scholarly journals Ultrafast pore-loop dynamics in a AAA+ machine point to a Brownian-ratchet mechanism for protein translocation

2021 ◽  
Vol 7 (36) ◽  
Author(s):  
Hisham Mazal ◽  
Marija Iljina ◽  
Inbal Riven ◽  
Gilad Haran
Keyword(s):  
Protein Translocation ◽  
Brownian Ratchet ◽  
Ratchet Mechanism ◽  
Loop Dynamics

scholarly journals Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
William John Allen ◽  
Robin Adam Corey ◽  
Peter Oatley ◽  
Richard Barry Sessions ◽  
Steve A Baldwin ◽  
...  
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Protein Translocation ◽  
Md Simulations ◽  
Atp Binding ◽  
Nucleotide Exchange ◽  
Brownian Ratchet ◽  
Ratchet Mechanism ◽  
Single Molecule Fret ◽  
Directional Movement

The essential process of protein secretion is achieved by the ubiquitous Sec machinery. In prokaryotes, the drive for translocation comes from ATP hydrolysis by the cytosolic motor-protein SecA, in concert with the proton motive force (PMF). However, the mechanism through which ATP hydrolysis by SecA is coupled to directional movement through SecYEG is unclear. Here, we combine all-atom molecular dynamics (MD) simulations with single molecule FRET and biochemical assays. We show that ATP binding by SecA causes opening of the SecY-channel at long range, while substrates at the SecY-channel entrance feed back to regulate nucleotide exchange by SecA. This two-way communication suggests a new, unifying 'Brownian ratchet' mechanism, whereby ATP binding and hydrolysis bias the direction of polypeptide diffusion. The model represents a solution to the problem of transporting inherently variable substrates such as polypeptides, and may underlie mechanisms of other motors that translocate proteins and nucleic acids.

scholarly journals Author response: Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation

2016 ◽  
Author(s):  
William John Allen ◽  
Robin Adam Corey ◽  
Peter Oatley ◽  
Richard Barry Sessions ◽  
Steve A Baldwin ◽  
...  
Keyword(s):  
Protein Translocation ◽  
Author Response ◽  
Brownian Ratchet ◽  
Ratchet Mechanism

scholarly journals Treadmilling FtsZ polymers drive the directional movement of sPG-synthesis enzymes via a Brownian ratchet mechanism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joshua W. McCausland ◽  
Xinxing Yang ◽  
Georgia R. Squyres ◽  
Zhixin Lyu ◽  
Kevin E. Bruce ◽  
...  
Keyword(s):  
Cell Wall ◽  
Single Molecule ◽  
Theoretical Modelling ◽  
Binding Potential ◽  
Central Component ◽  
Macromolecular Complex ◽  
Bacterial Cells ◽  
Brownian Ratchet ◽  
Ratchet Mechanism ◽  
Directional Movement

AbstractThe FtsZ protein is a central component of the bacterial cell division machinery. It polymerizes at mid-cell and recruits more than 30 proteins to assemble into a macromolecular complex to direct cell wall constriction. FtsZ polymers exhibit treadmilling dynamics, driving the processive movement of enzymes that synthesize septal peptidoglycan (sPG). Here, we combine theoretical modelling with single-molecule imaging of live bacterial cells to show that FtsZ’s treadmilling drives the directional movement of sPG enzymes via a Brownian ratchet mechanism. The processivity of the directional movement depends on the binding potential between FtsZ and the sPG enzyme, and on a balance between the enzyme’s diffusion and FtsZ’s treadmilling speed. We propose that this interplay may provide a mechanism to control the spatiotemporal distribution of active sPG enzymes, explaining the distinct roles of FtsZ treadmilling in modulating cell wall constriction rate observed in different bacteria.

scholarly journals Asymptotics of a Brownian ratchet for protein translocation

2010 ◽  
Vol 120 (6) ◽  
pp. 901-925 ◽  
Author(s):  
Andrej Depperschmidt ◽  
Peter Pfaffelhuber
Keyword(s):  
Protein Translocation ◽  
Brownian Ratchet

scholarly journals Ultrafast Brownian-ratchet mechanism for protein translocation by a AAA+ machine

2020 ◽  
Author(s):  
Hisham Mazal ◽  
Marija Iljina ◽  
Inbal Riven ◽  
Gilad Haran
Keyword(s):  
Single Molecule ◽  
Protein Translocation ◽  
Conformational Dynamics ◽  
Brownian Ratchet ◽  
Time Dynamics ◽  
Single Molecule Fret ◽  
Differential Behavior ◽  
Amplitude Fluctuations ◽  
Translocation Mechanism ◽  
Substrate Proteins

AbstractAAA+ ring-shaped machines, such as ClpB and Hsp104, mediate substrate translocation through their central channel by a set of pore loops. Recent structural studies suggested a universal hand-over-hand translocation mechanism, in which pore loops are moving rigidly in tandem with their corresponding subunits. However, functional and biophysical studies are in discord with this model. Here, we directly measure the real-time dynamics of the pore loops of ClpB and their response to substrate binding, using single-molecule FRET spectroscopy. All pore loops undergo large-amplitude fluctuations on the microsecond timescale, and change their conformation upon interaction with substrate proteins. Pore-loop conformational dynamics are modulated by nucleotides and strongly correlate with disaggregation activity. The differential behavior of the pore loops along the axial channel points to a fast Brownian-ratchet translocation mechanism, which likely acts in parallel to the much slower hand-over-hand process.

scholarly journals HDX-MS reveals nucleotide-regulated, anti-correlated opening and closure of SecA and SecY channels of the bacterial translocon

2019 ◽  
Author(s):  
Zainab Ahdash ◽  
Euan Pyle ◽  
William J. Allen ◽  
Robin A. Corey ◽  
Ian Collinson ◽  
...  
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Protein Transport ◽  
Atp Hydrolysis ◽  
Protein Translocation ◽  
Conformational Dynamics ◽  
Brownian Ratchet ◽  
Exchange Mass Spectrometry ◽  
Dependent Transport ◽  
Hdx Ms

AbstractThe bacterial Sec translocon is a multi-component protein complex responsible for translocating diverse proteins across the plasma membrane. For post-translational protein translocation, the Sec-channel – SecYEG – associates with the motor protein SecA to mediate the ATP-dependent transport of unfolded pre-proteins across the membrane. Based on the structure of the machinery, combined with ensemble and single molecule analysis, a diffusional based Brownian ratchet mechanism for protein secretion has been proposed [Allen et al. eLife 2016;5:e15598]. However, the conformational dynamics required to facilitate this mechanism have not yet been fully resolved. Here, we employ hydrogen-deuterium exchange mass spectrometry (HDX-MS) to reveal striking nucleotide-dependent conformational changes in the Sec protein-channel. In addition to the ATP-dependent opening of SecY, reported previously, we observe a counteracting, also ATP-dependent, constriction of SecA around the mature regions of the pre-protein. Thus, ATP binding causes SecY to open and SecA to close, while ATP hydrolysis has the opposite effect. This alternating behaviour could help impose the directionality of the Brownian ratchet for protein transport through the Sec machinery, and possibly in translocation systems elsewhere. The results highlight the power of HDX-MS for interrogating the dynamic mechanisms of diverse membrane proteins; including their interactions with small molecules such as nucleotides (ATPases and GTPases) and inhibitors (e.g. antibiotics).

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