Useful links

Positions Available

We will soon be announcing positions as follows:

  • Two PhD studentship to research unsual gyrases funded by OPUS

  • One postdoctoral fellow to research unusual gyrases funded by OPUS

  • One technician (part time) fellow to research unusual gyrases funded by OPUS

  • Testimonials

    • Professor Heddle is undoubtedly the greatest genius of our age

      Jonathan Heddle
    • I thought I was applying to a different lab

      Soumyananda Chakraborti
    • Joining the lab is simply a small part of a much larger plan to take over the world

      Dmitry Ghilarov
    • I went to sleep in Tokyo and woke up in Poland. I think I may have been kidnapped

      Yusuke Sakai


    We are grateful to the various bodies who fund our research:
  • The Malopolska Centre of Biotechnology





  • FNP Homing

  • Our team

    Jonathan Heddle

    Fearless Leader.

    Soumyananda Chakraborti

    I am originally from India, working as postdoctoral fellow in MCB. In Heddle lab I am working with different protein cages their Biophysical characterization and their cellular delivery. I am experienced researcher; before joining MCB, Poland I worked in Indiana University, USA and Institute Curie, Paris. My two major areas of expertise are synthetic and chemical biology. I did my PhD from Calcutta University, India in the year 2013 in the field of Biophysics. Other than science I am interested in travelling and reading.

    Dmitry Ghilarov

    Biochemist from Moscow, Russia. After several years of postdoctoral studies in Russia and UK I joined the Heddle lab as an independent fellow. I hope that together with Jonathan we can find the answer to one of the scientific questions that bothered me for a long time - how Qnr proteins protect gyrase against fluoroquinolones. I'm passionate about science and ballroom dancing and enjoy travelling, tasting good food, studying arts and history. You can access my POLONEZ project page here

    Yusuke Sakai

    I’m a DNA nanotechnology researcher in Heddle lab. I have researched about DNA origami nanomechanical device in Japan before and I’m currently dedicating myself to developing innovative nano-scale devices made of DNA. I’m also attracted to and investigated RNA biochemistry and gene expression system, a sophisticated decoding machinery equipped in all organisms.

    Izabela Stupka

    TRAP is a naturally occurring protein which role is to control the tryptophan synthesis in some bacterial species. This 11-sided protein, after incorporation of specific mutations and its incubation with nanogold particles, was found out to form special cage-like structures, which could have some interesting medical applications and could give us new insight into the rules of protein geometry. I take part in the research which aims to understand the formation of these structures but most of all I am involved in the production of novel proteins and testing the assembled ones for their interactions with various eukaryotic cell lines. My findings may help to design a new system for the safe cargo delivery, like drug molecules, to the inside of cells.

    Łukasz Mazurek

    DNA gyrase is an important antibiotic target and understanding and developing new inhibitors against it will be a useful weapon in the fight against antibacterial resistance, which is a growing threat to human survival. Topoisomerase-targeting pentapeptide repeat proteins (TTPRPs) may help us achieve this goal. My goal is to understand PRP action using structural biology methods. It will be helpful in the fight against antibacterial resistance.I am also interested in discovering other anti-microbials like bacteriocins. My other scientific interest is recombinant proteins production (especially hard cases).

    Karolina Majsterkiewicz

    Put together gold nanoparticles and mutated TRAP protein (containing cysteine) and what will you get? Intriguing nanostructures - stable and with unique geometrical arrangements. Recent work in the Heddle Laboratory has suggested that certain gold nanoparticles can interact with proteins containing cysteine residues to promote protein-protein bonds, which can result in production of highly stable artificial protein cages. The recipe sounds simple but chemistry behind it is quite complex. The role of gold nanoparticles in forming these protein cages is crucial but not really understood. In this project, I focus on finding what kind of gold nanoparticles (in terms of size, shape and surface chemistry) and reaction conditions can promote cage formation. Establishing the mechanism of this process would be a great step towards developing new ways of assembling proteins into interesting nanostructures.

    Agnieszka Kowalczyk

    I'm a PhD math student at the Jagiellonian University always ready to broaden my horizons in different fields. My goal in Heddle's Lab is to understand the geometry of protein cages. Professionally - particularly interested in the rigidity theory and mathematical aspects of origami. Privately incurable dance lover (especially cuban salsa), mountain hiker and yerba mate fan.

