Macromolecular Biochemistry

Teaching

Research projects for students of the University of Leiden and other Dutch Universities are often available at the MacBio group. The research lines are also described in the Research section. For details of specific projects contact the supervisor (Ubbink, Dame, Boyle, Jeuken or Wentink).

Protein Interactions: Enzymes and complexes

Supervisor: Marcellus Ubbink
Duration: variable

The research of Prof. Ubbink is aimed at understanding how proteins really work at the atomic level. Analysis of protein structure and dynamics are combined with functional studies. We focus at understanding enzymes that are important for human health. For example, the evolutionary combat between beta-lactamases and beta-lactam antibiotics is studied. Mutagenesis, kinetics, crystallography and NMR are used to characterize these interactions, with the ultimate aim to develop inhibitors that are no longer prone to induce evasive evolution of the lactamase enzyme.

We also study membrane proteins in Nanodiscs (small packets of membrane bilayer), e.g. the influenza spike protein and the caffeine detecting GPCR. Last, we develop NMR-tools, paramagnetic metal complexes that are designed and applied to protein in collaboration with the biosynthetic organic chemistry group.
 
Student projects generally involve protein production using recombinant expression systems and protein purification. Then, various biophysical measurements are performed to characterize the protein and its interactions at the atomic level. The analysis of such data requires a certain interest in quantitative experiments and computer work.

Molecular basis of genome organization and activity

Supervisor: Remus Dame
Duration: variable

Research in the group of Dr. Dame is focused on understanding the mechanisms by which chromatin is structured and functionally organized in bacteria and archaea. Transcription of genes occurs in a chromatin context and extensive interplay exists between genome structure and genome activity. Moreover, genome folding is affected by changes in cellular growth conditions and these changes are translated in altered gene expression and cellular behavior.

Genome organization across the three domains of life appears different, but upon closer inspection it becomes clear that many principles are shared. The group aims at determining fundamental principles of organization and to determine evolutionary relationships.

In order to be able to mechanistically dissect and understand these processes the group applies an extensive toolbox of techniques ranging from molecular genetics, conventional and single-molecule biochemistry to life cell microscopy and other state-of-the art in vivo approaches.

Research projects are typically connected to projects currently running within the group. In terms of techniques, projects are generally tailored depending on the interests and capacities of the candidate.

Self-assembly properties and applications of metal-binding peptides and proteins

Supervisor: Aimee Boyle
Duration: variable

Research in Aimee Boyle’s group is focused on designing metal-binding peptides and proteins to probe fundamental research questions but also to develop these structures for use in a range of applications. 

At a structural level, the group is interested in understanding how peptide/protein folding is influenced by the presence of metals. To investigate this, new peptides and proteins are designed, synthesised, and characterised to uncover which metals bind to different scaffolds and to understand why some metals interact and others don’t. It’s also of interest to test whether we can use our understanding to design scaffolds that are specific for a certain metal. 

In terms of applications of metal-binding structures, the group is interested in creating biosensors and hydrogels. Biosensing devices are important for detecting metal contamination in water sources and soil samples for example, whilst metal-containing hydrogels could have antibacterial properties if the correct metal is coordinated, and this is interesting for various medical applications.

Projects encompass a wide range of skills including peptide synthesis, recombinant protein production, peptide/protein purification, and UV-Vis spectroscopy, transmission electron microscopy, circular dichroism spectroscopy, NMR, and mass spectrometry (amongst others) for characterisation. 

We are a new lab and so there are lots of possibilities for projects. Exactly what is investigated and what techniques are used can be tailored to the student’s interests and capabilities. For more information, please email Aimee.

Nanoparticle – redox protein biohybrids

Supervisor: Lars Jeuken
Duration: variable

Lars Jeuken’s group uses a range of biophysical and biochemical techniques to study and exploit respiratory enzymes, in particular membrane enzymes. We aim to understand respiratory membrane enzymes in molecular detail, but we also develop applications in biotechnology and health, such as semi-artificial photosynthesis or the study of respiratory enzymes as a novel target space for antibiotics.

Current projects in the lab include the development of ‘biohybrids’ for photobiocatalysis and the production of solar fuels. Biohybrids are systems in which nanoparticle photosensitisers, such as carbon dots, are coupled to biocatalyst, like (membrane) proteins and whole bacteria. In the lab we work to optimise biohybrid systems for electron transfer between excited-state photosensitisers and respiratory proteins. To stabilise membrane enzymes for biocatalysis we are exploring so-called hybrid membranes, which are mixtures between amphiphilic copolymers and (phospho)lipids, provind biocompatibility within a mechanical and chemical robust environment. Finally, we study bacterial respiratory enzymes with the aim to understand their function in molecular detail. In the latter, we focus on the development and application of novel biophysical techniques, including single-enzyme methods, to drive our understanding beyond the state-of-the-art.    

As a project student you can expect to use a wide range of techniques in the lab. Depending on the project, you will express and purify (membrane) proteins, prepare lipid or hybrid vesicles, chemically modify nanoparticles and react these biomacromolecules. You will study these systems with a range of biochemical and biophysical techniques, including, but not limited to, dynamic light scattering, NMR, bioelectrochemistry, life-time fluorescence spectroscopy and UV-vis spectroscopy. For more information, please contact Lars Jeuken.

Molecular chaperones in neurodegenerative disease

Supervisor: Anne Wentink
Duration: variable

Molecular chaperones are important quality control factors that ensure proteins fold to their native state and maintain this conformation throughout their lifetime. When things go wrong, chaperones can prevent and reverse protein aggregation and promote the degradation of damaged proteins. A failure to do so can lead to pathological protein aggregation into amyloid fibres that are a hallmark of neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease.

The research of Anne Wentink’s group aims to understand the role of the Hsp70 chaperone in the formation, clearance and propagation of amyloid fibres and the key role of co-chaperones in enabling these diverse Hsp70 activities. To do this, we use a combination of structural biology (NMR spectroscopy and Electron Microscopy), fluorescence-based activity and binding assays, and cell biology techniques. The mechanistic insights into this fundamental process of protein quality control are then translated into the design of synthetic chaperones that can replicate selected chaperone activities in a highly specific manner on disease relevant substrates.

Student projects are designed around ongoing research in the group, taking into account the interests and capabilities of the student. For more information, please email Anne.