Single molecule and cell biophysics for Biomedicine - Hatzakis Lab

In spite of their immense importance, current understanding on enzymatic behaviour relies primarily on static pictures and ensemble functional assays and thus dynamic characteristics remain masked due to ensemble averaging. We therefore employ single molecule techniques to interrogate the behaviour of individual enzymes and elicit a detailed understanding of the molecular level details underlying enzymatic function and regulation. Using state of the art fluorescent microscopy techniques, we investigate how the complex protein conformational dynamics facilitate catalysis, as well as the existence and life times of enzymatic functional states and how point mutations, posttranslational modifications or effectors, redistribute them.

Advancing our understanding of functional protein dynamics will lead both to the design of novel pharmaceutics and the in silico design of novel biocatalysts with tailor made functionalities for biotechnological applications. 

The Hatzakis Group labs are equipped with everything needed to perform state of the art experiments on a variaty of protein, enzyme and related experiments. Most experiments in the group are build around fluorescent microscopy, performed on one (or both) of two microscopes:

• An IX81 Olympus confocal microscope
• An Olympus Total Internal Reflection Fluorescence microscope (TIRFm) set up for super resolution microscopy 
• State of the art Olympus SpinSR10 Confocal Super Resolution Microscope

The primary focus of our lab is to provide the molecular level mechanisms that underlie and control protein behavior with emphasis on structure function correlations and biomolecular interactions. The ultimate target is to utilize the attained knowledge for improving human health and for the design of tailor made biocatalysts for biotechnological, green energy, solutions. To succeed in this, and often inspired by nature, we develop biophysical assays in native-like membrane environments and employ biophysical tools that allow molecular interrogations with the unprecedented sensitivity of single-molecule readouts.

Focusing on a spectrum of biological systems, we investigate how the personality of a nanometer-dimension enzyme propagates to biological phenomena. As such, interrogating the structural and functional dynamics of an enzyme allows us to provide links between nanometer motions and ultrafast structural dynamics to human diseases, clinical phenotypes and industrial performance (e.g. detergents in industry). In a way, we strive to provide links of protein landscapes to clinical and industrial phenotypes.

All our projects are in tight collaboration with industrial partners (e.g. Novozymes), medical doctors, and biological labs and are at the interface between chemistry, biology, medicine and clinical biochemistry.

In 2015, Nikos S Hatzakis was awarded the prestigious Villum Young Investigator funding, that is directed to especially talented up-and-coming researchers in science and technology with ambitions of creating their own, independent research identity. With this grant, we equipped our lab with state-ofthe-art super-resolution single-molecule microscopes along with hiring new members.

Selected publications

• Stella et al Cell 2018
• Laursen et al Science 2016, 354, 890-893
• Veshaguri at el Science 2016, 351, 1469-1473
• Li et al J. Am. Chem. Soc. 2015, 137, 16055-16063
• Larsen et al Nat. Chem. Biol. 2015, 11, 192-U176
• Hatzakis et al Biophys. Chem. 2014, 186, 46-54
• Laursen et al ACS Chem. Biol. 2014, 9, 630-634
• Hatzakis et al J. Am. Chem. Soc. 2012, 134, 9296-9302
• Christensen et al Nat. Nanotech. 2012, 7, 51-55

• 2014: Villum Foundation, Young Investigator Fellowship 

• 2016: Novozymes A/S & The Henning Holck-Larsen Foundation, Guest Post-doctoral Fellowship 

• 2016: Novo Scholarship Programme

• 2017: Carlsberg Foundation, Most Distinguished Associate Professor Fellowship 

• 2017: Marie Curie, Post Doc Fellowship

• 2017: Lundbeck fonden, Post Doc Fellowship

• 2017: Velux foundation Center: Advanced Biomolecular Engineering

• 2018: Innovation Foundation Denmark, Industrial Post-doc

Associate Professor, group leader

Nikos S Hatzakis

Hatzakis lab
Nano Science Center
Department of Chemistry
Faculty of Science
Phone: 50202951
E-mail:hatzakis@nano.ku.dk

Nikos Hatzakis' main research interest is to obtain a fundamental understanding of the parameters underlying regulation of enzymatic function. Enzymes regulate a plethora of vital cellular processes and aberration in their function can result in countless disease states. They are also essential components in multiple industrial applications including drug synthesis and detergent development. Harnessing the biomolecular insights of current single molecule experiments allows us to unmask the structural and functional dynamics of major drug metabolism enzymes. Understanding how these enzymes operate paves the way for the design of novel pharmaceutics.

DeepFRET

Rapid and automated single molecule FRET data classification using deep learning.

Extraction of liposome intensity

Python based script for extraction and analysis of .tif formatted image files. The script can extract the intensity from individual liposomes based in a changeable ROI size given initially and subtract local background.

Cell analyzer HEK293/PYY/eYFP

Python based script for extraction and analysis of .tif formatted image files. The script will identify cells on a image based on set thresholds and parameters. From this a mask will be created to extract the intensity from up to three channels, here corresponding to signal from membrane stain (blue), yellow fluorescent protein (YFP, green) and Cy5/Atto655 (red).

Single Particle Tracking of Lipases

Python Script for analysing .tif movies of lipases diffusing on a surface. Code used to make data for Bohr, S. S.-R. et al. Scientific Reports, 2019.