Laboratory of Structural Bioinformatics of Proteins

Strukturní a funkční vlastnosti biologicky významných molekul a jejich interakcí pomocí nástrojů strukturní bioinformatiky a molekulového modelování.

Group leader: Ing. Jiří Černý, Ph.D.

Ing. Jiří Černý, Ph.D.The research concentrates on understanding the structural and functional features of biologically relevant molecules and their interactions employing the tools of Structural Bioinformatics and Molecular Modeling. We closely collaborate with researchers within IBT and BIOCEV as well as with external groups on analysis of structural data, rational design of protein mutations, and design of ligands and inhibitors of studied proteins.

 
Studied systems
  • Analysis of conformational behavior of oligopeptide blocks in proteins.
  • Design and identification of stable protein folds suitable for mutagenesis.
  • Identification of key protein residues involved in recognition and strength of interaction.
  • Development and testing of computational methods and procedures for modeling of structure and properties of biomolecules and their complexes.
  • Development of novel computational methods and parameter optimization for description of designed ligands and inhibitors and their interactions.
 
Methods
  • Homology modeling.
  • Molecular dynamics simulations (MD).
  • Ab initio quantum chemical calculations.
  • In silico mutagenesis.
  • Protein/protein and protein/small molecule docking.
Aliakbartehrani Zahra
Baran Sahra Setenay
Božíková Paulína, Mgr.
Černý Jiří, Ing., Ph.D.
Prchalová Terezie
Schramlová Barbora, Mgr.
Tomović Eni

2024

  • Novakova Z, Tehrani ZA, Jurok R, Motlova L, Kutil Z, Pavlicek J, Shukla S, Choy CJ, Havlinova B, Baranova P, Berkman CE, Kuchar M, Cerny J, Barinka C (2024) "Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors", 10.1021/acs.jcim.3c01542

  • Polak M, Cerny J, Novak P (2024) "Isotopic Depletion Increases the Spatial Resolution of FPOP Top-Down Mass Spectrometry Analysis", 10.1021/acs.analchem.3c03759

  • Kysilov B, Kuchtiak V, Krausova BH, Balik A, Korinek M, Fili K, Dobrovolski M, Abramova V, Chodounska H, Kudova E, Bozikova P, Cerny J, Smejkalova T, Vyklicky, L (2024) "Disease-associated nonsense and frame-shift variants resulting in the truncation of the GluN2A or GluN2B C-terminal domain decrease NMDAR surface expression and reduce potentiating effects of neurosteroids", 10.1007/s00018-023-05062-6

2023

  • Abramova V, Leal Alvarado V, Hill M, Smejkalova T, Maly M, Vales K, Dittert I, Bozikova P, Kysilov B, Hrcka Krausova B, Vyklicky V, Balik A, Fili K, Korinek M, Chodounska H, Kudova E, Ciz D, Martinovic J, Cerny J, Bartunek P, Vyklicky L. (2023)"Effects of Pregnanolone Glutamate and Its Metabolites on GABAA and NMDA Receptors and Zebrafish Behavior." ACS Chem Neurosci.14(10):1870-1883. doi: 10.1021/acschemneuro.3c00131.

  • Flores SC, Maly M, Hrebík D, Plevka P, Cerny J (2023) "Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses",10.1093/nar/gkad1153

  • Malý M, Kolenko P, Stránský J, Švecová L, Dušková J, Koval' T, Skálová T, Trundová M, Adámková K, Černý J, Božíková P, Dohnálek J. (2023)"Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia." Acta Crystallogr F Struct Biol Commun. 79(Pt 7):180-192. doi: 10.1107/S2053230X23005381.

  • Schneider, B., Sweeney, BA., Bateman, A., Cerny, J., Zok, T., Szachniuk, M.(2023)"When will RNA get its AlphaFold moment?"Nucleic Acids Res. doi: 10.1093/nar/gkad726.

  • Svoboda J, Berdár D, Kolenko P, Černý J, Nováková Z, Pavlíček J, Schneider B. (2023)"Conformation-based refinement of 18-mer DNA structures."Acta Crystallogr D Struct Biol.79(Pt 7):655-665. doi: 10.1107/S2059798323004679.

2022

  • Aliakbar Tehrani Z, Rulíšek L, Černý J.(2022)"Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein."J Biomol Struct Dyn.40(20):10250-10264. doi: 10.1080/07391102.2021.1942213.

  • Biedermannová L, Černý J, Malý M, Nekardová M, Schneider B.(2022)" Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks." Acta Crystallogr D Struct Biol.1;78(Pt 8):1032-1045. doi: 10.1107/S2059798322006234.

