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Izzi G, Campanile M, Del Vecchio P, Graziano G. On the Stabilizing Effect of Aspartate and Glutamate and Its Counteraction by Common Denaturants. Int J Mol Sci 2024; 25:9360. [PMID: 39273310 PMCID: PMC11395698 DOI: 10.3390/ijms25179360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
By performing differential scanning calorimetry(DSC) measurements on RNase A, we studied the stabilization provided by the addition of potassium aspartate(KAsp) or potassium glutamate (KGlu) and found that it leads to a significant increase in the denaturation temperature of the protein. The stabilization proves to be mainly entropic in origin. A counteraction of the stabilization provided by KAsp or KGlu is obtained by adding common denaturants such as urea, guanidinium chloride, or guanidinium thiocyanate. A rationalization of the experimental data is devised on the basis of a theoretical approach developed by one of the authors. The main contribution to the conformational stability of globular proteins comes from the gain in translational entropy of water and co-solute ions and/or molecules for the decrease in solvent-excluded volume associated with polypeptide folding (i.e., there is a large decrease in solvent-accessible surface area). The magnitude of this entropic contribution increases with the number density and volume packing density of the solution. The two destabilizing contributions come from the conformational entropy of the chain, which should not depend significantly on the presence of co-solutes, and from the direct energetic interactions between co-solutes and the protein surface in both the native and denatured states. It is the magnitude of the latter that discriminates between stabilizing and destabilizing agents.
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Affiliation(s)
- Guido Izzi
- Institute of Biostructure and Bioimaging, National Research Council, Via P. Castellino, 80131 Naples, Italy
| | - Marco Campanile
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, Via F. De Sanctis, 82100 Benevento, Italy
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2
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Role of N-Terminal Extensional Long α-Helix in the Arylesterase from Lacticaseibacillus rhamnosus GG on Catalysis and Stability. Catalysts 2023. [DOI: 10.3390/catal13020441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
In the α/β hydrolases superfamily, the extra module modulated enzymatic activity, substrate specificity, and stability. The functional role of N-terminal extensional long α-helix (Ala2-Glu29, designated as NEL-helix) acting as the extra module in the arylesterase LggEst from Lacticaseibacillus rhamnosus GG had been systemically investigated by deletion mutagenesis, biochemical characterization, and biophysical methods. The deletion of the NEL-helix did not change the overall structure of this arylesterase. The deletion of the NEL-helix led to the shifting of optimal pH into the acidity and the loss of thermophilic activity. The deletion of the NEL-helix produced a 10.6-fold drop in catalytic activity towards the best substrate pNPC10. NEL-Helix was crucial for the thermostability, chemical resistance, and organic solvents tolerance. The deletion of the NEL-helix did not change the overall rigidity of enzyme structure and only reduced the local rigidity of the active site. Sodium deoxycholate might partially replenish the loss of activity caused by the deletion of the NEL-helix. Our research further enriched the functional role of the extra module on catalysis and stability in the α/β hydrolase fold superfamily.
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Cozzolino S, Tortorella A, Del Vecchio P, Graziano G. General Counteraction Exerted by Sugars against Denaturants. Life (Basel) 2021; 11:652. [PMID: 34357025 PMCID: PMC8303697 DOI: 10.3390/life11070652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
The conformational stability of globular proteins is strongly influenced by the addition to water of different co-solutes. Some of the latter destabilize the native state, while others stabilize it. It is emerging that stabilizing agents are able to counteract the action of destabilizing agents. We have already provided experimental evidence that this counteraction is a general phenomenon and offered a rationalization. In the present work, we show that four different sugars, namely fructose, glucose, sucrose, and trehalose, counteract the effect of urea, tetramethylurea, sodium perchlorate, guanidinium chloride, and guanidinium thiocyanate despite the chemical and structural differences of those destabilizing agents. The rationalization we provide is as follows: (a) the solvent-excluded volume effect, a purely entropic effect, stabilizes the native state, whose solvent-accessible surface area is smaller than the one of denatured conformations; (b) the magnitude of the solvent-excluded volume effect increases markedly in ternary solutions because the experimental density of such solutions is larger than that of pure water.
