1st year u/g students, 2nd year u/g students, 3rd year u/g students
Student Responsibilty with support from IIP and/or Host Organization
International Internship Program
Academy of Sciences of the Czech Republic, Center for Nanobiology and Structural Biology About: The Center for Nanobiology and Structural Biology was founded in 2002 as a joint laboratory of the Institute of Systems Biology and Ecology of the Academy of Sciences and the Institute of Physical Biology of the University of South Bohemia named Laboratory of High Performance Computing. The laboratory combines methods ranging from computational and spectroscopic to molecular biological and biochemical and, in collaboration with the Kuta Smatanova, lab protein crystallization. With its focus on molecular systems biology, the relationship between structure and function of proteins, dynamic changes related to functional processes on the level of proteins, and the mutual interaction of co-factors and sub-units in protein complexes, the laboratory is an integral part of the new research concept of the Institute.
Intern Responsibilities: IIP interns will be introduced to the computational methods for building and investigation of biological systems and will be able to analyze dynamical changes in systems and learn how to interpret generated data. IIP interns will use special software for modeling biological systems and carrying out molecular dynamics simulations, partly using massive parallel calculations on a beowulf-computer cluster. The underlying experimental basis of all structural information comes from protein crystallography done in house. After receiving intense training during the first weeks, IIP interns will each be responsible for a sub-project that leads to a clear outcome/prediction that can be experimentally verified.
Possible sub-projects include a computational project and an experimental project. The IIP interns may also have the opportunity to participate in a symposium on Structure Systems Biology in Bratislava, Slovakia, and/or the opportunity to visit biomedical institutes of the Academy of Sciences in Prague. Each IIP intern will be assigned to one of the following two projects:
Modeling interactions in and between biomolecules and complex biologically relevant systems - The IIP intern will mainly work with computational tools on data, that are produced by experimentalists in house. After getting intense training during the first weeks, she/he/they will be responsible for a sub-project that leads to a clear outcome/prediction that can be experimentally verified. The IIP intern will also get an insight how the experimental data, like the X-ray structures, are generated and will collaborate directly with the scientists working on that.
Protelike for example restriction modification system EcoR124I or the cation translocation system TrK1). The IIP intern would not repeat something somebody has done already, but would use a unique mutant, that should alter the functionality. In this sense this is a new and un-characterized protein, as we do not know its actual functionality unless the IIP intern will find out! This project involves: 1) Polymerase chain reaction using primers that would introduce the mutation, amplification of the DNA, 2) Growing of e.coli or yeast cells used later for over-expression, 3) Over-expression of protein in e.coli or yeast cells, 4) French pressing the cells to disrupt them, 5) isolation of protein from the crude extract using gel filtration and affinity and ion exchange chromatography, 6) In vitro assays to monitor protein activity , 7) Ligand-binding studies like ITC/SPR/fluorescence/microscale thermophoresis 8) limited proteolysis. In nearly all steps SDS-phage electrophoresis is used to monitor either the successful amplificiation, the overexpression, the protein purity or the fragments after cleavage.
The experimental basis for modeling interactions in and between biomolecules - This would be a combined experimental and computational project focusing on protein crystallization and X-ray diffraction of mutants of type I restriction-modification systems to resolve the three-dimensional structure of these proteins. In parallel with the lab work the IIP intern would work computationally on: 1) Solving the X-ray structure and homology modeling 2) Ligand-docking 3) Molecular dynamics simulation of the system in simple-point water, 4) calculation of binding energy.
Qualifications: IIP candidates should have academic interest in life sciences, an understanding of biologically relevant systems and how they can be understood by computational modeling, a good background in physics and mathematics;, and a good relation to computers as a scientific tool. General UNIX knowledge is welcome, but no programming is required.