Future Events connected with Project:

Year 2022

Seminar Speaker Series’ of project StruBioMol

 

 

Past Events connected with Project:

Year 2022

2nd StruBioMol Workshop: Isolation, Characterization and Crystallization of Proteins

When:

14.06.2022 – 15.06.2022

Where:

Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, Bratislava, Slovakia

Topics:

The workshop will provide an introduction into the isolation, purification, thermal stability and crystallization of proteins. The covered techniques will be differential scanning fluorimetry (nanoDSF and Thermofluor), and protein crystallization (Manual and high-throughput techniques using Formulatrix crystallization robots). The workshop is divided into two sections (morning with lectures and afternoon with practical`s) and is intended for Masters’ and PhD students, postdocs and other researchers in the Vienna-Bratislava cross-border region. The number of attendees for practicals is limited and there will be selection from registered participants, but all registered participants can attend the morning lectures section.

The participants could bring their own protein samples for testing after prior consultation with organizers.

Travel grants:

A limited number of travel grants and accommodations are available for participants. Applicants do not need to apply separately for travel grants for this event but should indicate on the registration form if they wish to be considered for a travel grant. Selection of awardees is handled directly by the organizer who will notify all eligible participants.

Registration:

until 26.05. 2022 at 12.00 CET

 

https://docs.google.com/forms/d/e/1FAIpQLSd4T7xEx2w7F-W0nfGJenuqxbVKaf_MnIAwvkrFdig2AYdJIA/viewform

Contact:

In case of any questions, please contact: biochemiaumb@gmail.com

 

Organizers, Speakers and Tutors:

Kristina Djinovic Carugo, Max Perutz Labs, University of Vienna

Eva Kutejová, Institute of Molecular Biology SAS, Bratislava

Vladimír Pevala, Institute of Molecular Biology SAS, Bratislava

Antonio Sponga, Max Perutz Labs, University of Vienna

Pavlina Maloy Rezacova, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague

Sami Kereïche, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague

Cyril Bařinka, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague

Jacob Bauer, Institute of Molecular Biology SAS, Bratislava

Vladena Bauerová, Institute of Molecular Biology SAS, Bratislava

Nina Kunová, Institute of Molecular Biology SAS, Bratislava

Gabriela Ondrovičová, Institute of Molecular Biology SAS, Bratislava 

 

Program:

Tuesday 14th June

 9:00 - 9:15     Welcome and Introduction

Kristina Djinovic Carugo, Eva Kutejova

9:15 - 10:15      Protein expression

Cyril Bařinka

10:15 - 11:15     Protein purification for biochemical and structural studies

Antonio Sponga

11:15 - 11:30     Coffee break

11:30 - 12:30    Protein thermal stability - differential scanning fluorimetry

Vladena Bauerová

12:30 - 13:15    Lunch + Discussions

13:15 -  15:45   Practicals on nanoDSF and thermofluor

15:45 - 16:00    Coffee break

16:00 - 18:00    Practicals on nanoDSF and thermofluor

 

Wednesday 15th June

9:00 - 10:00      Crystallisation of macromolecules

Jacob Bauer

10:00 - 11:00     X-ray crystallography in drug discovery

Pavlina Maloy Rezacova

11:00 - 11:15     Coffee break

11:15 - 12:00     Electron microscopy in protein structure determination

Sami Kereïche

12:00 - 13:00     Lunch + Discussions

13:00 -  15:00    Practicals on crystallisation

15:00 - 15:15    Coffee break

 

15:15 - 18:00    Practicals on crystallisation

 

 

Rok 2021:

Dr. Dominika Fričová

Institute of Neuroimmunology SAS, Bratislava, Slovakia

What can we learn from Parkinson’s disease-related mutations? 

