanoencapsulation of its T conformer. PLoS One 2014; 9:e96536. [PMID: 24787711 PMCID: PMC4008608 DOI: 10.1371/journal.pone.0096536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/08/2014] [Indexed: 11/24/2022] Open
Abstract
The role of tertiary conformational changes associated to ligand binding was explored using the allosteric enzyme glucosamine-6-phosphate (GlcN6P) deaminase from Escherichia coli (EcGNPDA) as an experimental model. This is an enzyme of amino sugar catabolism that deaminates GlcN6P, giving fructose 6-phosphate and ammonia, and is allosterically activated by N-acetylglucosamine 6-phosphate (GlcNAc6P). We resorted to the nanoencapsulation of this enzyme in wet silica sol-gels for studying the role of intrasubunit local mobility in its allosteric activation under the suppression of quaternary transition. The gel-trapped enzyme lost its characteristic homotropic cooperativity while keeping its catalytic properties and the allosteric activation by GlcNAc6P. The nanoencapsulation keeps the enzyme in the T quaternary conformation, making possible the study of its allosteric activation under a condition that is not possible to attain in a soluble phase. The involved local transition was slowed down by nanoencapsulation, thus easing the fluorometric analysis of its relaxation kinetics, which revealed an induced-fit mechanism. The absence of cooperativity produced allosterically activated transitory states displaying velocity against substrate concentration curves with apparent negative cooperativity, due to the simultaneous presence of subunits with different substrate affinities. Reaction kinetics experiments performed at different tertiary conformational relaxation times also reveal the sequential nature of the allosteric activation. We assumed as a minimal model the existence of two tertiary states, t and r, of low and high affinity, respectively, for the substrate and the activator. By fitting the velocity-substrate curves as a linear combination of two hyperbolic functions with Kt and Kr as KM values, we obtained comparable values to those reported for the quaternary conformers in solution fitted to MWC model. These results are discussed in the background of the known crystallographic structures of T and R EcGNPDA conformers. These results are consistent with the postulates of the Tertiary Two-States (TTS) model.
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Wheeler KE, Nocek JM, Hoffman BM. NMR Spectroscopy Can Characterize Proteins Encapsulated in a Sol-Gel Matrix. J Am Chem Soc 2006; 128:14782-3. [PMID: 17105269 DOI: 10.1021/ja066244m] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins encapsulated within sol-gel matrices (SG) have the potential to fill many scientific and technological roles, but these applications are hindered by the limited means of probing possible structural consequences of encapsulation. We here present the first demonstration that it is possible to obtain high-resolution, solution NMR measurements of proteins encapsulated within a SG matrix. With the aim of determining the breadth of this approach, we have encapsulated three paramagnetic proteins with different overall charges: the highly acidic human Fe3+ cytochrome b5 (cyt b5); the highly basic horse heart cytochrome c (cyt c); and the nearly neutral, sperm whale cyanomet-myoglobin. The encapsulated anionic and neutral proteins (cyt b5; myoglobin) undergo essentially free rotation, but show minor conformational perturbations as revealed by shifts of contact-shifted peaks associated with the heme and nearby amino acids.
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Affiliation(s)
- Korin E Wheeler
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
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Massari AM, Finkelstein IJ, Fayer MD. Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy. J Am Chem Soc 2006; 128:3990-7. [PMID: 16551107 PMCID: PMC2532503 DOI: 10.1021/ja058745y] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectrally resolved infrared stimulated vibrational echo spectroscopy is used to measure the fast dynamics of heme-bound CO in carbonmonoxy-myoglobin (MbCO) and -hemoglobin (HbCO) embedded in silica sol-gel glasses. On the time scale of approximately 100 fs to several picoseconds, the vibrational dephasing of the heme-bound CO is measurably slower for both MbCO and HbCO relative to that of aqueous protein solutions. The fast structural dynamics of MbCO, as sensed by the heme-bound CO, are influenced more by the sol-gel environment than those of HbCO. Longer time scale structural dynamics (tens of picoseconds), as measured by the extent of spectral diffusion, are the same for both proteins encapsulated in sol-gel glasses compared to that in aqueous solutions. A comparison of the sol-gel experimental results to viscosity-dependent vibrational echo data taken on various mixtures of water and fructose shows that the sol-gel-encapsulated MbCO exhibits dynamics that are the equivalent of the protein in a solution that is nearly 20 times more viscous than bulk water. In contrast, the HbCO dephasing in the sol-gel reflects only a 2-fold increase in viscosity. Attempts to alter the encapsulating pore size by varying the molar ratio of silane precursor to water (R value) used to prepare the sol-gel glasses were found to have no effect on the fast or steady-state spectroscopic results. The vibrational echo data are discussed in the context of solvent confinement and protein-pore wall interactions to provide insights into the influence of a confined environment on the fast structural dynamics experienced by a biomolecule.
