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Kortheerakul C, Kageyama H, Waditee-Sirisattha R. Molecular and functional insights into glutathione S-transferase genes associated with salt stress in Halothece sp. PCC7418. PLANT, CELL & ENVIRONMENT 2021; 44:3583-3596. [PMID: 34347891 DOI: 10.1111/pce.14161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Evolution and function of glutathione S-transferase (GST) in primordial oxygenic phototrophs such as cyanobacteria are poorly understood. In this study, we identified and functionally characterized the GST gene family in the halotolerant cyanobacterium Halothece sp. PCC7418. Four putative Halothece-GSTs had very low homology, which implies evolutionary divergence. Of these, H0647, H0729 and H3557 were differentially expressed by oxidative stress whereas H3557 was highly and specifically upregulated under salt stress. In vitro analysis revealed that the recombinant H3557 exhibited GST activity toward 1-chloro-2, 4-dinitrobenzene (CDNB) and glutathione (GSH). H3557 displayed a broad range of activity at pH 6.5-10.5. Kinetic parameters showed the apparent Km for CDNB and GSH was 0.14 and 0.75 mM, respectively. H3557 remained catalytically active in the presence of NaCl. Structural modelling supported that H3557 is salt-adaptive enzyme with highly acidic residues on the protein surface. The vital function of H3557 in heterologous expression system was evaluated. The H3557-expressing cells were more tolerant to H2 O2 -induced oxidative stress compared with other GST-expressing cells and conferred salt tolerance. Taken together, the findings of this study provide insights into the molecular and cellular functions of GST in cyanobacteria, particularly under salt stress, which is less understood compared with other species.
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Affiliation(s)
- Chananwat Kortheerakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- The Chemical Approaches for Food Applications Research Group, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Hakuto Kageyama
- Department of Chemistry, Faculty of Science and Technology, Meijo University, Nagoya, Japan
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Japan
| | - Rungaroon Waditee-Sirisattha
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- The Chemical Approaches for Food Applications Research Group, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Papageorgiou L, Papakonstantinou E, Salis C, Polychronidou E, Hagidimitriou M, Maroulis D, Eliopoulos E, Vlachakis D. Drugena: A Fully Automated Immunoinformatics Platform for the Design of Antibody-Drug Conjugates Against Neurodegenerative Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1194:203-215. [PMID: 32468536 DOI: 10.1007/978-3-030-32622-7_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antibodies are proteins that are the first line of defense in the adaptive immune response of vertebrates. Thereby, they are involved in a multitude of biochemical mechanisms and clinical manifestations with significant medical interest, such as autoimmunity, the regulation of infection, and cancer. An emerging field in antibody science that is of huge medicinal interest is the development of novel antibody-interacting drugs. Such entities are the antibody-drug conjugates (ADCs), which are a new type of targeted therapy, which consist of an antibody linked to a payload drug. Overall, the underlying principle of ADCs is the discerning delivery of a drug to a target, hoping to increase the potency of the original drug. Drugena suite is a pioneering platform that employs state-of-the-art computational biology methods in the fight against neurodegenerative diseases using ADCs. Drugena encompasses an up-to-date structural database of specialized antibodies for neurological disorders and the NCI database with over 96 million entities for the in silico development of ADCs. The pipeline of the Drugena suite has been divided into several steps and modules that are closely related with a synergistic fashion under a user-friendly graphical user interface.
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Affiliation(s)
- Louis Papageorgiou
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece.,Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens, Greece.,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Constantinos Salis
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | | | - Marianna Hagidimitriou
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitris Maroulis
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens, Greece
| | - Elias Eliopoulos
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Vlachakis
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece. .,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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3
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Raftopoulou S, Nicolaides NC, Papageorgiou L, Amfilochiou A, Zakinthinos SG, George P, Eliopoulos E, Chrousos GP, Vlachakis D. Structural Study of the DNA: Clock/Bmal1 Complex Provides Insights for the Role of Cortisol, hGR, and HPA Axis in Stress Management and Sleep Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1195:59-71. [PMID: 32468460 DOI: 10.1007/978-3-030-32633-3_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Herein, we deploy an in silico pipeline of structural bioinformatics, thermodynamics, and molecular dynamics to investigate the role of cortisol in circadian rhythms, biorhythms, stress response, and even sleep disorders. Our study shows that high concentrations of cortisol intercalate in the minor groove of DNA. This phenomenon widens the adjacent major grooves and provides the Clock/Bmal1 complex with more space to dock and interact with DNA. Then, the strong charges of cortisol pull the alpha helices of the Clock/Bmal1 complex and bend it inward, thus establishing stronger interactions and prolonged signaling. Our results indicate that elevated cortisol levels play an important role in stress, inflammation, and sleep disorders as a result of prolonged and stronger dsDNA - Clock/Bmal1 interactions.
