Laboratory of Structural Biology and Cell Signaling

News

2022/07/21:

Our work on top-down FPOP, highlighting the benefits of exact gas-phase isolation of selected protein species and multiple fragmentation modes, is now available in the Analytical Chemistry!

2022/06/22:

Another popularization event with Aleš & Co. participation - Věda Fest!

2022/06/10:

Congratulations to Aleš on becoming a group leader at the 1st Faculty of Medicine where he will continue with Víťa in their adventures. Good luck! We enjoyed the time together and are glad that we stay in close contact and will still work together.

2022/06/04:

Our PhDs lead by Aleš were presenting at the Science Fair (Veletrh vědy). Great event! Some pictures here - one, two, three... ;)

2022/06/02:

Another great paper on NQO1, now about cavity making mutantions and allostery in flavoproteins. Excellent multilaboratory collaboration lead by Angel L. Pey from the University of Granada. Thanks to EPIC-XS H2020 Project for support!

2022/05/19:

This is big. Fantastic collaboration with Moshe and Yoni on cis-prenyltransferase continues with another great outcome. Paper now published in Sci. Adv. reveals how these enzymes synthesize long products via small active site!

2022/02/14:

Happy to help Klara and her team (KH lab) with the work deciphering evolution of early protein-RNA interaction. Paper supported by Terka and The Boss is now in high-ranking Mol. Biol. Evol. journal!

2022/02/09:

Marok's work on FPOP combined with top-down for transcription factor::dsDNA interaction is now published in Anal. Chem.! Very nice complement to our previus HDX and X-linking studies, now with residue level resolution.

2021/12/08:

Our team is growing! Welcome Maartje and Michael! We now have two real experts to expand MS into a second dimension and shoot the protein ions with all electron and laser guns we have. Top-down era of our lab is now making a huge leap forward.

2021/12/06:

Happy news! We received funding from the Czech Science Foundation to expand structural proteomics tools by developing new reagents, enhancing the existing ones and diving into transmembrane proteins.

2021/12/01:

Great success of Jarin and Fiji who have their protein fast-fluoralkylation tricks now published in prestigious  J Am Chem Soc. Also thanks for fruitful collaboration - Beier group and CF Plus Chemicals.

2021/11/25:

Highly productive collaboration with Angel Pey led to another publication on mammalian NQO1 flavoproteins. This time on phosphorylation and a specific evolutionary divergent mutation close to it. Available in FEBS Letters. Thanks to EU_FT-ICR_MS H2020 Project for support!

2021/11/04:

Our systematic structural characterization of haptoglobin-hemoglobin interaction resulted in a first paper, Hp-Hb interaction studied by FPOP.

2021/09/23:

Congratulations to Honza (Fiji), now officially PhD in biochemistry!

2021/09/22:

Active and productive collaboration with Sergei Strelkov's lab resulted in another paper on lamin assembly. Work was done under EU_FT-ICR_MS H2020 Project.

2021/09/01:

After several years of post-docking in Hamburg, Alan returns to our lab. Welcome home Alan!

2021/08/20:

Great collaboration with Angel Luis Pey from the University of Granada resulted in a very nice multidisciplinary study on the effect of mutations in human flavoproteins. Now available in Redox Biology! Thanks to EU_FT-ICR_MS H2020 Project for support!

2021/06/15:

We are organizing 2nd Advanced User School under the H2020 EU_FT-ICR_MS consortium. The school will be held in Prague/Vestec, Czech Republic on September 26-30, 2021 and will be stuffed with basics and applications of FT-ICR MS. Participation fee, accommodation and meals covered for 50 selected participants. Registration form can be found HERE. Deadline for application - Aug 23, 2021. Entry to CZ is regulated according to actual COVID situation.

2021/05/31:

Petr's collaboration with the Volf's lab and Austrian's parasitologists is now published in Parasit. Vectors.

