Kemisk Institut > Forskning > Biofysisk kemi > Projekter for studerende

Inspiration for possible student projects at the Biophysical Chemistry group

(projects particularly suitable for Medicinal Chemistry students are marked with *)

Leila Lo Leggio (LLL) (Leila@kemi.ku.dk)
Anders Kadziola (AK) (kadziola@kemi.ku.dk)
Sine Larsen (SL) (sine@kemi.ku.dk)
Anders Ø. Madsen (AØM) (madsen@kemi.ku.dk)
Axel Hunding (AH) (axhun@osc.kiku.dk )
Preben Graae Sørensen (PGS) (pgs@osc.kiku.dk)
Salim Abdali (SA) (abdali@kemi.ku.dk )

Structural basis of enzyme thermostability and pH optimum (LLL/JHJ)

Enzymes are the biological catalysts, and are usually vastly superior to chemical catalysts with respect of specificity of catalyzed reactions. This is a great advantage in industrial reactions when a specific product is desired. A disadvantage ofenzymes as industrial catalysts is their sensitivity to both temperature andpH.  Can enzyme activity and stabilitywith respect to pH be modulated at will by computationally designed changes inthe amino acid sequence? As part of a collaboration with computational chemists in the Scientific Computing Group, several projects are available. The predicted effect of mutations designed to improve enzyme characteristics will be tested by making the enzyme variants, testing their activity and stability, determining the 3-dimensional structure by X-ray crystallography and rationalizing the results in terms of the original prediction. The results will teach us more about the forces governing protein thermal and pH stability and help in improving design in the future.

ResearchGroup: Biophysical Chemistry

*Structure determination of glycosidase-ligand complexes (LLL)

Glycosidase are enzymes of great importance both for a variety of biological functions and as catalysts in a variety of industrial applications (eg. bioethanol production). They are very diverse in terms of specificity and in some cases also mechanism. In order to try and understand the structural basis of specificity, the 3-dimensional structure of a glycosidase can be determined by X-ray crystallography in complex with natural or synthetic ligands (substrates, products and substrate analogues). There are several projects available in this area, where the structure of the glycosidase free of ligand is already known. For the ambitious student, some projects are available where the structure of the glycosidase is yet unknown and will have to be determined first.

ResearchGroup: Biophysical Chemistry

Crystallographic investigations of PRPP-synthase from Sulfolobussolfataricus (AK)

PRPP-synthase is a key enzyme in nucleotide metabolism. It synthesizes  PhosphoRibosylPyroPhospate, which is one of the substrates for the various phosphoribosyltransferases synthesizing mono-phospho-nucleotides. During the last decade crystal structures of PRPP-synthase from Bacillus subtilis,Methanocaldococcus jannaschii and human have been determined. The aim is to determine the structure of PRPP-synthase from the thermophile archaeon Sulfolobus solfataricus in complex with various ligands (products and substrate analogs). The structures are to be compared with other PRPP-synthases in order to deduce information about reaction mechanism for this type of enzymes.

ResearchGroup: Biophysical Chemistry

Metabolic oscillations in yeast. (PGS)

Glucose degradation via glycolysis is a central part of the energy metabolism of living systems. The complexity of the chemistry involved makes it very difficult to model the connection between biological function of the cell and the biochemical network. Metabolic oscillations is a primitive example of biological function.

Possible projects within this area are:

a) Use of experimental or computer model perturbations of oscillatory yeast cells to get information on network dynamics.

b) Setup of an experimental system for investigating oscillations in yeast cells fixed in an agarose media.

c) Numerical investigations of robustness in a population of yeast cells.

ResearchGroup: Biophysical Chemistry

*Crystal engineering: Structural and computational investigations of polymorphic crystals (AØM).

The quest for, and the identification and characterization of, different crystal forms(polymorphs) of the same molecule, is one of the most active and challenging research areas of modern solid-state chemistry.

However, our ability to predict or control the occurrence of polymorphism is still embryonic. The project aims at a better understanding of polymorphism, which may be seen as a hurdle for e.g. the pharmaceutical industry, but as a great opportunity for crystal engineers, if the phenomenon can be understood and controlled. 

The project involves crystallization of known polymorphic systems, as well as searching for and characterization of new polymorphs. Projects can be focused on the laboratory-based crystallization and characterization by X-ray diffraction or directed towards theoretical investigations at the computer, depending on the interests and abilities of the student.

Research Group:Biophysical Chemistry

Electron transfer and ligand binding indihydroorotate dehydrogenase B from Lactococcus lactis.

