... Head of the Laboratory of Biomolecular Recognition at
the
Institute of Biotechnology Academy of Sciences of the Czech Republic (IBT).
We study interactions between biomolecules, proteins and nucleic acids, by biophysical and bioinformatic tools.
The Lab has five members, Dr. Jiri Cerny, Dr. Lada Biedermannova, PhD student Pavel Mikulecky, x-ray equipment specialist Karel Pufler, and myself.
We want to understand especially interactions driving specific recognition between biomolecules with potential diagnostic, medical or biotechnological use.
Our current major project is increasing affinity between interferon-gamma and extracellular part of its receptor. We want to improve the binding by rational design of mutations in either of the involved proteins, currently we concentrate on the modifications of the receptor molecules.
I am also involved in several bioinformatics projects, mostly on structural aspects of interactions between nucleic acids and proteins.
My second major responsibility is to coordinate research program of
Structural biology and protein engineering
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 molecular recognition is the Holy Grail of structural biology,
at least as I understand goals of structural biology...
I help to reach this goal by studying structure, dynamics, and
solvation of nucleic acids, and --since 2010-- by examination of
protein-protein interactions of cytokines, mostly interferon gamma and
its receptor.
... and of course, also by involvement 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
Facilities for Prokaryotic expression and purification
Rooms for Eukaryotic tissue cultures
A devoted crystallization room operated at 18 degrees C equipped with crystallization robots
A diffractometer Rigaku, a gift by Prof. Stephen Neidle and Dr. Gary
Parkinson from School of Pharmacy, University of London. This generous
gift includes rotating anode Rigaku RU-H3R with image plate detector
Raxis4 and cryo-protection by Oxford Cryosystem Cooler 600.
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-at-img.cas.cz
