CS
Prof. Mgr. Lubomír Rulíšek, CSc. DSc.

Prof. Mgr. Lubomír Rulíšek, CSc. DSc.

mail lubomir.rulisekinvalid-email-name@invalid-email-domainuochb.cas.cz
phone +420 220 183 263
Group leader
Lubomír Rulíšek Group
Theoretical Bioinorganic Chemistry

Profile

Date of birth: January 10, 1972


•    EDUCATION
26/04/2001    Ph.D. in Organic Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia (IOCB, Prague);  Supervisor: Dr. Zdeněk Havlas
1995    Master (Mgr.) in Physical Chemistry, Faculty of Science, Charles University, Prague, Czechia;  Supervisor: Dr. Zdeněk Havlas


•    CURRENT POSITIONS
2012-     Senior Research Group Leader, Theoretical Bioinorganic Chemistry Group, IOCB, Prague
2022-     Full Professor (External Faculty), Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czechia


•    PREVIOUS POSITIONS
2007–2012    Junior Research Group Leader position, IOCB, Prague
2004–2006    Head of the Theoretical Chemistry Group under the Dept. of Molecular Modelling, IOCB, Prague
2002–2004    Postdoctoral Fellow at the Dept. of Theoretical Chemistry, Lund University, Sweden, under the supervision of Prof. Ulf Ryde
2001–2002    Junior Researcher at the Dept. of Theoretical Chemistry, IOCB, Prague


•    RESEARCH SABBATICALS
07/2022-08/2022    Stanford University, CA, U. S. A. (Edward I. Solomon)
09/2014-11/2014    Stanford University, CA, U. S. A. (Edward I. Solomon) – Fulbright scholar
06/2014-07/2014    Gilead Sciences, Inc., Foster City, CA, U. S. A. (Uli Schmitz/William A. Lee)


•    RESEARCH INTERESTS
Theoretical bioinorganic chemistry, ab initio predictions of protein structure, biomolecular design, conformational sampling, quantum and molecular mechanical (QM/MM) methods, organic reactivity, protein–ligand interactions, computational electrochemistry, theoretical spectroscopy


•    PEER RECOGNITION: PRIZES, AWARDS
2021        Werner von Siemens Award – the best achievement in basic research in Czechia
2014        Fulbright-Masaryk Fellowship – Sabbatical stay at Stanford University
2006        Wichterle Prize of the Czech Acd. Sci.– for an outstanding young researcher
2001        Hlavka Prize – an annual award for outstanding Ph.D. students in the Czech Republic


•    INVITED (PLENARY OR KEYNOTE) LECTURES AT INTERNATIONAL CONFERENCES
Approximately 20 invited (plenary, keynote) talks at International Conferences, numerous departmental seminars at universities and research laboratories in Europe, USA


•    TEACHING ACTIVITIES
2008-     MSc/PhD Course ‘Computer Modelling of Chemical Reactions in Condensed Phase and Biomolecules’, Faculty of Science, Charles University, Prague
2016-2020    MSc./Bc. Course ‘Chemical Structure’, Faculty of Science, Charles University, Prague


•    SUPERVISION OF GRADUATE STUDENTS AND POSTDOCTORAL FELLOWS
2005-     Supervisor of seven Ph.D. students, fifteen postdoctoral fellows, five diploma (MSc.) students, one bachelor (Bc.) student, and co-supervisor of three Ph.D. students, all except one doing their research at IOCB, Prague, all enrolled in the study program at the Charles University in Prague and the University of Chemistry and Technology in Prague

•    ALUMNI: CONTRUBUTION TO CAREERS OF EARLY-STAGE RESEARCHERS
Many of the former Ph.D. students and postdocs found subsequent research jobs in academia or industrial R&D. Dr. Martin Srnec, department chair the J. H.-Inst. Physical Chemistry, CAS, recipient of numerous awards, including Preamium Acedamie can be highlighted. Other promising early-career researcher is Dr. Daniel Bím, who recently obtained an independent position at UCT, Prague, following two successful postdoc stays (UCLA, and Caltech as Marie Curie Fellow). Dr. Martin Culka (postdoc at Columbia Univ.), and Dr. Andras Rokob (vice-president at MSCI, Inc., Hungary) should be mentioned, too

•    MAJOR SCIENTIFIC COLLABORATIONS (LAST 10 YEARS, 2015-2024)
International:    Edward I. Solomon (Stanford Univ., USA), Ulf Ryde (Lund Univ., Sweden), Jana Roithová (Radboud Univ., Nijmegen, Netherlands), František Tureček (Univ. Washington, Seattle, USA), Michal S. Shoshan (Univ. Zürich, Switzerland), Mirco Natali (Univ. Ferrara, Italy), Albert Ruggi (Univ. Fribourg, Switzerland)
Domestic:     Cyril Bařinka (Inst. Biotechnology, CAS and BIOCEV, Vestec), Martin Srnec (J. H. Inst. Physical Chemistry, CAS, Prague), Milan Pour (Charles Univ., Hradec Králové) Aleš Růžička (Univ. Pardubice),
IOCB:     Petr Beier, Michal Hocek, Ullrich Jahn, Jan Konvalinka, Josef Michl(†), Jan Řezáč, Evžen Bouřa, Radim Nencka, Gabriel Birkuš, Jiří Vondrášek, Pavel Kočovský, Martin Dračínský


•    MEMBERSHIPS OF SCIENTIFIC SOCIETIES
2018-    Founding Member of the Quantum Bio·Inorganic Chemistry Society, Vice-Chair in 2018-2020
2016-     Member of the Royal Society of Chemistry