(SL with KajFrank Jensen from Biologisk Institut)

Dihydroorotatedehydrogenase (DHOD) is the only redox enzyme in the de novo pyrimidinebiosynthesis. The Class IB DHOD exemplified by the enzyme from Lactococcus lactis is a heterotetramercomprised of two different subunits that both contain flavin groups.

The projectinvolves protein chemical investigations (site directed mutagenesis, kineticstudies and crystal structure determinations) that all serve to elucidate theelectron transfer and ligand binding of the Class 1 B DHODs.

ResearchGroup: Biophysical Chemistry

Resolution of racemates (SL/AØM)

A frequently used method to resolve a racemate into its enantiomers is to crystallize it with a suitable optically active compound. The resulting diastereomeric salts may differ so much in their physico-chemical properties that a separation is possible. The project aims at elucidating the resolution process by physico-chemical characterization and structural studies of suitablediastereomeric crystal pairs and of their (saturated) solutions.

ResearchGroup: Biophysical Chemistry

Investigation of the milk-clotting protease chymosin

(SL in cooperation with Chr. Hansen A/S and PhD student Jesper Langholm Jensen)

Chymosin is an aspartate protease expressed in suckling infants, where it selectively digests their main nutrition, milk. The enzyme is used commercially for coagulation of milk in cheese production. It is our aim to understand the working mechanism of chymosin in detail by comparing the chymosin enzymes from cow and camel, which was triggered by the camel enzyme being superior in the clotting of bovine milk compared to the bovine enzyme.

Available student projects:

1. Prochymosin. This project aims to solve the structure of the inactive precursor in order to have a better understanding of the activation. This project involves molecular biology techniques (cloning and protein expression) and structural biology (X-ray crystallography).

2. Glycosylation. Chymosin is produced recombinantly in the fungus Aspergillus niger. The resulting enzyme is glycosylated and the preliminary results indicate that this affects the activity and stability of the enzyme. The project will test this through the construction and characterization of various glycosylation mutants with molecular biology techniques (cloning and protein expression) and protein characterization (SDS-PAGE, activity assay, etc.).

3. Chymosin's substrates (the casein protein micelles in milk) are very large and surface loops located close to the active site of chymosin are believed to affect this interaction. In addition, it was recently found that the N-terminal of camel chymosin adopts a different conformation compared to other enzymes in the same family. The aim of this project is to investigate the role of these loops as well as the folding of camel chymosin's N-terminal by NMR spectroscopy.

Crystallographic investigations of transcription factors (LLL)

Transcription factors are essential DNA-binding proteins in all realms of life and are involved in regulation of gene transcription. Projects are available in various collaborative projects, in particular:

1) Crystallization of NAC proteins, which are essential plant specific transcription factors, involved in plant development and defence. So far we have determined the only structure available of a NAC-DNA binding domain, and more structural information on this family is highly needed, especially regarding DNA binding.

2) Transcription factors involved in a phage lysogenic/lytic switch system, where key proteins have been identified, but the full regulation mechanism and protein-protein and protein-DNA interactions have not yet been elucidated, 

ResearchGroup: Biophysical Chemistry

* Nanoparticles coatings for treatment of cancer tumor (SA/LLL)

In this project the student will learn how to produce nanoparticles designed, i.e. material and size, for specific antibodies, which in turn are chosen for specific cancer protein. The antibodies will be used to recognize the target, e.g. the tumor, and subsequently get attached to it. By letting the target exposed to monochromatic light, a laser, the nanoparticles will absorb the light faster and more than the tissue, and thus, heat transfer will take place. With the right design of nanoparticles, the specific antibodies and light wavelength, it will be possible to heat the area so much that the tumor will be burned without affecting other parts of the body.

Although we have reached a control of this method, the optimization of the chemical process and the effect of the different type of nanoparticles-coating are still unknown. This project aims to find the optimal conditions for coatings, antibodies interaction with the nanoparticles and with the target, i.e. cancer protein.

In this project tools like SEC, SEM, DLS and Raman will be used.

ResearchGroup: Biophysical Chemistry

* Raman studies of cancer progressing protein S100A4 (SA/LLL)

In this project the cancer progressing protein S100A4 will be the subject of the study. This study will be carried out by Raman spectroscopy (RS) and its surface enhanced technique, called SERS, which enables study of single molecules.

The S100A4 is found to have different conformational structures depending whether the cancer is in its tumor of metastate phase. This means that the development of the disease could be determined if structural information of this protein is determined. Therefore, the project aims to provide structural information, finger prints, of different species of the protein, and thus, information of the development of the disease stage (in time) will be achieved.

In this project, tools like SEC, DLS and Raman will be used.

ResearchGroup: Biophysical Chemistry