1
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Dave U, Khan S, Gomes J. Characterization of E121K mutation of D-amino acid oxidase - Insights into mechanisms leading to amyotrophic lateral sclerosis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140947. [PMID: 37558109 DOI: 10.1016/j.bbapap.2023.140947] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/29/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
D-amino acid oxidase (DAO) maintains the intracellular d-serine level which modulates the activity of the N-methyl-d-aspartate receptor and its dysfunction has been linked to several neurodegenerative disorders. In targeted next-generation sequencing study by our group, E121K mutation in DAO was associated with amyotrophic lateral sclerosis (ALS) in patients from India. However, variations in molecular mechanisms caused by this mutation which leads to ALS have not been studied. Hence, we carried out comparative biophysical characterization and assay studies of the wildtype- and mutant E121K-DAO. We observed that the purified E121K-DAO was inactive and exhibited a lower affinity for the FAD cofactor and benzoate inhibitor. Structural studies revealed that the E121K mutant has higher beta-sheet content, melting temperature, and oligomeric states compared to the wildtype. Kinetic study of aggregation of the variants using thioflavin-T confirmed that the E121K-DAO was more prone to aggregation. Microscopic visualization showed that the aggregation proceeds through an intermediate step involving the formation of fibrillar structures in the E121K mutant. Our results give insights into the underlying mechanisms leading to ALS pathogenesis.
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Affiliation(s)
- Upma Dave
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shumayila Khan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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2
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Structural mechanism of Fab domain dissociation as a measure of interface stability. J Comput Aided Mol Des 2023; 37:201-215. [PMID: 36918473 PMCID: PMC10049950 DOI: 10.1007/s10822-023-00501-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/23/2023] [Indexed: 03/16/2023]
Abstract
Therapeutic antibodies should not only recognize antigens specifically, but also need to be free from developability issues, such as poor stability. Thus, the mechanistic understanding and characterization of stability are critical determinants for rational antibody design. In this study, we use molecular dynamics simulations to investigate the melting process of 16 antigen binding fragments (Fabs). We describe the Fab dissociation mechanisms, showing a separation in the VH-VL and in the CH1-CL domains. We found that the depths of the minima in the free energy curve, corresponding to the bound states, correlate with the experimentally determined melting temperatures. Additionally, we provide a detailed structural description of the dissociation mechanism and identify key interactions in the CDR loops and in the CH1-CL interface that contribute to stabilization. The dissociation of the VH-VL or CH1-CL domains can be represented by conformational changes in the bend angles between the domains. Our findings elucidate the melting process of antigen binding fragments and highlight critical residues in both the variable and constant domains, which are also strongly germline dependent. Thus, our proposed mechanisms have broad implications in the development and design of new and more stable antigen binding fragments.
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3
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Jin R, Grasso M, Zhou M, Marmorstein R, Baumgart T. Unfolding Mechanisms and Conformational Stability of the Dimeric Endophilin N-BAR Domain. ACS OMEGA 2021; 6:20790-20803. [PMID: 34423187 PMCID: PMC8374900 DOI: 10.1021/acsomega.1c01905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Endophilin, which is a member of the Bin-amphiphysin-Rvs (BAR) domain protein superfamily, contains a homodimeric N-BAR domain of a characteristic crescent shape. The N-BAR domain comprises a six-helix bundle and is known to sense and generate membrane curvature. Here, we characterize aspects of the unfolding mechanism of the endophilin A1 N-BAR domain during thermal denaturation and examine factors that influence the thermal stability of this domain. Far-UV circular dichroism (CD) spectroscopy was applied to monitor changes in the secondary structure above room temperature. The protein's conformational changes were further characterized through Foerster resonance energy transfer and cross-linking experiments at varying temperatures. Our results indicate that thermal unfolding of the endophilin N-BAR is (minimally) a two-step process, with a dimeric intermediate that displays partial helicity loss. Furthermore, a thermal shift assay and temperature-dependent CD were applied to compare the unfolding processes of several truncated versions of endophilin. The melting temperature of the N-BAR domain decreased when we deleted either the N-terminal H0 helix or the unstructured linker of endophilin. This result suggests that these intrinsically disordered domains may play a role in structurally stabilizing the functional N-BAR domain in vivo. Finally, we show that single-site mutations can also compromise endophilin's thermal stability.
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Affiliation(s)
- Rui Jin
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael Grasso
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Mingyang Zhou
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson
Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ronen Marmorstein
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson
Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Tobias Baumgart
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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4
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Rosini E, Volpi NA, Ziffels B, Grimaldi A, Sacchi S, Neri D, Pollegioni L. An antibody-based enzymatic therapy for cancer treatment: The selective localization of D-amino acid oxidase to EDA fibronectin. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 36:102424. [PMID: 34174417 DOI: 10.1016/j.nano.2021.102424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/12/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022]
Abstract
In order to generate an antibody directed enzyme prodrug therapy, here we designed a chimeric protein by fusing the F8 antibody that recognizes the EDA of fibronectin (expressed on the tumor neovasculature) and an evolved variant of the ROS-generating enzyme D-amino acid oxidase (DAAO). The F8(scFv)-DAAO-Q144R recombinant protein is expressed by both CHO-S and E. coli cells. The F8(scFv)-DAAO-Q144R from E. coli cells is fully soluble, shows a high specific activity, is more thermostable in blood than the native DAAO, possesses a binding affinity for EDA well suited for efficient tumor accumulation, and localizes in tumor tissues. Notably, the F8(scFv)-DAAO-Q144R conjugate generates a stronger cytotoxicity to tumor cells than the native enzyme, especially when an inhibitor of heme oxygenase-1 (HO-1) is used, making it a promising candidate for a selective antitumor oxidative therapy controlled by the substrate addition, in the so called "activity on demand", thus sparing normal tissue from damage.