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Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Attila Tortorella
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Pompea Del Vecchio
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università degli Studi del Sannio, Via Francesco de Sanctis snc, 82100 Benevento, Italy
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Structural and Functional Characterization of New SsoPox Variant Points to the Dimer Interface as a Driver for the Increase in Promiscuous Paraoxonase Activity. Int J Mol Sci 2020; 21:ijms21051683. [PMID: 32121487 PMCID: PMC7084321 DOI: 10.3390/ijms21051683] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/02/2020] [Accepted: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
Increasing attention is more and more directed toward the thermostable Phosphotriesterase-Like-Lactonase (PLL) family of enzymes, for the efficient and reliable decontamination of toxic nerve agents. In the present study, the DNA Staggered Extension Process (StEP) technique was utilized to obtain new variants of PLL enzymes. Divergent homologous genes encoding PLL enzymes were utilized as templates for gene recombination and yielded a new variant of SsoPox from Saccharolobus solfataricus. The new mutant, V82L/C258L/I261F/W263A (4Mut) exhibited catalytic efficiency of 1.6 × 105 M−1 s−1 against paraoxon hydrolysis at 70°C, which is more than 3.5-fold and 42-fold improved in comparison with C258L/I261F/W263A (3Mut) and wild type SsoPox, respectively. 4Mut was also tested with chemical warfare nerve agents including tabun, sarin, soman, cyclosarin and VX. In particular, 4Mut showed about 10-fold enhancement in the hydrolysis of tabun and soman with respect to 3Mut. The crystal structure of 4Mut has been solved at the resolution of 2.8 Å. We propose that, reorganization of dimer conformation that led to increased central groove volume and dimer flexibility could be the major determinant for the improvement in hydrolytic activity in the 4Mut.
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Tang L, Yang J, Chen J, Zhang J, Yu H, Shen Z. Design of salt-bridge cyclization peptide tags for stability and activity enhancement of enzymes. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Cozzolino S, Oliva R, Graziano G, Del Vecchio P. Counteraction of denaturant-induced protein unfolding is a general property of stabilizing agents. Phys Chem Chem Phys 2018; 20:29389-29398. [PMID: 30451257 DOI: 10.1039/c8cp04421j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DSC measurements on RNase A at neutral pH show that five stabilizing agents, namely trimethylamine N-oxide, glucose, sucrose, betaine and sodium sulfate, can counteract the destabilizing action of urea, sodium perchlorate, guanidinium chloride and guanidinium thiocyanate. This is an important finding inferring that counteraction has a common physical origin, regardless of the chemical differences among the stabilizing agents and among the destabilizing ones. A rationalization is provided grounded on the following line of reasoning: (a) the decrease in solvent-excluded volume effect is the main stabilizing contribution of the native state; (b) its magnitude increases on increasing the density of the aqueous solution; (c) the density increases significantly in the ternary solutions containing water, a stabilizing agent and a destabilizing one, as indicated by the present experimental data.
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Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia - 80126 Napoli, Italy.
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7
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Rusko J, Febbraio F. Development of an automated multienzymatic biosensor for risk assessment of pesticide contamination in water and food. EFSA J 2018; 16:e16084. [PMID: 32626055 PMCID: PMC7015495 DOI: 10.2903/j.efsa.2018.e16084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The goal of this research is to better address the problems related to the widespread presence of pesticides in the environment. Despite the unquestionable utility of the pesticides against various pests in the agricultural field, most pesticides and the corresponding pesticide residues are toxic to the environment and hazardous to human health. The recent literature on organophosphate compounds emphasises a clear correlation between their use and the occurrence of disorders in the nervous system, especially in children. The conventional systems for the detection and analysis of these compounds are expensive, time‐consuming and require highly specialised operators; moreover, no online automated screening systems are yet available, that would allow the identification and quantification of the presence of these chemicals in samples from industrial sectors such as the food industry. Esterase‐based biosensors represent a viable alternative to this problem. In this fellowship programme, we aim to develop a robust and sensitive methodology that enables the screening of toxic compounds using a streamlined process, using an automated robotic system to achieve a continuous monitoring for risk assessment of pesticides.
