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Ausili A. Despite their structural similarities, the cytosolic isoforms of human Hsp90 show different behaviour in thermal unfolding due to their conformation: An FTIR study. Arch Biochem Biophys 2023; 740:109599. [PMID: 37028636 DOI: 10.1016/j.abb.2023.109599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/16/2023] [Accepted: 04/05/2023] [Indexed: 04/09/2023]
Abstract
Heat shock proteins 90 (Hsp90) are chaperones that promote the proper folding of other proteins under high temperature stress situations. Hsp90s are highly conserved and ubiquitous proteins, and in mammalian cells, they are localized in the cytoplasm, endoplasmic reticulum, and mitochondria. Cytoplasmic Hsp90 are named Hsp90α and Hsp90β and differ mainly in their expression pattern: Hsp90α is expressed under stress conditions, while Hsp90β is a constitutive protein. Structurally, both share the same characteristics by presenting three well-conserved domains, one of which, the N-terminal domain, has a binding site for ATP to which various drugs targeting this protein, including radicicol, can bind. The protein is mainly found in dimeric form and adopts different conformations depending on the presence of ligands, co-chaperones and client proteins. In this study, some aspects of structure and thermal unfolding of cytoplasmic human Hsp90 were analysed by infrared spectroscopy. The effect on Hsp90β of binding with a non-hydrolysable ATP analogue and radicicol was also examined. The results obtained showed that despite the high similarity in secondary structure the two isoforms exhibit substantial differences in their behaviour during thermal unfolding, as Hsp90α exhibits higher thermal stability, slower denaturation process and different event sequence during unfolding. Ligand binding strongly stabilizes Hsp90β and slightly modifies the secondary structure of the protein as well. Most likely, these structural and thermostability characteristics are closely related to the conformational cycling of the chaperone and its propensity to exist in monomer or dimer form.
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Affiliation(s)
- Alessio Ausili
- Institute of Plant Biochemistry and Photosynthesis (IBVF), Consejo Superior de Investigaciones Científicas, 41092, Seville, Spain.
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Ausili A, Corbalán-García S, Gómez-Fernández JC. The binding of different model membranes with PKCε C2 domain is not dependent on membrane curvature but affects the sequence of events during unfolding. Arch Biochem Biophys 2021; 705:108910. [PMID: 33991498 DOI: 10.1016/j.abb.2021.108910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/12/2021] [Accepted: 05/01/2021] [Indexed: 11/28/2022]
Abstract
The C2 domain of novel protein kinases C (nPKC) binds to membranes in a Ca2+-independent way contributing to the activation of these enzymes. We have studied the C2 domain of one of these nPKCs, namely PKCε, and confirmed that it establishes a strong interaction with POPA, which is clearly visible through changes in chemical shifts detected through 31P-MAS-NMR and the protection that it exerts on the domain against thermal denaturation seen through DSC and FT-IR. In this study, using two-dimensional correlation analysis (2D-COS) applied to infrared spectra, we determined the sequence of events that occur during the thermal unfolding of the domain and highlighted some differences when phosphatidic acid or cardiolipin are present. Finally, by means of FRET and DLS experiments, we wanted to determine the effect of membrane curvature on the domain/membrane interaction by using lysophosphatidylcholine to introduce positive curvature as a control and we observed that the effect of these phospholipids on the protein binding is not exerted through the change of membrane curvature.
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Affiliation(s)
- Alessio Ausili
- Departamento de Bioquímica y Biología Molecular (A), Facultad de Veterinaria, International Campus of Excellence Mare Nostrum, Universidad de Murcia, Apartado. 4021, E-30100, Murcia, Spain.