  • Daniel Lišková V, Kosztyu P, Kuchař M, Černý J, Bharadwaj S, Petroková H, Vroblová E, Křupka M, Malý M, Zosinčuková T, Šulc J, Rašková Kafková L, Raška M, Malý P. (2022) "Myomedin replicas of gp120 V3 loop glycan epitopes recognized by PGT121 and PGT126 antibodies as non-cognate antigens for stimulation of HIV-1 broadly neutralizing antibodies." Front Immunol. 13:1066361. doi: 10.3389/fimmu.2022.1066361.

  • Hadrava Vanova K, Pang Y, Krobova L, Kraus M, Nahacka Z, Boukalova S, Pack SD, Zobalova R, Zhu J, Huynh TT, Jochmanova I, Uher O, Hubackova S, Dvorakova S, Garrett TJ, Ghayee HK, Wu X, Schuster B, Knapp PE, Frysak Z, Hartmann I, Nilubol N, Cerny J, Taieb D, Rohlena J, Neuzil J, Yang C, Pacak K. (2022) "Germline SUCLG2 Variants in Patients With Pheochromocytoma and Paraganglioma."J Natl Cancer Inst. 11;114(1):130-138. doi: 10.1093/jnci/djab158.

  • Vondrakova J, Frolikova M, Ded L, Cerny J, Postlerova P, Palenikova V, Simonik O, Nahacka Z, Basus K, Valaskova E, Machan R, Pacey A, Holubcova Z, Koubek P, Ezrova Z, Park S, Liu R, Partha R, Clark N, Neuzil J, Ikawa M, Erickson K, Lam KS, Moore H, Komrskova K. (2022) "MAIA, Fc receptor-like 3, supersedes JUNO as IZUMO1 receptor during human fertilization. "Sci Adv.;8(36):eabn0047. doi: 10.1126/sciadv.abn0047

2021

  • Filandrová R, Vališ K, Černý J, Chmelík J, Slavata L, Fiala J, Rosůlek M, Kavan D, Man P, Chum T, Cebecauer M, Fabris D, Novák P. (2020) "Motif orientation matters: Structural characterization of TEAD1 recognition of genomic DNA. "Structure.1;29(4):345-356.e8. doi: 10.1016/j.str.2020.11.018.

  • Hirschfeldova K, Cerny J, Bozikova P, Kuchtiak V, Rausch T, Benes V, Spaniel F, Gregus D, Horacek J, Vyklicky L, Balik A. (2021)"Evidence for the Association between the Intronic Haplotypes of Ionotropic Glutamate Receptors and First-Episode Schizophrenia." J Pers Med.;11(12):1250. doi: 10.3390/jpm11121250.

  • Kuchař M, Kosztyu P, Daniel Lišková V, Černý J, Petroková H, Vróblová E, Malý M, Vaňková L, Křupka M, Rašková Kafková L, Turánek Knotigová P, Dušková J, Dohnálek J, Mašek J, Turánek J, Raška M, Malý P.(2021) "Myomedin scaffold variants targeted to 10E8 HIV-1 broadly neutralizing antibody mimic gp41 epitope and elicit HIV-1 virus-neutralizing sera in mice." Virulence. 2021 Dec;12(1):1271-1287. doi: 10.1080/21505594.2021.1920251.

  • Pham, P. N., Huliciak, M., Biedermannova, L., Cerny, J., Charnavets, T., Fuertes, G., Herynek, S., Kolarova, L., Kolenko, P., Pavlicek, J., Zahradnik, J., Mikulecky, P., & Schneider, B. (2021). "Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution." Viruses, 13(2). 

2020

  • Cerny, J., Bozikova, P., Maly, M., Tykac, M., Biedermannova, L., & Schneider, B. (2020). "Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org." Acta Crystallogr D Struct Biol, 76(Pt 9), 805-813.

  • Cerny, J., P. Bozikova, J. Svoboda and B. Schneider (2020). "A unified dinucleotide alphabet describing both RNA and DNA structures." Nucleic Acids Research. doi 10.1093/nar/gkaa383

  • Jankovicova, J., Frolikova, M., Palenikova, V., Valaskova, E., Cerny, J., Secova, P., Bartokova, M., Horovska, L., Manaskova-Postlerova, P., Antalikova, L., Komrskova, K. (2020)  Expression and distribution of CD151 as a partner of alpha6 integrin in male germ cells. Sci Rep 10, 4374 (2020). https://doi.org/10.1038/s41598-020-61334-2

  • Kolenko, P., Svoboda, J., Černý, J., Charnavets, T., Schneider, B., (2020) „Structural variability of CG-rich DNA 18-mers accommodating double T–T mismatches“ StructBiol 76 (1233-1243) doi 10.1107/S2059798320014151

2019

  • Cerny, J., P. Bozikova, A. Balik, S. M. Marques and L. Vyklicky (2019). "NMDA Receptor Opening and Closing-Transitions of a Molecular Machine Revealed by Molecular Dynamics." Biomolecules 9(10).

