1
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Lacombe J, Ferron M. Vitamin K-dependent carboxylation in β-cells and diabetes. Trends Endocrinol Metab 2024; 35:661-673. [PMID: 38429160 DOI: 10.1016/j.tem.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 03/03/2024]
Abstract
Vitamin K is an essential micronutrient and a cofactor for the enzyme γ-glutamyl carboxylase, which adds a carboxyl group to specific glutamic acid residues in proteins transiting through the secretory pathway. Higher vitamin K intake has been linked to a reduced incidence of type 2 diabetes (T2D) in humans. Preclinical work suggests that this effect depends on the γ-carboxylation of specific proteins in β-cells, including endoplasmic reticulum Gla protein (ERGP), implicated in the control of intracellular Ca2+ levels. In this review we discuss these recent advances linking vitamin K and glucose metabolism, and argue that identification of γ-carboxylated proteins in β-cells is pivotal to better understand how vitamin K protects from T2D and to design targeted therapies for this disease.
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Affiliation(s)
- Julie Lacombe
- Molecular Physiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7, Canada.
| | - Mathieu Ferron
- Molecular Physiology Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7, Canada; Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, H3T 1J4, Canada; Département de Médecine, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
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2
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Diachenko AI, Rodin IA, Krasnova TN, Klychnikov OI, Nefedova LN. The Role of Vitamin K in the Development of Neurodegenerative Diseases. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S57-S70. [PMID: 38621744 DOI: 10.1134/s0006297924140049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 04/17/2024]
Abstract
Neurodegenerative diseases are a growing global health problem with enormous consequences for individuals and society. The most common neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases, can be caused by both genetic factors (mutations) and epigenetic changes caused by the environment, in particular, oxidative stress. One of the factors contributing to the development of oxidative stress that has an important effect on the nervous system is vitamin K, which is involved in redox processes. However, its role in cells is ambiguous: accumulation of high concentrations of vitamin K increases the content of reactive oxygen species increases, while small amounts of vitamin K have a protective effect and activate the antioxidant defense systems. The main function of vitamin K is its involvement in the gamma carboxylation of the so-called Gla proteins. Some Gla proteins are expressed in the nervous system and participate in its development. Vitamin K deficiency can lead to a decrease or loss of function of Gla proteins in the nervous system. It is assumed that the level of vitamin K in the body is associated with specific changes involved in the development of dementia and cognitive abilities. Vitamin K also influences the sphingolipid profile in the brain, which also affects cognitive function. The role of vitamin K in the regulation of biochemical processes at the cellular and whole-organism levels has been studied insufficiently. Further research can lead to the discovery of new targets for vitamin K and development of personalized diets and therapies.
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Affiliation(s)
- Anna I Diachenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Igor A Rodin
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Tatiana N Krasnova
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Oleg I Klychnikov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Lidia N Nefedova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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3
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Singh DK, Basit A, Rettie AE, Alade N, Thummel K, Prasad B. Characterization of Gla proteoforms and non-Gla peptides of gamma carboxylated proteins: Application to quantification of prothrombin proteoforms in human plasma. Anal Chim Acta 2023; 1284:341972. [PMID: 37996163 PMCID: PMC10789187 DOI: 10.1016/j.aca.2023.341972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Gamma (γ) carboxylation is an essential post-translational modification in vitamin K-dependent proteins (VKDPs), involved in maintaining critical biological homeostasis. Alterations in the abundance or activity of these proteins have pharmacological and pathological consequences. Importantly, low levels of fully γ-carboxylated clotting factors increase plasma des-γ-carboxy precursors resulting in little or no biological activity. Therefore, it is important to characterize the levels of γ-carboxylation that reflect the active state of these proteins. The conventional enzyme-linked immunosorbent assay for protein induced by vitamin K absence or antagonist II (PIVKA-II) quantification uses an antibody that is not applicable to distinguish different γ-carboxylation states. Liquid chromatography-mass spectrometry (LC-MS) approaches have been utilized to distinguish different γ-carboxylated proteoforms, however, these attempts were impeded by poor sensitivity due to spontaneous neutral loss of CO2 and simultaneous cleavage of the backbone bond in the collision cell. In this study, we utilized an alkaline mobile phase in combination with polarity switching (positive and negative ionization modes) to simultaneously identify and quantify γ-carboxylated VKDPs. The method was applied to compare Gla proteomics of prothrombin (FII) in 10 μL plasma samples of healthy control and warfarin-treated adults. We also identified surrogate non-Gla peptides for seven other VKDPs to quantify total (active plus inactive) protein levels. The total protein approach (TPA) was used to quantify absolute levels of the VKDPs in human plasma.
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Affiliation(s)
- Dilip Kumar Singh
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Abdul Basit
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Nathan Alade
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Kenneth Thummel
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA.
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4
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Coates RJ, Young MT, Scofield S. Optimising expression and extraction of recombinant proteins in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1074531. [PMID: 36570881 PMCID: PMC9773421 DOI: 10.3389/fpls.2022.1074531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Recombinant proteins are of paramount importance for research, industrial and medical use. Numerous expression chassis are available for recombinant protein production, and while bacterial and mammalian cell cultures are the most widely used, recent developments have positioned transgenic plant chassis as viable and often preferential options. Plant chassis are easily maintained at low cost, are hugely scalable, and capable of producing large quantities of protein bearing complex post-translational modification. Several protein targets, including antibodies and vaccines against human disease, have been successfully produced in plants, highlighting the significant potential of plant chassis. The aim of this review is to act as a guide to producing recombinant protein in plants, discussing recent progress in the field and summarising the factors that must be considered when utilising plants as recombinant protein expression systems, with a focus on optimising recombinant protein expression at the genetic level, and the subsequent extraction and purification of target proteins, which can lead to substantial improvements in protein stability, yield and purity.
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Affiliation(s)
| | | | - Simon Scofield
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
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5
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Kemp JA, Alvarenga L, Cardozo LFMF, Dai L, Stenvinkel P, Shiels PG, Hackeng TM, Schurgers LJ, Mafra D. Dysbiosis in Patients with Chronic Kidney Disease: Let Us Talk About Vitamin K. Curr Nutr Rep 2022; 11:765-779. [PMID: 36138326 DOI: 10.1007/s13668-022-00438-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW This narrative review aimed to summarize the current evidence on the connection between dysbiosis and vitamin K deficiency in patients with chronic kidney disease (CKD). The presence of dysbiosis (perturbations in the composition of the microbiota) has been described in several non-communicable diseases, including chronic kidney disease, and it has been hypothesized that dysbiosis may cause vitamin K deficiency. Patients with CKD present both vitamin K deficiency and gut dysbiosis; however, the relationship between gut dysbiosis and vitamin K deficiency remains to be addressed. RECENT FINDINGS Recently, few studies in animals have demonstrated that a dysbiotic environment is associated with low production of vitamin K by the gut microbiota. Vitamin K plays a vital role in blood coagulation as well as in the cardiovascular and bone systems. It serves as a cofactor for γ-glutamyl carboxylases and thus is essential for the post-translational modification and activation of vitamin K-dependent calcification regulators, such as osteocalcin, matrix Gla protein, Gla-rich protein, and proteins C and S. Additionally, vitamin K executes essential antioxidant and anti-inflammatory functions. Dietary intake is the main source of vitamin K; however, it also can be produced by gut microbiota. This review discusses the effects of uremia on the imbalance in gut microbiota, vitamin K-producing bacteria, and vitamin K deficiency in CKD patients, leading to a better understanding and raising hypothesis for future clinical studies.
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Affiliation(s)
- Julie Ann Kemp
- Graduate Program in Cardiovascular Sciences, Fluminense Federal University (UFF), Niterói, Brazil
| | - Livia Alvarenga
- Graduate Program in Medical Sciences, Fluminense Federal University (UFF), Niterói, Brazil
| | - Ludmila F M F Cardozo
- Graduate Program in Cardiovascular Sciences, Fluminense Federal University (UFF), Niterói, Brazil
| | - Lu Dai
- Division of Renal Medicine and Baxter Novum, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, Stockholm, Sweden
| | - Peter Stenvinkel
- Division of Renal Medicine and Baxter Novum, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, Stockholm, Sweden
| | - Paul G Shiels
- Wolfson Wohl Translational Research Centre, University of Glasgow, Glasgow, UK
| | - Tilman M Hackeng
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Leon J Schurgers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Denise Mafra
- Graduate Program in Medical Sciences, Fluminense Federal University (UFF), Niterói, Brazil.
- Graduate Program in Biological Sciences, Physiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- Unidade de Pesquisa Clínica, Rua Marquês Do Paraná, Niterói, RJ, 30324033-900, Brazil.