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Smaldone G, Balasco N, Vigorita M, Ruggiero A, Cozzolino S, Berisio R, Del Vecchio P, Graziano G, Vitagliano L. Domain communication in Thermotoga maritima Arginine Binding Protein unraveled through protein dissection. Int J Biol Macromol 2018; 119:758-769. [PMID: 30059738 DOI: 10.1016/j.ijbiomac.2018.07.172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022]
Abstract
Substrate binding proteins represent a large protein family that plays fundamental roles in selective transportation of metabolites across membrane. The function of these proteins relies on the relative motions of their two domains. Insights into domain communication in this class of proteins have been here collected using Thermotoga maritima Arginine Binding Protein (TmArgBP) as model system. TmArgBP was dissected into two domains (D1 and D2) that were exhaustively characterized using a repertoire of different experimental and computational techniques. Indeed, stability, crystalline structure, ability to recognize the arginine substrate, and dynamics of the two individual domains have been here studied. Present data demonstrate that, although in the parent protein both D1 and D2 cooperate for the arginine anchoring; only D1 is intrinsically able to bind the substrate. The implications of this finding on the mechanism of arginine binding and release by TmArgBP have been discussed. Interestingly, both D1 and D2 retain the remarkable thermal/chemical stability of the parent protein. The analysis of the structural and dynamic properties of TmArgBP and of the individual domains highlights possible routes of domain communication. Finally, this study generated two interesting molecular tools, the two stable isolated domains that could be used in future investigations.
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Affiliation(s)
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Marilisa Vigorita
- Department of Sciences and Technologies, Università del Sannio, via Port'arsa 11, 82100 Benevento, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Serena Cozzolino
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Giuseppe Graziano
- Department of Sciences and Technologies, Università del Sannio, via Port'arsa 11, 82100 Benevento, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
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9
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Vigorita M, Cozzolino S, Oliva R, Graziano G, Del Vecchio P. Counteraction ability of TMAO toward different denaturing agents. Biopolymers 2018; 109:e23104. [DOI: 10.1002/bip.23104] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/22/2017] [Accepted: 01/16/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Marilisa Vigorita
- Dipartimento di Scienze e Tecnologie; Università degli Studi del Sannio, Via Port'Arsa 11; Benevento 82100 Italy
| | - Serena Cozzolino
- Dipartimento di Scienze Chimiche; Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia; Napoli 80126 Italy
| | - Rosario Oliva
- Dipartimento di Scienze Chimiche; Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia; Napoli 80126 Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie; Università degli Studi del Sannio, Via Port'Arsa 11; Benevento 82100 Italy
| | - Pompea Del Vecchio
- Dipartimento di Scienze Chimiche; Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia; Napoli 80126 Italy
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10
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Hunt CJ, Tanksale A, Haritos VS. Biochemical characterization of a halotolerant feruloyl esterase from Actinomyces spp.: refolding and activity following thermal deactivation. Appl Microbiol Biotechnol 2015; 100:1777-1787. [DOI: 10.1007/s00253-015-7044-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/13/2015] [Accepted: 09/24/2015] [Indexed: 11/28/2022]
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11
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Fluorescence spectroscopy approaches for the development of a real-time organophosphate detection system using an enzymatic sensor. SENSORS 2015; 15:3932-51. [PMID: 25671511 PMCID: PMC4367393 DOI: 10.3390/s150203932] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/02/2015] [Indexed: 01/28/2023]
Abstract
Organophosphates are organic substances that contain a phosphoryl or a thiophosphoryl bond. They are mainly used around the world as pesticides, but can also be used as chemical warfare agents. Their detection is normally entrusted to techniques like GC- and LC-MS that, although sensitive, do not allow their identification on site and in real time. We have approached their identification by exploiting the high-affinity binding of these compounds with the esterase 2 from Alicyclobacillus acidocaldarius. Using an in silico analysis to evaluate the binding affinities of the enzyme with organophosphate inhibitors, like paraoxon, and other organophosphate compounds, like parathion, chlorpyriphos, and other organophosphate thio-derivatives, we have designed fluorescence spectroscopy experiments to study the quenching of the tryptophan residues after esterase 2 binding with the organophosphate pesticides. The changes in the fluorescence signals permitted an immediate and quantitative identification of these compounds from nano- to picomolar concentrations. A fluorescence based polarity-sensitive probe (ANS) was also employed as a means to understand the extent of the interactions involved, as well as to explore other ways to detect organophosphate pesticides. Finally, we designed a framework for the development of a biosensor that exploits fluorescence technology in combination with a sensitive and very stable bio-receptor.