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Cannone F, Bologna S, Campanini B, Diaspro A, Bettati S, Mozzarelli A, Chirico G. Tracking unfolding and refolding of single GFPmut2 molecules. Biophys J 2005; 89:2033-45. [PMID: 15994904 PMCID: PMC1366706 DOI: 10.1529/biophysj.105.064584] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The unfolding and refolding kinetics of >600 single GFPmut2 molecules, entrapped in wet nanoporous silica gels, were followed by monitoring simultaneously the fluorescence emission of the anionic and neutral state of the chromophore, primed by two-photon excitation. The rate of unfolding, induced by guanidinium chloride, was determined by counting the number of single molecules that disappear in fluorescence images, under conditions that do not cause bleaching or photoinduced conversion between chromophore protonation states. The unfolding rate is of the order of 0.01 min(-1), and its dependence on denaturant concentration is very similar to that previously reported for high protein load gels. Upon rinsing the gels with denaturant-free buffer, the GFPmut2 molecules refold with rates >10 min(-1), with an apparently random distribution between neutral and anionic states, that can be very different from the preunfolding equilibrium. A subsequent very slow (lifetime of approximately 70 min) relaxation leads to the equilibrium distribution of the protonation states. This mechanism, involving one or more native-like refolding intermediates, is likely rate limited by conformational rearrangements that are undetectable in circular dichroism experiments. Several unfolding/refolding cycles can be followed on the same molecules, indicating full reversibility of the process and, noticeably, a bias of denaturated molecules toward refolding in the original protonation state.
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Affiliation(s)
- Fabio Cannone
- Department of Physics, University of Milan Bicocca, 20126 Milan, Italy
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Pioselli B, Bettati S, Mozzarelli A. Confinement and crowding effects on tryptophan synthase alpha2beta2 complex. FEBS Lett 2005; 579:2197-202. [PMID: 15811341 DOI: 10.1016/j.febslet.2005.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2004] [Revised: 02/07/2005] [Accepted: 03/04/2005] [Indexed: 11/25/2022]
Abstract
Biological molecules experience in vivo a highly crowded environment. The investigation of the functional properties of the tryptophan synthase alpha(2)beta(2) complex either entrapped in wet nanoporous silica gels or in the presence of the crowding agents dextran 70 and ficoll 70 indicates that the rates of the conformational transitions associated to catalysis and regulation are reduced, and an open and less catalytically active conformation is stabilized.
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Affiliation(s)
- Barbara Pioselli
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
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Campanini B, Bologna S, Cannone F, Chirico G, Mozzarelli A, Bettati S. Unfolding of Green Fluorescent Protein mut2 in wet nanoporous silica gels. Protein Sci 2005; 14:1125-33. [PMID: 15802645 PMCID: PMC2253256 DOI: 10.1110/ps.041190805] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Many of the effects exerted on protein structure, stability, and dynamics by molecular crowding and confinement in the cellular environment can be mimicked by encapsulation in polymeric matrices. We have compared the stability and unfolding kinetics of a highly fluorescent mutant of Green Fluorescent Protein, GFPmut2, in solution and in wet, nanoporous silica gels. In the absence of denaturant, encapsulation does not induce any observable change in the circular dichroism and fluorescence emission spectra of GFPmut2. In solution, the unfolding induced by guanidinium chloride is well described by a thermodynamic and kinetic two-state process. In the gel, biphasic unfolding kinetics reveal that at least two alternative conformations of the native protein are significantly populated. The relative rates for the unfolding of each conformer differ by almost two orders of magnitude. The slower rate, once extrapolated to native solvent conditions, superimposes to that of the single unfolding phase observed in solution. Differences in the dependence on denaturant concentration are consistent with restrictions opposed by the gel to possibly expanded transition states and to the conformational entropy of the denatured ensemble. The observed behavior highlights the significance of investigating protein function and stability in different environments to uncover structural and dynamic properties that can escape detection in dilute solution, but might be relevant for proteins in vivo.