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6
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Jimenez EC. Post-translationally modified conopeptides: Biological activities and pharmacological applications. Peptides 2021; 139:170525. [PMID: 33684482 DOI: 10.1016/j.peptides.2021.170525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 10/25/2022]
Abstract
Conus venoms comprise a large variety of biologically active peptides (conopeptides or conotoxins) that are employed for prey capture and other biological functions. Throughout the course of evolution of the cone snails, they have developed an envenomation scheme that necessitates a potent mixture of peptides, most of which are highly post-translationally modified, that can cause rapid paralysis of their prey. The great diversity of these peptides defines the ecological interactions and evolutionary strategy of cone snails. Such scheme has led to some pharmacological applications for pain, epilepsy, and myocardial infarction, that could be further explored to ultimately find unique peptide-based therapies. This review focuses on ∼ 60 representative post-translationally modified conopeptides that were isolated from Conus venoms. Various conopeptides reveal post-translational modifications of specific amino acids, such as hydroxylation of proline and lysine, gamma-carboxylation of glutamate, formation of N-terminal pyroglutamate, isomerization of l- to d-amino acid, bromination of tryptophan, O-glycosylation of threonine or serine, sulfation of tyrosine, and cysteinylation of cysteine, other than the more common disulfide crosslinking and C-terminal amidation. Many of the post-translationally modified peptides paved the way for the characterization, by alternative analytical methods, of other pharmacologically important peptides that are classified under 27 conopeptide families denoting pharmacological classes.
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Affiliation(s)
- Elsie C Jimenez
- Department of Physical Sciences, College of Science, University of the Philippines Baguio, Baguio City, 2600, Philippines.
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7
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Beato S, Toledo-Solís FJ, Fernández I. Vitamin K in Vertebrates' Reproduction: Further Puzzling Pieces of Evidence from Teleost Fish Species. Biomolecules 2020; 10:E1303. [PMID: 32917043 PMCID: PMC7564532 DOI: 10.3390/biom10091303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Vitamin K (VK) is a fat-soluble vitamin that vertebrates have to acquire from the diet, since they are not able to de novo synthesize it. VK has been historically known to be required for the control of blood coagulation, and more recently, bone development and homeostasis. Our understanding of the VK metabolism and the VK-related molecular pathways has been also increased, and the two main VK-related pathways-the pregnane X receptor (PXR) transactivation and the co-factor role on the γ-glutamyl carboxylation of the VK dependent proteins-have been thoroughly investigated during the last decades. Although several studies evidenced how VK may have a broader VK biological function than previously thought, including the reproduction, little is known about the specific molecular pathways. In vertebrates, sex differentiation and gametogenesis are tightly regulated processes through a highly complex molecular, cellular and tissue crosstalk. Here, VK metabolism and related pathways, as well as how gametogenesis might be impacted by VK nutritional status, will be reviewed. Critical knowledge gaps and future perspectives on how the different VK-related pathways come into play on vertebrate's reproduction will be identified and proposed. The present review will pave the research progress to warrant a successful reproductive status through VK nutritional interventions as well as towards the establishment of reliable biomarkers for determining proper nutritional VK status in vertebrates.
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Affiliation(s)
- Silvia Beato
- Campus de Vegazana, s/n, Universidad de León (ULE), 24071 León, Spain;
| | - Francisco Javier Toledo-Solís
- Consejo Nacional de Ciencia y Tecnología (CONACYT, México), Av. Insurgentes Sur 1582, Col. Crédito Constructor, Alcaldía Benito Juárez, C.P. 03940 Ciudad de Mexico, Mexico;
- Department of Biology and Geology, University of Almería, 04120 Almería, Spain
| | - Ignacio Fernández
- Center for Aquaculture Research, Agrarian Technological Institute of Castile and Leon, Ctra. Arévalo, s/n, 40196 Zamarramala, Segovia, Spain
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8
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Hassan MO, Gassim DA, Albakrye AM, Elnasri HA, Khaier MA. In silico analysis of likely pathogenic variants in human GGCX gene. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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9
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Amann T, Schmieder V, Faustrup Kildegaard H, Borth N, Andersen MR. Genetic engineering approaches to improve posttranslational modification of biopharmaceuticals in different production platforms. Biotechnol Bioeng 2019; 116:2778-2796. [PMID: 31237682 DOI: 10.1002/bit.27101] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/27/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022]
Abstract
The number of approved biopharmaceuticals, where product quality attributes remain of major importance, is increasing steadily. Within the available variety of expression hosts, the production of biopharmaceuticals faces diverse limitations with respect to posttranslational modifications (PTM), while different biopharmaceuticals demand different forms and specifications of PTMs for proper functionality. With the growing toolbox of genetic engineering technologies, it is now possible to address general as well as host- or biopharmaceutical-specific product quality obstacles. In this review, we present diverse expression systems derived from mammalians, bacteria, yeast, plants, and insects as well as available genetic engineering tools. We focus on genes for knockout/knockdown and overexpression for meaningful approaches to improve biopharmaceutical PTMs and discuss their applicability as well as future trends in the field.
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Affiliation(s)
- Thomas Amann
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valerie Schmieder
- acib GmbH-Austrian Centre of Industrial Biotechnology, Graz, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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10
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Luo S, Dong SH. Recent Advances in the Discovery and Biosynthetic Study of Eukaryotic RiPP Natural Products. Molecules 2019; 24:molecules24081541. [PMID: 31003555 PMCID: PMC6514808 DOI: 10.3390/molecules24081541] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/22/2022] Open
Abstract
Natural products have played indispensable roles in drug development and biomedical research. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a group of fast-expanding natural products attribute to genome mining efforts in recent years. Most RiPP natural products were discovered from bacteria, yet many eukaryotic cyclic peptides turned out to be of RiPP origin. This review article presents recent advances in the discovery of eukaryotic RiPP natural products, the elucidation of their biosynthetic pathways, and the molecular basis for their biosynthetic enzyme catalysis.
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Affiliation(s)
- Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
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11
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Bahrami S, Ghaffari M, Zomorodipour A. Production of recombinant human factor IX by propeptide modification in Drosophila S2 cell line. Biotechnol Lett 2019; 41:347-355. [PMID: 30673933 DOI: 10.1007/s10529-019-02643-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/01/2019] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To compare the effect of pre-propeptide (pre-pro) of the human prothrombin (hPT), with both the native and an R-9N mutant forms of the human factor IX (hFIX) pre-pro on the hFIX carboxylation, in Drosophila cell. RESULTS The three different pre-pro sequences, equipped with Drosophila Kozak, were joined to the mature hFIX cDNA and were subjected to transient expression analysis of hFIX in the S2 Drosophila cells, compared to that of a native hFIX cDNA, with its native Kozak. Replacement of the hFIX pre-pro sequence with that of hPT increased the biological activity of hFIX, significantly. The highest total level of hFIX expression occurred for the native hFIX with the Drosophila Kozak. However, the hFIX secretion efficiency with this construct was less than that of the native hFIX with its native Kozak. The R-9N substitution, in the hFIX propeptide, with no apparent effect on the FIX γ-carboxylation, reduced the FIX expression efficiency. CONCLUSION Potential of the hPT pre-pro sequence for FIX expression in Drosophila cells, was confronted by γ-glutamyl carboxylase (GGCX) saturation in ER, besides the functional importance of -9 amino acid in propeptide is described; these are noteworthy for production of γ-carboxylated proteins.
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Affiliation(s)
- Samira Bahrami
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, P.O. Box: 14965/161, Tehran, Iran
- Department of Biochemistry, Institute of Biochemistry and Biophysics, Tehran University, Tehran, Iran
- Biotechnology Department, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahmoud Ghaffari
- Department of Biochemistry, Institute of Biochemistry and Biophysics, Tehran University, Tehran, Iran
| | - Alireza Zomorodipour
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, P.O. Box: 14965/161, Tehran, Iran.
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Reshetnyak VI, Zhuravel SV, Kuznetsova NK, Pisarev VМ, Klychnikova EV, Syutkin VЕ, Reshetnyak ТM. The System of Blood Coagulation in Normal and in Liver Transplantation (Review). GENERAL REANIMATOLOGY 2018. [DOI: 10.15360/1813-9779-2018-5-58-84] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The review dwells on the problem of hemostatic disorders in patients undergoing liver transplantation and their correction in the perioperative period. The physiology of the hemostatic system, disorders of the blood coagulation system in patients at various stages of liver transplantation, correction of hemostatic disorders during and after orthotopic liver transplantation are discussed. Liver transplantation is performed in patients with liver diseases in the terminal stage of liver failure. At the same time, changes in the hemostatic system of these patients pose a significant risk of developing bleeding and/or thrombosis during and after liver transplantation. The hypothesis is suggested that the personalized correction of hemostasis disorder in liver transplantation should be based on considerating the nosological forms of the liver damage, mechanisms of development of recipient’s hemostatic disorders, and the stage of the surgery.