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Affiliation(s)
- Sofia Raftopoulou
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece.,Affidea Healthcare Company, Athens, Greece
| | - Nicolas C Nicolaides
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Louis Papageorgiou
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece.,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Anastasia Amfilochiou
- Sismanoglio General Hospital of Attica, Respiratory Function & Sleep Study Unit, Marousi, Greece
| | - Spyros G Zakinthinos
- Critical Care and Pulmonary Services, Evangelismos Hospital, Medical School of Athens University, Athens, Greece
| | | | - Elias Eliopoulos
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - George P Chrousos
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Dimitrios Vlachakis
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece. .,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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Papageorgiou L, Maroulis D, Chrousos GP, Eliopoulos E, Vlachakis D. Antibody Clustering Using a Machine Learning Pipeline that Fuses Genetic, Structural, and Physicochemical Properties. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1194:41-58. [PMID: 32468522 DOI: 10.1007/978-3-030-32622-7_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibody V domain clustering is of paramount importance to a repertoire of immunology-related areas. Although several approaches have been proposed for antibody clustering, still no consensus has been reached. Numerous attempts use information from genes, protein sequences, 3D structures, and 3D surfaces in an effort to elucidate unknown action mechanisms directly related to their function and to either link them directly to diseases or drive the discovery of new medicines, such as antibody drug conjugates (ADC). Herein, we describe a new V domain antibody clustering method based on the comparison of the interaction sites between each antibody and its antigen. A more specific clustering analysis of the antibody's V domain was provided using deep learning and data mining techniques. The multidimensional information was extracted from the structural resolved antibodies when they were captured to interact with other proteins. The available 3D structures of protein antigen-antibody (Ag-Ab) interfaces contain information about how antibody V domains recognize antigens as well as about which amino acids are involved in the recognition. As such, the antibody surface holds information about antigens' folding that reside with the Ab-Ag interface residues and how they interact. In order to gain insight into the nature of such interactions, we propose a new simple philosophy to transform the conserved framework (fragment regions, complementarity-determining regions) of antibody V domain in a binary form using structural features of antibody-antigen interactions, toward identifying new antibody signatures in V domain binding activity. Finally, an advanced three-level hybrid classification scheme has been set for clustering antibodies in subgroups, which can combine the information from the protein sequences, the three-dimensional structures, and specific "key patterns" of recognized interactions. The clusters provide multilevel information about antibodies and antibody-antigen complexes.
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Affiliation(s)
- Louis Papageorgiou
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens, Greece.,Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitris Maroulis
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens, Greece
| | - George P Chrousos
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece.,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Elias Eliopoulos
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Vlachakis
- Genetics and Computational Biology Group, Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece. .,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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Olive Oil Polyphenols in Neurodegenerative Pathologies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1195:77-91. [PMID: 32468462 DOI: 10.1007/978-3-030-32633-3_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Neurodegenerative diseases lead to the death of nerve cells in the brain or the spinal cord. A wide range of diseases are included within the group of neurodegenerative disorders, with the most common ones being dementia, Alzheimer's, and Parkinson's diseases. Millions of older people are suffering from such pathologies. The global increase of life expectancy unavoidably leads to a consequent increase in the number of people who will be at some degree affected by neurodegenerative-related diseases. At this moment, there is no effective therapy or treatment that can reverse the loss of neurons. A growing number of studies highlight the value of the consumption of medical foods, and in particular olive oil, as one of the most important components of the Mediterranean diet. A diet based on extra virgin olive oil seems to contribute toward the lowering of risk of age-related pathologies due to high phenol concentration. The link of a polyphenol found in extra virgin olive oil, namely, tyrosol, with the protein tyrosinase, associated to Parkinson's disease is underlined as a paradigm of affiliation between polyphenols and neurodegenerative disorders.
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