2021/04/21:

Proteomic analysis of F. pinicola secretome leading to expression and characterization of two laccases (collaboration with the Ludwig Lab) has just been accepted in Enzyme Microb Technol

2021/04/09:

Structural analysis of human haptoglobin by FPOP and the benefits of ion mobility (TIMS/PASEF) for such analysis is now published in ACS Omega

2021/03/25:

Structural aspects of Von Willebrand factor binding and processing by metallopeptidase ADAMTS-13 studiedby integrative structural biology. Trans-national access via the EPIC-XS resulted in a joint publication in J. Mol. Biol.

2021/03/10:

The results of collaboration with the parasitology groups from Charles University and Morroco are now published in Transboundary and Emerging Diseases

2021/03/08:

Our software LinX for interpretation of chemical cross-linking data, with special features for homodimer elucidation or protein:DNA cross-links is now available on GitHub and related paper published in J Prot Res

2021/02/05:

Nice colaboration with Erik Sedlak's group on cytochrome c oxidation is now available in Int J Biol Macromol. Thanks EU_FT-ICR_MS H2020 Project for supporting this trans-national access! Enjoy 50 days of free access using the link above (till Mar 27, 2021).

2021/01/31:

New joint paper with Ales, from the times he was not part of our lab. FEBS J paper on Ku70/80 intramolecular interactions combining cryoEM and structural MS.

2021/01/08:

Collaboration with the Ludwig lab resulted in another paper on wood degrading enzymes. This time about chimeric CDHs in ACS Catalysis.

2020/12/18:

Paper on TEAD1-DNA interaction is now published in Structure. Enjoy 50 days of free access (till Feb 4, 2021).

2020/12/14:

Congratulations to Paja, now officially PhD in biochemistry!

2020/12/11:

Our HDX workflow combined with Ruza's experience on protein-DNA interaction studies was compiled into Methods Mol. Biol. chapter that has just been published.

2020/11/20:

Two new papers employing MALDI biotyping of sand flies are now in Parasit. Vectors. Collaboration of Petr with the Volf's lab.

2020/10/19:

Pleasant colaboration with Haitin Lab on cis-prenyltrasferase made it from BioRXiv to Nature Communications!. Thanks EU_FT-ICR_MS H2020 Project for support!

2020/10/12:

Petr contributed to another community-wide paper stuffed with ideas and recommendations toward transparency and accessibility of data from cross-linking mass spectrometry. Check the full text!

2020/09/24:

Congratulations to Franta, now officially PhD in biochemistry!

2020/09/17:

Collaborative work with the team of Vaclav Veverka is now available in Structure.

2020/09/09:

Karel Vališ joined the Reviewer Board of Metabolites.

2020/09/07:

3D printing of MALDI targets is now published in Analytical Chemistry.

2020/09/07:

Files for hands-on sessions at 21. Czech MS School are available under Downloads.

2020/07/14:

Collaboration with Sergei Strelkov's lab on lamin assembly is now published. Work was done under EU_FT-ICR_MS H2020 Project.

2020/06/28:

We are organizing 7th Short Course Structural Proteomics: Analysis of protein surface accessibility by Top Down mass spectrometry under the H2020 EU_FT-ICR_MS consortium. The course will be held in Prague/Vestec, Czech Republic on August 16-19, 2020. There are still free places so do not hesitate to apply. Please be aware that travel restriction may apply and the situation may change till half of August.

2020/06/18:

Nice work and pleasant collaboration with the Haitin Lab on soluble chloride channel Clic-5 now out in The FASEB J.
Thanks EU_FT-ICR_MS H2020 Project for support!

2020/06/12:

Another collaborative work with Haitin Lab done under EU_FT-ICR_MS H2020 Project this time on cis-prenyltrasferase is available as preprint on bioRXiv.

2020/06/01:

Ales Hnizda joined our lab. He is funded by Marie Sklodowska-Curie Action Individual Fellowship (Widening). Welcome Ales!