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Affiliation(s)
- V. I. Reshetnyak
- V. A. Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology
| | - S. V. Zhuravel
- N.V. Sklifosovsky Research Institute of Emergency Care, Moscow Healthcare Department
| | - N. K. Kuznetsova
- N.V. Sklifosovsky Research Institute of Emergency Care, Moscow Healthcare Department
| | - V. М. Pisarev
- V. A. Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology
| | - E. V. Klychnikova
- N.V. Sklifosovsky Research Institute of Emergency Care, Moscow Healthcare Department
| | - V. Е. Syutkin
- N.V. Sklifosovsky Research Institute of Emergency Care, Moscow Healthcare Department
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13
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Möller C, Dovell S, Melaun C, Marí F. Definition of the R-superfamily of conotoxins: Structural convergence of helix-loop-helix peptidic scaffolds. Peptides 2018; 107:75-82. [PMID: 30040981 DOI: 10.1016/j.peptides.2018.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/13/2018] [Accepted: 06/18/2018] [Indexed: 10/28/2022]
Abstract
The F14 conotoxins define a four-cysteine, three-loop conotoxin scaffold that produce tightly folded structures held together by two disulfide bonds with a CCCC arrangement (conotoxin framework 14). Here we describe the precursors of the F14 conotoxins from the venom of Conus anabathrum and Conus villepinii. Using transcriptomic and cDNA cloning analysis, the full-length of the precursors of flf14a and flf14b from the transcriptome of C. anabathrum revealed a unique signal sequence that defines the new conotoxin R-superfamily. Using the signal sequence as a primer, we cloned seven additional previously undescribed toxins of the R-superfamily from C. villepinii. The propeptide regions of the R-conotoxins are unusually long and with prevalent proline residues in repeating pentads which qualifies them as Pro-rich motifs (PRMs), which can be critical for protein-protein interactions or they can be cleaved to release short linear peptides that may be part of the envenomation mélange. Additionally, we determined the three-dimensional structure of vil14a by solution 1H-NMR and found that the structure of this conotoxin displays a cysteine-stabilized α-helix-loop-helix (Cs α/α) fold. The structure is well-defined over the helical regions (backbone RMSD for residues 2-13 and 17-26 is 0.63 ± 0.14 Å), with conformational flexibility in the triple Gly region of the second loop as well as the N- and C- termini. Structurally, the F14 conotoxins overlap with the Cs α/α scorpion toxins and other peptidic natural products, and in spite of their different exogenomic origins, there is convergence into this scaffold from several classes of living organisms that express these peptides.
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Affiliation(s)
- Carolina Möller
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991, USA
| | - Sanaz Dovell
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991, USA
| | - Christian Melaun
- Justus Liebig Universität Giessen, Institut für Allg. Zoologie und Entwicklungsbiologie, Giessen, Germany
| | - Frank Marí
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991, USA; Marine Biochemical Sciences, Chemical Sciences Division, National Institute of Standards and Technology, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, USA.
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14
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Montacir O, Montacir H, Eravci M, Springer A, Hinderlich S, Mahboudi F, Saadati A, Parr MK. Bioengineering of rFVIIa Biopharmaceutical and Structure Characterization for Biosimilarity Assessment. Bioengineering (Basel) 2018; 5:bioengineering5010007. [PMID: 29351237 PMCID: PMC5874873 DOI: 10.3390/bioengineering5010007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 01/04/2023] Open
Abstract
Eptacog alfa (NovoSeven®) is a vitamin K-dependent recombinant Factor VIIa produced by genetic engineering from baby hamster kidney (BHK) cells as a single peptide chain of 406 residues. After activation, it consists of a light chain (LC) of 152 amino and a heavy chain (HC) of 254 amino acids. Recombinant FVIIa undergoes many post-translational modifications (PTMs). The first ten glutamic acids of the N-terminal moiety are γ-carboxylated, Asn145 and Asn322 are N-glycosylated, and Ser52 and Ser60 are O-glycosylated. A head-to-head biosimilarity study was conducted for the originator and the first biosimilar AryoSeven™ to evaluate comparable bioengineering. Physicochemical properties were analyzed based on mass spectrometry, including intact mass, PTMs and higher-order structure. Both biotherapeutics exhibit a batch-to-batch variability in their N-glycan profiles. N-Glycopeptide analysis with UHPLC-QTOF-MSE confirmed N-glycosylation sites as well as two different O-glycopeptide sites. Ser60 was found to be O-fucosylated and Ser52 had O-glucose or O-glucose-(xylose)1,2 motifs as glycan variants. Ion mobility spectrometry (TWIMS) and NMR spectroscopy data affirm close similarity of the higher-order structure of both biologicals. Potency of the biodrugs was analyzed by a coagulation assay demonstrating comparable bioactivity. Consequently, careful process optimization led to a stable production process of the biopharmaceuticals.
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Affiliation(s)
- Othman Montacir
- Institute of Pharmacy, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
- Labor für Biochemie, Department of Life Sciences & Technology, Beuth Hochschule für Technik Berlin, Seestraße 64, 13347 Berlin, Germany.
| | - Houda Montacir
- Institute of Pharmacy, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
| | - Murat Eravci
- Institut für Chemie and Biochemie, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany.
| | - Andreas Springer
- Core Facility BioSupraMol, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany.
| | - Stephan Hinderlich
- Labor für Biochemie, Department of Life Sciences & Technology, Beuth Hochschule für Technik Berlin, Seestraße 64, 13347 Berlin, Germany.
| | - Fereidoun Mahboudi
- AryoGen Pharmed, No. 140, Cross Tajbakhsh Street, 24th Kilometer Makhsous Road, Tehran, Iran.
| | - Amirhossein Saadati
- Biopharmaceutical Research Center, AryoGen Pharmed Inc., Alborz University of Medical Sciences, Karaj, Iran.
| | - Maria Kristina Parr
- Institute of Pharmacy, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
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Structure and function of μ-conotoxins, peptide-based sodium channel blockers with analgesic activity. Future Med Chem 2015; 6:1677-98. [PMID: 25406007 DOI: 10.4155/fmc.14.107] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
μ-Conotoxins block voltage-gated sodium channels (VGSCs) and compete with tetrodotoxin for binding to the sodium conductance pore. Early efforts identified µ-conotoxins that preferentially blocked the skeletal muscle subtype (NaV1.4). However, the last decade witnessed a significant increase in the number of µ-conotoxins and the range of VGSC subtypes inhibited (NaV1.2, NaV1.3 or NaV1.7). Twenty µ-conotoxin sequences have been identified to date and structure-activity relationship studies of several of these identified key residues responsible for interactions with VGSC subtypes. Efforts to engineer-in subtype specificity are driven by in vivo analgesic and neuromuscular blocking activities. This review summarizes structural and pharmacological studies of µ-conotoxins, which show promise for development of selective blockers of NaV1.2, and perhaps also NaV1.1,1.3 or 1.7.
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Incorporation of post-translational modified amino acids as an approach to increase both chemical and biological diversity of conotoxins and conopeptides. Amino Acids 2013; 46:125-51. [DOI: 10.1007/s00726-013-1606-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 10/17/2013] [Indexed: 02/06/2023]
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Fedosov AÉ, Moshkovskiĭ SA, Kuznetsova KG, Olivera BM. [Conotoxins: from the biodiversity of gastropods to new drugs]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2013; 59:267-94. [PMID: 23987066 DOI: 10.18097/pbmc20135903267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A review describes general trends in research of conotoxins that are peptide toxins isolated from sea gastropods of the Conus genus, since the toxins were discovered in 1970th. There are disclosed a conotoxin classification, their structure diversity and different ways of action to their molecular targets, mainly, ion channels. In the applied aspect of conotoxin research, drug discovery and development is discussed, the drugs being based on conotoxin structure. A first exemplary drug is a ziconotide, which is an analgesic of new generation.
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Ul-Hasan S, Burgess DM, Gajewiak J, Li Q, Hu H, Yandell M, Olivera BM, Bandyopadhyay PK. Characterization of the peptidylglycine α-amidating monooxygenase (PAM) from the venom ducts of neogastropods, Conus bullatus and Conus geographus. Toxicon 2013; 74:215-24. [PMID: 23994590 DOI: 10.1016/j.toxicon.2013.08.054] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/15/2013] [Accepted: 08/21/2013] [Indexed: 11/29/2022]
Abstract
Cone snails, genus Conus, are predatory marine snails that use venom to capture their prey. This venom contains a diverse array of peptide toxins, known as conotoxins, which undergo a diverse set of posttranslational modifications. Amidating enzymes modify peptides and proteins containing a C-terminal glycine residue, resulting in loss of the glycine residue and amidation of the preceding residue. A significant fraction of peptides present in the venom of cone snails contain C-terminal amidated residues, which are important for optimizing biological activity. This study describes the characterization of the amidating enzyme, peptidylglycine α-amidating monooxygenase (PAM), present in the venom duct of cone snails, Conus bullatus and Conus geographus. PAM is known to carry out two functions, peptidyl α-hydroxylating monooxygenase (PHM) and peptidylamido-glycolate lyase (PAL). In some animals, such as Drosophila melanogaster, these two functions are present in separate polypeptides, working as individual enzymes. In other animals, such as mammals and in Aplysia californica, PAM activity resides in a single, bifunctional polypeptide. Using specific oligonucleotide primers and reverse transcription-polymerase chain reaction we have identified and cloned from the venom duct cDNA library, a cDNA with 49% homology to PAM from A. californica. We have determined that both the PHM and PAL activities are encoded in one mRNA polynucleotide in both C. bullatus and C. geographus. We have directly demonstrated enzymatic activity catalyzing the conversion of dansyl-YVG-COOH to dansyl-YV-NH2 in cloned cDNA expressed in Drosophila S2 cells.