•    INSTITUTIONAL RESPONSIBILITIES
2012-2017    Chairman of the IOCB Board
2009-2011     Member of the IOCB Board


•    SCIENTIFIC COMMUNITY ACTIVITIES
2022-         Member of the Scientific Board of the Faculty of Chemical Engineering of the University of  
2017-2021    Member and Chairman (2020 2021) of the P208 (Physical and Analytical Chemistry) Panel of the Czech Science Foundation
2017-2018    Member of the Board of the Institute of Molecular Genetics
2012        Member of the COST Evaluation Panel (CMST Domain)
2010        Leader of the ‘IOCB at EXPO2010’ team (Molecules for Life) in Shanghai, China


•    EDITORIAL BOARD OF SCIENTIFIC JOURNALS
2021-         Associate Editor, RSC Advances
2008-2011    Associate Editor, Collection of Czechoslovak Chemical Communications


•    REVIEWING ACTIVITIES
Peer-reviewing for various international journals, and several foreign or domestic grant agencies (incl. European Research Council), foreign universities (e.g. Ph.D. opponent Univ. Stockholm, 2017, Univ. Bayreuth, 2017, EPFL, Lausanne 2019); currently with a frequency of ~40 (manuscripts/projects/grants)/year


•    ORGANISATION OF CONFERENCES
2004-2024    Chair and co-chair (since 2014) of the weekly ‘IOCB Theoretical Chemistry Seminars’
2011, 2018    Chair of the 4th and 7th Japan-Czech-Slovak Symposium in Theoretical Chemistry
2016        Chair of the ECOSTBio “Spin States in Biochemistry” conference (Prague, April 2016)
2011        Chair of the Quantum Bioinorganic Chemistry Conference (Český Krumlov

•    BIBLIOGRAPHIC OVERVIEW
Approximately 140 research articles (including approx. 10 reviews or perspectives), mostly in leading international journals. LR is the first or corresponding (senior) author of ~75 papers. About 35 papers have been published in top-ranked journals, e.g. J. Am. Chem. Soc. (9), Chem. Eur. J. (14), Chem. Sci. (3), Angew. Chem. Int. Ed. (4) and Proc. Natl. Acad. Sci. U. S. A. (4). The work has been cited ~4700 times (with ~3700 fully independent citations, i.e. with all forms of self-citations excluded; source: ISI WoS Core Collection, August 27, 2024); H-index 41 (35 without all sort of self-citations excluded)


•    PATENTS
‘Rationally designed MALDI matrices for analysis of metabolites and other small molecules’ (WO2010031588) with MPI for Chemical Ecology, Jena, Germany (PI contribution 10%)

All publications

Selected papers

What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments
What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments
Z. Osifová T. Kalvoda J. Galgonek M. Culka J. Vondrášek P. Bouř L. Bednárová V. Andrushchenko M. Dračínský L. Rulíšek
Chemical Science 15 (2): 594-608 (2024)
Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically β-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-‘α-helical’ in proteins), KAM(α), ALA(α), DIC(α), EKF(α), IYI(pro-β-sheet or more generally, pro-extended), and VIV(β), and the reference α-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly…
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Elucidation of the tyrosinase/O2/monophenol ternary intermediate that dictates the monooxygenation mechanism in melanin biosynthesis
I. Kipouros A. Stańczak J. W. Ginsbach P. C. Andrikopoulos L. Rulíšek E. I. Solomon
Proceedings of the National Academy of Sciences of the United States of America 119 (33): e2205619119 (2022)
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Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein
M. Smola O. Gutten M. Dejmek M. Kožíšek T. Evangelidis Z. Aliakbar Tehrani B. Novotná R. Nencka G. Birkuš L. Rulíšek E. Bouřa
Angewandte Chemie International Edition 60 (18): 10172-10178 (2021)
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Exhaustive Mapping of the Conformational Space of Natural Dipeptides by the DFT-D3//COSMO-RS Method
T. Kalvoda M. Culka L. Rulíšek E. Andris
Journal of Physical Chemistry B 126 (32): 5949–5958 (2022)
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All publications

Latest publications

Acidity constants and protonation sites of cyclic dinucleotides determined by capillary electrophoresis, quantum chemical calculations, and NMR spectroscopy
S. Štěpánová E. Andris O. Gutten M. Buděšínský M. Dejmek P. Břehová L. Rulíšek V. Kašička
Electrophoresis 45 (7–8): 687–705 (2024)
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What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments
Z. Osifová T. Kalvoda J. Galgonek M. Culka J. Vondrášek P. Bouř L. Bednárová V. Andrushchenko M. Dračínský L. Rulíšek
Chemical Science 15 (2): 594-608 (2024)
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Experimental Evidence and Mechanistic Description of the Phenolic H-Transfer to the Cu2O2 Active Site of oxy-Tyrosinase
I. Kipouros A. Stańczak E. M. Dunietz J. W. Ginsbach M. Srnec L. Rulíšek E. I. Solomon
Journal of the American Chemical Society 145 (42): 22866–22870 (2023)
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Synthesis of highly polarized [3]dendralenes and their Diels–Alder reactions
R. Antal M. Staś S. M. Perdomo M. Štemberová Z. Brůža P. Matouš J. Kratochvíl A. Růžička L. Rulíšek J. Kuneš P. Kočovský E. Andris M. Pour
Organic Chemistry Frontiers 10 (22): 5568-5578 (2023)
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