  • Frolikova, M., E. Valaskova, J. Cerny, A. Lumeau, N. Sebkova, V. Palenikova, N. Sanches-Hernandez, A. Pohlova, P. Manaskova-Postlerova and K. Dvorakova-Hortova (2019). "Addressing the Compartmentalization of Specific Integrin Heterodimers in Mouse Sperm." Int J Mol Sci 20(5).

  • Kosztyu, P., M. Kuchar, J. Cerny, L. Barkocziova, M. Maly, H. Petrokova, L. Czernekova, V. Liskova, L. Raskova Kafkova, P. Knotigova, J. Masek, J. Turanek, P. Maly and M. Raska (2019). "Proteins mimicking epitope of HIV-1 virus neutralizing antibody induce virus-neutralizing sera in mice." EBioMedicine 47: 247-256.

  • Peter, E. K. and J. Cerny (2019). "A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints." Int J Mol Sci 20(2).

  • Plavec, T. V., M. Kuchar, A. Benko, V. Liskova, J. Cerny, A. Berlec and P. Maly (2019). "Engineered Lactococcus lactis Secreting IL-23 Receptor-Targeted REX Protein Blockers for Modulation of IL-23/Th17-Mediated Inflammation." Microorganisms 7(5).

2018

  • Frolikova, M., P. Manaskova-Postlerova, J. Cerny, J. Jankovicova, O. Simonik, A. Pohlova, P. Secova, J. Antalikova and K. Dvorakova-Hortova (2018). "CD9 and CD81 Interactions and Their Structural Modelling in Sperm Prior to Fertilization." Int J Mol Sci 19(4).

  • Hlavnickova, M., M. Kuchar, R. Osicka, L. Vankova, H. Petrokova, M. Maly, J. Cerny, P. Arenberger and P. Maly (2018). "ABD-Derived Protein Blockers of Human IL-17 Receptor A as Non-IgG Alternatives for Modulation of IL-17-Dependent Pro-Inflammatory Axis." Int J Mol Sci 19(10).

  • Peter, E. K. and J. Cerny (2018). "Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank." Int J Mol Sci 19(11).

  • Schneider, B., P. Boaeikova, I. Necasova, P. Cech, D. Svozil and J. Cerny (2018). "A DNA structural alphabet provides new insight into DNA flexibility." Acta Crystallogr D Struct Biol 74(Pt 1): 52-64.

  • Skrlec, K., P. Zadravec, M. Hlavnickova, M. Kuchar, L. Vankova, H. Petrokova, L. Krizova, J. Cerny, A. Berlec and P. Maly (2018). "p19-Targeting ILP Protein Blockers of IL-23/Th-17 Pro-Inflammatory Axis Displayed on Engineered Bacteria of Food Origin." Int J Mol Sci 19(7).

  • Zahradnik, J., P. Kolenko, A. Palyzova, J. Cerny, L. Kolarova, E. Kyslikova, H. Maresova, M. Grulich, J. Nunvar, M. Sulc, P. Kyslik and B. Schneider (2018). "The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form." Plos One 13(4): e0195299.

2017

  • Cerny, J., B. Schneider and L. Biedermannova (2017). "WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations." Phys Chem Chem Phys 19(26): 17094-17102.

  • Krizova, L., M. Kuchar, H. Petrokova, R. Osicka, M. Hlavnickova, O. Pelak, J. Cerny, T. Kalina and P. Maly (2017). "p19-targeted ABD-derived protein variants inhibit IL-23 binding and exert suppressive control over IL-23-stimulated expansion of primary human IL-17+ T-cells." Autoimmunity 50(2): 102-113.

  • Rohlenova, K., K. Sachaphibulkij, J. Stursa, A. Bezawork-Geleta, J. Blecha, B. Endaya, L. Werner, J. Cerny, R. Zobalova, J. Goodwin, T. Spacek, E. Alizadeh Pesdar, B. Yan, M. N. Nguyen, M. Vondrusova, M. Sobol, P. Jezek, P. Hozak, J. Truksa, J. Rohlena, L. F. Dong and J. Neuzil (2017). "Selective Disruption of Respiratory Supercomplexes as a New Strategy to Suppress Her2(high) Breast Cancer." Antioxid Redox Signal 26(2): 84-103.