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Affiliation(s)
- Sabah Ul-Hasan
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
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19
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Lee JS, Tung CH. Osteotropic cancer diagnosis by an osteocalcin inspired molecular imaging mimetic. Biochim Biophys Acta Gen Subj 2013; 1830:4621-7. [PMID: 23688398 DOI: 10.1016/j.bbagen.2013.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 04/20/2013] [Accepted: 05/09/2013] [Indexed: 01/30/2023]
Abstract
BACKGROUND Although microcalcifications of hydroxyapatite can be found in both benign and malignant osteotropic tumors, they are mostly seen in proliferative lesions, including carcinoma. The aim of this present study is to develop a molecular imaging contrast agent for selective identification of hydroxyapatite calcification in human osteotropic tumor tissues ex vivo and in human osteosarcoma cells in vitro. METHODS A bioinspired biomarker, hydroxyapatite binding peptide (HABP), was designed to mimic natural protein osteocalcin property in vivo. A fluorescein isothiocyanate dye conjugated HABP (HABP-19) was utilized to characterize hydroxyapatite on human osteotropic tumor tissue sections ex vivo and to selectively image hydroxyapatite calcifications in human osteosarcoma cells in vitro. RESULTS Using a HABP-19 molecular imaging probe, we have shown that it is possible to selectively image hydroxyapatite calcifications in osteotropic cancers ex vivo and in human SaOS-2 osteosarcoma cells in vitro. CONCLUSION Hydroxyapatite calcifications were selectively detected in osteotropic tissues ex vivo and in the early stage of the calcification process of SaOS-2 human osteosarcoma in vitro using our HABP-19 molecular imaging probe. This new target-selective molecular imaging probe makes it possible to study the earliest events associated with hydroxyapatite deposition in various osteotropic cancers at the cellular and molecular levels. GENERAL SIGNIFICANCE It potentially could be used to diagnose and treat osteotropic cancer or to anchor therapeutic agents directing the local distribution of desired therapy at calcified sites.
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Affiliation(s)
- Jae Sam Lee
- Department of Translational Imaging, Weill Medical College of Cornell University, Houston, TX 77030, USA.
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Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013; 30:108-60. [PMID: 23165928 DOI: 10.1039/c2np20085f] [Citation(s) in RCA: 1466] [Impact Index Per Article: 133.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
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Affiliation(s)
- Paul G Arnison
- Prairie Plant Systems Inc, Botanical Alternatives Inc, Suite 176, 8B-3110 8th Street E, Saskatoon, SK, S7H 0W2, Canada
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21
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Zhang N, Li BQ, Gao S, Ruan JS, Cai YD. Computational prediction and analysis of protein γ-carboxylation sites based on a random forest method. MOLECULAR BIOSYSTEMS 2012; 8:2946-55. [PMID: 22918520 DOI: 10.1039/c2mb25185j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The glutamate γ-carboxylation plays a pivotal part in a number of important human diseases. However, traditional protein γ-carboxylation site detection by experimental approaches are often laborious and time-consuming. In this study, we initiated an attempt for the computational prediction of protein γ-carboxylation sites. We developed a new method for predicting the γ-carboxylation sites based on a Random Forest method. As a result, 90.44% accuracy and 0.7739 MCC value were obtained for the training dataset, and 89.83% accuracy and 0.7448 MCC value for the testing dataset. Our method considered several features including sequence conservation, residual disorder, secondary structures, solvent accessibility, physicochemical/biochemical properties and amino acid occurrence frequencies. By means of the feature selection algorithm, an optimal set of 327 features were selected; these features were considered as the ones that contributed significantly to the prediction of protein γ-carboxylation sites. Analysis of the optimal feature set indicated several important factors in determining the γ-carboxylation and a possible consensus sequence of the γ-carboxylation recognition site (γ-CRS) was suggested. These may shed some light on the in-depth understanding of the mechanisms of γ-carboxylation, providing guidelines for experimental validation.
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Affiliation(s)
- Ning Zhang
- Department of Biomedical Engineering Tianjin University, Tianjin Key Lab of BME Measurement, Tianjin, 300072, PR China
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22
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Rishavy MA, Berkner KL. Vitamin K oxygenation, glutamate carboxylation, and processivity: defining the three critical facets of catalysis by the vitamin K-dependent carboxylase. Adv Nutr 2012; 3:135-48. [PMID: 22516721 PMCID: PMC3648714 DOI: 10.3945/an.111.001719] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vitamin K-dependent carboxylase uses vitamin K oxygenation to drive carboxylation of multiple glutamates in vitamin K-dependent proteins, rendering them active in a variety of physiologies. Multiple carboxylations of proteins are required for their activity, and the carboxylase is processive, so that premature dissociation of proteins from the carboxylase does not occur. The carboxylase is unique, with no known homology to other enzyme families, and structural determinations have not been made, rendering an understanding of catalysis elusive. Although a model explaining the relationship of oxygenation to carboxylation had been developed, until recently almost nothing was known of the function of the carboxylase itself in catalysis. In the past decade, discovery and analysis of naturally occurring carboxylase mutants has led to identification of functionally relevant residues and domains. Further, identification of nonmammalian carboxylase orthologs has provided a basis for bioinformatic analysis to identify candidates for critical functional residues. Biochemical analysis of rationally chosen carboxylase mutants has led to breakthroughs in understanding vitamin K oxygenation, glutamate carboxylation, and maintenance of processivity by the carboxylase. Protein carboxylation has also been assessed in vivo, and the intracellular environment strongly affects carboxylase function. The carboxylase is an integral membrane protein, and topological analysis, coupled with biochemical determinations, suggests that interaction of the carboxylase with the membrane is an important facet of function. Carboxylase homologs, likely acquired by horizontal transfer, have been discovered in some bacteria, and functional analysis of these homologs has the potential to lead to the discovery of new roles of vitamin K in biology.
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Clark RJ, Akcan M, Kaas Q, Daly NL, Craik DJ. Cyclization of conotoxins to improve their biopharmaceutical properties. Toxicon 2012; 59:446-55. [DOI: 10.1016/j.toxicon.2010.12.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 12/01/2010] [Indexed: 10/18/2022]
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Dan H, Simsa-Maziel S, Reich A, Sela-Donenfeld D, Monsonego-Ornan E. The role of matrix gla protein in ossification and recovery of the avian growth plate. Front Endocrinol (Lausanne) 2012; 3:79. [PMID: 22787455 PMCID: PMC3392708 DOI: 10.3389/fendo.2012.00079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 05/31/2012] [Indexed: 11/13/2022] Open
Abstract
Extracellular matrix mineralization is an essential physiologic process in bone, teeth, and hypertrophic cartilage. Matrix Gla protein (MGP), an inhibitor of mineralization, is expressed by chondrocytes and vascular smooth muscle cells to inhibit calcification of those soft tissues. Tibial dyschondroplasia (TD), a skeletal abnormality apparent as a plug of non-vascularized, non-mineralized, white opaque cartilage in the tibial growth plate of avian species can serve as a good model for studying process and genes involved in matrix mineralization and calcification. In this work, we studied the involvement of MGP in the development of TD, as well as in the processes of spontaneous and induced recovery from this syndrome. First, we found that during normal bone development, MGP is expressed in specific time and locations, starting from wide-spread expression in the yet un-ossified diaphysis during embryonic development, to specific expression in hypertrophic chondrocytes adjacent to the chondro-osseous junction and the secondary ossification center just prior to calcification. In addition, we show that MGP is not expressed in the impaired TD lesion, however when the lesion begins to heal, it strongly express MGP prior to its calcification. Moreover, we show that when calcification is inhibited, a gap is formed between the expression zones of MGP and BMP2 and that this gap is closed during the healing process. To conclude, we suggest that MGP, directly or through interaction with BMP2, plays a role as ossification regulator that acts prior to ossification, rather then simple inhibitor.
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Affiliation(s)
- Harel Dan
- Institute of Biochemistry and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew UniversityRehovot, Israel
| | - Stav Simsa-Maziel
- Institute of Biochemistry and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew UniversityRehovot, Israel
| | - Adi Reich
- Institute of Biochemistry and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew UniversityRehovot, Israel
| | - Dalit Sela-Donenfeld
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew UniversityRehovot, Israel
| | - Efrat Monsonego-Ornan
- Institute of Biochemistry and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew UniversityRehovot, Israel
- *Correspondence: Efrat Monsonego-Ornan, Institute of Biochemistry and Nutrition, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University, P.O. Box 12, Rehovot 76100, Israel. e-mail:
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Lee TY, Lu CT, Chen SA, Bretaña NA, Cheng TH, Su MG, Huang KY. Investigation and identification of protein γ-glutamyl carboxylation sites. BMC Bioinformatics 2011; 12 Suppl 13:S10. [PMID: 22372765 PMCID: PMC3278826 DOI: 10.1186/1471-2105-12-s13-s10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Carboxylation is a modification of glutamate (Glu) residues which occurs post-translation that is catalyzed by γ-glutamyl carboxylase in the lumen of the endoplasmic reticulum. Vitamin K is a critical co-factor in the post-translational conversion of Glu residues to γ-carboxyglutamate (Gla) residues. It has been shown that the process of carboxylation is involved in the blood clotting cascade, bone growth, and extraosseous calcification. However, studies in this field have been limited by the difficulty of experimentally studying substrate site specificity in γ-glutamyl carboxylation. In silico investigations have the potential for characterizing carboxylated sites before experiments are carried out. RESULTS Because of the importance of γ-glutamyl carboxylation in biological mechanisms, this study investigates the substrate site specificity in carboxylation sites. It considers not only the composition of amino acids that surround carboxylation sites, but also the structural characteristics of these sites, including secondary structure and solvent-accessible surface area (ASA). The explored features are used to establish a predictive model for differentiating between carboxylation sites and non-carboxylation sites. A support vector machine (SVM) is employed to establish a predictive model with various features. A five-fold cross-validation evaluation reveals that the SVM model, trained with the combined features of positional weighted matrix (PWM), amino acid composition (AAC), and ASA, yields the highest accuracy (0.892). Furthermore, an independent testing set is constructed to evaluate whether the predictive model is over-fitted to the training set. CONCLUSIONS Independent testing data that did not undergo the cross-validation process shows that the proposed model can differentiate between carboxylation sites and non-carboxylation sites. This investigation is the first to study carboxylation sites and to develop a system for identifying them. The proposed method is a practical means of preliminary analysis and greatly diminishes the total number of potential carboxylation sites requiring further experimental confirmation.
