Research Programmes

• Advanced Nanotechnologies and Microtechnologies
  • Functional Properties of Nanostructures
  • Submicron Systems and Nanodevices
  • Experimental Biophotonics
  • Fabrication and Characterisation of Nanostructures
  • Development of Methods for Analysis and Measuring
  • X-ray Micro CT and Nano CT
  • Optoelectronic Characterisation of Nanostructures
  • Micro and Nanotribology
  • Plasma Technologies
  • Synthesis and Analysis of Nanostructures
  • Transport and Magnetic Properties
• Advanced Materials
  • Advanced Ceramic Materials
  • Materials for Sensors and Technological Processes Control Systems
  • Advanced Polymers and Composites
  • Advanced Metallic Materials and Metal Based Composites
  • Structure and Phase Analysis
• Structural Biology
  • Bioinformatics
  • CD Spectroscopy of Nucleic Acids and Proteins
  • CryoEM
  • Glycobiochemistry
  • RNA Quality Control
  • Nanobiotechnology
  • Biomolecular NMR Spectroscopy
  • NMR Spectroscopy II
  • NMR Spectroscopy III
  • Protein/RNA Interactions
  • X-ray Crystallography I
  • X-ray Crystallography II
  • Structure and Dynamics of Nucleic Acids
  • Structure and Interaction of Biomolecules at Surfaces
  • Computational Chemistry
• Genomics and Proteomics of Plant Systems
  • Bioanalytical Instrumentation
  • Plant Cytogenomics
  • Functional Genomics and Proteomics of Plants
  • Hormonal Crosstalk in Plant Development
  • Metabolomics
  • Core Facility – Proteomics
  • Developmental and Cell Biology of Plants
  • Chromatin Molecular Complexes
  • Developmental and Production Biology – Omics Approaches
• Molecular Medicine
  • Medical Genomics
  • Molecular Oncology I – Hematooncology
  • Molecular Oncology II – Solid Cancer
  • Inherited Diseases I – Genetic Research
  • Inherited Diseases II – Transcriptional Regulation
  • Molecular Immunology and Microbiology
  • Molecular Gastroenterology and Hepatology
  • Genome Dynamics
  • Core Facility – Genomics
  • Laboratory of Human Molecular Genetics
• Brain and Mind Research
  • Cellular and Molecular Neurobiology
  • Molecular and Functional Neuroimaging
  • Experimental and Applied Neuropsychopharmacology
  • Psychophysiology
  • Behavioural and Social Neuroscience
  • Applied Neuroscience
• Molecular Veterinary Medicine
  • Molecular Virology
  • Molecular Bacteriology
  • Parasitology
  • Food Safety
  • Orthopaedics and Surgery
  • Animal Imunogenomics
  • Animal Cytogenomics
  • Mammalian Reproduction

Biomolecular NMR Spectroscopy

Prof. RNDr. Vladimír Sklenář, DrSc.
Research Group Leader

THEMATIC RESEARCH FOCUS

RESEARCH AREAS

• NMR methodology (fast acquisition, non-linear sampling, C-13 detection)
• 3D structure determination of proteins and nucleic acids from NMR measurements
• Structural characterisation of small, biologically interesting molecules
• Ab initio calculations of NMR parameters

MAIN OBJECTIVES

• Development of new methodologies for investigating the structure, interactions, and dynamics of biomolecules.
• Investigations of the structure and interactions of biomacromolecules and their relation to the functions of living systems, disease and therapy.

CONTENT OF RESEARCH

The progress of structural biology during the past decade has been closely linked with the developments of new experimental methods, data evaluation procedures, and improvements of computational protocols to provide detailed information about the spatial structure and dynamic properties of biomolecular systems. The new equipment acquired as a part of the CEITEC infrastructure for structural biology will be used to continue with methodological developments in NMR spectroscopy.

