Ogfod2 protein. Characterization of a Fe(II) and oxoglutarate (2OG) dependant oxygenase with unknown function
(2014) MOBT15 20132Degree Projects in Molecular Biology
- Abstract
- ABSTRACT
Ferrous iron and 2-oxoglutarate (2OG) dependant oxygenases are an important family of enzymes that catalyse hydroxylation and oxidative demethylation reactions in humans. Proteins, lipids, nucleic acids and small molecules can all be substrates of these enzymes. Previous studies showed that hydroxylation of prolyl and asparaginyl residues of the hypoxia-inducible transcription factor (HIF) are important in sensing low oxygen levels (hypoxia) in cells.
Based on sequence similarities Ogfod2 protein belongs to this family of enzymes and is most similar to pro-collagen-lysine, 2-oxoglutarate 5-dioxygenases (PLODs), which are important proteins in collagen biosynthesis. However, to date there is no published data about Ogfod2. - Abstract
- Popular science summary:
Untangling the mystery of Ogfod2 protein
Human body consists of tens of thousands of proteins. Some of them have been studied in depth and their functions are well known. Others, however, have not been studied at all and nobody can tell if the protein has some very important function or not. One of these unstudied proteins is the human Ogfod2 protein.
Human Ogfod2 protein is a member of a large family of enzymes with about 60 different members in human cells. These enzymes are called ferrous iron (Fe(II)) and 2-oxoglutarate (2OG) dependant oxygenases. Members of this enzyme family modify other proteins by adding a small chemical tag. In particular these oxygenases can add an oxygen atom to a protein in... (More) - Popular science summary:
Untangling the mystery of Ogfod2 protein
Human body consists of tens of thousands of proteins. Some of them have been studied in depth and their functions are well known. Others, however, have not been studied at all and nobody can tell if the protein has some very important function or not. One of these unstudied proteins is the human Ogfod2 protein.
Human Ogfod2 protein is a member of a large family of enzymes with about 60 different members in human cells. These enzymes are called ferrous iron (Fe(II)) and 2-oxoglutarate (2OG) dependant oxygenases. Members of this enzyme family modify other proteins by adding a small chemical tag. In particular these oxygenases can add an oxygen atom to a protein in order to alter the function of the modified protein.
In the 1960s the first 2OG oxygenases have been identified. Hutton and co-workers identified small chemical tags on collagen. Collagen is the most abundant protein in human body and can be found all through it – in skin, bones, cartilage, tendon, hair, organs, etc. For collagen to form a proper 3D structure, three different enzymes of the 2OG oxygenase family have to modify the collagen.
In the meantime many other 2OG oxygenases with a lot of different substrates were identified. Improper work of some of these oxygenases can be linked to diseases such as scurvy, cancer or brittle bone disease. In recent years scientists tried to elucidate the 2OG oxygenase working mechanisms and to modify their activity in order to cure these diseases. The Ogfod2 protein is a 2OG oxygenase with a function which is not yet known.
How to unravel the mechanism of action of a protein of unknown function?
There are several methods to elucidate the function of a protein that I have used for characterization of Ogfod2 protein.
• Proteins in different cellular compartments have different functions. Therefore, knowing the location of Ogfod2 in cells can help to understand its function. I stained cells with an antibody recognizing the Ogfod2 protein and found that it is located in the cytoplasm of the cell within a structure around the nucleus.
• Proteins are often functioning in larger protein complexes. Identification of interaction partners with known functions would tell about involvement of Ogfod2 in cellular mechanisms. For finding out about proteins which might be interacting with Ogfod2 I did pull-down experiments. I pulled Ogfod2 protein out of cells and tried to see if I would co-purify other proteins, because they were interacting with Ogfod2.
• I tried to eliminate Ogfod2 from the cells using a method called knockdown and see how the cells change in the absence of this protein.
There is much unknown about the human Ogfod2 protein, but my research starts decoding the mystery of Ogfod2.
Advisor: Alexander Wolf
Institute of Molecular Pharmacology and Toxicology,
Helmholtz Zentrum München
Master’s Degree project in Molecular Biology, 60 ECTS, 2014 (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/4499976
- author
- Mikuciauskaite, Juste
- supervisor
- organization
- course
- MOBT15 20132
- year
- 2014
- type
- H2 - Master's Degree (Two Years)
- subject
- language
- English
- id
- 4499976
- date added to LUP
- 2014-06-25 09:20:00
- date last changed
- 2014-06-25 09:20:00
@misc{4499976,
abstract = {{Popular science summary:
Untangling the mystery of Ogfod2 protein
Human body consists of tens of thousands of proteins. Some of them have been studied in depth and their functions are well known. Others, however, have not been studied at all and nobody can tell if the protein has some very important function or not. One of these unstudied proteins is the human Ogfod2 protein.
Human Ogfod2 protein is a member of a large family of enzymes with about 60 different members in human cells. These enzymes are called ferrous iron (Fe(II)) and 2-oxoglutarate (2OG) dependant oxygenases. Members of this enzyme family modify other proteins by adding a small chemical tag. In particular these oxygenases can add an oxygen atom to a protein in order to alter the function of the modified protein.
In the 1960s the first 2OG oxygenases have been identified. Hutton and co-workers identified small chemical tags on collagen. Collagen is the most abundant protein in human body and can be found all through it – in skin, bones, cartilage, tendon, hair, organs, etc. For collagen to form a proper 3D structure, three different enzymes of the 2OG oxygenase family have to modify the collagen.
In the meantime many other 2OG oxygenases with a lot of different substrates were identified. Improper work of some of these oxygenases can be linked to diseases such as scurvy, cancer or brittle bone disease. In recent years scientists tried to elucidate the 2OG oxygenase working mechanisms and to modify their activity in order to cure these diseases. The Ogfod2 protein is a 2OG oxygenase with a function which is not yet known.
How to unravel the mechanism of action of a protein of unknown function?
There are several methods to elucidate the function of a protein that I have used for characterization of Ogfod2 protein.
• Proteins in different cellular compartments have different functions. Therefore, knowing the location of Ogfod2 in cells can help to understand its function. I stained cells with an antibody recognizing the Ogfod2 protein and found that it is located in the cytoplasm of the cell within a structure around the nucleus.
• Proteins are often functioning in larger protein complexes. Identification of interaction partners with known functions would tell about involvement of Ogfod2 in cellular mechanisms. For finding out about proteins which might be interacting with Ogfod2 I did pull-down experiments. I pulled Ogfod2 protein out of cells and tried to see if I would co-purify other proteins, because they were interacting with Ogfod2.
• I tried to eliminate Ogfod2 from the cells using a method called knockdown and see how the cells change in the absence of this protein.
There is much unknown about the human Ogfod2 protein, but my research starts decoding the mystery of Ogfod2.
Advisor: Alexander Wolf
Institute of Molecular Pharmacology and Toxicology,
Helmholtz Zentrum München
Master’s Degree project in Molecular Biology, 60 ECTS, 2014}},
author = {{Mikuciauskaite, Juste}},
language = {{eng}},
note = {{Student Paper}},
title = {{Ogfod2 protein. Characterization of a Fe(II) and oxoglutarate (2OG) dependant oxygenase with unknown function}},
year = {{2014}},
}