23.11.2021 o 14:00

Zoom online video presentation:

https://us02web.zoom.us/j/202574764?pwd=QjlDQ2tiU09RSUJKQkZVQUVQbWRZUT09

Abstract: 

Mitochondrial dysfunction has been hypothesized to play a central role in the pathobiology of Parkinson’s disease (PD). The identification of mutations in genes encoding PINK1 (PTEN-induced kinase 1) and Parkin (E3 ubiquitin ligase) in familial PD and their functional association with mitochondrial quality control provided further support to this hypothesis. We have recently identified a heterozygous missense mutation in PINK1 changing glycine 411 (G411) to serine (S) that increases the risk for PD. Our studies in PD patient’s fibroblasts and derived iNeurons carrying heterozygous PINK1 p.G411S mutation revealed aberrant auto-phosphorylation of PINK1 p.G411S and significant reduction of PINK1 kinase activity. We uncovered a partial loss-of-function as well as a dominant-negative effect of the PINK1 p.G411S due to its interaction with WT PINK1. Subsequent impairment in cytoprotective functions of the PINK1/Parkin-mediated mitochondrial quality control then causes later manifestation of the disease in heterozygous p.G411S mutation carriers than homozygous loss-of-function mutations in PD cases. In order to analyze the molecular mechanisms of p.G411S mutation-mediated pathobiology in greater detail we employed CRISPR/Cas9 technique and introduced p.G411S mutation in HEK293T cells. As a control for our experiments, we introduced in the same genetic background a point mutation which doesn’t allow aberrant PINK1 phosphorylation - PINK1 G411 to alanine (A). Our experiments indicate that aberrant phosphorylation of S411, alters substrate binding and reduces the activity of PINK1 towards Ub and Parkin phosphorylation. Surprisingly, introduction of non-phosphorylatable residue A411 dramatically increased the activity of PINK1 towards these substrates. Our findings are supported by structural modeling and dynamics simulations that suggest higher receptivity of PINK1 A411 across different PINK1 substrates. Importantly, the increase of PINK1 A411 activity translates to higher mitochondrial turnover after mitochondrial damage induction with potential cytoprotective impact.

 

Prof. Tony Wilkinson

Head of York Structural Biology Laboratory, Department of Chemistry, University of York, UK

Post-translational modification systems as targets for inhibition in Leishmania therapy 

04.05.2021 at 14:00

Zoom online video presentation:

https://us02web.zoom.us/j/202574764?pwd=QjlDQ2tiU09RSUJKQkZVQUVQbWRZUT09

Abstrakt: Leishmaniases are a group of neglected tropical diseases caused by protozoan Leishmania parasites, which are transmitted by sand flies. There are three main forms of the disease with cutaneous leishmaniasis (CL) the most common and visceral leishmaniasis (VL) the most severe and usually fatal if untreated. Up to one billion people live in areas of the world where leishmania is endemic leading to over 1 million new CL cases and 30,000 new VL cases each year. There is no vaccine available so chemotherapy is the principal method of intervention. Current drugs suffer from various drawbacks including toxic side effects, lack of oral formulation, prolonged treatment times, high costs of treatment and the emergence of drug resistance. As a result, there is a pressing need to discover and develop new drugs for the treatment of leishmaniasis. With this in mind, we have been carrying out drug target validation of post-translational modification (PTM) enzymes of Leishmania. PTM systems have proved fertile territory for therapeutic intervention in human disease with many current therapies targeting PTM components. We belong to a Neglected Tropical Diseases Network involving groups in Asia and South America that is using gene knock-out/knock-down technologies to identify essential PTM genes in Leishmania species. We are especially interested in genes required for parasite differentiation from the promastigote form, which is transmitted by the sand fly, to the amastigote form that establishes infection and causes human disease. Targets identified and characterised in studies of the parasite ubiquitination/deubiquitination system will be discussed (1).

The talk will then describe an in-depth study of N-myristoyltransferase (NMT) an enzyme which catalyses the co-translational attachment of a C14 fatty acid to the amino terminal glycine residue of a subset of proteins. NMT is an essential enzyme in L. donovani and a promising target for drug discovery. In a collaborative study, we carried out high-throughput screens for inhibitors (2) and followed this is up with a combination of Medicinal Chemistry, Structural Biology and Parasitology to develop several compound series into potent and specific inhibitors (3, 4). As part of this work, inhibitors of the human host NMT were discovered, which showed potential for the treatment of diseases caused by picornaviruses including the common cold.