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Affiliation(s)
- Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.
| | - Noemi Antonella Volpi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Barbara Ziffels
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zurich, Switzerland
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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5
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Shimekake Y, Hirato Y, Funabashi R, Okazaki S, Goto M, Furuichi T, Suzuki H, Kera Y, Takahashi S. X-ray structure analysis of a unique D-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA. Acta Crystallogr F Struct Biol Commun 2020; 76:517-523. [PMID: 33135670 PMCID: PMC7605106 DOI: 10.1107/s2053230x20013333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/05/2020] [Indexed: 11/11/2022] Open
Abstract
D-Amino-acid oxidases (DAAOs) catalyze the oxidative deamination of neutral and basic D-amino acids. The DAAO from the thermophilic fungus Rasamsonia emersonii strain YA (ReDAAO) has a high thermal stability and a unique broad substrate specificity that includes the acidic D-amino acid D-Glu as well as various neutral and basic D-amino acids. In this study, ReDAAO was crystallized by the hanging-drop vapor-diffusion method and its crystal structure was determined at a resolution of 2.00 Å. The crystal structure of the enzyme revealed that unlike other DAAOs, ReDAAO forms a homotetramer and contains an intramolecular disulfide bond (Cys230-Cys285), suggesting that this disulfide bond is involved in the higher thermal stability of ReDAAO. Moreover, the structure of the active site and its vicinity in ReDAAO indicates that Arg97, Lys99, Lys114 and Ser231 are candidates for recognizing the side chain of D-Glu.
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Affiliation(s)
- Yuya Shimekake
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yuki Hirato
- Department of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Rikako Funabashi
- Department of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Sayoko Okazaki
- Department of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Masaru Goto
- Department of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Takehiro Furuichi
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Hideyuki Suzuki
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Yoshio Kera
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Shouji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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6
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Key factors behind autofluorescence changes caused by ablation of cardiac tissue. Sci Rep 2020; 10:15369. [PMID: 32958843 PMCID: PMC7506017 DOI: 10.1038/s41598-020-72351-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/25/2020] [Indexed: 11/30/2022] Open
Abstract
Radiofrequency ablation is a commonly used clinical procedure that destroys arrhythmogenic sources in patients suffering from atrial fibrillation and other types of cardiac arrhythmias. To improve the success of this procedure, new approaches for real-time visualization of ablation sites are being developed. One of these promising methods is hyperspectral imaging, an approach that detects lesions based on changes in the endogenous tissue autofluorescence profile. To facilitate the clinical implementation of this approach, we examined the key variables that can influence ablation-induced spectral changes, including the drop in myocardial NADH levels, the release of lipofuscin-like pigments, and the increase in diffuse reflectance of the cardiac muscle beneath the endocardial layer. Insights from these experiments suggested simpler algorithms that can be used to acquire and post-process the spectral information required to reveal the lesion sites. Our study is relevant to a growing number of multilayered clinical targets to which spectral approaches are being applied.
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7
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Ocal N, L’enfant M, Charmantray F, Pollegioni L, Martin J, Auffray P, Collin J, Hecquet L. d-Serine as a Key Building Block: Enzymatic Process Development and Smart Applications within the Cascade Enzymatic Concept. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nazim Ocal
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Mélanie L’enfant
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Franck Charmantray
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, Università degli Studi dell’Insubria, 21100 Varese, Italy
| | - Juliette Martin
- Protéus by Seqens, 70 Allée Graham Belln, F-30035 Nîmes, France
| | - Pascal Auffray
- Protéus by Seqens, 70 Allée Graham Belln, F-30035 Nîmes, France
| | - Jérôme Collin
- Protéus by Seqens, 70 Allée Graham Belln, F-30035 Nîmes, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
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8
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L'enfant M, Bruna F, Lorillière M, Ocal N, Fessner W, Pollegioni L, Charmantray F, Hecquet L. One‐Pot Cascade Synthesis of (3 S)‐Hydroxyketones Catalyzed by Transketolase viaHydroxypyruvate Generated in Situfrom d‐Serine by d‐Amino Acid Oxidase. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mélanie L'enfant
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Felipe Bruna
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Marion Lorillière
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Nazim Ocal
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Wolf‐Dieter Fessner
- Institut für Organische Chemie und BiochemieTechnische Universität Darmstadt 64287 Darmstadt Germany
| | - Loredano Pollegioni
- Department of Biotechnology and Life SciencesUniversità degli Studi dell'Insubria Varese Italy
| | - Franck Charmantray
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
| | - Laurence Hecquet
- Université Clermont AuvergneCNRSSIGMA Clermont, Institut de Chimie de Clermont-Ferrand (ICCF) F-63000 Clermont-Ferrand France
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9
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Takahashi S, Osugi K, Shimekake Y, Shinbo A, Abe K, Kera Y. Characterization and improvement of substrate-binding affinity of D-aspartate oxidase of the thermophilic fungus Thermomyces dupontii. Appl Microbiol Biotechnol 2019; 103:4053-4064. [PMID: 30937498 DOI: 10.1007/s00253-019-09787-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/05/2019] [Accepted: 03/19/2019] [Indexed: 12/23/2022]
Abstract
D-Aspartate oxidase (DDO) is a valuable enzyme that can be utilized in the determination of acidic D-amino acids and the optical resolution of a racemic mixture of acidic amino acids, which require its higher stability, higher catalytic activity, and higher substrate-binding affinity. In the present study, we identified DDO gene (TdDDO) of a thermophilic fungus, Thermomyces dupontii, and characterized the recombinant enzyme expressed in Escherichia coli. In addition, we generated a variant that has a higher substrate-binding affinity. The recombinant TdDDO expressed in E. coli exhibited oxidase activity toward acidic D-amino acids and a neutral D-amino acid, D-Gln, with the highest activity toward D-Glu. The Km and kcat values for D-Glu were 2.16 mM and 217 s-1, respectively. The enzyme had an optimum pH and temperature 8.0 and 60 °C, respectively, and was stable between pH 5.0 and 10.0, with a T50 of ca. 51 °C, which was much higher than that in DDOs from other origins. Enzyme stability decreased following a decrease in protein concentration, and externally added FAD could not repress the destabilization. The mutation of Phe248, potentially located in the active site of TdDDO, to Tyr residue, conserved in DDOs and D-amino acid oxidases, markedly increased substrate-binding affinity. The results showed the great potential of TdDDO and the variant for practical applications.