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Affiliation(s)
- Barbara Campanini
- Department of Public Health, University of Parma, Via Volturno 39, 43100 Parma, Italy
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Pioselli B, Bettati S, Demidkina TV, Zakomirdina LN, Phillips RS, Mozzarelli A. Tyrosine phenol-lyase and tryptophan indole-lyase encapsulated in wet nanoporous silica gels: Selective stabilization of tertiary conformations. Protein Sci 2004; 13:913-24. [PMID: 15044726 PMCID: PMC2280055 DOI: 10.1110/ps.03492904] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The pyridoxal 5'-phosphate-dependent enzymes tyrosine phenol-lyase and tryptophan indole-lyase were encapsulated in wet nanoporous silica gels, a powerful method to selectively stabilize tertiary and quaternary protein conformations and to develop bioreactors and biosensors. A comparison of the enzyme reactivity in silica gels and in solution was carried out by determining equilibrium and kinetic parameters, exploiting the distinct spectral properties of catalytic intermediates and reaction products. The encapsulated enzymes exhibit altered distributions of ketoenamine and enolimine tautomers, increased values of inhibitors dissociation constants, slow attaining of steady-state in the presence of substrate and substrate analogs, modified steady-state distribution of catalytic intermediates, and a sixfold-eightfold decrease of specific activities. This behavior can be rationalized by a reduced conformational flexibility for the encapsulated enzymes and a selective stabilization of either the open (inactive) or the closed (active) form of the enzymes. Despite very similar structures and catalytic mechanisms, the influence of encapsulation is more pronounced for tyrosine phenol-lyase than tryptophan indole-lyase. This finding indicates that subtle structural and dynamic differences can lead to distinct interactions of the protein with the gel matrix.
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Affiliation(s)
- Barbara Pioselli
- Department of Biochemistry and Molecular Biology, University of Parma, Via Parco delle Scienze 23/A, 43100 Parma, Italy
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Wheeler KE, Lees NS, Gurbiel RJ, Hatch SL, Nocek JM, Hoffman BM. Electrostatic Influence on Rotational Mobilities of Sol−Gel-Encapsulated Solutes by NMR and EPR Spectroscopies. J Am Chem Soc 2004; 126:13459-63. [PMID: 15479102 DOI: 10.1021/ja046659c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rotational mobilities of small solute molecules encapsulated in tetramethyl orthosilicate (TMOS) sol-gels have been investigated by EPR spectroscopy of encapsulated nitroxide probes and by high-resolution NMR spectroscopic measurements of transferred NOE's (trNOE's), of T(1)'s, and of T(1)'s in the rotating frame (T(1)rho). The two spectroscopic methods are sensitive to motions on different time scales and hence, are nicely complementary. Suites of neutral, positively, and negatively charged nitroxide probes (EPR) and of simple diamagnetic small molecules (NMR) were selected to disclose influences of electrostatic interactions with the sol-gel walls and to probe the presence of multiple populations of molecules in distinct regions of the sol-gel pores. For neutral and negatively charged solute probes, both techniques disclose a single population with a significantly increased average rotational correlation time, which we interpret at least in part as resulting from exchange between free-volume and transiently immobilized surface populations. The electrostatic attraction between cationic probes and the negatively charged sol-gel walls causes the positively charged probes to be more effectively immobilized and/or causes a greater percentage of probes to undergo this transient immobilization. The EPR spectra directly disclose a population of cationic probes which are immobilized on the X-band EPR time scale: tau(c) greater than or approximately equal 10(-7) s. However, NMR measurements of trNOE's and of T(1)rho demonstrate that this population does exchange with the free-volume probes on the slower time scale of NMR. This approach is equally applicable to the study of solutes within other types of confined spaces, as well.
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Affiliation(s)
- Korin E Wheeler
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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Jin W, Brennan JD. Properties and applications of proteins encapsulated within sol–gel derived materials. Anal Chim Acta 2002. [DOI: 10.1016/s0003-2670(02)00229-5] [Citation(s) in RCA: 416] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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