    Kinga Borzęcka-Solarz

    My research interests include cell biology, cancer biology and immunology. During PhD studies my research focused on molecular mechanisms of activation receptors of immune cells and participation of proteins, like tyrosine kinases, in activation of cells with microbial components. In my current research I am using of various approaches, based on both biochemistry and bioinformatics, to study the structure of TRAP protein. My interest focuses on the use of mutated TRAP proteins, especially their capacity for forming a cage-like structures in the presence of gold nanoparticles, as potential nanodevices for cell-targeting. To pursue this goal I’m going to conduct tests on different cell lines using wide arrange of biochemical and imaging techniques.

    Artur Biela

    After several years came back to academia from industry - technology transfer - you're doing it wrong! ;) But being more serious. I am a structural biologist with an expertise in X-ray macromolecular crystallography. For the past several years I've been working in private sector of science, purifying, crystallizing and solving 3D structures of proteins and protein complexes. Recently I've decided to broaden my horizons as a structural biologist, and start to investigate structures of protein complexes by using cryo-EM..

    Jan Różycki

    I received my Ph.D. in Chemistry from University of Gdansk (Poland) and carried out my postdoctoral research at National Cancer Institute, NIH, Bethesda, USA. My research focuses on peptide and protein design as an approach to understanding macromolecule structure and function. I have particular interest in peptide design and synthesis, enzymology and developing new enzyme inhibitors. In the Heddle Lab I carried out a structure–activity relationship (S.A.R.) study of the TRAP protein sequence to define the importance of each residue and the effect of a single substitution on the self assembly properties.

    Elizabeth Michalczyk

    After working for a brief time in industry where I was involved in topoisomerase production and testing I moved to the Heddle lab where I am helping to investigate how Qnr and related proteins interact with DNA gyrase.

    Michal Kobiałka

    I am a PhD Student in the field: biological sciences, the discipline of biology, Jagiellonian University, Institute of Zoology, specialization: genetics and biology of reproduction. The basic aim of the Ph.D studies in my department is to examine the distribution, ultrastructure, mode of transovarial transmission and systematic affinity of symbionts in bodies of selected insects, phylogenetic relations between them and their host (Preludium 9, NCN grant for the young researchers). In the Heddle lab I work as a technician on the Symfonia project as a specialist of protein electron microscopy. Main tasks: preparation protein samples for TEM (Jeol JEM 2100), Cryo-electron microscopy (Cryo-EM); handling and using Vitrobot, TEM/Cryo-EM; data collection and analysis from TEM/Cryo-EM. More information about scientific achievements here.

    Gerrit Wilkens

    Originally coming from Germany, I joined the Heddle lab as a PhD student. During my PhD project I am working on stabilisation hydrophobic proteins using DNA origami based devices. Before I started this project, I studied Biology in Hamburg, Germany. During my master at the university hospital of Eppendorf I did research on the structure of biofilm inducing proteins.

    Joanna Markiewicz

    Origami refers to the art of folding and sculpting a flat sheet of paper into arbitrarily shaped objects and you can do almost the same with DNA. DNA origami allows us to easily design and build arbitrary structures using DNA strands as building block. In Heddle Lab I work as technician on the POLONEZ3 project focused on producing a programmable DNA nanorobots with an ability to act as drug carry capsules. It is still a new and an exciting field which may be fruitful in developing novel drug delivery systems. Before joining Heddle's Lab I was working as QC scientist in pharmaceutical industry.

    Dhanasekaran Balakrishnan

    I am a Bioinformatician from India and have joined Heddle's lab as a PhD student and here I am trying to develop a DNA nanodevice which captures for interaction with artificial cells. Before joining Heddle's lab, I was working in Indian Institute of Science as a Research Assistant and completed couple of projects. Outside of the lab, I am interested in Photography and travelling

    Martyna Adamiak

    I am currently a Masters student at Jagiellonian University in Bioinformatics and Applied Biophysics, after obtaining a BSc in Biochemistry. My primary scientific interests are Synthetic Biology and general Drug Development, along with novel Drug Delivery systems. Here, at Heddle Lab, II am involved in a POLONEZ3 research project, which aims to develop a system of drug delivery based on a programmable DNA robot. I am trying to focus on Biophysical approach to this subject. During my previous studies, I have researched the pathogenesis of neuropsychiatric diseases

    Zuzanna Pakosz

    DNA gyrase is one of the most important targets for antibacterial drugs. However, recently it was found in single cell eukaryotic parasites such as Plasmodium which causes malaria and Toxoplasma which causes toxoplasmosis. Better understanding their structure and mechanism of working could lead to future drug discovery. In my project, I will focus on characterisation of Toxoplasma gyrase – both biochemically and structurally.

