Protein Structure and Dynamics

Plots of J values as functions of the residue number.

Project description:

Structures and molecular motions of proteins and their interactions with other biologically relevant molecules are studied mostly by methods of nuclear magnetic resonance. Application of standard NMR techniques to interesting biological systems is combined with our own methodological development. Examples of proteins recently and currently studied in our laboratory are briefly reviewed below.

Mouse major urinary protein I (MUP-I) has been recently investigated in our group as an example of a mammalian pheromone-binding protein. Standard NMR techniques have been used to study structural details of MUP-I in complex with a natural pheromone. NMR relaxation measurements have been employed in mapping internal dynamics of free and pheromone-bound MUP-I [1]. Analysis of data obtained at various temperatures was used to improve reliability of the measured values and to obtain additional information about dynamical and thermodynamical changes upon binding. The results have been compared to molecular dynamic simulations [2,3]. Both NMR relaxation and MD simulations indicated that the pheromone binding does not rigidify the MUP-I structure. On the conrary, several regions of increased flexibility have been identified in the protein-pheromone complex.

Chemosensory protein 1 (CSP1) of Bombyx mori is believed to bind small hydrophobic, like MUP-I. In spite of the functional similarity structures of CSP1 (and related insect proteins) differes from the typical lipocalin fold of MUP-I. In collaboration with the Department of Ecology at the Lund University, 3D structure of CSP1 has been solved in our laboratory based on NMR data [4].

A protein putatively involved in molybdopterin synthesis has been studied as target TA1019 of the Thermoplasma acidophillum structural genomic project at the University of Toronto. Due to the low solubility and limited stability, TA1019 has been excluded from the automated protocol of structure determination. Based on data obtained at experimentally challenging conditions, a structural model of TA1019 has been built in our laboratory.

Other proteins which our group is interested in include mammalian lectin-like receptor domains, plant lipid-transfer proteins, bacterial RNA polymerases, retroviral proteases etc. Structural investigations of these proteins are usually combined with binding studies and various biological assays perfored in collaborating groups (mostly at the institutes of the Czech Academy of Sciences). Our goal is to provide a complex description of the systems and thus help to understand their biological roles.


Design © oliver 2007