Strukturní virologie - Pavel Plevka

Research areas

• X-ray crystallography of proteins, macromolecular complexes, and icosahedral viruses.
• Cryo-electron microscopy and single particle reconstruction of viruses in complexes with antibodies or cellular receptors.
• Cryo-electron tomography of virus assembly and cell entry intermediates.

Main objectives

Obtain structural understanding of virus life-cycles and use it to develop anti-viral therapies.

Content of research

Viruses are the smallest self-replicating organisms. Even though individually viruses are rather simple, as a group they are exceptionally diverse in both replication strategies and structures. Many viruses are important human pathogens.

We use X-ray crystallography, cryo-electron microscopy, and molecular biology to study the life cycle of human viruses. We investigate macromolecular interactions associated with virus cell entry, genome replication, assembly, and maturation. Viruses are simple enough that we can aspire to understand their biology at a molecular level. Our efforts are directed towards using structural information for the development of anti-viral drugs and vaccines.

Our research is focused on three projects:

1.) Rhinoviruses and Enteroviruses that usually cause common colds, but may induce more serious symptoms such as foot, hand, and mouth disease or encephalitis.

2.) Viruses from the order picornavirales that infect honeybees and contribute to the collapse of honeybee colonies.

3.) Leishmania RNA Virus 1 that infects Leishmania and enables the parasite to evade human immune system. This results in a more serious form of leishmaniasis.

seznam / vizitky

VYBRANÉ PUBLIKACE

2017

• FIALA, T; LUDVIKOVA, L; HEGER, D; SVEC, J; SLANINA, T; VETRAKOVA, L; BABIAK, M; NECAS, M; KULHANEK, P; KLAN, P; SINDELAR, V, 2017:Bambusuril as a One-Electron Donor for Photoinduced Electron Transfer to Methyl Viologen in Mixed Crystals. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 139 (7), p. 2597 - 2603.
• JASNOVIDOVA, O; KLUMPLER, T; KUBICEK, K; KALYNYCH, S; PLEVKA, P; STEFL, R, 2017:Structure and dynamics of the RNAPII CTDsome with Rtt103. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114 (42), p. 11133 - 11138.
• SKUBNIK, K; NOVACEK, J; FUZIK, T; PRIDAL, A; PAXTON, RJ; PLEVKA, P, 2017:Structure of deformed wing virus, a major honey bee pathogen. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114 (12), p. 3210 - 3215.
• SPURNY, R; PRIDAL, A; PALKOVE, L; TRAN KIEM, H. K; DE MIRANDA, J R; PLEVKA,, 2017:Virion structure of black queen cell virus, a common honeybee pathogen. JOURNAL OF VIROLOGY
• STYSKALIK, A; BABIAK, M; MACHAC, P; RELICHOVA, B; PINKAS, J, 2017:New Adamantane-like Silicophosphate Cage and Its Reactivity toward Tris(pentafluorophenyl)borane. INORGANIC CHEMISTRY 56 (17), p. 10699 - 10705.