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Affiliation(s)
- Shouji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan.
| | - Kohei Osugi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Yuya Shimekake
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Akira Shinbo
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Katsumasa Abe
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Yoshio Kera
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
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10
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Properties of l-amino acid deaminase: En route to optimize bioconversion reactions. Biochimie 2019; 158:199-207. [DOI: 10.1016/j.biochi.2019.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/18/2019] [Indexed: 12/24/2022]
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11
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Ball J, Gannavaram S, Gadda G. Structural determinants for substrate specificity of flavoenzymes oxidizing d-amino acids. Arch Biochem Biophys 2018; 660:87-96. [PMID: 30312594 DOI: 10.1016/j.abb.2018.10.002] [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: 08/28/2018] [Revised: 10/01/2018] [Accepted: 10/08/2018] [Indexed: 12/26/2022]
Abstract
The oxidation of d-amino acids is relevant to neurodegenerative diseases, detoxification, and nutrition in microorganisms and mammals. It is also important for the resolution of racemic amino acid mixtures and the preparation of chiral building blocks for the pharmaceutical and food industry. Considerable biochemical and structural knowledge has been accrued in recent years on the enzymes that carry out the oxidation of the Cα-N bond of d-amino acids. These enzymes contain FAD as a required coenzyme, share similar overall three-dimensional folds and highly conserved active sites, but differ in their specificity for substrates with neutral, anionic, or cationic side-chains. Here, we summarize the current biochemical and structural knowledge regarding substrate specificity on d-amino acid oxidase, d-aspartate oxidase, and d-arginine dehydrogenase for which a wealth of biochemical and structural studies is available.
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Affiliation(s)
- Jacob Ball
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Swathi Gannavaram
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Giovanni Gadda
- Departments of Chemistry, Georgia State University, Atlanta, GA, 30302-3965, USA; Departments of Biology, Georgia State University, Atlanta, GA, 30302-3965, USA; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30302-3965, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302-3965, USA.
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12
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Molla G. Competitive Inhibitors Unveil Structure/Function Relationships in Human D-Amino Acid Oxidase. Front Mol Biosci 2017; 4:80. [PMID: 29250527 PMCID: PMC5715370 DOI: 10.3389/fmolb.2017.00080] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/13/2017] [Indexed: 02/02/2023] Open
Abstract
D-amino acid oxidase (DAAO) catalyzes the oxidative deamination of several neutral D-amino acids and is the enzyme mainly responsible (together with serine racemase) for degrading D-serine (D-Ser) in the central nervous system of mammals. This D-amino acid, which binds the coagonist site of the N-methyl-D-aspartate receptor, is thus a key neuromodulator of glutamatergic neurotransmission. Altered D-Ser metabolism results in several pathological conditions (e.g., amylotrophic lateral sclerosis or schizophrenia, SZ) for which effective "broad spectrum" pharmaceutical drugs are not yet available. In particular, the correlation between reduced D-Ser concentration and SZ led to a renaissance of biochemical interest in human DAAO (hDAAO). In the last 10 years, public and corporate research laboratories undertook huge efforts to study the structural, enzymatic, and physiological properties of the human flavoenzyme and to identify novel effective inhibitors which, acting as pharmaceutical drugs, could decrease hDAAO activity, thus restoring the physiological concentration of D-Ser. Although, none of the identified hDAAO inhibitors has reached the market yet, from a biochemical point of view, these compounds turned out to be invaluable for gaining a detailed understanding of the structure/function relationships at the molecular level in the mammalian DAAO, in particular of the interaction between ligand and the enzyme. This detailed knowledge, together with several recent studies concerning the interaction of the human enzyme with other protein regulative partners, its subcellular localization, and in vivo degradation, contributed to gaining comprehensive knowledge of the structure, function, and physiopathological role of this important human enzyme.
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Affiliation(s)
- Gianluca Molla
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,The Protein Factory Research Center, Politecnico of Milano and University of Insubria, Milan, Italy
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13
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Rosini E, Allegretti C, Melis R, Cerioli L, Conti G, Pollegioni L, D'Arrigo P. Cascade enzymatic cleavage of the β-O-4 linkage in a lignin model compound. Catal Sci Technol 2016. [DOI: 10.1039/c5cy01591j] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The optimized Lig enzymatic system reached the full bioconversion of a racemic mixture of GGE, a lignin model compound.
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Affiliation(s)
- Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
- The Protein Factory
| | - Chiara Allegretti
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Roberta Melis
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Lorenzo Cerioli
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Gianluca Conti
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
- The Protein Factory
| | - Paola D'Arrigo
- The Protein Factory
- Politecnico di Milano and Università degli Studi dell'Insubria
- 20131 Milano
- Italy
- Dipartimento di Chimica
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14
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Cappelletti P, Piubelli L, Murtas G, Caldinelli L, Valentino M, Molla G, Pollegioni L, Sacchi S. Structure-function relationships in human d-amino acid oxidase variants corresponding to known SNPs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1150-9. [PMID: 25701391 DOI: 10.1016/j.bbapap.2015.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/05/2015] [Accepted: 02/07/2015] [Indexed: 12/11/2022]
Abstract
In the brain, d-amino acid oxidase plays a key role in modulating the N-methyl-d-aspartate receptor (NMDAR) activation state, catalyzing the stereospecific degradation of the coagonist d-serine. A relationship between d-serine signaling deregulation, NMDAR dysfunction, and CNS diseases is presumed. Notably, the R199W substitution in human DAAO (hDAAO) was associated with familial amyotrophic lateral sclerosis (ALS), and further coding substitutions, i.e., R199Q and W209R, were also deposited in the single nucleotide polymorphism database. Here, we investigated the biochemical properties of these different hDAAO variants. The W209R hDAAO variant shows an improved d-serine degradation ability (higher activity and affinity for the cofactor FAD) and produces a greater decrease in cellular d/(d+l) serine ratio than the wild-type counterpart when expressed in U87 cells. The production of H2O2 as result of excessive d-serine degradation by this hDAAO variant may represent the factor affecting cell viability after stable transfection. The R199W/Q substitution in hDAAO altered the protein conformation and enzymatic activity was lost under conditions resembling the cellular ones: this resulted in an abnormal increase in cellular d-serine levels. Altogether, these results indicate that substitutions that affect hDAAO functionality directly impact on d-serine cellular levels (at least in the model cell system used). The pathological effect of the expression of the R199W hDAAO, as observed in familial ALS, originates from both protein instability and a decrease in kinetic efficiency: the increase in synaptic d-serine may be mainly responsible for the neurotoxic effect. This information is expected to drive future targeted treatments.
