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Energy landscape steering mediates dynamic coupling in ATP-driven protein translocation by the bacterial Sec machinery

https://doi.org/10.1101/793943
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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A Reducing and Oxidizing System Minimizes Photobleaching and Blinking of Fluorescent Dyes
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Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy
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SecA protein hydrolyzes ATP and is an essential component of the protein translocation ATPase of Escherichia coli.
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Translocation can drive the unfolding of a preprotein domain.
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PrlA suppressor mutations cluster in regions corresponding to three distinct topological domains.
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The crystal structure Escherichia coli Spy
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Suppressor mutations that restore export of a protein with a defective signal sequence
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A temperature-sensitive mutant of E. coli exhibiting slow processing of exported proteins
inferredcites →https://doi.org/10.1016/0092-8674(90)90111-qopenalex-snapshot
The purified E. coli integral membrane protein is sufficient for reconstitution of SecA-dependent precursor protein translocation
inferredcites →https://doi.org/10.1016/0092-8674(90)90160-gopenalex-snapshot
The binding cascade of SecB to SecA to SecYE mediates preprotein targeting to the E. coli plasma membrane
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VMD: Visual molecular dynamics
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Identifying Molecular Dynamics in Single-Molecule FRET Experiments with Burst Variance Analysis
inferredcites →https://doi.org/10.1016/j.cell.2014.03.063openalex-snapshot
A “Push and Slide” Mechanism Allows Sequence-Insensitive Translocation of Secretory Proteins by the SecA ATPase
inferredcites →https://doi.org/10.1016/j.celrep.2011.11.003openalex-snapshot
Structure of the SecY Complex Unlocked by a Preprotein Mimic
inferredcites →https://doi.org/10.1016/j.celrep.2015.10.025openalex-snapshot
Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State
inferredcites →https://doi.org/10.1016/j.jbc.2022.102572openalex-snapshot
Inner membrane YfgM–PpiD heterodimer acts as a functional unit that associates with the SecY/E/G translocon and promotes protein translocation
inferredcites →https://doi.org/10.1016/j.jmb.2007.09.086openalex-snapshot
A Large Conformational Change Couples the ATP Binding Site of SecA to the SecY Protein Channel
inferredcites →https://doi.org/10.1016/j.jmb.2019.03.007openalex-snapshot
A High-Resolution Luminescent Assay for Rapid and Continuous Monitoring of Protein Translocation across Biological Membranes
inferredcites →https://doi.org/10.1016/j.jmb.2021.166929openalex-snapshot
Structure and Function of Chromatin Remodelers
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SF1 and SF2 helicases: family matters
inferredcites →https://doi.org/10.1016/j.sbi.2017.10.007openalex-snapshot
Protein folding transition path times from single molecule FRET
inferredcites →https://doi.org/10.1016/j.str.2010.04.010openalex-snapshot
Dynamics of SecY Translocons with Translocation-Defective Mutations
inferredcites →https://doi.org/10.1016/j.str.2016.02.001openalex-snapshot
Unlocking the Bacterial SecY Translocon
inferredcites →https://doi.org/10.1016/j.str.2018.10.006openalex-snapshot
The Preprotein Binding Domain of SecA Displays Intrinsic Rotational Dynamics
inferredcites →https://doi.org/10.1021/ac000877gopenalex-snapshot
An Experimental Comparison of the Maximum Likelihood Estimation and Nonlinear Least-Squares Fluorescence Lifetime Analysis of Single Molecules
inferredcites →https://doi.org/10.1021/acs.biochem.8b00907openalex-snapshot
Hinge–Linker Elements in the AAA+ Protein Unfoldase ClpX Mediate Intersubunit Communication, Assembly, and Mechanical Activity
inferredcites →https://doi.org/10.1021/acs.jpcb.6b02776openalex-snapshot
Molecular Motors: Power Strokes Outperform Brownian Ratchets
inferredcites →https://doi.org/10.1021/acs.jpcb.6b10726openalex-snapshot
Photon-by-Photon Hidden Markov Model Analysis for Microsecond Single-Molecule FRET Kinetics
inferredcites →https://doi.org/10.1021/ja00752a042openalex-snapshot
Thiophosphate analogs of nucleoside di- and triphosphates
inferredcites →https://doi.org/10.1021/ja0780481openalex-snapshot
Single Molecule Conformational Dynamics of Adenylate Kinase: Energy Landscape, Structural Correlations, and Transition State Ensembles
inferredcites →https://doi.org/10.1021/ja105725eopenalex-snapshot
