Genome structure and organisation, Protein-DNA interaction, Protein and DNA photooxidation, Protein purification method development.
Current Project Area
DNA structural codes in genomes.
The sequence of genomic DNA contains information on several levels, ranging from simple coding of protein and RNA gene products over controlling the temporal and spatial expression of these to the physical structure and compaction (in nucleosomes and chromatin) of the genome in the cell nucleus, and therefore the evolutionary constraint on the genome sequence is multidimensional. Almost all genomic bioinformatics analyses focus on primary DNA sequence without taking into account or being able to interpret second and third order etc. effects of the DNA sequence, as for instance DNA helix conformation, electrostatics and flexibility which is as well “encoded” by the DNA sequence, and has direct impact on protein recognition and physical DNA properties. This project is aimed at understanding these sequence derived effects on DNA helix conformation, in particular in terms of genome function and thus evolutionary impact, as well as developing bioinformatics tools which allow direct sequence based genomic interrogation of DNA helix conformation and minor groove electrostatics, thereby obtaining a deeper genome wide understanding of the functional importance (also in terms of disease) of these.
Novel Biotechnology-based method for synthesis of amidated peptide pharmaceuticals.
In this project we propose an entirely new strategy for producing amidated peptides from E. coli fermentation both solving enrichment and amidation efficiency of the peptide. The technology is based on uranyl (UO2 2+) photo-cleavage of a novel C-terminal peptide tag that specifically binds to uranyl with high affinity. UV irradiation efficiently induces a site-specific cleavage of the peptide tag yielding a C-terminally amidated peptide and a uranyl-bound peptide tag. The purpose of this project is to develop a general method for production in E.coli of therapeutically relevant amidated peptides by developing a one-step peptide enrichment and amidation technology. This project is in collaboration with Proffs. Frank Kjeldsen and Thomas Jørgensen, University of Southern Denmark.
Photooxidation of DNA binding proteins.
It is widely established that exposure of cells to oxidants can result in cell dysfunction and death. Oxidation can result from many biological processes (e.g. inflammation, mitochondrial electron leakage, metabolic pathways, enzyme activity), as well as exposure to UV and high energy radiation, minerals, pesticides, and pollutants. We have shown that some DNA binding proteins are highly susceptible to biologically-relevant wavelengths and doses of UV light, with this resulting in protein aggregation and selective damage to the DNA to which the protein is bound. These exciting observations provide a new paradigm for modulating gene expression and growth of cells. This project is in collaboration with Prof. Michael Davies, BMI, Faculty of Health and Medical Sciences, KU.
- Elnegaard, R.L.B., Mollegaard, NE., Zhang, Q., Kjeldsen, F. and Jorgensen, T.J.D. Uranyl Photocleavage of Phosphopeptides Yields Truncated C-Terminally Amidated Peptide Products. Chembiochem 18, 1117-1122 (2017).
- Gjerstorff, M., Relster, M., Greve, KBV, Møller, JB., Elias, D.1, Lindgreen, JN.,Schmidt,, S., Mollenhauer, J, Voldborg, B, Møllegård, NE. and Ditzel, HJ. SSX2 is a novel DNA-binding protein that antagonizes polycomb group body formation and gene repression. Nucleic Acids Research. 42(18):433-46. (2014)
- Zhang, Q, Jørgensen, TJD, Nielsen, PE., and Møllegaard NE. A phosphorylation tag for uranyl mediated protein purification and photo assisted tag removal. PLoS One. 9(3):e91138. (2014).
- Lindemose S, Nielsen PE, Valentin-Hansen P., Møllegaard NE A novel indirect readout component in the E. coli cyclic AMP receptor protein operator. ACS Chem Biol. 9(3):752-60. (2014).
- Gjerstorff MF, Rösner HI, Pedersen CB, Greve KB, Schmidt S, Wilson KL, Mollenhauer J, Besir H, Poulsen FM, Møllegaard NE, Ditzel HJ. GAGE cancer-germline antigens are recruited to the nuclear envelope by germ cell-less (GCL). PLoS One. 7(9):e45819. (2012).
- Lindemose S, Nielsen PE, Hansen, M., Møllegaard NE. A DNA minor groove electronegative potential genome map based on photo-chemical probing. Nucleic Acids Research. 39(14):6269-76. (2011).
Michael J. Davies, Department of Biomedical science, KU
Thomas JD Jørgensen, Department of Biochemistry and Molecular Biology, SDU
Frank Kjeldsen, Department of Biochemistry and Molecular Biology, SDU
Morten Gjerstoff, Department for Cancer and Inflammation Research, SDU
Peter E. Nielsen, Department of Cellular and Molecular Medicine, KU
Niels Erik Møllegaard
Program for prediction of DNA electrostatic potential based on uranyl photocleavage can be downloaded here.
This link replace the link in the paper by Lindemose et al. 2011
Niels Erik Møllegaard
Further information in:
Lindemose S, Nielsen PE, Hansen, M., Møllegaard NE. A DNA minor groove electronegative potential genome map based on photo-chemical probing. Nucleic Acids Res. 39(14):6269-76. (2011).