scholarly journals Translocation of structured biomolecule through a vibrating nanopore

2018 ◽  
Author(s):  
M. A. Shahzad
Keyword(s):  
Protein Transport ◽  
Protein Translocation ◽  
Intermediate Frequency ◽  
Global Maximum ◽  
Cylindrical Pore ◽  
Transport Dynamics ◽  
Frequency Regime ◽  
Translocation Time ◽  
Static Channel ◽  
Resonant Activation

ABSTRACTWe study the effect of fluctuating environment in protein transport dynamics. In particular, we investigate the translocation of a structured biomolecule (protein) across a temporally modulated nano-pore. We allow the radius of the cylindrical pore to oscillate harmonically with certain frequency and amplitude about an average radius. The protein is imported inside the pore whose dynamics is influences by the fluctuating nature of the pore. We investigate the dynamic and thermodynamical properties of the translocation process by revealing the statistics of translocation time as a function of the pulling inward force acting along the axis of the pore, and the frequency of the time dependent radius of the channel. We also examine the distribution of translocation time in the intermediate frequency regime. We observe that the shaking mechanism of pore leads to accelerate the translocation process as compared to the static channel that has a radius equal to the mean radius of oscillating pore. Moreover, the translocation time shows a global maximum as a function of frequency of the oscillating radius, hence revealing a resonant activation phenomenon in the dynamics of protein translocation.

scholarly journals Greybody Factors for Schwarzschild Black Holes: Path-Ordered Exponentials and Product Integrals

Universe ◽  
2018 ◽  
Vol 4 (9) ◽  
pp. 93 ◽  
Author(s):  
Finnian Gray ◽  
Matt Visser
Keyword(s):  
Black Holes ◽  
High Frequency ◽  
Low Frequency ◽  
Intermediate Frequency ◽  
General Context ◽  
Matrix Formalism ◽  
Barrier Penetration ◽  
Frequency Regime ◽  
Transfer Matrix Formalism ◽  
Numerical Approaches

In earlier work concerning the sparsity of the Hawking flux, we found it necessary to re-examine what is known regarding the greybody factors of black holes, with a view to extending and expanding on some old results from the 1970s. Focusing specifically on Schwarzschild black holes, we have re-calculated and re-assessed the greybody factors using a path-ordered-exponential approach, a technique which has the virtue of providing a pedagogically useful semi-explicit formula for the relevant Bogoliubov coefficients. These path-ordered-exponentials, being based on a variant of the “transfer matrix” formalism, are closely related to so-called “product integrals”, leading to quite straightforward and direct numerical evaluation, while side-stepping any need for numerically solving the relevant ordinary differential equations. Furthermore, while considerable analytic information is already available regarding both the high-frequency and low-frequency asymptotics of these greybody factors, numerical approaches seem better adapted to finding suitable “global models” for these greybody factors in the intermediate frequency regime, where most of the Hawking flux is actually concentrated. Working in a more general context, these path-ordered-exponential techniques are also likely to be of interest for generic barrier-penetration problems.

scholarly journals Substrate Proteins Take Shape at an Improved Bacterial Translocon

2018 ◽  
Vol 201 (1) ◽  
Author(s):  
Donald Oliver
Keyword(s):  
Protein Transport ◽  
Protein Translocation ◽  
Membrane Vesicles ◽  
Transport Models ◽  
Content Type ◽  
Rate Limiting ◽  
Substrate Proteins

ABSTRACTCharacterization of Sec-dependent bacterial protein transport has often relied on anin vitroprotein translocation system comprised in part ofEscherichia coliinverted inner membrane vesicles or, more recently, purified SecYEG translocons reconstituted into liposomes using mostly a single substrate (proOmpA). A paper published in this issue (P. Bariya and L. Randall, J Bacteriol 201:e00493-18, 2019, https://doi.org/10.1128/JB.00493-18) finds that inclusion of SecA protein during SecYEG proteoliposome reconstitution dramatically improves the number of active translocons. This experimentally useful and intriguing result that may arise from SecA membrane integration properties is discussed here. Furthermore, determination of the rate-limiting transport step for nine different substrates implicates the mature region distal to the signal peptide in the observed rate constant differences, indicating that more nuanced transport models that respond to differences in protein sequence and structure are needed.

scholarly journals Two Endoplasmic Reticulum (ER) Membrane Proteins That Facilitate ER-to-Golgi Transport of Glycosylphosphatidylinositol-anchored Proteins