    Marcin Wasylewski

    My education is related to fields of chemistry and biology and focuses on biochemistry, primarily on protein biochemistry. My research topics include protein – ligand and protein-protein interactions, biochemical reaction kinetics which includes enzyme kinetics and kinetics of other reactions. I have worked on energetics of biochemical reactions and systems using calorimetric techniques. I have worked on protein stability and structure in solution which includes chemical and thermal denaturation processes. In my research I have used HPLC techniques for analytical and semi-preparation scale with respect to peptides, alkaloids, polyphenols, steroids and sugars and others.

    Karolina Miszczak

    Currently I am a Biochemistry Master student on the Jagiellonian Univeristy. During my Bachelor studies I was working with cancer cells and lentiviral vectors but I decided to change completely field of my interesting. I have joined Heddle Lab and I will be doing research on TRAP protein. I want to make TRAP cages but instead of gold nanoparticles I will be using a new approach. This project is something totally new for me so I am very curious about my future results

    Anna Świetlikowska

    I am a master student at molecular biotechnology at Jagiellonian University, my former experience during my bachelor studies focused mainly in bacterial genetics. As a part of DNA origami group in Heddle Lab we are aiming to develop molecular systems for manipulation of proteins for use in artificial cells. For this purpose we will use (yes, you guessed well) DNA origami! Personally, I am also interested in cinematography, languages and travelling.

    Mohit Sharma

    I am from extreme northern part of India i,e Jammu and Kashmir State (the paradise on earth). I work in bioinformatics, which I define very generally as anything that can be done on a computer and which is relevant to the biological sciences. I am a passionate and enthusiastic science communicator and have a wealth of experience in organismic, running and delivering excellent scientific events especially in the area of Bioinformatics. Before joining Heddle Lab I was in University of Jammu. In University of Jammu, I was responsible for the creation of bioinformatics facility to enable the lab to work with biological data. At Heddle’s Lab, I am focusing on structural biology particularly on dynamics, modeling and designing of proteins by using computational approaches. When I'm not working, you can find me socializing via different medias. I like to update myself with current affairs, cooking and travel.

    Dorota Nowińska-Bąk

    I graduated in mathematics from Jagiellonian University. I also completed postgraduate studies in Controlling and finances of enterprises at Cracow University of Economics and have PRINCE2® Foundation Certificate in Project Management. In my previous jobs I gained experience in administration, finances and controlling. I also used to collaborate a lot with many people. In the Heddle Lab I have a wide remit which I hope will improve the functioning of our lab. I am really glad that I have a chance to be a part of such briliant, international team.

    Piotr Stępień

    Polish biophysicist with expertise in membrane mimetic systems and various spectroscopic techniques. Interplay between proteins and lipids always fascinated me so why not add DNA into the mix? Add to this my passion for LEGO bricks and problem solving and the only answer is bionanoscience! In Heddle lab I am trying to prepare DNA-based nanorobots for delivery of membrane proteins in oriented fashion. My other interests include: Electron Paramagnetic Resonance and making music — that’s why they call me true resonance man.

    Md. Sirajul Islam

    I am working as a Postdoctoral Researcher in the Heddle lab. My current researches focus on exploring methodology for controlled interaction of proteins merging diverse techniques such as DNA nanorobots and microfluidics. I also worked as Postdoctoral Fellow in Hokkaido University and Kansai University, Japan. I received my PhD in Biophysics from Hokkaido University, Japan. Before that I achieved my Bachelor and Master’s degrees from the Department of Chemistry, University of Dhaka, Bangladesh. My research experiences include the purification and handling of cytoskeletal and membrane proteins, designing, synthesizing and building of the DNA origami and its interaction with proteins.

    Wojciech Czyszczoń

    I am a Master student at Jagiellonian University. In Heddle lab I am working on topoisomerase-targeting pentapeptide repeat proteins to understand their role in DNA gyrase protection against fluoroquinolones. Personally, I am interested in ethnography and traveling. I am also a passionate of mountain hiking - especially Beskid Niski and Bieszczady with the culture of Lemkos and Boykos which I find very fascinating.

