Future Events connected with Project:
Year 2022
Seminar Speaker Series’ of project StruBioMol
3rd StruBioMol Workshop: Macromolecular structure determination, analysis and validation
When:
02.11.2022 – 03.11.2022
Where:
Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna
Topics:
The workshop will provide the overview to macromolecular crystallography, solution of phase problem, refinement and model building, structure validation, analysis and databases.
Practicals will focus to MR structure solution and refinement (1st day afternoon, 2nd day morning), structure validation, analysis and databases analysis.
The workshop is divided into two sections (1st day morning with lectures and with practical`s in 1st day afternoon, 2nd day morning) 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 (20) and there will be selection from registered participants.
Registration:
until 26.10. 2022 at 12.00 CET
https://forms.gle/zXfD3awmPTTwfEKV8
Contact:
In case of any questions, please contact: admin.vbc5@univie.ac.at
Program:
Wednesday 2nd November
9:15 - 09:30 Welcome
9:30 - 10:30 Overview to macromolecular crystallography
Kristina Djinovic Carugo
10:30 - 11:30 Coffee break
11:30 - 12:15 Solution of phase problem (focus on MR)
Vladena Bauerova
12:15 - 13:00 Refinement and model building
Jacob Bauer
13:00 - 14:15 Lunch + Discussions
14:30 - 16:00 Practicals 1 - Molecular replacement, model building, refinement
Georg Mlynek
Thursday 3rd November
9:30 - 10:15 Structure validation and analysis and databases
Jacob Bauer
10:15 - 10:30 Coffee break
10:30 – 12:20 Practicals 2 - structure validation, analysis
Georg Mlynek
12:30 - 13:30 Lunch + Discussions
13:30 - 16:00 Practicals 2 - databases analysis
Vladena Bauerova
16:00 Closing remarks
Organizers and Speakers:
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
Georg Mlynek, Max Perutz Labs, University of Vienna
Jacob Bauer, Institute of Molecular Biology SAS, Bratislava
Vladena Bauerová, Institute of Molecular Biology SAS, Bratislava
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
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
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 metho&l