| | - Senena Corbalán-García
- Departamento de Bioquímica y Biología Molecular (A), Facultad de Veterinaria, International Campus of Excellence Mare Nostrum, Universidad de Murcia, Apartado. 4021, E-30100, Murcia, Spain
| | - Juan C Gómez-Fernández
- Departamento de Bioquímica y Biología Molecular (A), Facultad de Veterinaria, International Campus of Excellence Mare Nostrum, Universidad de Murcia, Apartado. 4021, E-30100, Murcia, Spain
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Suleiman M, Krüger A, Antranikian G. Biomass-degrading glycoside hydrolases of archaeal origin. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:153. [PMID: 32905355 PMCID: PMC7469102 DOI: 10.1186/s13068-020-01792-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
During the last decades, the impact of hyperthermophiles and their enzymes has been intensively investigated for implementation in various high-temperature biotechnological processes. Biocatalysts of hyperthermophiles have proven to show extremely high thermo-activities and thermo-stabilities and are identified as suitable candidates for numerous industrial processes with harsh conditions, including the process of an efficient plant biomass pretreatment and conversion. Already-characterized archaea-originated glycoside hydrolases (GHs) have shown highly impressive features and numerous enzyme characterizations indicated that these biocatalysts show maximum activities at a higher temperature range compared to bacterial ones. However, compared to bacterial biomass-degrading enzymes, the number of characterized archaeal ones remains low. To discover new promising archaeal GH candidates, it is necessary to study in detail the microbiology and enzymology of extremely high-temperature habitats, ranging from terrestrial to marine hydrothermal systems. State-of-the art technologies such as sequencing of genomes and metagenomes and automated binning of genomes out of metagenomes, combined with classical microbiological culture-dependent approaches, have been successfully performed to detect novel promising biomass-degrading hyperthermozymes. In this review, we will focus on the detection, characterization and similarities of archaeal GHs and their unique characteristics. The potential of hyperthermozymes and their impact on high-temperature industrial applications have not yet been exhausted.
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Affiliation(s)
- Marcel Suleiman
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Anna Krüger
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
| | - Garabed Antranikian
- Institute of Technical Microbiology, University of Technology Hamburg, Hamburg, Germany
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Aragón-Muriel A, Ausili A, Sánchez K, Rojas A OE, Londoño Mosquera J, Polo-Cerón D, Oñate-Garzón J. Studies on the Interaction of Alyteserin 1c Peptide and Its Cationic Analogue with Model Membranes Imitating Mammalian and Bacterial Membranes. Biomolecules 2019; 9:biom9100527. [PMID: 31557903 PMCID: PMC6843542 DOI: 10.3390/biom9100527] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 01/17/2023] Open
Abstract
Antimicrobial peptides (AMPs) are effector molecules of the innate immune system and have been isolated from multiple organisms. Their antimicrobial properties are due to the fact that they interact mainly with the anionic membrane of the microorganisms, permeabilizing it and releasing the cytoplasmic content. Alyteserin 1c (+2), an AMP isolated from Alytes obstetricans and its more cationic and hydrophilic analogue (+5) were synthesized using the solid phase method, in order to study the interaction with model membranes by calorimetric and spectroscopic assays. Differential scanning calorimetry (DSC) showed that both peptides had a strong effect when the membrane contained phosphatidylcholine (PC) alone or was mixed with phosphatidylglycerol (PG), increasing membrane fluidization. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was used to study the secondary structure of the peptide. Peptide +2 exhibited a transition from β-sheet/turns to β-sheet/α-helix structures after binding with model membranes, whereas peptide +5 had a transition from aggregation/unordered to β-sheet/α-helix structures after binding with membrane-contained PC. Interestingly, the latter showed a β-sheet structure predominantly in the presence of PG lipids. Additionally, molecular dynamics (MD) results showed that the carboxy-terminal of the peptide +5 has the ability to insert into the surface of the PC/PG membranes, resulting in the increase of the membrane fluidity.
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Affiliation(s)
- Alberto Aragón-Muriel
- Facultad de Ciencias Naturales y Exactas, Departmento de Química, Laboratorio of Investigación en Catalisis and Procesos (LICAP), Universidad del Valle, Cali 760001, Colombia.
| | - Alessio Ausili
- Departmento de Bioquímica y Biología Molecular-A, Facultad de Medicina Veterinaria, Campus of International Excellence Mare, Universidad de Murcia, E-30100 Murcia, Spain.
| | - Kevin Sánchez
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760031, Colombia.
| | - Oscar E Rojas A
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760031, Colombia.
| | - Juan Londoño Mosquera
- Facultad de Ciencias Naturales y Exactas, Departmento de Química, Laboratorio of Investigación en Catalisis and Procesos (LICAP), Universidad del Valle, Cali 760001, Colombia.
| | - Dorian Polo-Cerón
- Facultad de Ciencias Naturales y Exactas, Departmento de Química, Laboratorio of Investigación en Catalisis and Procesos (LICAP), Universidad del Valle, Cali 760001, Colombia.
| | - Jose Oñate-Garzón
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760031, Colombia.