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Affiliation(s)
- Pamela Cappelletti
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Luciano Piubelli
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Giulia Murtas
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Laura Caldinelli
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Mattia Valentino
- The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy; CNR, Istituto di Chimica del Riconoscimento Molecolare, Sezione Adolfo Quilico, via M. Bianchi 9, 20131 Milano, Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Silvia Sacchi
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy.
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15
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Takahashi S, Furukawara M, Omae K, Tadokoro N, Saito Y, Abe K, Kera Y. A Highly Stable D-Amino Acid Oxidase of the Thermophilic Bacterium Rubrobacter xylanophilus. Appl Environ Microbiol 2014; 80:7219-29. [PMID: 25217016 PMCID: PMC4249180 DOI: 10.1128/aem.02193-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/09/2014] [Indexed: 01/31/2023] Open
Abstract
d-Amino acid oxidase (DAO) is a biotechnologically attractive enzyme that can be used in a variety of applications, but its utility is limited by its relatively poor stability. A search of a bacterial genome database revealed a gene encoding a protein homologous to DAO in the thermophilic bacterium Rubrobacter xylanophilus (RxDAO). The recombinant protein expressed in Escherichia coli was a monomeric protein containing noncovalently bound flavin adenine dinucleotide as a cofactor. This protein exhibited oxidase activity against neutral and basic d-amino acids and was significantly inhibited by a DAO inhibitor, benzoate, but not by any of the tested d-aspartate oxidase (DDO) inhibitors, thus indicating that the protein is DAO. RxDAO exhibited higher activities and affinities toward branched-chain d-amino acids, with the highest specific activity toward d-valine and catalytic efficiency (kcat/Km) toward d-leucine. Substrate inhibition was observed in the case of d-tyrosine. The enzyme had an optimum pH range and temperature of pH 7.5 to 10 and 65°C, respectively, and was stable between pH 5.0 and pH 8.0, with a T50 (the temperature at which 50% of the initial enzymatic activity is lost) of 64°C. No loss of enzyme activity was observed after a 1-week incubation period at 30°C. This enzyme was markedly inactivated by phenylmethylsulfonyl fluoride but not by thiol-modifying reagents and diethyl pyrocarbonate, which are known to inhibit certain DAOs. These results demonstrated that RxDAO is a highly stable DAO and suggested that this enzyme may be valuable for practical applications, such as the determination and quantification of branched-chain d-amino acids, and as a scaffold to generate a novel DAO via protein engineering.
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Affiliation(s)
- Shouji Takahashi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Makoto Furukawara
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Keishi Omae
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Namiho Tadokoro
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yayoi Saito
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Katsumasa Abe
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yoshio Kera
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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16
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D’Arrigo P, Allegretti C, Tamborini S, Formantici C, Galante Y, Pollegioni L, Mele A. Single-batch, homogeneous phase depolymerization of cellulose catalyzed by a monocomponent endocellulase in ionic liquid [BMIM][Cl]. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.04.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Kopf J, Hormigo D, García JL, Acebal C, de la Mata I, Arroyo M. Inhibition of Recombinant D-Amino Acid Oxidase from Trigonopsis variabilisby Salts. Enzyme Res 2011; 2011:158541. [PMID: 21423676 PMCID: PMC3057018 DOI: 10.4061/2011/158541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 01/01/2011] [Indexed: 11/20/2022] Open
Abstract
Inhibition of recombinant D-amino acid oxidase fromTrigonopsis variabilis(TvDAAO) activity in the presence of different sodium salts and potassium chloride is reported. A competitive inhibition pattern by sodium chloride was observed, and an inhibition constant value ofKi=85 mM was calculated. Direct connection of NaCl inhibition with FAD cofactor dissociation was confirmed by measuring the fluorescence of tryptophanyl residues of the holoenzyme.
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Affiliation(s)
- Jessica Kopf
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain
| | - Daniel Hormigo
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain
| | - José Luis García
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carmen Acebal
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain
| | - Isabel de la Mata
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain
| | - Miguel Arroyo
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain
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18
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Zhukovsky MA, Basmaciogullari S, Pacheco B, Wang L, Madani N, Haim H, Sodroski J. Thermal stability of the human immunodeficiency virus type 1 (HIV-1) receptors, CD4 and CXCR4, reconstituted in proteoliposomes. PLoS One 2010; 5:e13249. [PMID: 20967243 PMCID: PMC2954141 DOI: 10.1371/journal.pone.0013249] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 09/13/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The entry of human immunodeficiency virus (HIV-1) into host cells involves the interaction of the viral exterior envelope glycoprotein, gp120, and receptors on the target cell. The HIV-1 receptors are CD4 and one of two chemokine receptors, CCR5 or CXCR4. METHODOLOGY/PRINCIPAL FINDINGS We created proteoliposomes that contain CD4, the primary HIV-1 receptor, and one of the coreceptors, CXCR4. Antibodies against CD4 and CXCR4 specifically bound the proteoliposomes. CXCL12, the natural ligand for CXCR4, and the small-molecule CXCR4 antagonist, AMD3100, bound the proteoliposomes with affinities close to those associated with the binding of these molecules to cells expressing CXCR4 and CD4. The HIV-1 gp120 exterior envelope glycoprotein bound tightly to proteoliposomes expressing only CD4 and, in the presence of soluble CD4, bound weakly to proteoliposomes expressing only CXCR4. The thermal stability of CD4 and CXCR4 inserted into liposomes was examined. Thermal denaturation of CXCR4 followed second-order kinetics, with an activation energy (E(a)) of 269 kJ/mol (64.3 kcal/mol) and an inactivation temperature (T(i)) of 56°C. Thermal inactivation of CD4 exhibited a reaction order of 1.3, an E(a) of 278 kJ/mol (66.5 kcal/mol), and a T(i) of 52.2°C. The second-order denaturation kinetics of CXCR4 is unusual among G protein-coupled receptors, and may result from dimeric interactions between CXCR4 molecules. CONCLUSIONS/SIGNIFICANCE Our studies with proteoliposomes containing the native HIV-1 receptors allowed an examination of the binding of biologically important ligands and revealed the higher-order denaturation kinetics of these receptors. CD4/CXCR4-proteoliposomes may be useful for the study of virus-target cell interactions and for the identification of inhibitors.
