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I am ...

  • ... a structural biologist, Head of the Laboratory of Biomolecular Recognition at the Institute of Biotechnology Academy of Sciences of the Czech Republic (IBT).

    In my lab, we study interactions between biomolecules, proteins and nucleic acids, by biophysical and bioinformatic tools.

  • The Lab has a good balance of senior scientists, Dr. Jiri Cerny, Dr. Lada Biedermannova, and students, PhD students Pavel Mikulecky, Iva Zuskova, Jiri Zahradnik, and Phuong Ngoc Pham, and diploma students, Paulina Bozikova and Lucie Kolarova. Jaroslav Nunvar graduated in Winter 2014. Technical issues and also a good deal of the paperwork is dealt with by Karel Pufler.
  • We want to understand interactions driving specific recognition between biomolecules with potential diagnostic, medical or biotechnological use.
  • We are involved in several projects dealing with Interferon gamma and its recpetors. A major effort has been devoted to a project in which we increased affinity between interferon-gamma and extracellular part of its receptor R1. We improved the binding by rational design of mutations in the receptor. One paper describes how to increase R1 affinity to IFNg by mutation analysis of the receptor residues at the interaction interface with the IFNg molecule (Mikulecky et al. (2013), doi: 10.1155/2013/752514.), the other aimed at modifications of amino acids in receptor 1 cavities (Cerny et al. (2015), doi: 10.1155/2015/716945.).

    We study protein/DNA interactions in a system of bacterial non-coding REP sequences (Repetitive palindromic sequences) associated with so called RAYT transposase. Oligonucleotides with sequences of REP elements have extremely interesting and unexpected structural behavior (Charnavets et al.: Biopolymers (2015), doi: 10.1002/bip.22666. ).

    The lab is involved in several exciting bioinformatics projects, mostly on structural aspects of interactions between nucleic acids and proteins.

    We have recently published a paper analyzing the geometry of the protein/DNA interfaces (Schneider et al.: Bioinformatic analysis of the protein/DNA interface. Nucleic Acids Res. 42, 3381 (2014). ).

    The above analysis has been based on the original method of assignemnt of DNA conformations we published earlier, (Cech_et al.: BMCBioinfo_14,_205_(2013). ).

    We have built a web interface to classify DNA structures and DNA/protein structures; a test version that classifies DNA is at the website dnatco.org.

  • My second major responsibility is to coordinate research program of Structural biology and protein engineering at the center BIOCEV, Biotechnological Center Vestec, the project funded by the European Regional Development Fund.

  • Some papers I co-authored and are of more general interest can be found under the link "papers" above. Wherever it is legal I provide their pdf versions.

    References to most my papers can be found at the end of my curriculum vitae also linked above as "cv".

    My Interests

  • Intermolecular interactions & recognition of biomolecules
  • Understading mechanisms of molecular recognition is the Holy Grail of structural biology, at least as I understand goals of structural biology...
    To reach this goal, I study structure, dynamics, and solvation of nucleic acids, and proteins.

    I have also been involved in development of structural databases, the indispensable tool of all structural studies.

  • Nucleic Acid Structure and Dynamics
  • Both DNA and RNA dinucleotides form a limited set of conformers. Some, as BI ("b-one") or "canonical A" (also called "AI") are very abundant and form the scaffold of DNA double helices (BI) or RNA complex architectures (AI). Other conformers are rare but occur at structurally and functionally critical points. Especially RNA molecules with their complicated 3D folds employ a repertoire of unusual but structurally well defined conformers.
    More can be found in papers in the above link "papers".

  • Hydration and solvation of nucleic acids
  • Solvation, water activity, presence and concentration of ions, especially cations, is important for structural integrity of nucleic acids and therefore for their function.
    Since the early ninetees, I have been involved in research of structural aspects of DNA solvation in the lab of Prof. Helen Berman at Rutgers University, NJ and later in Prague. I believe that most of our results are still valid because all our conclusions have been drawn solely from experimental crystal data with no bias of any "theoretical" model.
    The resulting "Hydrated Building Blocks" are summarized at the web I dared to copy from now defunct NDB beta site.

  • Design, development, and maintenance of structural databases
  • I have been priviledged to work with Prof. Helen Berman at Rutgers University on development of two important databases of molecular structures, the Nucleic Acid Database, NDB and on the Protein Data Bank, PDB .
    Between years 1998 and 2008 I was a member of the team maintaining the NDB and I annotated structures deposited to the PDB. In years 2000-2008, after I returned to Prague, structures deposited at Rutgers were annotated in Prague taking advantage of the portable architecture of the RCSB annotation and deposition system developed primarily by John Westbrook and Zukang Feng from RCSB at Rutgers University.

    What is annotation of biomolecular structures? If you really want to know, you can read a paper where three annotators explain what is involved before a molecular structure can be loaded into the PDB: A Biocurator Perspective: Annotation at the RCSB. Burkhardt, Schneider, Ory: PLOS Comp.Biol. 2, 1186 (2006).

    Equipment available at the IBT

    Lab equipment for biophysical characterization of Biomolecules:
  • Circular dischroism and UV spectrometers
  • Isothermal Titration Calorimetry
  • Surface Plasmon Resonance - ProteOn by Bio-Rad
  • Microscale Thermophoresis - Monolith MT115 by nanoTemper
  • Dynamic light dispersion - Zetasizer Nano90 by Malvern
  • Facilities for prokaryotic expression and purification
  • Rooms for Eukaryotic tissue cultures
  • A devoted crystallization room equipped with crystallization robots
  • A diffractometer Bruker

    You are welcome to contact me:

    Bohdan Schneider
    Institute of Biotechnology AS CR
    Videnska 1083, CZ-142 20 Prague, Czech Republic
    Phone: +420 241 063 624,
    Cell: +420 728 303 566
    e-mail: bohdan.schneider-at-gmail.com
  •  
    Bohdan Schneider 2008-2015