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Scirè A, Tanfani F, Ausili A. A Spectroscopic Study on Secondary Structure and Thermal Unfolding of the Plant Toxin Gelonin Confirms Some Typical Structural Characteristics and Unravels the Sequence of Thermal Unfolding Events. Toxins (Basel) 2019; 11:toxins11090483. [PMID: 31443430 PMCID: PMC6783991 DOI: 10.3390/toxins11090483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 11/17/2022] Open
Abstract
Gelonin from the Indian plant Gelonium multiflorum belongs to the type I ribosome-inactivating proteins (RIPs). Like other members of RIPs, this toxin glycoprotein inhibits protein synthesis of eukaryotic cells; hence, it is largely used in the construction of immunotoxins composed of cell-targeted antibodies. Lysosomal degradation is one of the main issues in targeted tumor therapies, especially for type I RIP-based toxins, as they lack the translocation domains. The result is an attenuated cytosolic delivery and a decrease of the antitumor efficacy of these plant-derived toxins; therefore, strategies to permit their release from endosomal vesicles or modifications of the toxins to make them resistant to degradation are necessary to improve their efficacy. Using infrared spectroscopy, we thoroughly analyzed both the secondary structure and the thermal unfolding of gelonin. Moreover, by the combination of two-dimensional correlation spectroscopy and phase diagram method, it was possible to deduce the sequence of events during the unfolding, confirming the typical characteristic of the RIP members to denature in two steps, as a sequential loss of tertiary and secondary structure was detected at 58 °C and at 65 °C, respectively. Additionally, some discrepancies in the unfolding process between gelonin and saporin-S6, another type I RIP protein, were detected.
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Affiliation(s)
- Andrea Scirè
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Fabio Tanfani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Alessio Ausili
- Departamento de Bioquímica y Biología Molecular "A", Facultad de Veterinaria, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, 30100 Murcia, Spain.
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Tao Y, Wu Y, Zhang L. Advancements of two dimensional correlation spectroscopy in protein researches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 197:185-193. [PMID: 29409703 DOI: 10.1016/j.saa.2018.01.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 01/09/2018] [Accepted: 01/13/2018] [Indexed: 05/26/2023]
Abstract
The developments of two-dimensional correlation spectroscopy (2DCOS) applications in protein studies are discussed, especially for the past two decades. The powerful utilities of 2DCOS combined with various analytical techniques in protein studies are summarized. The emphasis is on the vibration spectroscopic techniques including IR, NIR, Raman and optical activity (ROA), as well as vibration circular dichroism (VCD) and fluorescence spectroscopy. In addition, some new developments, such as hetero-spectral 2DCOS, moving-window correlation, and model based correlation, are also reviewed for their utility in the investigation of the secondary structure, denaturation, folding and unfolding changes of protein. Finally, the new possibility and challenges of 2DCOS in protein research are highlighted as well.
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Affiliation(s)
- Yanchun Tao
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
| | - Yuqing Wu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China.
| | - Liping Zhang
- Department of Foundation, Jilin Business and Technology College, No. 1666 Kalunhu Street, Changchun 130507, China.
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Wu Y, Zhang L, Jung YM, Ozaki Y. Two-dimensional correlation spectroscopy in protein science, a summary for past 20years. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 189:291-299. [PMID: 28823970 DOI: 10.1016/j.saa.2017.08.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/04/2017] [Indexed: 05/26/2023]
Abstract
Two-dimensional correlation spectroscopy (2DCOS) has been widely used to Infrared, Raman, Near IR, Optical Activity (ROA), Vibrational Circular Dichroism (VCD) and Fluorescence spectroscopy. In addition, several new developments, such as 2D hetero-correlation analysis, moving-window two-dimensional (MW2D) correlation, model based correlation (βν and kν correlation analyses) have also well incorporated into protein research. They have been used to investigate secondary structure, denaturation, folding and unfolding changes of protein, and have contributed greatly to the field of protein science. This review provides an overview of the applications of 2DCOS in the field of protein science for the past 20 year, especially to memory our old friend, Dr. Boguslawa Czarnik-Matusewicz, for her great contribution in this research field. The powerful utility of 2DCOS combined with various analytical techniques in protein studies is summarized. The noteworthy developments and perspective of 2DCOS in this field are highlighted finally.
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Affiliation(s)
- Yuqing Wu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
| | - Liping Zhang
- Department of Foundation, Jilin Business and Technology College, No. 1666 Kalunhu Street, Changchun 130507, China.