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Affiliation(s)
- Mikhail A. Zhukovsky
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Pathology, Division of AIDS, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Structural Dynamics of (Bio)chemical Systems, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stéphane Basmaciogullari
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Pathology, Division of AIDS, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Beatriz Pacheco
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Pathology, Division of AIDS, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Liping Wang
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Pathology, Division of AIDS, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Navid Madani
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Pathology, Division of AIDS, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hillel Haim
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Pathology, Division of AIDS, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joseph Sodroski
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Pathology, Division of AIDS, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
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19
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The role of residues Arg169 and Arg220 in intersubunit interactions of yeast D-amino acid oxidase. Russ Chem Bull 2010. [DOI: 10.1007/s11172-010-0072-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Caldinelli L, Molla G, Sacchi S, Pilone MS, Pollegioni L. Relevance of weak flavin binding in human D-amino acid oxidase. Protein Sci 2009; 18:801-10. [PMID: 19309736 DOI: 10.1002/pro.86] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In the brain, the human flavoprotein D-amino acid oxidase (hDAAO) is involved in the degradation of the gliotransmitter D-serine, an important modulator of NMDA-receptor-mediated neurotransmission; an increase in hDAAO activity (that yields a decrease in D-serine concentration) was recently proposed to be among the molecular mechanisms leading to the onset of schizophrenia susceptibility. This human flavoenzyme is a stable homodimer (even in the apoprotein form) that distinguishes from known D-amino acid oxidases because it shows the weakest interaction with the flavin cofactor in the free form. Instead, cofactor binding is significantly tighter in the presence of an active site ligand. In order to understand how hDAAO activity is modulated, we investigated the FAD binding process to the apoprotein moiety and compared the folding and stability properties of the holoenzyme and the apoprotein forms. The apoprotein of hDAAO can be distinguished from the holoenzyme form by the more "open" tertiary structure, higher protein fluorescence, larger exposure of hydrophobic surfaces, and higher sensitivity to proteolysis. Interestingly, the FAD binding only slightly increases the stability of hDAAO to denaturation by urea or temperature. Taken together, these results indicate that the weak cofactor binding is not related to protein (de)stabilization or oligomerization (as instead observed for the homologous enzyme from yeast) but rather should represent a means of modulating the activity of hDAAO. We propose that the absence in vivo of an active site ligand/substrate weakens the cofactor binding, yielding the inactive apoprotein form and thus avoiding excessive D-serine degradation.
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Affiliation(s)
- Laura Caldinelli
- Department of Biotechnology and Molecular Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
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21
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Analysis of oligomeric proteins during unfolding by pH and temperature. J Mol Model 2009; 15:1013-25. [PMID: 19205760 DOI: 10.1007/s00894-008-0365-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022]
Abstract
During thermal transition and variation of pH, structural properties of 35 proteins and their complexes (bound with substrate and co-factor) were analyzed in detail. During pH alteration, these proteins were shown to have substantial differences in conformations. pH conformers were analyzed in detail. Free energy and other energy parameters were also estimated for these proteins at various pH and temperatures. Detailed structural analysis and binding interfaces of various substrates, inhibitors and cofactor of these proteins were also investigated using docking and molecular dynamic simulation.
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22
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Mora MF, Giacomelli CE, Garcia CD. Interaction of D-amino acid oxidase with carbon nanotubes: implications in the design of biosensors. Anal Chem 2009; 81:1016-22. [PMID: 19132842 PMCID: PMC2646172 DOI: 10.1021/ac802068n] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have investigated the interaction of d-amino acid oxidase (DAAO) with single-walled carbon nanotubes (CNT) by spectroscopic ellipsometry. Dynamic adsorption experiments were performed at different experimental conditions. In addition, the activity of the enzyme adsorbed at different conditions was studied. Our results indicate that DAAO can be adsorbed to CNT at different pH values and concentrations by a combination of hydrophobic and electrostatic interactions. Considering that the highest enzymatic activity was obtained by adsorbing the protein at pH 5.7 and 0.1 mg x mL(-1), our results indicate that DAAO can adopt multiple orientations on the surface, which are ultimately responsible for significant differences in catalytic activity.
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Affiliation(s)
- Maria F. Mora
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249, USA
| | | | - Carlos D. Garcia
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249, USA
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23
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Crystal structure of chlorite dismutase, a detoxifying enzyme producing molecular oxygen. J Mol Biol 2009; 387:192-206. [PMID: 19361444 DOI: 10.1016/j.jmb.2009.01.036] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 01/16/2009] [Accepted: 01/20/2009] [Indexed: 11/22/2022]
Abstract
Chlorite dismutase (Cld) is a key enzyme of perchlorate and chlorate respiration. This heme-based protein reduces the toxic compound chlorite into the innocuous chloride anion in a very efficient way while producing molecular oxygen. A sequence comparison between Cld homologues shows a highly conserved family. The crystal structure of Azospira oryzae strain GR-1 Cld is reported to 2.1 A resolution. The structure reveals a hexameric organization of the Cld, while each monomer exhibits a ferredoxin-like fold. The six subunits are organized in a ring structure with a maximal diameter of 9 nm and an inner diameter of 2 nm. The heme active-site pocket is solvent accessible both from the inside and the outside of the ring. Moreover, a second anion binding site that could accommodate the assumed reaction intermediate ClO(-) for further transformation has been identified near the active site. The environment of the heme cofactor was investigated with electron paramagnetic resonance spectroscopy. Apart from the high-spin ferric signal of the five-coordinate resting-state enzyme, two low-spin signals were found corresponding to six-coordinate species. The current crystal structure confirms and complements a recently proposed catalytic mechanism that proceeds via a ferryl species and a ClO(-) anion. Our structural data exclude cooperativity between the iron centers.