2020/05/05:

Collaboration with RECAMO team on heat shock proteins and co-chaperones resulted in another paper The interaction of the mitochondrial protein importer TOMM34 with HSP70 is regulated by TOMM34 phosphorylation and binding to 14-3-3 adaptors. which is now available in J Biol Chem.

2020/05/03:

New review Targeting ERK-Hippo Interplay in Cancer Therapy. from Karel is now published in Int. J. Mol. Sci..

2020/03/26:

CIISB offers priority and free-of-charge access for COVID-19 research proposals! More here

2020/03/05:

Another TNA access under EU_FT-ICR_MS H2020 Project resulted in joint paper with Erik Sedlak from Kosice. Now published in Scientific Reports.

2020/03/05:

Cellulose degradation combo by Franta. Two papers arising from collaboration with Roland Ludwig and Daniel Kracher are out. One in Biomolecules and another in Biotechnol. Biofuels.

2020/03/03:

Dmitry Loginov joined our lab. Welcome Dmitry!

2020/02/28:

Our systematic effort to understand what is going in chemical cross-linking resulted in another paper. This time about the cross-linker polarity. Enjoy author's copy available for 50 days.

2020/01/23:

Collaboration with Obsil's team on the interaction between 14-3-3 and caspase-2 was accepted in FEBS J.

2020/01/21:

We are proud of our IMIC colleagues Zdenek and Lucka for making this JACS paper a reality. And very happy to help with our MS skills!

2020/01/08:

Our new computational platform for biomolecular language processing called MatrixMotif is now available for download.

2020/01/07:

Petr Novak became the chair of the Czech Proteomics Society. Congratulations! :)

2020/01/07:

6th Short Course on FT-ICR-MS aimed at "Mapping post-translational modifications through FT-ICR" will be held in Lisbon in March 2020. Apply now, no participation fee, accommodation and meals covered!

2019/12/18:

Long-lasting, nice and enjoyable collaboration with Gill Norris from Massey University (NZ) resulted in one more paper on bacterions. Now published in FEBS Letters.

2019/12/12:

Results of another TNA access under EU_FT-ICR_MS H2020 Project are now in the FEBS Journal. Collaboration with the University of Pavia, Italy.

2019/12/11:

TNA access under EU_FT-ICR_MS H2020 Project gave rise to this nice paper on NQO1 dynamics. Collaboration with Angel L. Pey from the University of Granada, Spain.

2019/11/08:

Our collaboration with RECAMO team resulted in paper HSPA1A conformational mutants reveal a conserved structural unit in Hsp70 proteins. which is now available in BBA General Subjects.
Enjoy free author's access until Dec 27(using the hyperlink above)!

2019/10/28:

Petr Novak joined the Editorial Board of Biomolecules.

2019/10/10:

Joint paper with Volf's lab showing identification of blood sources of Hematophagous arthropods is now in PLOS Neglected Tropical Diseases..

2019/10/04:

Our new publication combining ambient ion landing of proteases with structural biology is now in Catalyst.

2019/09/27:

The EPIC-XS proposal submission system is now online. Proposal can be submitted here.

2019/09/26:

Our paper describing characterization of transcription factor/DNA interaction by structural mass spectrometry has just been accepted!

2019/09/25:

Collaboration between IMIC, IOCB and CF Plus Chemicals resulted in a publication which is now available in Chemistry journal.

2019/08/05:

5th Short Course on FT-ICR-MS aimed at "Basics of FT-ICR: dynamic harmonization and computer simulation" will be held in early October in Moscow. Apply now, no participation fee, accommodation and meals covered!

2019/07/24:

Preprint version of our paper combining structural MS approaches for characterization of transcription factor / DNA interaction is now available in Biomolecules.

2019/07/19:

Chromatin Proteomics Workshop coorganized by EPIC-XS H2020 consortium will be on Sep 22-27, 2019 in Greece. Deadline (Jul 29) is approaching!.

2019/07/15:



Two new papers dealing with HDX-MS are out. In one we contributed to very important community wide guidelines paper in Nat. Methods - Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Antoher one is a joint Anal. Chem. paper with Kasper Rand's lab on HDX-compatible digestion of membrane proteins.