Accurate Distance Determination of Nucleic Acids via Förster Resonance Energy Transfer: Implications of Dye Linker Length and Rigidity
inferredcites →https://doi.org/10.1021/ja809117zopenalex-snapshot
On the Mechanism of Trolox as Antiblinking and Antibleaching Reagent
inferredcites →https://doi.org/10.1038/nature02218openalex-snapshot
X-ray structure of a protein-conducting channel
inferredcites →https://doi.org/10.1038/nature07335openalex-snapshot
Structure of a complex of the ATPase SecA and the protein-translocation channel
inferredcites →https://doi.org/10.1038/nature08559openalex-snapshot
Signal peptides are allosteric activators of the protein translocase
inferredcites →https://doi.org/10.1038/nature12720openalex-snapshot
Structure of the SecY channel during initiation of protein translocation
inferredcites →https://doi.org/10.1038/nature17163openalex-snapshot
Crystal structure of a substrate-engaged SecY protein-translocation channel
inferredcites →https://doi.org/10.1038/ncb2939openalex-snapshot
Structural mechanism of the dynein power stroke
inferredcites →https://doi.org/10.1038/ncomms5103openalex-snapshot
Visualization of a polytopic membrane protein during SecY-mediated membrane insertion
inferredcites →https://doi.org/10.1038/ncomms6263openalex-snapshot
Lateral opening of the bacterial translocon on ribosome binding and signal peptide insertion
inferredcites →https://doi.org/10.1038/nsmb.2016openalex-snapshot
Genetic selection designed to stabilize proteins uncovers a chaperone called Spy
inferredcites →https://doi.org/10.1038/nsmb.2941openalex-snapshot
The energy landscape of adenylate kinase during catalysis
inferredcites →https://doi.org/10.1038/s41467-019-09474-6openalex-snapshot
Tunable microsecond dynamics of an allosteric switch regulate the activity of a AAA+ disaggregation machine
inferredcites →https://doi.org/10.1038/s41467-019-10918-2openalex-snapshot
Structure of the substrate-engaged SecA-SecY protein translocation machine
inferredcites →https://doi.org/10.1038/s41467-022-28632-xopenalex-snapshot
Multi-parameter photon-by-photon hidden Markov modeling
inferredcites →https://doi.org/10.1038/s42003-018-0133-4openalex-snapshot
Large conformational changes of a highly dynamic pre-protein binding domain in SecA
inferredcites →https://doi.org/10.1039/b708995copenalex-snapshot
Design principles for Brownian molecular machines: how to swim in molasses and walk in a hurricane
inferredcites →https://doi.org/10.1039/c4cp01222dopenalex-snapshot
Accounting for dye diffusion and orientation when relating FRET measurements to distances: three simple computational methods
inferredcites →https://doi.org/10.1039/c4cp02489copenalex-snapshot
Fast single-molecule FRET spectroscopy: theory and experiment
inferredcites →https://doi.org/10.1042/bcj20220480openalex-snapshot
Interaction of the periplasmic chaperone SurA with the inner membrane protein secretion (SEC) machinery
inferredcites →https://doi.org/10.1073/pnas.0809592106openalex-snapshot
Energy transduction in protein transport and the ATP hydrolytic cycle of SecA
inferredcites →https://doi.org/10.1073/pnas.0901178106openalex-snapshot
Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories
inferredcites →https://doi.org/10.1073/pnas.0905466106openalex-snapshot
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
inferredcites →https://doi.org/10.1073/pnas.1303289110openalex-snapshot
Stoichiometry of SecYEG in the active translocase of Escherichia coli varies with precursor species
inferredcites →https://doi.org/10.1073/pnas.1315901111openalex-snapshot
Membrane protein insertion and proton-motive-force-dependent secretion through the bacterial holo-translocon SecYEG–SecDF–YajC–YidC
inferredcites →https://doi.org/10.1073/pnas.1720448115openalex-snapshot
Direct observation of ultrafast large-scale dynamics of an enzyme under turnover conditions
inferredcites →https://doi.org/10.1073/pnas.1816184116openalex-snapshot
Hydrogen exchange reveals Hsp104 architecture, structural dynamics, and energetics in physiological solution
inferredcites →https://doi.org/10.1073/pnas.2010906117openalex-snapshot
Refined measurement of SecA-driven protein secretion reveals that translocation is indirectly coupled to ATP turnover
inferredcites →https://doi.org/10.1073/pnas.2100474118openalex-snapshot
Lateral gate dynamics of the bacterial translocon during cotranslational membrane protein insertion
inferredcites →https://doi.org/10.1073/pnas.2208070120openalex-snapshot
Structural basis of SecA-mediated protein translocation
inferredcites →https://doi.org/10.1073/pnas.88.15.6545openalex-snapshot
Reconstitution of a protein translocation system containing purified SecY, SecE, and SecA from Escherichia coli.
inferredcites →https://doi.org/10.1073/pnas.93.12.5953openalex-snapshot
prlA suppressors in Escherichia coli relieve the proton electrochemical gradient dependency of translocation of wild-type precursors.