  • Schneider, B., P. Bozikova, P. Cech, D. Svozil and J. Cerny (2017). "A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle." Genes (Basel) 8(10).

  • Valis, K., V. Grobarova, L. Hernychova, M. Buganova, D. Kavan, M. Kalous, J. Cerny, E. Stodulkova, M. Kuzma, M. Flieger, J. Cerny and P. Novak (2017). "Reprogramming of leukemic cell metabolism through the naphthoquinonic compound Quambalarine B." Oncotarget 8(61): 103137-103153.

2016

  • Boukalova, S., J. Stursa, L. Werner, Z. Ezrova, J. Cerny, A. Bezawork-Geleta, A. Pecinova, L. Dong, Z. Drahota and J. Neuzil (2016). "Mitochondrial Targeting of Metformin Enhances Its Activity against Pancreatic Cancer." Mol Cancer Ther 15(12): 2875-2886.

  • Cerny, J., P. Bozikova and B. Schneider (2016). "DNATCO: assignment of DNA conformers at dnatco.org." Nucleic Acids Research 44(W1): W284-287.

  • Mikulecky, P., J. Zahradnik, P. Kolenko, J. Cerny, T. Charnavets, L. Kolarova, I. Necasova, P. N. Pham and B. Schneider (2016). "Crystal structure of human interferon-gamma receptor 2 reveals the structural basis for receptor specificity." Acta Crystallogr D Struct Biol 72(Pt 9): 1017-1025.

  • Novakova, Z., J. Cerny, C. J. Choy, J. R. Nedrow, J. K. Choi, J. Lubkowski, C. E. Berkman and C. Barinka (2016). "Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities." FEBS J 283(1): 130-143.

  • Taherkhani, M., A. Armentano, J. Černý and K. Müller-Dethlefs (2016). "Threshold ionization spectroscopic investigation of supersonic jet-cooled, laser-desorbed Tryptophan." Chemical Physics Letters 657: 142-147.

2015

  • Osicka, R., A. Osickova, S. Hasan, L. Bumba, J. Cerny and P. Sebo (2015). "Bordetella adenylate cyclase toxin is a unique ligand of the integrin complement receptor 3." Elife 4: e10766.

2014

  • Vymetal, J., S. R. Bathula, J. Cerny, R. Chaloupkova, L. Zidek, V. Sklenar and J. Vondrasek (2014). "Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition." Protein Eng Des Sel 27(12): 463-472.

2012

  • Rozbesky, D., P. Man, D. Kavan, J. Chmelik, J. Cerny, K. Bezouska and P. Novak (2012). "Chemical cross-linking and H/D exchange for fast refinement of protein crystal structure." Anal Chem 84(2): 867-870.

2011

  • Armentano, A., J. Cerny, M. Riese, M. Taherkhani, M. Ben Yezzar and K. Muller-Dethlefs (2011). "Spectral shifts and structures of phenol...Ar(n) clusters." Phys Chem Chem Phys 13(13): 6077-6084.

  • Cerny, J., M. Pitonak, K. E. Riley and P. Hobza (2011). "Complete Basis Set Extrapolation and Hybrid Schemes for Geometry Gradients of Noncovalent Complexes." J Chem Theory Comput 7(12): 3924-3934.

  • Klusák, V., P. Dobeš, J. Černý and J. Vondrášek (2011). "How to fragment a polypeptide? An ab initio computational study of pair interactions between amino acids and ligand-amino acids in proteins." Collection of Czechoslovak Chemical Communications 76(5): 605-618.

2010

  • Cerny, J. and P. Hobza (2010). "Energy barriers between H-bonded and stacked structures of 9-methyladenine...1-methylthymine and 9-methylguanine...1-methylcytosine complexes." Chem Commun (Camb) 46(3): 383-385.

  • Riley, K. E., M. Pitonak, J. Cerny and P. Hobza (2010). "On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H...pi): WFT and DFT Calculations." J Chem Theory Comput 6(1): 66-80.

2009

  • Cerny, J., J. Vondrasek and P. Hobza (2009). "Loss of dispersion energy changes the stability and folding/unfolding equilibrium of the Trp-cage protein." J Phys Chem B 113(16): 5657-5660.

MEYS: LM2023055, J. Černý: Czech National Infrastructure for Biological Data. 2023 – 2026

MEYS: LM201547, Schneider: ELIXIR CZ: Czech National Infrastructure for Biological Data. 2016-2017.

MEYS: LM2018131, Černý: Czech National Infrastructure for Biological Data. 2020-2022