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The Department of Biomedicine

BBB Seminar: Igor N. Berezovsky

Protein stability, function and evolution

Igor N. Berezovsky
Computational Biology Unit, Uni Research, University of Bergen

My talk will cover three topics. First, protein stability and mechanisms of molecular adaptation will be discussed for the case of thermostability of protein complexes [1]. Tuning protein structure and sequences and adjustment of combinations of stabilizing forces in response to selective pressure of the environment will be analyzed. Second, a thermodynamical view of allosteric regulation [2] and communication [3] will be presented. The importance of considering conformational degrees of freedom, which determine fluctuations around the native conformation and switching from/to functional states will be discussed. It will be argued that ligand binding shifts conformational equilibrium of a protein, and transitions between states involved in function and its regulation are based on coherent conformational degrees of freedom. Third, the question of how it all started will be addressed. In other words we will try to understand how the first enzymes emerged and what their elementary building blocks were [4,5]. It will be illustrated how the polymer nature of proteins determined the units of protein structure and function.

References:

1. Ma, B.G., Goncearenco, A. & Berezovsky, I.N. 2010. Thermophilic adaptation of protein complexes inferred from proteomic homology modeling. Structure 18, 819-828.

2. Mitternacht, S. & Berezovsky, I.N. 2011. Binding leverage as a molecular basis for allosteric regulation. PLoS Comp Biol 7, e1002148.

3. Mitternacht, S. & Berezovsky, I.N. 2011. Coherent conformational degrees of freedom as a structural basis for allosteric communication. PLoS Comp Biol, in press.

4. Goncearenco, A. & Berezovsky, I.N. 2010. Prototypes of elementary functional loops unravel evolutionary connections between protein functions. Bioinformatics 26, i497-i503.

5. Goncearenco, A. & Berezovsky, I.N. 2011. Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins. Bioinformatics 27, 2368-2375.

Chair: Inge Jonassen , Department of Informatics