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24
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Properties and applications of microbial D-amino acid oxidases: current state and perspectives. Appl Microbiol Biotechnol 2008; 78:1-16. [DOI: 10.1007/s00253-007-1282-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 11/09/2007] [Accepted: 11/09/2007] [Indexed: 10/22/2022]
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25
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Caldinelli L, Iametti S, Barbiroli A, Fessas D, Bonomi F, Piubelli L, Molla G, Pollegioni L. Relevance of the flavin binding to the stability and folding of engineered cholesterol oxidase containing noncovalently bound FAD. Protein Sci 2008; 17:409-19. [PMID: 18218720 DOI: 10.1110/ps.073137708] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The flavoprotein cholesterol oxidase (CO) from Brevibacterium sterolicum is a monomeric flavoenzyme containing one molecule of FAD cofactor covalently linked to His69. The elimination of the covalent link following the His69Ala substitution was demonstrated to result in a significant decrease in activity, in the midpoint redox potential of the flavin, and in stability with respect to the wild-type enzyme, but does not modify the overall structure of the enzyme. We used CO as a model system to dissect the changes due to the elimination of the covalent link between the flavin and the protein (by comparing the wild-type and H69A CO holoproteins) with those due to the elimination of the cofactor (by comparing the holo- and apoprotein forms of H69A CO). The apoprotein of H69A CO lacks the characteristic tertiary structure of the holoprotein and displays larger hydrophobic surfaces; its urea-induced unfolding does not occur by a simple two-state mechanism and is largely nonreversible. Minor alterations in the flavin binding region are evident between the native and the refolded proteins, and are likely responsible for the low refolding yield observed. A model for the equilibrium unfolding of H69A CO that also takes into consideration the effects of cofactor binding and dissociation, and thus may be of general significance in terms of the relationships between cofactor uptake and folding in flavoproteins, is presented.
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Affiliation(s)
- Laura Caldinelli
- Department of Biotechnology and Molecular Sciences, University of Insubria, 21100 Varese, Italy
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26
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Fessas D, Staiano M, Barbiroli A, Marabotti A, Schiraldi A, Varriale A, Rossi M, D'Auria S. Molecular adaptation strategies to high temperature and thermal denaturation mechanism of the D-trehalose/D-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis. Proteins 2007; 67:1002-9. [PMID: 17373708 DOI: 10.1002/prot.21383] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The D-trehalose/D-maltose-binding protein (TMBP), a monomeric protein of 48 kDa, is one component of the trehalose and maltose uptake system. In the hyperthermophilic archaeon T. litoralis this is mediated by a protein-dependent ATP-binding cassette system transporter. The gene coding for a thermostable TMBP from the archaeon T. litoralis has been cloned, and the recombinant protein has been expressed in E. coli. The recombinant TMBP has been purified to homogeneity and characterized. It exhibits the same functional and structural properties as the native one. In fact, it is highly thermostable and binds both trehalose and maltose with high affinity. In this work we used differential scanning calorimetry studies together with a detailed analysis, at the molecular level, of the three-dimensional protein structure to shed light on the basis of the high thermostability exhibited by the recombinant TMBP from the archaeon T. litoralis. The obtained data suggest that the presence of trehalose does not change the overall mechanism of the denaturation of this protein but it selectively modifies the stability of the TMBP structural domains.
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Affiliation(s)
- Dimitrios Fessas
- Department of Food Science, Technology and Microbiology, University of Milan, Milan, Italy
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27
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Arroyo M, Menéndez M, García JL, Campillo N, Hormigo D, de la Mata I, Castillón MP, Acebal C. The role of cofactor binding in tryptophan accessibility and conformational stability of His-tagged d-amino acid oxidase from Trigonopsis variabilis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:556-65. [PMID: 17466607 DOI: 10.1016/j.bbapap.2007.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 03/07/2007] [Accepted: 03/07/2007] [Indexed: 11/30/2022]
Abstract
d-amino acid oxidase from Trigonopsis variabilis (TvDAAO) is a flavoenzyme with high biotechnological and industrial interest. The overexpression and purification of the apoprotein form of a recombinant His-tagged TvDAAO allowed us to go deep into the structural differences between apoenzyme and holoenzyme, and on the cofactor binding and its contribution to enzyme stability. A significant decrease in intrinsic fluorescence emission took place upon FAD binding, associated to cofactor induced conformational transitions or subunit dimerization that could affect the local environment of protein tryptophan residues. Furthermore, acrylamide-quenching experiments indicated that one of the five tryptophan residues of TvDAAO became less accessible upon FAD binding. A K(d)=1.5+/-0.1x10(-7) M for the dissociation of FAD from TvDAAO was calculated from binding experiments based on both quenching of FAD fluorescence and activity titration curves. Secondary structure prediction indicated that TvDAAO is a mixed alpha/beta protein with 8 alpha-helices and 14 beta-sheets connected by loops. Prediction results were in good agreement with the estimates obtained by circular dichroism which indicated that both the apoenzyme and the holoenzyme had the same structural component ratios: 34% alpha-helix content, 20% beta-structure content (14% antiparallel and 6% parallel beta-sheet), 15% beta-turns and 31% of random structure. Circular dichroism thermal-transition curves suggested single-step denaturation processes with apparent midpoint transition temperatures (T(m)) of 37.9 degrees C and 41.4 degrees C for the apoenzyme and the holoenzyme, respectively. A three-dimensional model of TvDAAO built by homology modelling and consistent with the spectroscopic studies is shown. Comparing our results with those reported for pig kidney (pkDAAO) and Rhodotorula gracilis (RgDAAO) d-amino acid oxidases, a "head-to-head" interaction between subunits in the TvDAAO dimer might be expected.