1. Burge RJ, Damianou A, Wilkinson AJ, Rodenko B, & Mottram JC (2020) Leishmania differentiation requires ubiquitin conjugation mediated by a UBC2-UEV1 E2 complex. PLoS Pathog 16(10):e1008784.
2. Brannigan J, et al. (2014) Diverse modes of binding in structures of Leishmania major N-myristoyltransferase with selective inhibitors. IUCr Journal 1:250-260.
3. Bell AS, et al. (2020) Novel Thienopyrimidine Inhibitors of Leishmania N-Myristoyltransferase with On-Target Activity in Intracellular Amastigotes. J Med Chem 63(14):7740-7765.
4. Mousnier A, et al. (2018) Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus. Nat Chem 10(6):599-606.
 

Dr. Jacob BAUER

Institute of Molecular Biology SAS, Dúbravská cesta 21, Bratislava, Slovakia

Normal Mode Analysis and Its Application to Protein Structure Studies

14.01.2021 at 14:00

Abstrakt: Normal Mode Analysis (NMA) is a computational technique that can be used to calculate the flexible states available to a protein from a given equilibrium conformation. It produces results comparable to those from molecular dynamics simulation combined with principal components analysis but at a fraction of the computational cost. Although it has been used for certain applications in protein crystallography for many years, it is still uncommon to find it a part of the analysis step in a protein crystal structure study. Here, I will briefly describe the theory and most common applications of NMA. I will illustrate some of its strengths and limitations using a case study from the literature, and will discuss a potential application to single-molecule optical tweezers experiments 

ZOOM Online videoprezentácia: https://zoom.us/j/91905230005?pwd=anZ0aXlJandMTEpEcCtQUzJoMmxtZz09

Meeting-ID: 919 0523 0005

Kenncode: 997466

Host: Kristina Djinovic-Carugo

https://www.maxperutzlabs.ac.at/news/lectures/l/normal-mode-analysis-and-its-application-to-protein-structure-studies-1003

 

Rok 2020:

Dr. Kvido Stříšovský

Kontrola kvality membránových proteínov a intramembránová proteolýza 

06.10.2020 o 13:00

 ZOOM Online videoprezentácia: https://us02web.zoom.us/j/202574764?pwd=QjlDQ2tiU09RSUJKQkZVQUVQbWRZUT09

 


Thomas Gohl, PhD. a Mayank Aggarwal, PhD.

FORMULATRIX Workflow solution

29.09.2020 o 14:00

Program: 

- Quick Introduction (TG)

- Systems – Specific features of systems for high throughput automation (TG)

               RI54 –                     Imager

               Formulator –           Screen Maker

               NT8 –                       Drop Setter

- Rock Maker – Protein Crystallization Software (MA)

               Grid Optimization

               Random Optimization

               Iterative Screen Optimization

               MARCO – Machine Recognition of Crystallization Outcomes

 

WebEx Online videoprezentácia: odkaz bude odoslaný registrovaným účastníkom

 

Registrácia: e-mailom na adresu biochemiaumb@gmail.com

 


Vyberte si nový zlatý štandard v charakterizácii stability proteínov

Piotr Wardega (NanoTemper)

Pondelok 20. júla 2020 o 13:00 v prednáškovej miestnosti ÚMB SAV

Prednáška bude obsahovať všeobecné informácie o diferenciálnej skenovacej fluorimetrii a princípoch práce s novým prístrojom nanoDSF Prometheus od NanoTemper

 


Inštruktážna prednáška k ultracentrifúge Beckman

Štvrtok 9. júla 2020 o 13:00 v prednáškovej miestnosti ÚMB SAV

Obsahom školenia budú všeobecné postupy pre ultracentrifugy, zásady práce s rotormi, skúmavkami a praktická ukážka u novo inštalovanej sálovej ultracentrifúgy Optima XPN

 


Dr. Cyril Bařinka

Štruktúra ligandov na zobrazovanie a terapiu rakoviny prostaty pomocou štruktúr

31.03.2020 o 14:00

Prednášková sála Ústavu molekulárnej biológie SAV, Dúbravská cesta 21, Bratislava, Slovensko

 


Rok 2019:

1. workshop StruBioMol: Biofyzikálna charakterizácia a kryštalizácia proteínov

Workshop sa uskutoční okamžite po workshope Interreg SK-AT „CAPSID“ na tému Úvod do prípravy, čistenia a hodnotenia kvality rekombinantného proteínu, ktorý sa bude konať 3-4. Decembra 2019 (capsid.vbcf.ac.at/events/), čo so sebou prináša veľa synergií medzi oboma projektmi.