2016

• KALYNYCH S; PŘIDAL A; PÁLKOVÁ L; LEVDANSKY Y; DE MIRANDA JR; PLEVKA P, 2016:Virion structure of iflavirus slow bee paralysis virus at 2.6Å resolution. JOURNAL OF VIROLOGY 90 (16), p. 7444 - 7455.
• KALYNYCH, S; PALKOVA, L; PLEVKA, P, 2016:The Structure of Human Parechovirus 1 Reveals an Association of the RNA Genome with the Capsid. JOURNAL OF VIROLOGY 90 (3), p. 1377 - 1386.
• KALYNYCH, S; PRIDAL, A; PALKOVA, L; LEVDANSKY, Y; DE MIRANDA, JR; PLEVKA, P, 2016:Virion Structure of Iflavirus Slow Bee Paralysis Virus at 2.6-Angstrom Resolution. JOURNAL OF VIROLOGY 90 (16), p. 7444 - 7455.
• MULLAPUDI E; NOVÁČEK J; PÁLKOVÁ L; KULICH P; LINDBERG AM; VAN KUPPEVELD FJ; PLEVKA P, 2016:Structure and genome release mechanism of human cardiovirus Saffold virus-3. JOURNAL OF VIROLOGY , p. [Epub ahead of print] - .
• MULLAPUDI E; PŘIDAL A; PÁLKOVÁ L; DE MIRANDA JR; PLEVKA P, 2016:Virion structure of Israeli acute bee paralysis virus. JOURNAL OF VIROLOGY 90 (18), p. 8150 - 8159.
• MULLAPUDI, E; NOVACEK, J; PALKOVA, L; KULICH, P; LINDBERG, AM; VAN KUPPEVELD, FJM; PLEVKA, P, 2016:Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3. JOURNAL OF VIROLOGY 90 (17), p. 7628 - 7639.
• NOVÁČEK J; ŠIBOROVÁ M; BENEŠÍK M; PANTŮČEK R; DOŠKAŘ J; PLEVKA P, 2016:Structure and genome release of Twort-like Myoviridae phage with a double-layered baseplate. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 113 (33), p. 9351 - 6.
• SABIN, C; FUZIK, T; SKUBNIK, K; PALKOVA, L; LINDBERG, AM; PLEVKA, P, 2016:Structure of Aichi Virus 1 and Its Empty Particle: Clues to Kobuvirus Genome Release Mechanism. JOURNAL OF VIROLOGY 90 (23), p. 10800 - 10810.
• SABIN, C; PLEVKA, P, 2016:The use of noncrystallographic symmetry averaging to solve structures from data affected by perfect hemihedral twinning. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 72 , p. 188 - 197.

2013

• MENG, G; ZHANG, XZ; PLEVKA, P; YU, Q; TIJSSEN, P; ROSSMANN, MG, 2013:The Structure and Host Entry of an Invertebrate Parvovirus. JOURNAL OF VIROLOGY 87 (23), p. 12523 - 12530.
• NEMECEK, D; BOURA, E; WU, WM; CHENG, NQ; PLEVKA, P; QIAO, J; MINDICH, L; HEYMANN, JB; HURLEY, JH; STEVEN, AC, 2013:Subunit Folds and Maturation Pathway of a dsRNA Virus Capsid. STRUCTURE 21 (8), p. 1374 - 1383.
• NEMECEK, D; PLEVKA, P; BOURA, E, 2013:Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage I center dot 6 Major Capsid Protein. PROTEIN JOURNAL 32 (8), p. 635 - 640.
• PRASAD, VM; WILLOWS, SD; FOKINE, A; BATTISTI, AJ; SUN, SY; PLEVKA, P; HOBMAN, TC; ROSSMANN, MG, 2013:Rubella virus capsid protein structure and its role in virus assembly and infection. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 110 (50), p. 20105 - 20110.
• WANG, ZQ; LI, L; PENNINGTON, JG; SHENG, J; YAP, ML; PLEVKA, P; MENG, G; SUN, L; JIANG, W; ROSSMANN, MG, 2013:Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody. JOURNAL OF VIROLOGY 87 (16), p. 8909 - 8915.
• ZHANG, XZ; SHENG, J; PLEVKA, P; KUHN, RJ; DIAMOND, MS; ROSSMANN, MG, 2013:Dengue structure differs at the temperatures of its human and mosquito hosts. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 110 (17), p. 6795 - 6799.