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Affiliation(s)
- Tzong-Yi Lee
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li 320, Taiwan.
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26
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Lu CT, Chen SA, Bretaña NA, Cheng TH, Lee TY. Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites. J Comput Aided Mol Des 2011; 25:987-95. [PMID: 22038416 DOI: 10.1007/s10822-011-9477-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 09/29/2011] [Indexed: 02/07/2023]
Abstract
In proteins, glutamate (Glu) residues are transformed into γ-carboxyglutamate (Gla) residues in a process called carboxylation. The process of protein carboxylation catalyzed by γ-glutamyl carboxylase is deemed to be important due to its involvement in biological processes such as blood clotting cascade and bone growth. There is an increasing interest within the scientific community to identify protein carboxylation sites. However, experimental identification of carboxylation sites via mass spectrometry-based methods is observed to be expensive, time-consuming, and labor-intensive. Thus, we were motivated to design a computational method for identifying protein carboxylation sites. This work aims to investigate the protein carboxylation by considering the composition of amino acids that surround modification sites. With the implication of a modified residue prefers to be accessible on the surface of a protein, the solvent-accessible surface area (ASA) around carboxylation sites is also investigated. Radial basis function network is then employed to build a predictive model using various features for identifying carboxylation sites. Based on a five-fold cross-validation evaluation, a predictive model trained using the combined features of amino acid sequence (AA20D), amino acid composition, and ASA, yields the highest accuracy at 0.874. Furthermore, an independent test done involving data not included in the cross-validation process indicates that in silico identification is a feasible means of preliminary analysis. Additionally, the predictive method presented in this work is implemented as Carboxylator ( http://csb.cse.yzu.edu.tw/Carboxylator/ ), a web-based tool for identifying carboxylated proteins with modification sites in order to help users in investigating γ-glutamyl carboxylation.
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Affiliation(s)
- Cheng-Tsung Lu
- Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003 Taiwan, ROC.
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27
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Rishavy MA, Hallgren KW, Berkner KL. The vitamin K-dependent carboxylase generates γ-carboxylated glutamates by using CO2 to facilitate glutamate deprotonation in a concerted mechanism that drives catalysis. J Biol Chem 2011; 286:44821-32. [PMID: 21896484 DOI: 10.1074/jbc.m111.249177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The γ-glutamyl carboxylase converts Glu to carboxylated Glu (Gla) to activate a large number of vitamin K-dependent proteins with diverse functions, and this broad physiological impact makes it critical to understand the mechanism of carboxylation. Gla formation is thought to occur in two independent steps (i.e. Glu deprotonation to form a carbanion that then reacts with CO(2)), based on previous studies showing unresponsiveness of Glu deprotonation to CO(2). However, our recent studies on the kinetic properties of a variant enzyme (H160A) showing impaired Glu deprotonation prompted a reevaluation of this model. Glu deprotonation monitored by tritium release from the glutamyl γ-carbon was dependent upon CO(2), and a proportional increase in both tritium release and Gla formation occurred over a range of CO(2) concentrations. This discrepancy with the earlier studies using microsomes is probably due to the known accessibility of microsomal carboxylase to water, which reprotonates the carbanion. In contrast, tritium incorporation experiments with purified carboxylase showed very little carbanion reprotonation and consequently revealed the dependence of Glu deprotonation on CO(2). Cyanide stimulated Glu deprotonation and carbanion reprotonation to the same extent in wild type enzyme but not in the H160A variant. Glu deprotonation that depends upon CO(2) but that also occurs when water or cyanide are present strongly suggests a concerted mechanism facilitated by His-160 in which an electrophile accepts the negative charge on the developing carbanion. This revised mechanism provides important insight into how the carboxylase catalyzes the reaction by avoiding the formation of a high energy discrete carbanion.
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Affiliation(s)
- Mark A Rishavy
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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Safavi-Hemami H, Siero WA, Gorasia DG, Young ND, Macmillan D, Williamson NA, Purcell AW. Specialisation of the venom gland proteome in predatory cone snails reveals functional diversification of the conotoxin biosynthetic pathway. J Proteome Res 2011; 10:3904-19. [PMID: 21707029 DOI: 10.1021/pr1012976] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Conotoxins, venom peptides from marine cone snails, diversify rapidly as speciation occurs. It has been suggested that each species can synthesize between 1000 and 1900 different toxins with little to no interspecies overlap. Conotoxins exhibit an unprecedented degree of post-translational modifications, the most common one being the formation of disulfide bonds. Despite the great diversity of structurally complex peptides, little is known about the glandular proteins responsible for their biosynthesis and maturation. Here, proteomic interrogations on the Conus venom gland led to the identification of novel glandular proteins of potential importance for toxin synthesis and secretion. A total of 161 and 157 proteins and protein isoforms were identified in the venom glands of Conus novaehollandiae and Conus victoriae, respectively. Interspecies differences in the venom gland proteomes were apparent. A large proportion of the proteins identified function in protein/peptide translation, folding, and protection events. Most intriguingly, however, we demonstrate the presence of a multitude of isoforms of protein disulfide isomerase (PDI), the enzyme catalyzing the formation and isomerization of the native disulfide bond. Investigating whether different PDI isoforms interact with distinct toxin families will greatly advance our knowledge on the generation of cone snail toxins and disulfide-rich peptides in general.
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Affiliation(s)
- Helena Safavi-Hemami
- Department of Biochemistry and Molecular Biology, University of Melbourne, Victoria, Australia.
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29
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Lee JS, Tung CH. Osteocalcin biomimic recognizes bone hydroxyapatite. Chembiochem 2011; 12:1669-73. [PMID: 21661088 DOI: 10.1002/cbic.201100162] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Indexed: 02/01/2023]
Affiliation(s)
- Jae Sam Lee
- Department of Radiology, The Methodist Hospital Research Institute, Weill Medical College of Cornell University, 6565 Fannin Street, Houston, TX 77030, USA
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Hu H, Bandyopadhyay PK, Olivera BM, Yandell M. Characterization of the Conus bullatus genome and its venom-duct transcriptome. BMC Genomics 2011; 12:60. [PMID: 21266071 PMCID: PMC3040727 DOI: 10.1186/1471-2164-12-60] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 01/25/2011] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The venomous marine gastropods, cone snails (genus Conus), inject prey with a lethal cocktail of conopeptides, small cysteine-rich peptides, each with a high affinity for its molecular target, generally an ion channel, receptor or transporter. Over the last decade, conopeptides have proven indispensable reagents for the study of vertebrate neurotransmission. Conus bullatus belongs to a clade of Conus species called Textilia, whose pharmacology is still poorly characterized. Thus the genomics analyses presented here provide the first step toward a better understanding the enigmatic Textilia clade. RESULTS We have carried out a sequencing survey of the Conus bullatus genome and venom-duct transcriptome. We find that conopeptides are highly expressed within the venom-duct, and describe an in silico pipeline for their discovery and characterization using RNA-seq data. We have also carried out low-coverage shotgun sequencing of the genome, and have used these data to determine its size, genome-wide base composition, simple repeat, and mobile element densities. CONCLUSIONS Our results provide the first global view of venom-duct transcription in any cone snail. A notable feature of Conus bullatus venoms is the breadth of A-superfamily peptides expressed in the venom duct, which are unprecedented in their structural diversity. We also find SNP rates within conopeptides are higher compared to the remainder of C. bullatus transcriptome, consistent with the hypothesis that conopeptides are under diversifying selection.
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Affiliation(s)
- Hao Hu
- Eccles institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, UT 84112, USA
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Abstract
Carbon dioxide (CO(2)) is a physiological gas found at low levels in the atmosphere and produced in cells during the process of aerobic respiration. Consequently, the levels of CO(2) within tissues are usually significantly higher than those found externally. Shifts in tissue levels of CO(2) (leading to either hypercapnia or hypocapnia) are associated with a number of pathophysiological conditions in humans and can occur naturally in niche habitats such as those of burrowing animals. Clinical studies have indicated that such altered CO(2) levels can impact upon disease progression. Recent advances in our understanding of the biology of CO(2) has shown that like other physiological gases such as molecular oxygen (O(2)) and nitric oxide (NO), CO(2) levels can be sensed by cells resulting in the initiation of physiological and pathophysiological responses. Acute CO(2) sensing in neurons and peripheral and central chemoreceptors is important in rapidly activated responses including olfactory signalling, taste sensation and cardiorespiratory control. Furthermore, a role for CO(2) in the regulation of gene transcription has recently been identified with exposure of cells and model organisms to high CO(2) leading to suppression of genes involved in the regulation of innate immunity and inflammation. This latter, transcriptional regulatory role for CO(2), has been largely attributed to altered activity of the NF-B family of transcription factors. Here, we review our evolving understanding of how CO(2) impacts upon gene transcription.