1999 ◽  
Vol 10 (4) ◽  
pp. 1043-1059 ◽  
Author(s):  
Wolfgang P. Barz ◽  
Peter Walter
Keyword(s):  
Endoplasmic Reticulum ◽  
Cell Surface ◽  
Secretory Pathway ◽  
Protein Transport ◽  
Protein Translocation ◽  
Sequence Similarity ◽  
Surface Proteins ◽  
Golgi Transport ◽  
Er Membrane

Many eukaryotic cell surface proteins are anchored in the lipid bilayer through glycosylphosphatidylinositol (GPI). GPI anchors are covalently attached in the endoplasmic reticulum (ER). The modified proteins are then transported through the secretory pathway to the cell surface. We have identified two genes inSaccharomyces cerevisiae, LAG1 and a novel gene termed DGT1 (for “delayed GPI-anchored protein transport”), encoding structurally related proteins with multiple membrane-spanning domains. Both proteins are localized to the ER, as demonstrated by immunofluorescence microscopy. Deletion of either gene caused no detectable phenotype, whereas lag1Δ dgt1Δ cells displayed growth defects and a significant delay in ER-to-Golgi transport of GPI-anchored proteins, suggesting thatLAG1 and DGT1 encode functionally redundant or overlapping proteins. The rate of GPI anchor attachment was not affected, nor was the transport rate of several non–GPI-anchored proteins. Consistent with a role of Lag1p and Dgt1p in GPI-anchored protein transport, lag1Δ dgt1Δ cells deposit abnormal, multilayered cell walls. Both proteins have significant sequence similarity to TRAM, a mammalian membrane protein thought to be involved in protein translocation across the ER membrane. In vivo translocation studies, however, did not detect any defects in protein translocation in lag1Δ dgt1Δcells, suggesting that neither yeast gene plays a role in this process. Instead, we propose that Lag1p and Dgt1p facilitate efficient ER-to-Golgi transport of GPI-anchored proteins.

scholarly journals SecA Dimer Cross-Linked at Its Subunit Interface Is Functional for Protein Translocation

2006 ◽  
Vol 188 (1) ◽  
pp. 335-338 ◽  
Author(s):  
Lucia B. Jilaveanu ◽  
Donald Oliver
Keyword(s):  
Conformational Changes ◽  
Protein Transport ◽  
Protein Translocation ◽  
Directed Mutagenesis ◽  
Subunit Interface ◽  
Cargo Proteins ◽  
Considerable Controversy ◽  
The Subject ◽  
Vitro Protein

ABSTRACT SecA facilitates protein transport across the eubacterial plasma membrane by its association with cargo proteins and the SecYEG translocon, followed by ATP-driven conformational changes that promote protein translocation in a stepwise manner. Whether SecA functions as a monomer or a dimer during this process has been the subject of considerable controversy. Here we utilize cysteine-directed mutagenesis along with the crystal structure of the SecA dimer to create a cross-linked dimer at its subunit interface, which was normally active for in vitro protein translocation.

scholarly journals Translocation of a Polymer through a Crowded Channel under Electrical Force

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Tingting Sun ◽  
Yunxin Gen ◽  
Hujun Xie ◽  
Zhouting Jiang ◽  
Zhiyong Yang
Keyword(s):  
Field Strength ◽  
Shape Factor ◽  
Cylindrical Channel ◽  
Protein Translocation ◽  
Scaling Exponent ◽  
Scaling Relation ◽  
Maximum Value ◽  
Translocation Time ◽  
Dynamics Simulations ◽  
Number Of Segments

The translocation of a polymer chain through a crowded cylindrical channel is studied using the Langevin dynamics simulations. The influences of the field strength F, the chain length N, and the crowding extent ρ on the translocation time are evaluated, respectively. Scaling relation τ~F-α is observed. With the crowding extent ρ increasing, the scaling exponent α becomes large. It is found that, for noncrowded channel, translocation probability drops when the field strength becomes large. However, for high-crowded channel, it is the opposite. Moreover, the translocation time and the average translocation time for all segments both have exponential growth with the crowding extent. The investigation of shape factor δ shows maximum value with increasing of the number of segments outside s. At last, the number of segments inside channel Nin in the process of translocation is calculated and a peak is observed. All the information from the study may benefit protein translocation.

scholarly journals ATP-induced asymmetric pre-protein folding: a driver of protein translocation?