    Mantu Kumar

    In the Heddle lab, my project is to design and produce highly programmable modular DNA Nano-robots for the delivery of therapeutic proteins. I will characterize the produced composite structure using various biophysical techniques including functional assays. Before joining the Heddle Lab, I have completed masters in biochemistry from the central university of Rajasthan and was working as project fellow in the area of biochemistry and structural biology at 'CSIR-centre for cellular and molecular biology' India.

    Yang Zheng

    I am a Master student in Jagiellonian University, majoring in Molecular Biotechnology, The reason why I have chosen the scientific area was due to its ability to inspire and boost people`s thinking, plus I am alway ready for new challenges in my life. I am working witht the protein engineering team in the Heddle lab. My hobby is reading and learning new languages, sometimes exercising in the gym as well.

    Samarpita Lahiri

    I ’m a bio-crystallographer working as a post-doctoral fellow in Heddle’s lab. I did my Ph.D. from Italy in biochemistry and bio-crystallography on DNA Repair Proteins. Prime domain of my research expertise deals with Recombinant protein production, Biochemical characterization, and X-ray Macromolecular Crystallography. Currently, in the Heddle lab my research is mainly focused on structural, biochemical, interaction studies of DNA gyrases. Apart from science, I am interested in singing (Indian classical music) and traveling.

    Sylwia Świątek

    I studied chemistry at Jagiellonian University and AGH University of Science and Technology. I will soon complete my PhD at Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science. During that time I studied structural and functional relationship of bovine beta-lactoglobulin with wide range of methods (X-ray diffraction, quartz crystal microbalance, dynamic light scattering). I am motivated to further broaden my experience and to enter the new field of protein structure biology by joining Heddle Lab as a technician. In my spare time I enjoy being in nature. I am interested in fitness, gardening and reptiles.

    Naoto Asai

    I am developing a detection device by combining an aptamer and a biosensor as an internship student in the Heddle lab. In Japan, I have studied improvement of the sensitivity of sensors by utilizing large surface areas nanostructures, as a 2nd year PhD student in Kansai University. My research mission is to manufacture a useful diagnosis device for promoting early detection, delivering it to people. Oligonucleotide-based aptamers are suitable due to several advantages, for example low cost synthesis, uniform activity and programable capability. Additionally, I am ensuring that some electronic elements are replaced by an bioelectronic element composed of DNA structure to allow high densities. As a first step, I am developing an aptamer-based biosensor in the Heddle lab.

    Yusuke Azuma

    I am an Adjunkt, assistant professor, working on protein cage engineering. I grew up in Japan and obtained my PhD from Kyoto University with Prof. Shiroh Futaki, where I was trained in peptide chemistry. To expand my scientific skills and knowledge in intelligent protein design and directed evolution, I had a short internship and postdoc training at the University of Potsdam with Prof. Katja Arndt and at ETH Zurich with Prof. Donald Hilvert, respectively. In 2018, I joined the Heddle group to acquire deep expertise in nanotechnology and to develop my own research career in artificial compartment design for storage and catalysis. All the while, my ever-long childhood dream is to become a professional baseball player or snowboard rider. You can find our more about me on research gate and orcid

    Abdulhalim Kiliç

    My degree in Molecular Biology-Genetics and Biotechnology (Turkey) with a specialization in “artificial cell membrane models” encouraged and led me to the area of “artificial cells” using a bottom-up approach and necessitated to extend my skills on the emerging technologies in the field of synthetic biology. To realize my ideal and gain experience, fortunately I joined to the Heddle lab as a Postdoctoral Researcher. My main focus is on the controlled reconstitution of membrane-proteins onto protocells via designed nanorobots in conjunction with a droplet-based microfluidic system. My research experiences include liposome production, functional lipid bilayer construction, cell– surface interactions, utilization of surface-sensitive techniques (QCM-D, SPR).

    Previous Members

    • Iga Niemiec. Iga worked with us an intern researching DNA gyrase.
    • Monika Zazula. Monika was our previous Lab Manager.
    • Renata Pałka. Renata was a Masters student working on protein bionanoscience.
    • Maciej Michalak. Maciej Michalak was a Masters student working on protein bionanoscience.