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Affiliation(s)
- Cormac T Taylor
- UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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Kraus NJ, Corneli PS, Watkins M, Bandyopadhyay PK, Seger J, Olivera BM. Against expectation: a short sequence with high signal elucidates cone snail phylogeny. Mol Phylogenet Evol 2010; 58:383-9. [PMID: 21147238 DOI: 10.1016/j.ympev.2010.11.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 10/11/2010] [Accepted: 11/23/2010] [Indexed: 11/30/2022]
Abstract
A short (259 nucleotide) conserved intronic sequence (CIS) is surprisingly informative for delineating deep phylogenetic relationships in cone snails. Conus species previously have been assigned to clades based on the evidence from mitochondrial 12S and 16S rRNA gene sequences (1129 bp). Despite their length, these genes lack the phylogenetic information necessary to resolve the relationships among the clades. Here we show that the relationships can be inferred from just 46 sites in the very short CIS sequence (a portion of "intron 9" of the γ-glutamyl carboxylase gene). This is counterintuitive because in short sequences sampling error (noise) often drowns out phylogenetic signal. The intron 9 CIS is rich in synapomorphies that define the divergence patterns among eight clades of worm- and fish-hunting Conus, and it contains almost no homoplasy. Parsimony, maximum likelihood and Bayesian analyses of the combined sequences (mt rRNA+CIS) confirm most of the relationships among 23 Conus sequences. This phylogeny implies that fish-hunting behavior evolved at least twice during the history of Conus-once among New World species and independently in the Indo-Pacific clades.
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Affiliation(s)
- Nicole J Kraus
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, United States
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Krossøy C, Lock EJ, Ørnsrud R. Vitamin K-dependent gamma-glutamylcarboxylase in Atlantic salmon (Salmo salar L.). FISH PHYSIOLOGY AND BIOCHEMISTRY 2010; 36:627-635. [PMID: 19685220 DOI: 10.1007/s10695-009-9335-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 05/12/2009] [Indexed: 05/28/2023]
Abstract
Due to problems with bone deformities in farmed Atlantic salmon, there is a growing interest in the possible involvement of vitamin K in normal bone development, and sensitive biomarkers for evaluating vitamin K status are therefore needed. The vitamin K-dependent (VKD) enzyme gamma-glutamylcarboxylase (GGCX, EC 6.4.x.x) requires vitamin K as a cofactor for its post-translational modification of glutamic acid (Glu) residues to gamma-carboxyglutamic acid (Gla) residues in VKD proteins, and is required for their function in haemostasis and bone metabolism. The present study was designed to evaluate the enzyme assay for GGCX activity in isolated liver microsomes and its distribution in the tissues of Atlantic salmon. The effect of KH(2) and menadione on the GGCX activity in salmon liver was also compared. Results from the present study show a widespread tissue distribution and expression of GGCX in Atlantic salmon. The GGCX activity and ggcx expression in all bony tissues examined imply the presence of vitamin K, and suggest the involvement of vitamin K in bone metabolism of Atlantic salmon. We propose the GGCX assay as a sensitive marker for vitamin K status, and confirm that menadione does not work as a cofactor for GGCX in Atlantic salmon liver.
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Affiliation(s)
- Christel Krossøy
- National Institute of Nutrition and Seafood Research (NIFES), PO Box 2029, Nordnes, 5817, Bergen, Norway
- Department of Biology, University of Bergen, 5020, Bergen, Norway
| | - Erik-Jan Lock
- National Institute of Nutrition and Seafood Research (NIFES), PO Box 2029, Nordnes, 5817, Bergen, Norway
| | - Robin Ørnsrud
- National Institute of Nutrition and Seafood Research (NIFES), PO Box 2029, Nordnes, 5817, Bergen, Norway.
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Kaas Q, Westermann JC, Craik DJ. Conopeptide characterization and classifications: an analysis using ConoServer. Toxicon 2010; 55:1491-509. [PMID: 20211197 DOI: 10.1016/j.toxicon.2010.03.002] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 02/25/2010] [Accepted: 03/01/2010] [Indexed: 10/19/2022]
Abstract
Cone snails are carnivorous marine gastropods that have evolved potent venoms to capture their prey. These venoms comprise a rich and diverse cocktail of peptide toxins, or conopeptides, whose high diversity has arisen from an efficient hypermutation mechanism, combined with a high frequency of post-translational modifications. Conopeptides bind with high specificity to distinct membrane receptors, ion channels, and transporters of the central and muscular nervous system. As well as serving their natural function in prey capture, conopeptides have been utilized as versatile tools in neuroscience and have proven valuable as drug leads that target the nervous system in humans. This paper examines current knowledge on conopeptide sequences based on an analysis of gene and peptide sequences in ConoServer (http://www.conoserver.org), a specialized database of conopeptide sequences and three-dimensional structures. We describe updates to the content and organization of ConoServer and discuss correlations between gene superfamilies, cysteine frameworks, pharmacological families targeted by conopeptides, and the phylogeny, habitat, and diet of cone snails. The study identifies gaps in current knowledge of conopeptides and points to potential directions for future research.
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Affiliation(s)
- Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, Brisbane, 4072 QLD, Australia
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Nuclear alpha NAC influences bone matrix mineralization and osteoblast maturation in vivo. Mol Cell Biol 2010; 30:43-53. [PMID: 19884350 DOI: 10.1128/mcb.00378-09] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nascent-polypeptide-associated complex and coactivator alpha (alpha NAC) is a protein shuttling between the nucleus and the cytoplasm. Upon phosphorylation at residue serine 43 by integrin-linked kinase, alpha NAC is translocated to the nuclei of osteoblasts, where it acts as an AP-1 coactivator to increase osteocalcin gene transcription. To determine the physiological role of nuclear alpha NAC, we engineered a knock-in mouse model with a serine-to-alanine mutation at position 43 (S43A). The S43A mutation resulted in a decrease in the amount of nuclear alpha NAC with reduced osteocalcin gene promoter occupancy, leading to a significant decrease in osteocalcin gene transcription. The S43A mutant bones also expressed decreased levels of alpha(1)(I) collagen mRNA and as a consequence had significantly less osteoid tissue. Transient transfection assays and chromatin immunoprecipitation confirmed the alpha(1)(I) collagen gene as a novel alpha NAC target. The reduced quantity of bone matrix in S43A mutant bones was mineralized faster, as demonstrated by the significantly reduced mineralization lag time, producing a lower volume of immature, woven-type bone characterized by poor lamellation and an increase in the number of osteocytes. Accordingly, the expression of the osteocyte differentiation marker genes DMP-1 (dentin matrix protein 1), E11, and SOST (sclerostin) was increased. The accelerated mineralization phenotype was cell autonomous, as osteoblasts isolated from the calvaria of S43A mutant mice mineralized their matrix faster than did wild-type cells. Thus, inhibition of alpha NAC nuclear translocation results in an osteopenic phenotype caused by reduced expression of osteocalcin and type I collagen, accelerated mineralization, and immature woven-bone formation.
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Abstract
Venomous marine cone snails harbour a variety of small disulfide-rich peptides called conotoxins, which target a broad range of ion channels, membrane receptors, and transporters. More than 700 species of Conus are thought to exist, each expressing a wide array of different peptides. Within this large repertoire of toxins, individual conotoxins are able to discriminate between different subtypes and isoforms of ion channels, making them valuable pharmacological probes or leads for drug design. This review gives a brief background to the discovery of conotoxins and describes their sequences, biological activities, and applications in drug design.
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Affiliation(s)
- Reena Halai
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
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37
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Locke D, Harris AL. Connexin channels and phospholipids: association and modulation. BMC Biol 2009; 7:52. [PMID: 19686581 PMCID: PMC2733891 DOI: 10.1186/1741-7007-7-52] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Accepted: 08/17/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND For membrane proteins, lipids provide a structural framework and means to modulate function. Paired connexin hemichannels form the intercellular channels that compose gap junction plaques while unpaired hemichannels have regulated functions in non-junctional plasma membrane. The importance of interactions between connexin channels and phospholipids is poorly understood. RESULTS Endogenous phospholipids most tightly associated with purified connexin26 or connexin32 hemichannels or with junctional plaques in cell membranes, those likely to have structural and/or modulatory effects, were identified by tandem electrospray ionization-mass spectrometry using class-specific interpretative methods. Phospholipids were characterized by headgroup class, charge, glycerol-alkyl chain linkage and by acyl chain length and saturation. The results indicate that specific endogenous phospholipids are uniquely associated with either connexin26 or connexin32 channels, and some phospholipids are associated with both. Functional effects of the major phospholipid classes on connexin channel activity were assessed by molecular permeability of hemichannels reconstituted into liposomes. Changes to phospholipid composition(s) of the liposome membrane altered the activity of connexin channels in a manner reflecting changes to the surface charge/potential of the membrane and, secondarily, to cholesterol content. Together, the data show that connexin26 and connexin32 channels have a preference for tight association with unique anionic phospholipids, and that these, independent of headgroup, have a positive effect on the activity of both connexin26 and connexin32 channels. Additionally, the data suggest that the likely in vivo phospholipid modulators of connexin channel structure-function that are connexin isoform-specific are found in the cytoplasmic leaflet. A modulatory role for phospholipids that promote negative curvature is also inferred. CONCLUSION This study is the first to identify (endogenous) phospholipids that tightly associate with connexin channels. The finding that specific phospholipids are associated with different connexin isoforms suggests connexin-specific regulatory and/or structural interactions with lipid membranes. The results are interpreted in light of connexin channel function and cell biology, as informed by current knowledge of lipid-protein interactions and membrane biophysics. The intimate involvement of distinct phospholipids with different connexins contributes to channel structure and/or function, as well as plaque integrity, and to modulation of connexin channels by lipophilic agents.