2017 ◽  
Author(s):  
Robin A. Corey ◽  
William J. Allen ◽  
Ian Collinson
Keyword(s):  
Secondary Structure ◽  
Structure Formation ◽  
Protein Transport ◽  
Protein Translocation ◽  
Protein Secondary Structure ◽  
Structural Data ◽  
Underlying Mechanism ◽  
Dynamics Simulation ◽  
Secondary Structure Formation ◽  
Atp Binding And Hydrolysis

AbstractThe transport of proteins across membranes is a fundamental and essential process, achieved in every cell by the ‘Sec’ translocon. In prokaryotes, SecYEG associates with the motor protein SecA to carry out ATP-driven pre-protein secretion – a vital step in the biogenesis of most periplasmic, outer membrane and secreted proteins. Structural data of the SecA-SecYEG complex has provided considerable insight into underlying mechanism of this process. Previously, we have proposed a Brownian ratchet model for protein translocation, whereby the free energy of ATP binding and hydrolysis favours the progression of pre-protein across the membrane from the cytosol toward the outside [Allen, Corey et al. eLife 2016]. Here, we use atomistic molecular dynamics simulation of a SecA-SecYEG complex engaged with preprotein to further address the mechanism underlying this process. The data describe pre-protein secondary structure formation within the channel, which exhibits a nucleotide-dependent asymmetry between the cytoplasmic and exterior cavities. The results suggest ATP-dependent pre-protein transport is partly driven by pre-protein secondary structure formation. The model previously described, and refined here, could easily be adapted for the transport of proteins across various other membranes, such as the endoplasmic reticular and mitochondrial inner membranes.

scholarly journals Transition to turbulence in pulsating pipe flow

2017 ◽  
Vol 831 ◽  
pp. 418-432 ◽  
Author(s):  
Duo Xu ◽  
Sascha Warnecke ◽  
Baofang Song ◽  
Xingyu Ma ◽  
Björn Hof
Keyword(s):  
Pipe Flow ◽  
Oscillation Amplitude ◽  
Intermediate Frequency ◽  
Finite Amplitude ◽  
Decay Rates ◽  
Transition To Turbulence ◽  
Pulsation Frequency ◽  
Onset Of Turbulence ◽  
Frequency Regime ◽  
The Impact

Fluid flows in nature and applications are frequently subject to periodic velocity modulations. Surprisingly, even for the generic case of flow through a straight pipe, there is little consensus regarding the influence of pulsation on the transition threshold to turbulence: while most studies predict a monotonically increasing threshold with pulsation frequency (i.e. Womersley number, $\unicode[STIX]{x1D6FC}$), others observe a decreasing threshold for identical parameters and only observe an increasing threshold at low $\unicode[STIX]{x1D6FC}$. In the present study we apply recent advances in the understanding of transition in steady shear flows to pulsating pipe flow. For moderate pulsation amplitudes we find that the first instability encountered is subcritical (i.e. requiring finite amplitude disturbances) and gives rise to localized patches of turbulence (‘puffs’) analogous to steady pipe flow. By monitoring the impact of pulsation on the lifetime of turbulence we map the onset of turbulence in parameter space. Transition in pulsatile flow can be separated into three regimes. At small Womersley numbers the dynamics is dominated by the decay turbulence suffers during the slower part of the cycle and hence transition is delayed significantly. As shown in this regime thresholds closely agree with estimates based on a quasi-steady flow assumption only taking puff decay rates into account. The transition point predicted in the zero $\unicode[STIX]{x1D6FC}$ limit equals to the critical point for steady pipe flow offset by the oscillation Reynolds number (i.e. the dimensionless oscillation amplitude). In the high frequency limit on the other hand, puff lifetimes are identical to those in steady pipe flow and hence the transition threshold appears to be unaffected by flow pulsation. In the intermediate frequency regime the transition threshold sharply drops (with increasing $\unicode[STIX]{x1D6FC}$) from the decay dominated (quasi-steady) threshold to the steady pipe flow level.

scholarly journals Inner nuclear membrane protein transport is mediated by multiple mechanisms

2008 ◽  
Vol 36 (6) ◽  
pp. 1373-1377 ◽  
Author(s):  
Nikolaj Zuleger ◽  
Nadia Korfali ◽  
Eric C. Schirmer
Keyword(s):  
Nuclear Envelope ◽  
Nuclear Pore Complex ◽  
Nuclear Membrane ◽  
Protein Transport ◽  
Protein Translocation ◽  
Lateral Diffusion ◽  
Membrane System ◽  
Nuclear Pore ◽  
Inner Nuclear Membrane ◽  
Classical Transport

