Seeing the invisible – Study of transiently formed protein conformation found in domain 1.1 of bacterial transcription factor

D. Tužinčin1,2, P. Kadeřávek1,2, P. Padrta1,2, L. Žídek1,2

1Central European Institute of Technology (CEITEC), Faculty of Science, Masaryk University, Kamenice 735/5, Brno, Czech Republic

2National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 735/5, Brno, Czech Republic


Biomolecules undergo a variety of motions at various timescales. Motions at microsecond to millisecond timescales are often associated with transitions between ground states and higher energy states. Methods of structural biology allow detailed characterization of ground state structure and dynamics. However, the studies of higher energy state conformations are more difficult, because of their low occupancies and short lifetimes. Due to this fact, studies of excited states are often omitted. But nuclear magnetic resonance provides methods to investigate motions associated with these transitions and structures of excited states.

In here, we investigate such conformational exchange, between well-defined ground state and transiently formed excited state which has been detected in domain 1.1 of primary sigma transcription factor from Bacillus subtillis. Sigma factor is essential for initiating the process of transcription, a fundamental cellular process. With the use of relaxation dispersion experiments we obtained structural information about orientations of bond vectors and secondary structure propensities within the excited state. Our results suggest that the excited state (populated only about 3% in the solution at 25 °C) has significantly lower propensity to form a stable secondary structure in the regions of helix I and helix III compared to the ground state.

This work was supported by Czech Science Foundation grant No. GJ18-04197Y, from European Regional Development Fund-Project MSCAfellow2@MUNI (No. CZ.02.2.69/0.0/0.0/18_070/0009846) CIISB, Instruct-CZ Centre of Instruct-ERIC EU consortium, funded by MEYS CR infrastructure project LM2018127, is gratefully acknowledged for the financial support of the measurements at the Josef Dadok National NMR Centre.