2019/07/10:



Joint paper with Valasek's lab describing how chemical cross-linking helps in structural characterization of 40S ribosomal subunit interacting with eIFs is now available in Nucleic Acid Research.

2019/07/10:

Short course on High Resolution Tandem Mass Spectrometry of Biomolecules will be organized by the EU_FT-ICR_MS H2020 consortium. Save the date and place: Aug 21-23, 2019, Warwick. Register here.

2019/06/24:



Few years ago, we helped Petrak's lab with the development of transmembrane proteome analysis. We are happy that Jirka's team is pushing it further and even happier we still keep in touch as this resulted in another nice J Proteomics paper.

2019/06/15:



Deadline for the first round of Transnational access proposal submission to EPIC-XS is apporaching (30th June 2019).

2019/06/12:



Congratulations to our Bc students (Zuzka, Verča, Týna, Kamila and Jana) on successful defense of their Bc theses.

2019/05/31:



Congratulations to Lucka Wallenfels (Hernychová) on successful defense of her PhD thesis and other happy life events. All the best in the future Lucka!.

2019/05/06:

Attempts to fully uderstand and somehow unify chemical cross-linking pushed further through interlaboratory comparion in which we participated. Read more in this community-wide Analytical Chemistry paper.

2019/05/05:

Short course on Ion-molecule reactions: fundamental and analytical aspects will be organized by the EU_FT-ICR_MS H2020 consortium. Save the date and place: June 25-27, 2019, Roma. Register here.

2019/04/29:

New publication about oligomerisation of NK cell receptors evaluated using homo-FRET and high resolution mass spectrometry - colaboration with Marek Cebecauer's group - is online in the International Journal of Molecular Sciences.

2019/03/02:

Advanced Users School on FT-ICR background will be organized by the EU_FT-ICR_MS H2020 consortium. Save the date and place: Apr 14-Apr18, 2019, Lisbon. Register here.

2019/01/26:

Joint paper with Ales Hnizda on structural characterization of pyrophosphatase NUDT15 and its thiopurine intolerance causing mutations is now available in Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics.

2018/11/28:

We recieved funding from Czech Science Foundation to study protein structure by reactive radical footprinting and top-down mass spectrometry.

2018/11/20:

Paper on Hsp70 dimerization - our collaboration with RECAMO team - has just been accepted in Mol Cell Proteomics.

2018/11/08:

Our work about structure of NK cell receptor Nkrp1b is now in Journal of Proteomics.

2018/09/13:

We are proud to be a part of another EU Horizon 2020 project called EPIC-XS (European Proteomics Infrastructure Consortium providing Access).

2018/07/19:

Our paper on MALDI chips suitable for detection of transferrin variants is now in Clinical Chemistry. So now we can detect who has serious problem with alcohol...

2018/07/13:

FEBS Congress 2018 in Prague is over. Thanks all who represented our lab at this event (one oral, one speed talk and four posters).

2018/07/12:

Joint paper with Veverka's group is now in PNAS.

2018/06/25:

Unique possibility to learn about FT-ICR MS opens to anyone through Summer school funded by EU FT-ICR MS Horizon project. Details available here. Number of places is limited, expenses are covered!

2018/06/14:

Prof. Dan Fabris from the University at Albany has just joined our group for half a year. Together we will work on DNA/RNA structure and interactions.

2018/06/09:

We returned from California where our lab presented three posters at the 66th ASMS Conference on Mass Spectrometry and Allied Topics

2018/06/07:

Joint paper with Sebo lab is now in FEBS Open Bio.

2018/04/14:

7th national MS conference at IMG in Prague was great! Thanks to all labmembers for their presentation (7poster talks + posters) and congratulations to Petra on the third place in Poster prize competition.

2018/03/05:

Trans-national access to our lab and the FT-ICR facility in BIOCEV is available for EU labs through EU-FTICR-MS project (Horizon 2020). You can apply here.