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Affiliation(s)
- Darren Locke
- Department of Pharmacology and Physiology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
| | - Andrew L Harris
- Department of Pharmacology and Physiology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
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Abstract
'Replaying the tape' is an intriguing 'would it happen again?' exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis -- although perhaps not oxygenic photosynthesis -- would also have evolved.
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Rishavy MA, Berkner KL. Insight into the coupling mechanism of the vitamin K-dependent carboxylase: mutation of histidine 160 disrupts glutamic acid carbanion formation and efficient coupling of vitamin K epoxidation to glutamic acid carboxylation. Biochemistry 2008; 47:9836-46. [PMID: 18717596 DOI: 10.1021/bi800296r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vitamin K-dependent (VKD) proteins become activated by the VKD carboxylase, which converts Glu's to carboxylated Glu's (Gla's) in their Gla domains. The carboxylase uses vitamin K epoxidation to drive Glu carboxylation, and the two half-reactions are coupled in 1:1 stoichiometry by an unknown mechanism. We now report the first identification of a residue, His160, required for coupling. A H160A mutant showed wild-type levels of epoxidation but substantially less carboxylation. Monitoring proton abstraction using a peptide with Glu tritiated at the gamma-carbon position revealed that poor coupling was due to impaired carbanion formation. H160A showed a 10-fold lower ratio of tritium release to vitamin K epoxidation than wild-type enzyme (i.e., 0.12 versus 1.14, respectively), which could fully account for the fold decrease in coupling efficiency. The Ala substitution in His160 did not affect the K m for vitamin K and caused only a 2-fold increase in the K m for Glu and 2-fold decrease in the activation of vitamin K epoxidation by Glu. The H160A K m for CO 2 was 5-fold higher than the wild-type enzyme. However, the k cat for H160A carboxylation was 8-9-fold lower than the wild-type enzyme with all three substrates (i.e., Glu, CO 2, and vitamin K), suggesting a catalytic role for His160 in carbanion formation. We propose that His160 facilitates the formation of the transition state for carbanion formation. His160 is highly conserved in metazoan VKD carboxylases but not in some bacterial orthologues (acquired by horizontal gene transfer), which has implications for how bacteria have adapted the carboxylase for novel functions.
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Affiliation(s)
- Mark A Rishavy
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
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40
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Conantokin-P, an unusual conantokin with a long disulfide loop. Toxicon 2008; 52:203-13. [PMID: 18586049 DOI: 10.1016/j.toxicon.2008.04.178] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 04/06/2008] [Accepted: 04/07/2008] [Indexed: 11/23/2022]
Abstract
The conantokins are a family of Conus venom peptides (17-27AA) that are N-methyl-d-aspartate (NMDA) receptor antagonists. Conantokins lack disulfide bridges (six out of seven previously characterized peptides are linear), but contain multiple residues of gamma-carboxyglutamate. These post-translationally modified amino acids confer the largely helical structure of conantokins by coordinating divalent metal ions. Here, we report that a group of fish-hunting cone snails, Conus purpurascens and Conus ermineus, express a distinctive branch of the conantokin family in their venom ducts. Two novel conantokins, conantokin-P (Con-P) and conantokin-E (Con-E) are 24AA long and contain five gamma-carboxyglutamate residues. These two peptides are characterized by a long disulfide loop (12 amino acids including two Gla residues between the Cys residues). The oxidative folding studies of Con-P revealed that the formation of the disulfide bond proceeded significantly faster in the presence of Ca(++) ions. Circular dichroism suggested that Con-P is less helical than other previously characterized conantokins. Con-P blocks NMDA receptors containing NR2B subunit with submicromolar potency. Furthermore, the subtype-selectivity for different NR2 subunits differs from that of the previously characterized conantokins. Our results suggest that different branches of the phylogenetic tree of cone snails have evolved distinct groups of conantokins, each with its own unique biochemical features.
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Abstract
Vitamin K-dependent (VKD) protein carboxylation uses vitamin K epoxidation to convert Glus to carboxylated Glus (Glas), rendering VKD proteins active in physiologies that include hemostasis, apoptosis, bone mineralization, calcium homeostasis, growth control, and signal transduction. Clusters of Glus are modified by a processive carboxylase, generating a calcium-binding module that allows binding to either hydroxyapatite in the extracellular matrices or cell surfaces where anionic phospholipids become exposed, for example, during apoptosis or cell activation. Naturally occurring carboxylase mutations have been informative for function and are associated with bleeding complications and, surprisingly, a pseudoxanthoma elasticum (PXE)-like phenotype. A major advance in defining carboxylase function is the identification of the base that initiates carboxylation, which raises interesting possibilities for how vitamin K epoxidation is regulated by Glu substrate and carboxylase membrane topology. Vitamin K oxidoreductase (VKOR), the target of warfarin, generates the reduced vitamin K cofactor used by the carboxylase. Oxidation of active site thiols during vitamin K reduction inactivates VKOR, and activity is regenerated by an unknown reductase. The amounts of reduced vitamin K limit the capacity for carboxylation in cells, and overexpression of VKOR, but not carboxylase, improves carboxylation. However, the effect of VKOR overexpression is small, possibly because the reductase that regenerates VKOR activity is saturated. The review discusses these advances, as well as the potential impact of secretory components on carboxylation, which occurs during VKD protein secretion. Also discussed is the role of the carboxylase in mammals and lower organisms, including the bacterial pathogen Leptospira interrogans that has acquired a VKD carboxylase by horizontal transfer.
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Affiliation(s)
- Kathleen L Berkner
- Department of Molecular Cardiology, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
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Bandyopadhyay PK. Vitamin K-dependent gamma-glutamylcarboxylation: an ancient posttranslational modification. VITAMINS AND HORMONES 2008; 78:157-84. [PMID: 18374194 DOI: 10.1016/s0083-6729(07)00008-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The vitamin K-dependent carboxylase carries out the posttranslational modification of specific glutamate residues in proteins to gamma-carboxy glutamic acid (Gla) in the presence of reduced vitamin K, molecular oxygen, and carbon dioxide. In the process, reduced vitamin K is converted to vitamin K epoxide, which is subsequently reduced to vitamin K, by vitamin K epoxide reductase (VKOR) for use in the carboxylation reaction. The modification has a wide range of physiological implications, including hemostasis, bone calcification, and signal transduction. The enzyme interacts with a high affinity gamma-carboxylation recognition sequence (gamma-CRS) of the substrate and carries out multiple modifications of the substrate before the product is released. This mechanism ensures complete carboxylation of the Gla domain of the coagulation factors, which is essential for their biological activity. gamma-Carboxylation, originally discovered in mammals, is widely distributed in the animal kingdom. It has been characterized in sea squirt (Ciona intestinalis), in flies (Drosophila melanogaster), and in marine snails (Conus textile), none of which have a blood coagulation system similar to mammals. The cone snails express a large array of gamma-carboxylated peptides that modulate the activity of ion channels. These findings have led to the suggestion that gamma-carboxylation is an extracellular posttranslational modification that antedates the divergence of molluscs, arthropods, and chordates. I will first summarize recent understanding of gamma-carboxylase and gamma-carboxylation gleaned from experiments using the mammalian enzyme, and then I will briefly describe the available information on gamma-carboxylation in D. melanogaster and C. textile.
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Affiliation(s)
- Pradip K Bandyopadhyay
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
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Möller C, Marí F. A vasopressin/oxytocin-related conopeptide with gamma-carboxyglutamate at position 8. Biochem J 2007; 404:413-9. [PMID: 17331075 PMCID: PMC1896288 DOI: 10.1042/bj20061480] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Vasopressins and oxytocins are homologous, ubiquitous and multifunctional peptides present in animals. Conopressins are vasopressin/oxytocin-related peptides that have been found in the venom of cone snails, a genus of marine predatory molluscs that envenom their prey with a complex mixture of neuroactive peptides. In the present paper, we report the purification and characterization of a unique conopressin isolated from the venom of Conus villepinii, a vermivorous cone snail species from the western Atlantic Ocean. This novel peptide, designated gamma-conopressin-vil, has the sequence CLIQDCPgammaG* (gamma is gamma-carboxyglutamate and * is C-terminal amidation). The unique feature of this vasopressin/oxytocin-like peptide is that the eighth residue is gamma-carboxyglutamate instead of a neutral or basic residue; therefore it could not be directly classified into either the vasopressin or the oxytocin peptide families. Nano-NMR spectroscopy of the peptide isolated directly from the cone snails revealed that the native gamma-conopressin-vil undergoes structural changes in the presence of calcium. This suggests that the peptide binds calcium, and the calcium-binding process is mediated by the gamma-carboxyglutamate residue. However, the negatively charged residues in the sequence of gamma-conopressin-vil may mediate calcium binding by a novel mechanism not observed in other peptides of this family.