Work in the nuclear transport field has led to an incredibly detailed description of protein translocation through the central channel of the nuclear pore complex, yet the mechanism by which nuclear envelope transmembrane proteins reach the inner nuclear membrane after synthesis in the endoplasmic reticulum is still hotly debated. Three different translocation models have gained experimental support: (i) simple lateral diffusion through the nuclear envelope membrane system; (ii) translocation by vesicle fusion events; and (iii) a variation on classical transport mediated by the nuclear pore complex. Although these models appear to be mutually exclusive, in the present paper we argue that they probably all function for different inner nuclear membrane proteins according to their unique characteristics.

scholarly journals Clustering of C-Terminal Stromal Domains of Tha4 Homo-oligomers during Translocation by the Tat Protein Transport System

2009 ◽  
Vol 20 (7) ◽  
pp. 2060-2069 ◽  
Author(s):  
Carole Dabney-Smith ◽  
Kenneth Cline
Keyword(s):  
Protein Transport ◽  
Transmembrane Domain ◽  
Protein Translocation ◽  
Proton Gradient ◽  
Receptor Complex ◽  
Tat Protein ◽  
Twin Arginine Translocation ◽  
Conducting Component ◽  
Cross Links ◽  
Folded Proteins

The chloroplast Twin arginine translocation (Tat) pathway uses three membrane proteins and the proton gradient to transport folded proteins across sealed membranes. Precursor proteins bind to the cpTatC-Hcf106 receptor complex, triggering Tha4 assembly and protein translocation. Tha4 is required only for the translocation step and is thought to be the protein-conducting component. The organization of Tha4 oligomers was examined by substituting pairs of cysteine residues into Tha4 and inducing disulfide cross-links under varying stages of protein translocation. Tha4 formed tetramers via its transmembrane domain in unstimulated membranes and octamers in membranes stimulated by precursor and the proton gradient. Tha4 formed larger oligomers of at least 16 protomers via its carboxy tail, but such C-tail clustering only occurred in stimulated membranes. Mutational studies showed that transmembrane domain directed octamers as well as C-tail clusters require Tha4's transmembrane glutamate residue and its amphipathic helix, both of which are necessary for Tha4 function. A novel double cross-linking strategy demonstrated that both transmembrane domain directed- and C-tail directed oligomerization occur in the translocase. These results support a model in which Tha4 oligomers dock with a precursor–receptor complex and undergo a conformational switch that results in activation for protein transport. This possibly involves accretion of additional Tha4 into a larger transport-active homo-oligomer.

scholarly journals Annotating eukaryotic and toxin-specific signal peptides using Razor

2020 ◽  
Author(s):  
Bikash K. Bhandari ◽  
Paul P. Gardner ◽  
Chun Shen Lim
Keyword(s):  
Signal Peptide ◽  
Web Application ◽  
Protein Transport ◽  
Protein Translocation ◽  
Recombinant Protein Expression ◽  
Disease Diagnosis ◽  
Signal Peptides ◽  
Specific Signal ◽  
Link Type ◽  
Command Line Tool

ABSTRACTMotivationSignal peptides are responsible for protein transport and secretion and are ubiquitous to all forms of life. The annotation of signal peptides is important for understanding protein translocation and toxin secretion, optimising recombinant protein expression, as well as for disease diagnosis and metagenomics.ResultsHere we explore the features of these signal sequences across eukaryotes. We find that different kingdoms have their characteristic distributions of signal peptide residues. Additionally, the signal peptides of secretory toxins have common features across kingdoms. We leverage these subtleties to build Razor, a simple yet powerful tool for annotating signal peptides, which additionally predicts toxin- and fungal-specific signal peptides based on the first 23 N-terminal residues. Finally, we demonstrate the usability of Razor by scanning all reviewed sequences from UniProt. Indeed, Razor is able to identify toxins using their signal peptide sequences only. Strikingly, we discover that many defensive proteins across kingdoms harbour a toxin-like signal peptide; some of these defensive proteins have emerged through convergent evolution, e.g. defensin and defensin-like protein families, and phospholipase families.Availability and implementationRazor is available as a web application (https://tisigner.com/razor) and a command-line tool (https://github.com/Gardner-BinfLab/Razor).

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