Controlling the Revolving and Rotating Motion Direction of Asymmetric Hexameric Nanomotor by Arginine Finger and Channel Chirality

Abstract

Nanomotors in nanotechnology are as important as engines in daily life. Many ATPases are nanoscale biomotors classified into three categories based on the motion mechanisms in transporting substrates: linear, rotating, and the recently discovered revolving motion. Most biomotors adopt a multisubunit ring-shaped structure that hydrolyzes ATP to generate force. How these biomotors control the motion direction and regulate the sequential action of their multiple subunits is intriguing. Many ATPases are hexameric with each monomer containing a conserved arginine finger. This review focuses on recent findings on how the arginine finger controls motion direction and coordinates adjacent subunit interactions in both revolving and rotating biomotors. Mechanisms of intersubunit interactions and sequential movements of individual subunits are evidenced by the asymmetrical appearance of one dimer and four monomers in high-resolution structural complexes. The arginine finger is situated at the interface of two subunits and extends into the ATP binding pocket of the downstream subunit. An arginine finger mutation results in deficiency in ATP binding/hydrolysis, substrate binding, and transport, highlighting the importance of the arginine finger in regulating energy transduction and motor function. Additionally, the roles of channel chirality and channel size are discussed as related to controlling one-way trafficking and differentiating the revolving and rotating mechanisms. Finally, the review concludes by discussing the conformational changes and entropy conversion triggered by ATP binding/hydrolysis, offering a view different from the traditional concept of ATP-mediated mechanochemical energy coupling. The elucidation of the motion mechanism and direction control in ATPases could facilitate nanomotor fabrication in nanotechnology.

High resolution structure of hexameric herpesvirus DNA-packaging motor elucidates revolving mechanism and ends 20-year fervent debate

“…Thus, most rotation motors contain a channel smaller than 2 nm. However, the diameter of many connector portal channels of procapsids/assembly intermediates in dsDNA bacteriophages are larger than the diameter of the dsDNA (Schwartz et al, 2013;Zhao et al, 2013;Guo et al, 2014Guo et al, , 2019. The channel of the herpesvirus motor as reported here is about 50% larger than that of dsDNA (Wang et al, 2020; Yang et al, 2020), indicative of an impossibility for nutand-bolt rotation.…”

“…This finding agrees with many recent findings on revolving biomotors such as phi29 bacteriophage DNA packaging motor, human 26S proteasome, FtsK DNA translocase, and SPP1 DNA packaging motor, etc. (Guo et al, 2019). With all the solid biophysical data, the authors were able to rule out the rotation motor model but support the revolving mechanism for DNA translocation driven by conformational change, and in turn shed light on the mechanism of the packaging motor.…”

“…Each subunit of the ATPase hexamer has the capability to bind ATP; however, saturation of the ATPase with ATP reveals that at least two of the subunits do not bind to ATP. Even when only a few of the subunits are able to bind ATP, ATPase function is still retained (Martin et al, 2005;Guo et al, 2019).…”

“…As stated before, in many hexameric ring-shaped ATPases, the arginine finger serves as the bridge between two of the ATPase subunits; the two adjacent subunits thus form a more compact dimer configuration that may appear as a monomer in low resolution cryo-EM images. The presence of one dimer complex and four monomers in the motor will result in an asymmetrical hexameric ring (Soultanas and Wigley, 2001;Lyubimov et al, 2012;Arai et al, 2013;Zhao et al, 2016;Puchades et al, 2017;Su et al, 2017;Sun et al, 2017;Zehr et al, 2017;Dong et al, 2019), which was processed into a seemingly pentamer (Guo et al, 2019), leading to a false pentameric configuration.…”

Direct structural evidence supporting a revolving mechanism in DNA packaging motors

“…Unlike linear motor kinesin, which consumes one ATP molecule for each 8 nm step with a hand-over-hand mechanism (Li et al 2018), and reversible rotary motor F o F 1 -ATPase, which synthesizes/ hydrolyzes one ATP molecule for each 120°step with a binding-change-mechanism (Shu and Lai 2008), the framework of the genome packaging motors remains elusive. Although rotational motion with tight mechanochemical coupling was long thought as a common mechanism for the DNA packaging motors (Hendrix 1998;Serwer 2003;Simpson et al 2000), a revolving framework of DNA translocation has recently been proposed for the /29 dsDNA packaging motor (Guo et al 2019;Schwartz et al 2013;Zhao et al 2016).…”