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Affiliation(s)
- Carolina Möller
- Department of Chemistry and Biochemistry, and Center of Excellence in Biomedical and Marine Biotechnology, Florida Atlantic University, Boca Raton, FL 33431, U.S.A
| | - Frank Marí
- Department of Chemistry and Biochemistry, and Center of Excellence in Biomedical and Marine Biotechnology, Florida Atlantic University, Boca Raton, FL 33431, U.S.A
- To whom correspondence should be addressed (email )
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Grant MA, Shanmugasundaram K, Rigby AC. Conotoxin therapeutics: a pipeline for success? Expert Opin Drug Discov 2007; 2:453-68. [DOI: 10.1517/17460441.2.4.453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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45
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Zhu A, Sun H, Raymond RM, Furie BC, Furie B, Bronstein M, Kaufman RJ, Westrick R, Ginsburg D. Fatal hemorrhage in mice lacking gamma-glutamyl carboxylase. Blood 2007; 109:5270-5. [PMID: 17327402 PMCID: PMC1890832 DOI: 10.1182/blood-2006-12-064188] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The carboxylation of glutamic acid residues to gamma-carboxyglutamic acid (Gla) by the vitamin K-dependent gamma-glutamyl carboxylase (gamma-carboxylase) is an essential posttranslational modification required for the biological activity of a number of proteins, including proteins involved in blood coagulation and its regulation. Heterozygous mice carrying a null mutation at the gamma-carboxylase (Ggcx) gene exhibit normal development and survival with no evidence of hemorrhage and normal functional activity of the vitamin K-dependent clotting factors IX, X, and prothrombin. Analysis of a Ggcx(+/-) intercross revealed a partial developmental block with only 50% of expected Ggcx(-/-) offspring surviving to term, with the latter animals dying uniformly at birth of massive intra-abdominal hemorrhage. This phenotype closely resembles the partial midembryonic loss and postnatal hemorrhage previously reported for both prothrombin- and factor V (F5)-deficient mice. These data exclude the existence of a redundant carboxylase pathway and suggest that functionally critical substrates for gamma-carboxylation, at least in the developing embryo and neonate, are primarily restricted to components of the blood coagulation cascade.
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Affiliation(s)
- Aihua Zhu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
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Abstract
The story I shall recount started in 1969, when I was given the opportunity to join the Department of Clinical Chemistry at the University Hospital in Malmö. I had just finished medical school at the university in the neighboring town of Lund. Parallel to pursuing my medical studies I had spent some time in the Department of Biochemistry. I did not know much about biochemistry, but it was enough for me to realize that I wanted to do laboratory research rather than developing a clinical career. I was happy to accept an offer to start working in the laboratory, particularly as the head of the department, Professor Carl-Bertil Laurell, had an excellent reputation. As it turned out, I came to spend almost all of my professional life in the laboratory.
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Affiliation(s)
- J Stenflo
- Department of Clinical Chemistry, University Hospital, Malmö, Sweden.
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47
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Kulman JD, Harris JE, Nakazawa N, Ogasawara M, Satake M, Davie EW. Vitamin K-dependent proteins in Ciona intestinalis, a basal chordate lacking a blood coagulation cascade. Proc Natl Acad Sci U S A 2006; 103:15794-9. [PMID: 17043233 PMCID: PMC1635082 DOI: 10.1073/pnas.0607543103] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have isolated and sequenced several cDNAs derived from the sea squirt Ciona intestinalis that encode vitamin K-dependent proteins. Four of these encode gamma-carboxyglutamic acid (Gla) domain-containing proteins, which we have named Ci-Gla1 through Ci-Gla4. Two additional cDNAs encode the apparent orthologs of gamma-glutamyl carboxylase and vitamin K epoxide reductase. Ci-Gla1 undergoes gamma-glutamyl carboxylation when expressed in CHO cells and is homologous to Gla-RTK, a putative receptor tyrosine kinase previously identified in a related ascidian. The remaining three Gla domain proteins are similar to proteins that participate in fundamental developmental processes, complement regulation, and blood coagulation. These proteins are generally expressed at low levels throughout development and exhibit either relatively constant expression (Ci-Gla1, gamma-glutamyl carboxylase, and vitamin K epoxide reductase) or spatiotemporal regulation (Ci-Gla2, -3, and -4). These results demonstrate the evolutionary emergence of the vitamin K-dependent Gla domain before the divergence of vertebrates and urochordates and suggest novel functions for Gla domain proteins distinct from their roles in vertebrate hemostasis. In addition, these findings highlight the usefulness of C. intestinalis as a model organism for investigating vitamin K-dependent physiological phenomena, which may be conserved among the chordate subphyla.
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Affiliation(s)
- John D. Kulman
- *Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Jeff E. Harris
- *Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Noriko Nakazawa
- Department of Biology, Faculty of Science, Chiba University, Chiba 263-8522, Japan; and
| | - Michio Ogasawara
- Department of Biology, Faculty of Science, Chiba University, Chiba 263-8522, Japan; and
| | - Masanobu Satake
- Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Earl W. Davie
- *Department of Biochemistry, University of Washington, Seattle, WA 98195
- To whom correspondence should be addressed. E-mail:
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48
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Czerwiec E, Kalume DE, Roepstorff P, Hambe B, Furie B, Furie BC, Stenflo J. Novel gamma-carboxyglutamic acid-containing peptides from the venom of Conus textile. FEBS J 2006; 273:2779-88. [PMID: 16817904 DOI: 10.1111/j.1742-4658.2006.05294.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The cone snail is the only invertebrate system in which the vitamin K-dependent carboxylase (or gamma-carboxylase) and its product gamma-carboxyglutamic acid (Gla) have been identified. It remains the sole source of structural information of invertebrate gamma-carboxylase substrates. Four novel Gla-containing peptides were purified from the venom of Conus textile and characterized using biochemical methods and mass spectrometry. The peptides Gla(1)-TxVI, Gla(2)-TxVI/A, Gla(2)-TxVI/B and Gla(3)-TxVI each have six Cys residues and belong to the O-superfamily of conotoxins. All four conopeptides contain 4-trans-hydroxyproline and the unusual amino acid 6-l-bromotryptophan. Gla(2)-TxVI/A and Gla(2)-TxVI/B are isoforms with an amidated C-terminus that differ at positions +1 and +13. Three isoforms of Gla(3)-TxVI were observed that differ at position +7: Gla(3)-TxVI, Glu7-Gla(3)-TxVI and Asp7-Gla(3)-TxVI. The cDNAs encoding the precursors of the four peptides were cloned. The predicted signal sequences (amino acids -46 to -27) were nearly identical and highly hydrophobic. The predicted propeptide region (-20 to -1) that contains the gamma-carboxylation recognition site (gamma-CRS) is very similar in Gla(2)-TxVI/A, Gla(2)-TxVI/B and Gla(3)-TxVI, but is more divergent for Gla(1)-TxVI. Kinetic studies utilizing the Conusgamma-carboxylase and synthetic peptide substrates localized the gamma-CRS of Gla(1)-TxVI to the region -14 to -1 of the polypeptide precursor: the Km was reduced from 1.8 mm for Gla (1)-TxVI lacking a propeptide to 24 microm when a 14-residue propeptide was attached to the substrate. Similarly, addition of an 18-residue propeptide to Gla(2)-TxVI/B reduced the Km value tenfold.
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Affiliation(s)
- Eva Czerwiec
- Marine Biological Laboratory, Woods Hole, MA, USA.
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49
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Jakubowski JA, Hatcher NG, Xie F, Sweedler JV. The first γ-carboxyglutamate-containing neuropeptide. Neurochem Int 2006; 49:223-9. [PMID: 16522341 DOI: 10.1016/j.neuint.2006.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Accepted: 01/19/2006] [Indexed: 11/18/2022]
Abstract
A key factor in the characterization of peptide transmitters used in neuronal signaling is the correct elucidation of post-translational modifications, especially as they are often required to confer biological activity. A rare carboxylation modification is described on the D-peptide from the insulin prohormone in the sea slug, Aplysia californica. Using liquid chromatography purification coupled with electrospray ionization and nanoelectrospray ionization-ion trap-mass spectrometry (ESI- and nanoESI-MS), the presence of this D-peptide within Aplysia insulin (AI)-producing neurons is confirmed. Further detailed mass spectrometric analyses demonstrate that the Aplysia insulin D-peptide is carboxylated on the single glutamate residue within the sequence. This gamma-carboxy D-peptide, along with other identified AI-related peptides, is secreted from the central nervous system in response to ionophore stimulation, thus suggesting a signaling role within the nervous system. Although carboxylated peptides have been described previously, the Aplysia gamma-carboxy D-peptide appears to be the first reported carboxylated neuropeptide.
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Affiliation(s)
- Jennifer A Jakubowski
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, 61801, USA
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50
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Abstract
In the four decades since toxinologists in Australia and elsewhere started to investigate the active constituents of venomous cone snails, a wealth of information has emerged on the various classes of peptides and proteins that make their venoms such potent bioactive cocktails. This article provides an overview of the current state of knowledge of these venom constituents, several of which are of interest as potential human therapeutics as a consequence of their high potency and exquisite target specificity. With the promise of as many as 50,000 venom components across the entire Conus genus, many more interesting peptides can be anticipated.
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Affiliation(s)
- Raymond S Norton
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3050, Victoria, Australia.
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