The role of structural equilibrium fluctuation in proteins

  Protein dynamics Copyright: © Fitter  

Conformational states of a protein can be assigned to different regions within the protein folding funnel (see left panel). These states (unfolded a-amylase in the upper part of the funnel, folded a-amylase in the lower part of the funnel) were dynamically characterized by quasi-elastic neutron scattering (right panel).


Biological macromolecules, such as enzymes or transport proteins share a structural complexity which is also reflected in a complex dynamical behavior. In particular fast stochastic fluctuations on a picosecond time-scale are relevant to overcome energy barriers which are given by the energy landscape of the biomolecules. These fluctuations can determine the kinetics of transitions between conformational (intermediate) states. In addition, these fluctuations contribute significantly to the conformational entropy of a biopolymer, and are therefore important for protein stability, protein folding and protein-ligand interactions. One of the most powerful techniques to study in particular fast fluctuations is given by neutron spectroscopy which in principle provides a detailed picture about motion in the time regime of 10-14 – 10-8 seconds with amplitudes in the order of 0.1 – 10 nanometer. So far we compare for various water soluble proteins (a-amylases, PGK, myoglobin) dynamical properties between the folded and various unfolded states (heat, GndHCl, or pH denatured states). One particular goal of our studies is to estimate the contribution of measured picosecond fluctuations to the conformational entropy change which is related unfolding/refolding transitions or to protein/ligand binding. In further studies neutron spin echo technique is employed to investigate domain movements (e.g., hinge bending) which are directly related to the catalytic actvitity of enzymes.


Related publications

Balacescu L, Schrader TE, Radulescu A, Zolnierczuk P, Holderer O, Pasini S, Fitter J and Stadler AM
Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions
Sci Rep. 10(1), 1570 (2020)

Mona Sarter, Doreen Niether, Bernd W. Koenig, Wiebke Lohstroh, Michaela Zamponi,
Niina H. Jalarvo, Simone Wiegand, Jörg Fitter and Andreas M. Stadler
Strong Adverse Contribution of Conformational Dynamics to Streptavidin−Biotin Binding
J. Phys. Chem. B. 124,324-335 (2019)

D. Niether, M. Sarter, B. König, M. Zamponi, J. Fitter, A.Stadler and S. Wiegand
Thermodiffusion as a probe of protein hydration for streptavidin and the streptavidin-biotin complex.
AIP Conference Proceedings, 1929, 020001, (2018)

A.M. Stadler, M. M. Koza, and J. Fitter
Determination of Conformational Entropy of Fully and Partially Folded Conformations of Holo- and Apomyoglobin.
J. Phys. Chem. B, 119, 72-82, (2015)

A.M. Stadler, E. Pellegrini, M. Johnson, J. Fitter, and G. Zaccai
Dynamics-Stability Relationships in Apo- and Holomyoglobin: A Combined Neutron and Molecular Dynamics Simulation Study.
Biophys. J, 102, 351-359, (2012 )

R. Inoue, R. Biehl, T. Rosenkanz, J. Fitter, M. Monkenbusch, A. Radelescu, B. Farago, D. Richter
Large domain fluctuations on 50 ns timescale enable catalytic function in phosphoglycerate kinase.
Biophys. J. 99, 2309-2317, (2010)

J. Fitter
A Measure of Conformational Entropy Change during Thermal Protein Unfolding using Neutron Spectroscopy.
Biophysical Journal, 84(6), 3924 -3930, (2003)