inferredcites →https://doi.org/10.1074/jbc.m110.175638openalex-snapshot
The Oligomeric State and Arrangement of the Active Bacterial Translocon
inferredcites →https://doi.org/10.1074/jbc.m312892200openalex-snapshot
Binding of SecA to the SecYEG Complex Accelerates the Rate of Nucleotide Exchange on SecA
inferredcites →https://doi.org/10.1074/jbc.m702066200openalex-snapshot
Allosteric Regulation of SecA
inferredcites →https://doi.org/10.1074/jbc.m901855200openalex-snapshot
The Lateral Gate of SecYEG Opens during Protein Translocation
inferredcites →https://doi.org/10.1074/jbc.ra119.010686openalex-snapshot
Noncompetitive binding of PpiD and YidC to the SecYEG translocon expands the global view on the SecYEG interactome in Escherichia coli
inferredcites →https://doi.org/10.1080/01621459.1963.10500845openalex-snapshot
Hierarchical Grouping to Optimize an Objective Function
inferredcites →https://doi.org/10.1083/jcb.201205191openalex-snapshot
Mobility of the SecA 2-helix-finger is not essential for polypeptide translocation via the SecYEG complex
inferredcites →https://doi.org/10.1093/bioinformatics/btl461openalex-snapshot
Bio3d: an R package for the comparative analysis of protein structures
inferredcites →https://doi.org/10.1093/bioinformatics/btp023openalex-snapshot
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics
inferredcites →https://doi.org/10.1093/emboj/16.10.2756openalex-snapshot
Distinct catalytic roles of the SecYE, SecG and SecDFyajC subunits of preprotein translocase holoenzyme
inferredcites →https://doi.org/10.1093/emboj/19.1.134openalex-snapshot
Discrimination between SRP‐ and SecA/SecB‐dependent substrates involves selective recognition of nascent chains by SRP and trigger factor
inferredcites →https://doi.org/10.1093/emboj/20.10.2462openalex-snapshot
Projection structure and oligomeric properties of a bacterial core protein translocase
inferredcites →https://doi.org/10.1101/2022.08.03.502619openalex-snapshot
Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins
inferredcites →https://doi.org/10.1109/5.18626openalex-snapshot
A tutorial on hidden Markov models and selected applications in speech recognition
inferredcites →https://doi.org/10.1126/sciadv.aat8797openalex-snapshot
Single-molecule observation of nucleotide induced conformational changes in basal SecA-ATP hydrolysis
inferredcites →https://doi.org/10.1126/science.1074424openalex-snapshot
Nucleotide Control of Interdomain Interactions in the Conformational Reaction Cycle of SecA
inferredcites →https://doi.org/10.1128/jb.170.8.3404-3414.1988openalex-snapshot
Nucleotide sequence of the secA gene and secA(Ts) mutations preventing protein export in Escherichia coli
inferredcites →https://doi.org/10.1146/annurev-biochem-011520-105201openalex-snapshot
Structural and Mechanistic Principles of ABC Transporters
inferredcites →https://doi.org/10.1182/blood.v128.22.2535.2535openalex-snapshot
Hydrogen Exchange Mass Spectrometry Reveals Allosteric Interactions Between the Distal and the Proximal Domains of Human ADAMTS13
inferredcites →https://doi.org/10.1371/journal.pone.0160716openalex-snapshot
FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET
inferredcites →https://doi.org/10.1385/cbb:38:2:191openalex-snapshot
Brownian Ratchet Models of Molecular Motors
inferredcites →https://doi.org/10.15252/embj.2018101140openalex-snapshot
Protein translocation by the SecA ATPase occurs by a power‐stroke mechanism
inferredcites →https://doi.org/10.15252/embr.201948191openalex-snapshot
Partially inserted nascent chain unzips the lateral gate of the Sec translocon
inferredcites →https://doi.org/10.15252/embr.202050905openalex-snapshot
Protease protection assays show polypeptide movement into the SecY channel by power strokes of the SecA ATPase
inferredcites →https://doi.org/10.1529/biophysj.105.064766openalex-snapshot
Pulsed Interleaved Excitation
inferredcites →https://doi.org/10.3109/10409238.2015.1102195openalex-snapshot
Single-molecule perspectives on helicase mechanisms and functions
inferredcites →https://doi.org/10.3389/fmicb.2019.01217openalex-snapshot
The Dynamic ATP-Driven Mechanism of Bacterial Protein Translocation and the Critical Role of Phospholipids
inferredcites →https://doi.org/10.3390/molecules25225268openalex-snapshot
ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter
inferredcites →https://doi.org/10.7554/elife.03035openalex-snapshot
A structural model of the active ribosome-bound membrane protein insertase YidC
inferredcites →https://doi.org/10.7554/elife.15598openalex-snapshot
Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation
inferredcites →https://doi.org/10.7554/elife.35112openalex-snapshot
Dynamic action of the Sec machinery during initiation, protein translocation and termination
inferredcites →https://doi.org/10.7554/elife.41803openalex-snapshot
ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery
inferredcites →https://doi.org/10.7554/elife.47402openalex-snapshot
HDX-MS reveals nucleotide-dependent, anti-correlated opening and closure of SecA and SecY channels of the bacterial translocon
inferredcites →https://doi.org/10.7554/elife.77586openalex-snapshot
Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s10867-021-09591-8openalex-snapshot
Energy landscapes and dynamics of ion translocation through membrane transporters: a meeting ground for physics, chemistry, and biology
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