Protein Structure Characterization by Advanced Mass Spectrometry

Protein Structure Characterization by Advanced Mass Spectrometry

RNDr. Petr Novák, Ph.D.

RNDr. Petr Novák, Ph.D. — Project head

About us

Laboratory of Structural Biology and Cell Signaling consists of a multidisciplinary team whose thematic focus is divided into two main directions.

Structural biology group produces proteins by recombinant expression technologies and characterizes the protein or protein-ligand structures and their dynamics utilizing advanced mass spectrometric techniques.

Cell signaling unit examines the linkages of cellular signaling to the metabolism of cancer cells using molecular biology and biochemistry methods.

Through the collaboration of the two groups a unique research platform is formed, wherein the results obtained by the study of biological systems can also be verified and explained at the molecular level.

More info at http://peterslab.org/

Publications

2018

Škerlová J, Bláha J, Pachl P, Hofbauerová K, Kukačka Z, Man P, Pompach P, Novák P, Otwinowski Z, Brynda J, Vaněk O, Řezáčová P (2018): Crystal structure of native β-N-acetylhexosaminidase isolated from Aspergillus oryzae sheds light onto its substrate specificity, high stability, and regulation by propeptide. FEBS J. 2018 Feb; 285(3): 580-598

Rozbesky D, Rosulek M, Kukacka Z, Chmelik J, Man P, Novak P(2018): Impact of Chemical Cross-Linking on Protein Structure and Function. Anal Chem 2018 Jan 16; 90(2):1104-1113

Stranava M, Man P, Skalova T, Kolenko P, Blaha J, Fojtikova V, Martinek V, Dohnalek J, Lengalova A, Rosulek M, Shimizu T, Martinkova M(2017): Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction. J Biol Chem 2017, in press

2017

Vališ K, Grobárová V, Hernychová L, Bugáňová M, Kavan D, Kalous M, Černý J, Stodůlková E, Kuzma M, Flieger M, Černý J, Novák P. (2017): Reprogramming of leukemic cell metabolism through the naphthoquinonic compound Quambalarine B. Oncotarget. 2017 Oct 7;8(61):103137-103153.

Tarbouriech N, Ducournau C, Hutin S, Mas PJ, Man P, Forest E, Hart DJ, Peyrefitte CN, Burmeister WP, Iseni F High-resolution structure of E9, the vaccinia virus DNA polymerase: Insight into the structural organization of the holoenzyme. Nat Commun 2017 Nov 13; 8(1): 1455

Gupta K, Watson AA, Scheer E, Köhler Ch, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson CV, Tora L, Berger I: Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID. eLife 2017 Nov 7; 6. pii: e30395

Bláha J, Kalousková B, Skořepa O, Pažický S, Novák P, Vaněk O. High-level expression and purification of soluble form of human natural killer cell receptor NKR-P1 in HEK293S GnTI- cells. Protein Expr Purif. 2017 Dec;140:36-43.

Kalabova D, Smidova A, Petrvalska O, Alblova M, Kosek D, Man P, Obsil T, Obsilova V. Human procaspase-2 phosphorylation at both S139 and S164 is required for 14-3-3 binding. Biochem Biophys Res Commun. 2017, 493:940-945.

Masin J, Roderova J, Osickova A, Novak P, Bumba L, Fiser R, Sebo P, Osicka R. (2017): The conserved tyrosine residue 940 plays a key structural role in membrane interaction of Bordetella adenylate cyclase toxin. Sci Rep. 2017 Aug;7(1):9330.

Giladi M, van Dijk L, Refaeli B, Almagor L, Hiller R, Man P, Forest E, Khananshvili D. (2017): Dynamic distinctions in the sodium-calcium exchanger adopting the inward- and outward-facing conformational states. J Biol Chem. 2017 Jul 21; 292(29):12311-12323.

Schräder CU, Lee L, Rey M, Sarpe V, Man P, Sharma S, Zabrouskov V, Larsen B, Schriemer DC. (2017): Neprosin, a Selective Prolyl Endoprotease for Bottom-up Proteomics and Histone Mapping. Mol Cell Proteomics. 2017 Jun;16(6):1162-1171.

Team

RNDr. Petr Novák, Ph.D.

RNDr.
Petr Novák, Ph.D.

Head of Group Protein Structure Characterization by Advanced Mass Spectrometry

pnovak@biomed.cas.cz
+420325873610
Mgr. Lyubina Adámková

Mgr.
Lyubina Adámková

Graduate student (currently on maternity leave)

ivanova@biomed.cas.cz
+420325873606
Mgr. Jan Fiala

Mgr.
Jan Fiala

Graduate student

jan.fiala@biomed.cas.cz
+420325873608
Mgr. František Filandr

Mgr.
František Filandr

Graduate student

frantisek.filandr@biomed.cas.cz
+420325873608
Mgr. Daniel Kavan, Ph.D.

Mgr.
Daniel Kavan, Ph.D.

Junior research scientist

kuan@natur.cuni.cz
+420325873609
Mgr. Zdeněk Kukačka, Ph.D.

Mgr.
Zdeněk Kukačka, Ph.D.

Junior research scientist

zdenek.kukacka@biomed.cas.cz
+420325873608
Mgr. Růžena Lišková

Mgr.
Růžena Lišková

Graduate student

ruzena.liskova@biomed.cas.cz
+420325873608
RNDr. Petr Man, Ph.D.

RNDr.
Petr Man, Ph.D.

Senior research scientist

pman@biomed.cas.cz
+420325873610

Ing.
Jana Nováková

Laboratory technician

jana.novakova@biomed.cas.cz
+420325873608
Mgr. Karel Vališ, Ph.D.

Mgr.
Karel Vališ, Ph.D.

Junior research scientist

karel.valis@biomed.cas.cz
+420325873606
Mgr. Pavla Vaňková

Mgr.
Pavla Vaňková

Graduate student

pavla.vankova@biomed.cas.cz
+420325873609
MSc. Ghazaleh Yassaghi

MSc.
Ghazaleh Yassaghi

Post-Doc

ghazaleh.yassaghi@biomed.cas.cz
+420325873606

Teaching

Offered topics

thesis author thesis name thesis type
Radical labeling of proteins as a tool for the validation of biological therapeutics. Diploma Thesis
Purification and characterization of aspergilopepsin and its use for protein cleavage in hydrogen / deuterium exchange experiments. Diploma Thesis
Preparation of oryzapsin for protein cleavage in hydrogen / deuterium exchange experiments. Diploma Thesis
Preparation of affinity surfaces for mass spectrometry Diploma Thesis
Preparation of fluorescently labeled NK cell receptor for the study of dynamics in mammalian cells. Diploma Thesis
Optimization of chemical crosslinking of protein with nucleic acid. Bachelor Thesis
Preparation of affinity media for clinical diagnostics. Bachelor Thesis
Protein production and purification using structural mass spectrometry. Bachelor Thesis
Computer processing of mass spectrometric data. Bachelor Thesis
Recombinant preparation of the extracellular portion of the murine Clrb receptor. Bachelor Thesis
The role of caspases during cell death induced by new naphthoquinones. Bachelor Thesis