NMR spectroscopy is the only method that can be used to determine the structure of proteins and protein complexes in complex native-like environments, both in solution and in membranes. Furthermore, NMR can rapidly assess the conformational properties of a protein, and easily identify whether the protein is well-structured, unfolded, or intrinsically disordered. NMR also has exceptional capabilities for studying molecular interactions in order to understand their biological functions and to guide pharmaceutical developments. The methodological developments will be directed to improving the effi ciency and throughput of NMR data collection routines and optimising the computational protocols for data processing, structure calculations of proteins and proteins-nucleic acid complexes, and interpreting NMR data in terms of molecular motions. The newly introduced NMR tools will meet the demands of experimentally addressing biological samples with limited stability, to study biological processes that occur on very fast time scales (protein folding, RNA folding in regulation, enzyme kinetics) and to investigate large multimeric complexes between proteins, nucleic acids and various ligands. The new developments will be applied to study proteins, nucleic acids and their assemblies of particular interest for projects embedded in work packages of Structural Biology programme as well as in other CEITEC life science programmes.

KEY RESEARCH EQUIPMENT

PLANNED RESEARCH INFRASTRUCTURE

Core Facility

The research group will be one of the principal users of the CEITEC High-field NMR Spectroscopy Core Facility.

CURRENT RESEARCH INFRASTRUCTURE

The NMR laboratory is currently equipped with a 600 MHz NMR spectrometer (Bruker Avance) with the TCI cryoprobe, a 500 MHz NMR spectrometer (Bruker Avance) for spectroscopy in liquids and the CP MAS accessory for solid state measurements, and a routine 300 MHz NMR system (Bruker Avance) for measurements in liquids. The lab has installed and mastered a full armoury of computational tools for studies of biomolecular structure and the dynamics of both proteins and nucleic acids.

MAIN PROJECTS

• Allosteric effects induced in 14-3-3 targets (235902), FP7-PEOPLE, EU, 2010-2013, V. Sklenař, Masaryk University.
• The Delta Subunit of RNA Polymerase from Gram positive Bacteria (GA204/09/0583), Czech Science Foundation, 2009-2012, L. Krasny, Institute of Microbiology AS CR, L. Židek, Masaryk University.
• East-NMR (228461), FP7-INFRASTRUCTURES, EU, 2009-2013, V. Sklenař, Masaryk University.
• Bio-NMR Facilities (261863), FP7-INFRASTRUCTURES, EU, 2010-2014, V. Sklenař, Masaryk University.
• Biomolecular centre (LC06030), Ministry of Education, Youth and Sports, 2006-2011, V. Sklenař, Masaryk University, Rychlik, Veterinary Research Institute, J. Šponer, Institute of Biophysics AS CR.

SELECTED PUBLICATIONS

• NOVACEK, J., ZAWADSKA-KAZIMIERCZUK, A., MOTACKOVA, V., ZIDEK, L., KOZMINSKI, W., SKLENAR, V., J. 5D 13C-detected NMR experiments for backbone assignment of unstructured proteins with a very low signal dispersion. J. Biomol. NMR. 2011, 50, p. 1–11.
• PRECECHTELOVA, J., NOVAK, P., MUNZAROVA, M., L., KAUPP, M., SKLENAR, V. 31P Chemical Shift and Chemical Shift Anisotropy Tensors in DNA: DFT and MD Study. J. Amer. Chem. Soc. 2010, 132, p. 17139–17148.
• MOTACKOVA, V., SANDEROVA, H., ZIDEK, L., NOVACEK, J., PADRTA, P., SVENKOVA, A., KORELUSOVA, J., JONAK, J., KRASNY, L., SKLENAR, V. Solution Structure of the N-terminal domain of Bacillus subtilis δ subunit of RNA polymerze and its classification based on structural homologues. PROTEINS. 2010, 78, p. 1807-1810.
• MACEK, P., CHMELIK, J., KRIZOVA, I., KADERAVEK, P., ZIDEK, L., WILDOVA, M., HADRAVOVA, R., CHALOUPKOVA, R., PICHOVA, I., RUML, T., RUMLOVA, M., SKLENAR, V. NMR structure of the N-terminal domain of capsid protein from the Mason-Pfizer monkey virus. J. Mol. Biol. 2009, 392, p. 100-114.
• KRIZOVA, H., ZIDEK, L., STONE, M., NOVOTNY, M., V., SKLENAR, V. Temperature Dependent Backbone Dynamics of Major Urinary Protein-I Complexed with the Pheromone 2-sec-butyl-4,5-dihydrothiazole. J. Biomol. NMR. 2004, 28, p. 369-384.