2018/02/26:

Results of fruitful collaboration with IOCB group were published in Leukemia.

2018/01/03:

Our lab is part of H2020 project European Network of Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry Centers.

2017/12/28:

The effect of Quambalarine B on leukemic cells is now published in Oncotarget.

2017/12/18:

Software LinX ready for download.

2017/12/15:

A paper about structure of beta-N-acetylhexosaminidase is now in FEBS J.

2017/12/14:

Our work describing influence of cross-linker on the protein structure is now in Analytical Chemistry (2017/12/14)

2017/11/03:

Paper about structure and dynamics of heme-containing gas sensing protein where three groups joint their expertise (Martinkova lab, Dohnalek lab and our group) has just been accepted in J Biol Chem (2017/11/01)

2017/11/03:

Three talks and five posters from the lab just presented at the 7th Symposium on Structural Biology which was again a great event! (2017/10/25)

2017/11/03:

Joint paper with Obsil’s group just published in BBRC (2017/10/09)

2017/09/13:

Publication Protein Chips Compatible with MALDI Mass Spectrometry Prepared by Ambient Ion Landing was awarded Vladimir Hanus prize! Congratulations to all authors.

2017/06/28:

Petr Novak’s presentation at Proteins in action – biophysical techniques for protein research can be downloaded here.

2017/06/07:

Five posters presented by our great PhDs (Petra, Růža, Lucka, Michal and Lukáš) at the 65th ASMS conference in Indianapolis.

2017/06/01:

Joint paper with Eric Forest and Daniel Khananshvili has just appeared in the Journal of Biological Chemistry

2017/05/17:

Pavla and Jirka just presented posters at the first HDXMS conference in Sweden.

2017/04/12:

Great collaboration with Dave Schriemer’s lab on carnivorous proteases continues. Newly identified acid protease neprosin and its use in proteomics now in Molecular and Cellular Proteomics!

2017/04/11:

Another brick in the 14-3-3 wall with Obsil’s lab now in Biophysical Journal

2017/03/31:

Our lab presented five posters (Pavla, Franta, Michal, Lukáš and Jirka) and gave two talks (Petra and Petr N.) at the Czech MS Conference in Olomouc.

2017/02/20:

Karel’s interview for NEURON is available here

2017/02/11:

Our work on cellobiose dehydrogenase function is available in Biochimica et Biophysica Acta

2017/02/05:

Petra turned her master thesis into a publication in the Journal of Proteomics!

2016/12/10:

Our contribution to understanding of the Hippo signalling pathway is now available in the Experimental Cell Research.

2016/10/19:

Great collaboration with Aleš Hnízda on misregulation of purine 5´-nucleotidase is now online in the BMC Biology.

2016/10/10:

Joint paper with Markéta Martínková’s group in now in Proteins

2016/10/01:

Two papers with Obsil’s lab appeared in Sep and Oct in FEBS Journal and Journal of Biological Chemistry

2016/09/23:

Work on anticancer effect of Quambalarine B is now online in Journal of Natural Products

2016/09/19:

PhD thesis from the lab defended! Congratulations to Alan Kadek

2016/09/13:

Lab in media: Pomohli jsme odhalit co zabíjí zimující netopýry. original article in Scientific Reports

2016/09/05:

Bachelor and diploma theses from the group defended! Congratulations to Jitka Smetanova and Pavla Vankova

2016/08/15:

Lab in media: Our joint work with Dave Schriemer’s group on nepenthes proteases holds promise for celiac patiens. original article in Scientific Reports

2016/05/26:

Two diploma theses from the group defended! Congratulations to Ruzena Liskova and Frantisek Filandr

2016/03/19:

Lab in media: Our joint work with Jiri Petrak’s group on membrane proteomics attracts attention of proteomic community. original article in Journal of Proteomics

2016/01/04:

Lab in media: Commentary to our work on functionalized surfaces for MALDI-MS original article in Clinical Chemistry