Kedy: 05.12.2019 - 06.12.2019

Kde: Katedra štruktúrnej a výpočtovej biológie, Max Perutz Labs, Viedenská univerzita, Campus Vienna Biocenter 5, A-1030, Viedeň

Zameranie:

Workshop poskytne úvod do biofyzikálnej charakterizácie a kryštalizácie proteínov. Pokryté biofyzikálne techniky budú chromatografia, dynamický a statický rozptyl svetla, diferenciálna skenovacia fluorimetria a kruhový dichroizmus (size exclusion chromatography, dynamic and static light scattering, differential scanning fluorimetry, and circular dichroism). Workshop je určený pre študentov magisterského a doktorandského štúdia, doktorandov a ďalších výskumných pracovníkov v cezhraničnom regióne Viedeň - Bratislava.

Kontakt:

V prípade akýchkoľvek otázok kontaktujte interreg86@gmail.com

Rečníci a lektori:

Kristina Djinovic Carugo, laboratóriá Maxa Perutza, Viedenská univerzita

Julius Kostan, Max Perutz Labs, Viedenská univerzita

Joan Lopez Arolas, laboratóriá Maxa Perutza, Viedenská univerzita

Dalibor Milic, Max Perutz Labs, Viedenská univerzita

Georg Mlynek, Max Perutz Labs, Viedenská univerzita

Arthur Sedivy, hlavné zariadenie Viedne BioCenter

Martin Puchinger, hlavné zariadenia Viedne BioCenter

Vladena Bauerová, Slovenská akadémia vied, Bratislava

Program:

Štvrtok 5. December

9:00 - 9:15      Welcome and Introduction

Kristina Djinovic Carugo, Eva Kutejova

 

9:15 - 10:30      Requirements on protein purity for biochemical and structural studies and size exclusion

chromatography

Kristina Djinovic Carugo

10:30 - 11:30    Static and dynamic light scattering

Kristina Djinovic Carugo/Arthur Sedivy

11:30 - 11:50     Coffee break

11:50 - 13:00    Assessment and optimisation of thermal stability with differential scanning fluorimetry

Georg Mlynek

13:00 - 14:00    Lunch

14:00 -  16:15   Practicals on biophysical methods

16:15 - 16:45   Coffee break

16:45 - 18:30   Practicals on biophysical methods

 

Piatok 6. December

9:00 - 10:00     Crystallisation of macromolecules - part I

Kristina Djinovic Carugo

10:00 - 11:00    Crystallisation of macromolecules - part II

Kristina Djinovic Carugo

11:00 - 11:30    Coffee break

11:30 - 13:00    Circular dichroism

Vladena Bauerová

13:00 - 14:00    Lunch

14:00 -  16:15   Practicals on crystallisation and CD

16:15 - 16:45   Coffee break

16:45 - 18:30   Practicals on crystallisation and CD

 

[28.06.2019 Bratislava]

28. júna sa v Bratislave stretli partneri projektu Max Perutz Labs a UMB SAV, aby zahájili projekt Interreg StruBioMol. Projekt je zameraný na zvýšenie medzinárodnej viditeľnosti výskumu štrukturálnej biológie v slovensko-rakúskom pohraničnom regióne. Spolu s 23 strategickými projektovými partnermi sa Viedenská univerzita - Max Perutz Labs vo Viedni a Ústav molekulárnej biológie Slovenskej akadémie vied v Bratislave spojili, aby zlepšili vedeckú komunikáciu v regióne a medzinárodnú viditeľnosť výskumnej komunity štruktúrnej biológie a molekulárnej biológie.

 

StruBioMol je spolufinancovaný z Európskeho fondu regionálneho rozvoja (EFRR) v rámci programu Interreg V-A Slovensko-Rakúsko.