Structural and dynamic aspects of protein clocks: how can they be so slow and stable?

Abstract

KaiC is a core protein of the cyanobacterial Kai oscillator, which persists without transcription-translation feedback. In the presence of KaiA and KaiB, KaiC reveals rhythmic activation/inactivation of its ATPase and autokinase/autophosphotase activities over approximately 24 h. Since the in vitro reconstruction of the Kai oscillator, the structures and functions of the Kai proteins have been studied extensively. Each protein's crystal structure and low-resolution views of Kai complexes have been reported. In addition, newer data are emerging on dynamic aspects such as assembly/disassembly of the Kai components and a ticking motion of KaiC, which is probably coupled to its slow, temperature-compensated ATPase activity. The accumulated evidence offers an ideal opportunity to revisit a fundamental question regarding biological circadian clocks: what determines the temperature-compensated 24 h period? In this review, I summarize the current understanding of the Kai oscillator's molecular mechanism and discuss emerging ideas on protein clocks.

Fig. 1

Crystal structures of Kai proteins. a Crystal structure of S. elongatus KaiA [18]. b Crystal structure of T. elongatus KaiB [28]. c Crystal structure of S. elongatus KaiC [35]. d Expanded view of dotted square in (c). A-loop and C-terminal tail are orange and magenta, respectively

Fig. 2

Structural models for KaiAC complex. a NMR-based T. elongatus KaiAC subcomplex (adapted from Ref. [26]). b EM-based S. elongatus KaiAC complex (tethered model) [25]. c EM-based S. elongatus KaiAC complex (engaged model) [25]. (b, c) Adapted from Ref. [29]. d Two orthogonal views of SAXS-based S. elongatus KaiAC complex (adapted from Ref. [24])

Fig. 3

Structural models for KaiBC complex. a EM-based T. elongatus KaiBC complex (adapted from Ref. [29]). b Two orthogonal views of SAXS-based S. elongatus KaiBC complex (adapted from Ref. [24])

Fig. 4

Expansion and contraction of KaiC interlocked with ATPase, phosphorylation state, and assembly/disassembly of Kai complexes in presence of KaiA and KaiB. a ATPase activity. b Relative abundance of four phosphorylation states (red KaiC^S/pT, blue KaiC^pS/pT, orange KaiC^pS/T, green KaiC^S/T). c Circadian fluctuation of Trp fluorescence in the C2 domain. d Weight-averaged molecular mass of Kai complexes from I(0) [24]. Adapted from Ref. [39]

Fig. 5

Expansion and contraction of C2 ring interlocked with ATPase in C1 ring. ATPase activity of KaiC is given as a relative value. Adapted from Ref. [39]

Fig. 6

Spatio-temporal scale of protein dynamics. Approximate time scales of motions were taken from Refs. [–54]