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12
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Pezzullo M, Del Vecchio P, Mandrich L, Nucci R, Rossi M, Manco G. Comprehensive analysis of surface charged residues involved in thermal stability in Alicyclobacillus acidocaldarius esterase 2. Protein Eng Des Sel 2012; 26:47-58. [DOI: 10.1093/protein/gzs066] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Sherrer SM, Maxwell BA, Pack LR, Fiala KA, Fowler JD, Zhang J, Suo Z. Identification of an unfolding intermediate for a DNA lesion bypass polymerase. Chem Res Toxicol 2012; 25:1531-40. [PMID: 22667759 DOI: 10.1021/tx3002115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sulfolobus solfataricus DNA Polymerase IV (Dpo4), a prototype Y-family DNA polymerase, has been well characterized biochemically and biophysically at 37 °C or lower temperatures. However, the physiological temperature of the hyperthermophile S. solfataricus is approximately 80 °C. With such a large discrepancy in temperature, the in vivo relevance of these in vitro studies of Dpo4 has been questioned. Here, we employed circular dichroism spectroscopy and fluorescence-based thermal scanning to investigate the secondary structural changes of Dpo4 over a temperature range from 26 to 119 °C. Dpo4 was shown to display a high melting temperature characteristic of hyperthermophiles. Unexpectedly, the Little Finger domain of Dpo4, which is only found in the Y-family DNA polymerases, was shown to be more thermostable than the polymerase core. More interestingly, Dpo4 exhibited a three-state cooperative unfolding profile with an unfolding intermediate. The linker region between the Little Finger and Thumb domains of Dpo4 was found to be a source of structural instability. Through site-directed mutagenesis, the interactions between the residues in the linker region and the Palm domain were identified to play a critical role in the formation of the unfolding intermediate. Notably, the secondary structure of Dpo4 was not altered when the temperature was increased from 26 to 87.5 °C. Thus, in addition to providing structural insights into the thermal stability and an unfolding intermediate of Dpo4, our work also validated the relevance of the in vitro studies of Dpo4 performed at temperatures significantly lower than 80 °C.
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Affiliation(s)
- Shanen M Sherrer
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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14
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Pagano B, Del Vecchio P, Mattia CA, Graziano G. Molecular dynamics study of the conformational stability of esterase 2 from Alicyclobacillus acidocaldarius. Int J Biol Macromol 2011; 49:1072-7. [DOI: 10.1016/j.ijbiomac.2011.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 08/30/2011] [Accepted: 09/01/2011] [Indexed: 11/16/2022]
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15
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Production and characterization of two N-terminal truncated esterases from Thermus thermophilus HB27 in a mesophilic yeast: Effect of N-terminus in thermal activity and stability. Protein Expr Purif 2011; 78:120-30. [DOI: 10.1016/j.pep.2011.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 03/18/2011] [Accepted: 04/05/2011] [Indexed: 11/20/2022]
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16
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Febbraio F, Merone L, Cetrangolo GP, Rossi M, Nucci R, Manco G. Thermostable Esterase 2 from Alicyclobacillus acidocaldarius as Biosensor for the Detection of Organophosphate Pesticides. Anal Chem 2011; 83:1530-6. [DOI: 10.1021/ac102025z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ferdinando Febbraio
- Istituto di Biochimica delle Proteine, CNR. Via P. Castellino 111, 80131 Naples, Italy
| | - Luigia Merone
- Istituto di Biochimica delle Proteine, CNR. Via P. Castellino 111, 80131 Naples, Italy
| | | | - Mosè Rossi
- Istituto di Biochimica delle Proteine, CNR. Via P. Castellino 111, 80131 Naples, Italy
| | - Roberto Nucci
- Istituto di Biochimica delle Proteine, CNR. Via P. Castellino 111, 80131 Naples, Italy
| | - Giuseppe Manco
- Istituto di Biochimica delle Proteine, CNR. Via P. Castellino 111, 80131 Naples, Italy
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Brod FCA, Vernal J, Bertoldo JB, Terenzi H, Arisi ACM. Cloning, Expression, Purification, and Characterization of a Novel Esterase from Lactobacillus plantarum. Mol Biotechnol 2009; 44:242-9. [DOI: 10.1007/s12033-009-9232-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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