| | - Young Mee Jung
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yukihiro Ozaki
- School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
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Bovine α1-acid glycoprotein, a thermostable version of its human counterpart: Insights from Fourier transform infrared spectroscopy and in silico modelling. Biochimie 2014; 102:19-28. [DOI: 10.1016/j.biochi.2014.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 02/04/2014] [Indexed: 11/19/2022]
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Okazaki H, Kaneko C, Hirahara M, Watanabe S, Tochio N, Kigawa T, Nishimura C. Long-range effects of tag sequence on marginally stabilized structure in HIV-1 p24 capsid protein monitored using NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1638-47. [PMID: 24960591 DOI: 10.1016/j.bbapap.2014.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 06/10/2014] [Accepted: 06/16/2014] [Indexed: 10/25/2022]
Abstract
N-terminal domain of HIV-1 p24 capsid protein is a globular fold composed of seven helices and two β-strands with a flexible structure including the α4-5 loop and both N- and C-terminal ends. However, the protein shows a high tendency (48%) for an intrinsically disordered structure based on the PONDR VL-XT prediction from the primary sequence. To assess the possibility of marginally stabilized structure under physiological conditions, the N-terminal domain of p24 was destabilized by the addition of an artificial flexible tag to either N- or C-terminal ends, and it was analyzed using T1, T2, hetero-nuclear NOE, and amide-proton exchange experiments. When the C-terminal tag (12 residues) was attached, the regions of the α3-4 loop and helix 6 as well as the α4-5 loop attained the flexible structures. Furthermore, in the protein containing the N-terminal tag (27 residues), helix 4 in addition to the above-mentioned area including α3-4 and α4-5 loops as well as helix 6 exhibited highly disordered structures. Thus, the long-range effects of the existence of tag sequence was observed in the stepwise manner of the appearance of disordered structures (step 1: α4-5 loop, step 2: α3-4 loop and helix 6, and step 3: helix 4). Furthermore, the disordered regions in tagged proteins were consistent with the PONDR VL-XT disordered prediction. The dynamic structure located in the middle part (α3-4 loop to helix 6) of the protein shown in this study may be related to the assembly of the viral particle.
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Affiliation(s)
- Honoka Okazaki
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
| | - Chie Kaneko
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
| | - Miyuki Hirahara
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
| | - Satoru Watanabe
- NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan
| | - Naoya Tochio
- NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan
| | - Takanori Kigawa
- NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan
| | - Chiaki Nishimura
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan.
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Liszka MJ, Clark ME, Schneider E, Clark DS. Nature Versus Nurture: Developing Enzymes That Function Under Extreme Conditions. Annu Rev Chem Biomol Eng 2012; 3:77-102. [DOI: 10.1146/annurev-chembioeng-061010-114239] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Elizabeth Schneider
- Department of Chemical and Biomolecular Engineering,
- UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley, California 94720; , , ,
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Baldassarre M, Scirè A, Tanfani F. Turning pyridoxal-5'-phosphate-dependent enzymes into thermostable binding proteins: D-Serine dehydratase from baker's yeast as a case study. Biochimie 2011; 94:479-86. [PMID: 21896305 DOI: 10.1016/j.biochi.2011.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 08/24/2011] [Indexed: 12/21/2022]
Abstract
D-serine dehydratase from Saccharomyces cerevisae is a recently discovered dimeric enzyme catalyzing the β-elimination of D-serine to pyruvate and ammonia. The reaction is highly enantioselective and depends on cofactor pyridoxal-5'-phosphate (PLP) and Zn(2+). In our work, the aldimine linkage tethering PLP to recombinant, tagged D-serine dehydratase (Dsd) has been reduced by treatment with NaBH(4) so as to yield an inactive form of the holoenzyme (DsdR), which was further treated with a protease in order to remove the amino-terminal purification tag. Fourier Transform infrared (FT-IR) spectroscopic analysis revealed that both the reduced form (DsdR) and the reduced/detagged form (DsdRD) maintain the overall secondary structure of Dsd, but featured a significant increased thermal stability. The observed T(m) values for DsdR and for DsdRD shifted to 71.5 °C and 73.3 °C, respectively, resulting in nearly 11 °C and 13 °C higher than the one measured for Dsd. Furthermore, the analysis of the FT-IR spectra acquired in the presence of D-serine and L-serine indicates that, though catalytically inert, DsdRD retains the ability to enantioselectively bind its natural substrate. Sequence analysis of D-serine dehydratase and other PLP-dependent enzymes also highlighted critical residues involved in PLP binding. In virtue of its intrinsic properties, DsdRD represents an ideal candidate for the design of novel platforms based on stable, non-consuming binding proteins aimed at measuring d-serine levels in biological fluids.
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Affiliation(s)
- Maurizio Baldassarre
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Ranieri, 60131 Ancona, Italy
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Nam ES, Kim MS, Lee HB, Ahn JK. β-Glycosidase of Thermus thermophilus KNOUC202: Gene and biochemical properties of the enzyme expressed in Escherichia coli. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810050091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Overexpression of β-glucosidase from Thermotoga maritima for the production of highly purified aglycone isoflavones from soy flour. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0121-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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