Laboratory for determination of the three-dimensional structure of proteins using x-ray diffraction

Laboratory for determination of the three-dimensional structure of proteins using x-ray diffraction 2008 – 2010
Budget: 1.428.000 lei
Project director: Stefan Szedlacsek
PN-II-Pi-CD-Investitii - 2008 - CAPACITATI (no.194/9.09.2008)

One of the most powerful techniques in modern biomedical research is the determination of the three dimensional structure of proteins. This project proposes to establish a laboratory for 3D protein structure determination using X-ray diffraction experiments.

The acquisition of a suitable protein crystal X-ray diffractometer and several component instruments would provide a fully functional national core facility for protein crystal structure solution. This investment would open a new direction in structural biology research for Romanian scientists, with an expected high impact on the level of research in the life sciences, an increased number of publications in top journals, high chances of Romanian research groups being accepted in European networks dedicated to structural genomics. In addition, this new facility can significantly stimulate the development of new biotechnological units focused on drug design.

Stefan Szedlacsek, Dr.
Stefan Szedlacsek, Dr.

Head of Department

Prof. Dr. Stefan Szedlacsek is the Head of the Enzymology Department at the Institute of Biochemistry of the Romanian Academy. He holds a PhD degree in Biotechnology from Polytechnical University of Bucharest as well as a MSc in Organic Synthesis (Polytechnical University, Bucharest) and MSc in Mathematics (University of Bucharest). As a visiting scientist, he performed research in the field of cholesterol metabolism at the University of Illinois at Urbana-Champaign (USA), where he succeeded to evidence a new pathway in the metabolism of oxysterols.  He is an “Alexander von Humboldt” fellow and worked in Germany, in the Institute of Biochem More...

Project coordinator: Dr.Ștefan Szedlacsek

Dr.Bălașu Mihaela Camelia  - Scientific researcher

Georgiana Petrăreanu          -  PhD student

Mihaela Pascaru                   -  PhD student

Rodica Badea                       -  PhD student

Creation of a dedicated space for the Protein Crystallography Laboratory.

Purchase of essential advanced research equipment for the laboratory.

Provide computing resources and software necessary for structural analysis.

The laboratory has been equipped to carry out high-level research in protein crystallography, meeting international standards and supporting further scientific progress.






Within the II stage of the project, it is proposed to purchase equipment necessary for the preparation and analysis of crystallisation plates.

Thus, part of the research equipment proposed in this project was purchased during this phase.

The protein crystallography laboratory has been equipped with:

- a rapid pipetting system for crystallisation plates,

- a system for transporting crystals under optimal conditions

- A vacuum pump for periodic evacuation of the CCD detector of the X-ray diffractometer,

- the continuous power source,

- incubator for thermostatting the crystallisation plates and Dewar flasks for keeping the crystals liquid in nitrogen.

2 st year 2009

During phase III of the project, a software package was purchased for the processing of the data obtained and the theoretical modelling of the protein structures.

The software purchased, Discovery Studio, offers a variety of tools in a single graphical interface, making it easier than ever to study the properties of protein molecules:

·        2D and 3D visualisation

·        2D and 3D descriptors

·        Quantum and classical mechanics

·        2D and 3D SAR and QSAR analysis

·        Bayesian statistics, neural networks

·        Database analysis

·        Modelling from databases

·        Conformation generation and analysis

·        Design based on or guided by the structure, docking, scoring

·        Ligand-receptor interaction analysis

·        Fragment based design

·        De novo design (LUDI)

·        Pharmacophore generation (catalyst)

·        3D database searching

·        Simulations, molecular mechanics and dynamics (CHARMm@)

·        Explicit and implicit solvated models

·        Transmembrane protein modelling

·        Homology-based modelling

·        Antibody-based model

·        Electrostatic calculations, ionisation and pK predictions

·        Protein modelling (MODELER) and analysis, protein engineering

·        Protein-Protein Docking and Refinement

·        Sequence analysis, sequence alignments, phylogenetic analysis

·        Analysis and refinement of X-ray diffraction structures (CNX).