**Marta Kolonko and Beata Greb-Markiewicz \***

Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrze ˙ze Wyspia ´nskiego 27, 50-370 Wroclaw, Poland

**\*** Correspondence: beata.greb-markiewicz@pwr.edu.pl

Received: 24 June 2019; Accepted: 16 July 2019; Published: 26 July 2019

**Abstract:** The basic helix–loop–helix/Per-ARNT-SIM (bHLH–PAS) proteins are a class of transcriptional regulators, commonly occurring in living organisms and highly conserved among vertebrates and invertebrates. These proteins exhibit a relatively well-conserved domain structure: the bHLH domain located at the N-terminus, followed by PAS-A and PAS-B domains. In contrast, their C-terminal fragments present significant variability in their primary structure and are unique for individual proteins. C-termini were shown to be responsible for the specific modulation of protein action. In this review, we present the current state of knowledge, based on NMR and X-ray analysis, concerning the structural properties of bHLH–PAS proteins. It is worth noting that all determined structures comprise only selected domains (bHLH and/or PAS). At the same time, substantial parts of proteins, comprising their long C-termini, have not been structurally characterized to date. Interestingly, these regions appear to be intrinsically disordered (IDRs) and are still a challenge to research. We aim to emphasize the significance of IDRs for the flexibility and function of bHLH–PAS proteins. Finally, we propose modern NMR methods for the structural characterization of the IDRs of bHLH–PAS proteins.

**Keywords:** bHLH–PAS transcription factor; intrinsically disordered region; IDR; C-terminus