2012

• BATTISTI, AJ; MENG, G; WINKLER, DC; MCGINNES, LW; PLEVKA, P; STEVEN, AC; MORRISON, TG; ROSSMANN, MG, 2012:Structure and assembly of a paramyxovirus matrix protein. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 109 (35), p. 13996 - 14000.
• BATTISTI, AJ; YODER, JD; PLEVKA, P; WINKLER, DC; PRASAD, VM; KUHN, RJ; FREY, TK; STEVEN, AC; ROSSMANN, MG, 2012:Cryo-Electron Tomography of Rubella Virus. JOURNAL OF VIROLOGY 86 (20), p. 11078 - 11085.
• PLEVKA, P; BATTISTI, AJ; WINKLER, DC; TARS, K; HOLDAWAY, HA; BATOR, CM; ROSSMANN, MG, 2012:Sample Preparation Induced Artifacts in Cryo-Electron Tomographs. MICROSCOPY AND MICROANALYSIS 18 (5), p. 1043 - 1048.
• PLEVKA, P; PERERA, R; CARDOSA, J; KUHN, RJ; ROSSMANN, MG, 2012:Crystal Structure of Human Enterovirus 71. SCIENCE 336 (6086), p. 1274 - 1274.
• PLEVKA, P; PERERA, R; CARDOSA, J; KUHN, RJ; ROSSMANN, MG, 2012:Structure determination of enterovirus 71. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 68 , p. 1217 - 1222.

2011

• KAUFMANN, B; EL-FAR, M; PLEVKA, P; BOWMAN, VD; LI, Y; TIJSSEN, P; ROSSMANN, MG, 2011:Structure of Bombyx mori Densovirus 1, a Silkworm Pathogen. JOURNAL OF VIROLOGY 85 (10), p. 4691 - 4697.
• ROSSMANN, MG; BATTISTI, AJ; PLEVKA, P, 2011:FUTURE PROSPECTS. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY, VOL 82: RECENT ADVANCES IN ELECTRON CRYOMICROSCOPY, PT B 82 , p. 101 - 121.

2010

• KAUFMANN, B; PLEVKA, P; KUHN, RJ; ROSSMANN, MG, 2010:Crystallization and preliminary X-ray diffraction analysis of West Nile virus. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS 66 , p. 558 - 562.
• PLEVKA, P; HAFENSTEIN, S; HARRIS, KG; CIFUENTE, JO; ZHANG, Y; BOWMAN, VD; CHIPMAN, PR; BATOR, CM; LIN, F; MEDOF, ME; ROSSMANN, MG, 2010:Interaction of Decay-Accelerating Factor with Echovirus 7. JOURNAL OF VIROLOGY 84 (24), p. 12665 - 12674.

GRANTY

• Strukturní studie potenciálního protibakteriálního agens, fága 812K1-420 infikujícího zlatého stafylokoka (GA15-21631Y), Czech Science Foundation - Junior grants, 2015 - 2017
• Structural studies of human and animal pathogens from the order Picornavirales, EMBO (European Molecular Biology Organization ) grants, 2015 - 2017
• Structural studies of human picornaviruses (335855), FP7 - Ideas - ERC Starting Grants, 2014 - 2018

PLANNED RESEARCH INFRASTRUCTURE

• BSL-2 tissue culture laboratory equipped for production and purification of human viruses.
• Equipment for protein crystallization and X-ray diffraction data collection.
• Instrumentation for preparation of samples for cryo-electron microscopy, Titan Krios, Versa 3D, and F20 electron microscopes.

1. Cryo-electron microscopy analysis of  influenza A replication in vivo

Supervisor:  Mgr. Pavel Plevka, Ph.D.

Annotation:

Influenza A virus causes hundreds of millions of infections, thousands of deaths, and economic losses of billions of US dollars every year. Still, the replication cycle of influenza A is not structurally characterized at molecular level. Cryo-electron microscopy allows observation of biological specimens in near-native state, but it faces the problem of decreased image quality for samples thicker than 300 nm. Focused ion beam milling can be used to prepare thin sections of vitrified cells to circumvent this issue. Subsequent cryo-electron tomography provides high-resolution structural information of complex cellular samples. Student will study replication and assembly of influenza A in vivo. Although three-dimensional structures of virus replication in vivo have been previously determined in fixed and stained cells, we intend on collecting data on cryo-preserved samples to enable the characterization of virus replication in near-native state without artifacts caused by heavy ion staining. The resulting tomograms will be analyzed with the help of pattern recognition and sub-tomogram averaging to obtain high-resolution details of the virus replication and assembly intermediates.

Keywords: Influenza A virus, replication cycle, cryo-electron microscopy, cryo-electron tomography