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Affiliation(s)
- Miguel Arroyo
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain.
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28
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Rasmussen P, Barbiroli A, Bonomi F, Faoro F, Ferranti P, Iriti M, Picariello G, Iametti S. Formation of structured polymers upon controlled denaturation of β-lactoglobulin with different chaotropes. Biopolymers 2007; 86:57-72. [PMID: 17315200 DOI: 10.1002/bip.20704] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Prolonged exposure (>90 days) of bovine beta-lactoglobulin (BLG) to subdenaturing concentrations of either urea or potassium thiocyanate resulted in the formation of ordered polymers in the form of fibrils. The fibrils obtained with each chaotrope showed major differences in morphology, surface properties, thiol accessibility, and stability to dissociating agents as a consequence of the different chemical bonds involved in their stabilization. Hydrophobic interactions between BLG monomers are predominant in thiocyanate-formed fibrils, whereas urea-formed fibrils are stabilized by intermolecular disulfides generated through a thiol-disulfide exchange reaction. The different features of fibrils obtained with each chaotrope relate to the peculiar structural features and chemical properties of the "active" monomers generated by subdenaturing chaotrope concentrations in the early phases of the polymerization process, as detected by spectroscopic and limited proteolysis/mass spectrometry studies in the earliest stages of the action of individual chaotropes. The chaotrope-specific features of these early intermediates in turn affect the polymerization mechanism, whose intermediates were studied by size-exclusion chromatography on the soluble fraction at different times of fibril formation. The potential of these findings for the production of protein-derived nanostructures having different and controlled geometries and chemical properties is also discussed.
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Affiliation(s)
- P Rasmussen
- Section of Biochemistry, Dipartimento di Scienze Molecolari Agroalimentari, University of Milan, Milan 20133, Italy
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29
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Caldinelli L, Molla G, Pilone MS, Pollegioni L. Tryptophan 243 affects interprotein contacts, cofactor binding and stability in D-amino acid oxidase from Rhodotorula gracilis. FEBS J 2006; 273:504-12. [PMID: 16420474 DOI: 10.1111/j.1742-4658.2005.05083.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The flavoenzyme d-amino acid oxidase from Rhodotorula gracilis is a homodimeric protein whose dimeric state has been proposed to occur as a result of (a) the electrostatic interactions between positively charged residues of the betaF5-betaF6 loop of one monomer and negatively charged residues belonging to the alpha-helices I3' and I3'' of the other monomer, and (b) the interaction of residues (e.g. Trp243) belonging to the two monomers at the mixed interface region. The role of Trp243 was investigated by substituting it with either tyrosine or isoleucine: both substitutions were nondisruptive, as confirmed by the absence of significant changes in catalytic activity, but altered the tertiary structure (yielding a looser conformation) and decreased the stability towards temperature and denaturants. The change in conformation interferes both with the interaction of the coenzyme to the apoprotein moiety (although the kinetics of the apoprotein-FAD complex reconstitution process are similar between wild-type and mutant D-amino acid oxidases) and with the interaction between monomers. Our results indicate that, in the folded holoenzyme, Trp243 is situated at a position optimal for increasing the interactions between monomers by maximizing van der Waals interactions and by efficiently excluding solvent.
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Affiliation(s)
- Laura Caldinelli
- Department of Biotechnology and Molecular Sciences, University of Insubria, Varese, Italy
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Caldinelli L, Iametti S, Barbiroli A, Bonomi F, Fessas D, Molla G, Pilone MS, Pollegioni L. Dissecting the structural determinants of the stability of cholesterol oxidase containing covalently bound flavin. J Biol Chem 2005; 280:22572-81. [PMID: 15817448 DOI: 10.1074/jbc.m500549200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cholesterol oxidase from Brevibacterium sterolicum is a monomeric flavoenzyme catalyzing the oxidation and isomerization of cholesterol to cholest-4-en-3-one. This protein is a class II cholesterol oxidases, with the FAD cofactor covalently linked to the enzyme through the His(69) residue. In this work, unfolding of wild-type cholesterol oxidase was compared with that of a H69A mutant, which does not covalently bind the flavin cofactor. The two protein forms do not show significant differences in their overall topology, but the urea-induced unfolding of the H69A mutant occurred at significant lower urea concentrations than wild-type (approximately 3 versus approximately 5 M, respectively), and the mutant protein had a melting temperature approximately 10-15 degrees C lower than wild-type in thermal denaturation experiments. The different sensitivity of the various spectroscopic features used to monitor protein unfolding indicated that in both proteins a two-step (three-state) process occurs. The presence of an intermediate was more evident for the H69A mutant at 2 m urea, where catalytic activity and tertiary structure were lost, and new hydrophobic patches were exposed on the protein surface, resulting in protein aggregation. Comparative analysis of the changes occurring upon urea and thermal treatment of the wild-type and H69A protein showed a good correlation between protein instability and the elimination of the covalent link between the flavin and the protein. This covalent bond represents a structural device to modify the flavin redox potentials and stabilize the tertiary structure of cholesterol oxidase, thus pointing to a specific meaning of the flavin binding mode in enzymes that carry out the same reaction in pathogenic versus non-pathogenic bacteria.
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Affiliation(s)
- Laura Caldinelli
- Department of Biotechnology and Molecular Sciences, University of Insubria, Varese, Italy
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D-amino acid oxidase: structure, catalytic mechanism, and practical application. BIOCHEMISTRY (MOSCOW) 2005. [DOI: 10.1007/pl00021754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Tishkov VI, Khoronenkova SV. D-amino acid oxidase: structure, catalytic mechanism, and practical application. BIOCHEMISTRY (MOSCOW) 2005. [DOI: 10.1007/s10541-005-0004-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Tishkov VI, Khoronenkova SV. D-amino acid oxidase: structure, catalytic mechanism, and practical application. BIOCHEMISTRY (MOSCOW) 2005. [DOI: 10.1007/s10541-005-0050-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Pollegioni L, Caldinelli L, Molla G, Sacchi S, Pilone MS. Catalytic properties of D-amino acid oxidase in cephalosporin C bioconversion: a comparison between proteins from different sources. Biotechnol Prog 2004; 20:467-73. [PMID: 15058991 DOI: 10.1021/bp034206q] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lacking an efficient process to produce 7-aminocephalosporanic acid from cephalosporin C in a single step, d-amino acid oxidase (DAAO) is of foremost importance in the industrial, two-step process used for this purpose. We report a detailed study on the catalytic properties of the three available DAAOs, namely, a mammalian DAAO and two others from yeast (Rhodotorula gracilis and Trigonopsis variabilis). In comparing the kinetic parameters determined for the three DAAOs, with both cephalosporin C and d-alanine as substrate, the catalytic efficiency of the two enzymes from microorganism is at least 2 orders of magnitude higher than that of pig kidney DAAO. Furthermore, the mammalian enzyme is more sensitive to product inhibition (from hydrogen peroxide and glutaryl-7-aminocephalosporanic acid). Therefore, enzymes from microorganisms appear to be by far more suitable catalysts for bioconversion, although some different minor differences are present between them (e.g., a higher activity of the R. gracilis enzyme when the bioconversion is carried out at saturating oxygen concentration). The mammalian DAAO, even being a poor catalyst, is more stable with respect to temperature than the R. gracilis enzyme in the free form. In any case, for industrial purposes DAAO is used only in the immobilized form where a strong enzyme stabilization occurs.
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Affiliation(s)
- Loredano Pollegioni
- Department of Structural and Functional Biology, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
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Wu X, Van Wie BJ, Kidwell DA. An enzyme electrode for amperometric measurement of d-amino acid. Biosens Bioelectron 2004; 20:879-86. [PMID: 15522605 DOI: 10.1016/j.bios.2004.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2004] [Revised: 03/17/2004] [Accepted: 04/01/2004] [Indexed: 11/25/2022]
Abstract
A carbon paste enzyme electrode has been developed for measurement of D-amino acids that employs a fatty acid modified FAD to prevent leaching of this essential cofactor to the surrounding aqueous environment and which serves as an enzyme stabilizing agent. The lower limit of detection is at least 10(-4) M and the electrode has a linear range of 10(-4) to 3 x 10(-3) M and a response time of 180 s. Twenty L-amino acids were tested and none of them elicited responses when electrodes were exposed to 0.5 mM concentration increases over a baseline level. On the other hand, some response was observed when exposed to 18 of 20 D-amino acids varying from 2 to 200% of the corresponding D-alanine response. Electrodes were shown to have longevities of over 30 days while maintaining 85% of their original sensitivity. Electrodes showed activity over a pH of 6.2-11.7 with a maximum at 9.2 and over temperatures of 10-47 degrees C with a maximum at 37 degrees C.
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Affiliation(s)
- Xiaoxi Wu
- School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164-2710, USA.
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Caldinelli L, Iametti S, Barbiroli A, Bonomi F, Piubelli L, Ferranti P, Picariello G, Pilone MS, Pollegioni L. Unfolding intermediate in the peroxisomal flavoprotein D-amino acid oxidase. J Biol Chem 2004; 279:28426-34. [PMID: 15102841 DOI: 10.1074/jbc.m403489200] [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: 11/06/2022] Open
Abstract
The flavoenzyme d-amino acid oxidase (DAAO) from Rhodotorula gracilis is a peroxisomal enzyme and a prototypical member of the glutathione reductase family of flavoproteins. DAAO is a stable homodimer with a FAD molecule tightly bound to each 40-kDa subunit. In this work, the urea-induced unfolding of dimeric DAAO was compared with that of a monomeric form of the same protein, a deleted dimerization loop mutant. By using circular dichroism spectroscopy, protein and flavin fluorescence, 1,8-anilinonaphtalene sulfonic acid binding and activity assays, we demonstrated that the urea-induced unfolding of DAAO is a three-state process, yielding an intermediate, and that this process is reversible. The intermediate species lacks the catalytic activity and the characteristic tertiary structure of native DAAO but has significant secondary structure and retains flavin binding. Unfolding of DAAO proceeds through formation of an expanded, partially unfolded inactive intermediate, characterized by low solubility, by increased exposure of hydrophobic surfaces, and by increased sensitivity to trypsin of the beta-strand F5 belonging to the FAD binding domain. The oligomeric state does not modify the inferred folding process. The strand F5 is in contact with the C-terminal alpha-helix containing the Ser-Lys-Leu sequence corresponding to the type 1 peroxisomal targeting signal, and this structural element interacts with the N-terminal betaalphabeta flavin binding motif (Rossmann fold). The expanded conformation of the folding intermediate (and in particular the higher disorder of the mentioned secondary structure elements) could match the structure of the inactive holoenzyme required for in vivo trafficking of DAAO through the peroxisomal membrane.
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Affiliation(s)
- Laura Caldinelli
- Department of Structural and Functional Biology, University of Insubria, via J. H. Dunant 3, Varese 21100, Italy
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Abstract
Flavoproteins are ubiquitous redox proteins that are involved in many biological processes. In the majority of flavoproteins, the flavin cofactor is tightly but noncovalently bound. Reversible dissociation of flavoproteins into apoprotein and flavin prosthetic group yields valuable insights in flavoprotein folding, function and mechanism. Replacement of the natural cofactor with artificial flavins has proved to be especially useful for the determination of the solvent accessibility, polarity, reaction stereochemistry and dynamic behaviour of flavoprotein active sites. In this review we summarize the advances made in the field of flavoprotein deflavination and reconstitution. Several sophisticated chromatographic procedures to either deflavinate or reconstitute the flavoprotein on a large scale are discussed. In a subset of flavoproteins, the flavin cofactor is covalently attached to the polypeptide chain. Studies from riboflavin-deficient expression systems and site-directed mutagenesis suggest that the flavinylation reaction is a post-translational, rather than a cotranslational, process. These genetic approaches have also provided insight into the mechanism of covalent flavinylation and the rationale for this atypical protein modification.
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Affiliation(s)
- Marco H Hefti
- Laboratory of Biochemistry, Wageningen University, The Netherlands
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