scholarly journals A molecular dynamics study on the resilience of Sec61 channel from open to closed state

RSC Advances ◽  
2019 ◽  
Vol 9 (26) ◽  
pp. 14876-14883
Author(s):  
Sujuan Sun ◽  
Shuangshuang Wang ◽  
Zhangfa Tong ◽  
Xingdong Yao ◽  
Jian Gao
Keyword(s):  
Molecular Dynamics ◽  
Chain Segment ◽  
Closed State ◽  
Nascent Chain ◽  
Lateral Gate ◽  
Sec61 Channel

The lateral gate of Sec61 is able to recover its partially-closed state rapidly after the nascent chain segment enters the bilayer, which triggers subsequent motions of the pore ring and plug.

scholarly journals Partially inserted nascent chain unzips the lateral gate of the Sec translocon

EMBO Reports ◽  
2019 ◽  
Vol 20 (10) ◽  
Author(s):  
Lukas Kater ◽  
Benedikt Frieg ◽  
Otto Berninghausen ◽  
Holger Gohlke ◽  
Roland Beckmann ◽  
...  
Keyword(s):  
Nascent Chain ◽  
Sec Translocon ◽  
Lateral Gate

scholarly journals Ribosome–SRP–FtsY cotranslational targeting complex in the closed state

2015 ◽  
Vol 112 (13) ◽  
pp. 3943-3948 ◽  
Author(s):  
Ottilie von Loeffelholz ◽  
Qiyang Jiang ◽  
Aileen Ariosa ◽  
Manikandan Karuppasamy ◽  
Karine Huard ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Protein Targeting ◽  
Signal Sequence ◽  
Signal Recognition Particle ◽  
Binding Pocket ◽  
Van Der Waals Interactions ◽  
Closed State ◽  
Chain Complexes ◽  
Nascent Chain ◽  
Srp Rna

The signal recognition particle (SRP)-dependent pathway is essential for correct targeting of proteins to the membrane and subsequent insertion in the membrane or secretion. In Escherichia coli, the SRP and its receptor FtsY bind to ribosome–nascent chain complexes with signal sequences and undergo a series of distinct conformational changes, which ensures accurate timing and fidelity of protein targeting. Initial recruitment of the SRP receptor FtsY to the SRP–RNC complex results in GTP-independent binding of the SRP–FtsY GTPases at the SRP RNA tetraloop. In the presence of GTP, a closed state is adopted by the SRP–FtsY complex. The cryo-EM structure of the closed state reveals an ordered SRP RNA and SRP M domain with a signal sequence-bound. Van der Waals interactions between the finger loop and ribosomal protein L24 lead to a constricted signal sequence-binding pocket possibly preventing premature release of the signal sequence. Conserved M-domain residues contact ribosomal RNA helices 24 and 59. The SRP–FtsY GTPases are detached from the RNA tetraloop and flexible, thus liberating the ribosomal exit site for binding of the translocation machinery.

scholarly journals How does Sec63 affect the conformation of Sec61 in yeast?

2021 ◽  
Vol 17 (3) ◽  
pp. e1008855
Author(s):  
Pratiti Bhadra ◽  
Lalitha Yadhanapudi ◽  
Karin Römisch ◽  
Volkhard Helms
Keyword(s):  
Endoplasmic Reticulum ◽  
Secretory Pathway ◽  
Endoplasmic Reticulum Membrane ◽  
Intermolecular Contact ◽  
Cryo Electron Microscopy ◽  
Ring Diameter ◽  
Lateral Gate ◽  
Co Precipitation ◽  
Dynamics Simulations ◽  
Sec61 Channel

The Sec complex catalyzes the translocation of proteins of the secretory pathway into the endoplasmic reticulum and the integration of membrane proteins into the endoplasmic reticulum membrane. Some substrate peptides require the presence and involvement of accessory proteins such as Sec63. Recently, a structure of the Sec complex from Saccharomyces cerevisiae, consisting of the Sec61 channel and the Sec62, Sec63, Sec71 and Sec72 proteins was determined by cryo-electron microscopy (cryo-EM). Here, we show by co-precipitation that the accessory membrane protein Sec62 is not required for formation of stable Sec63-Sec61 contacts. Molecular dynamics simulations started from the cryo-EM conformation of Sec61 bound to Sec63 and of unbound Sec61 revealed how Sec63 affects the conformation of Sec61 lateral gate, plug, pore region and pore ring diameter via three intermolecular contact regions. Molecular docking of SRP-dependent vs. SRP-independent peptide chains into the Sec61 channel showed that the pore regions affected by presence/absence of Sec63 play a crucial role in positioning the signal anchors of SRP-dependent substrates nearby the lateral gate.

scholarly journals Gating Mechanism of Hv1 Studied by Molecular Dynamic Simulations

2020 ◽  
Vol 4 (1) ◽  
pp. 20
Author(s):  
Thi Tuong Vy Phan
Keyword(s):  
Molecular Dynamics ◽  
Cancer Progression ◽  
Md Simulations ◽  
Proton Channel ◽  
Water Molecules ◽  
State Structure ◽  
Ph Homeostasis ◽  
Dynamic Simulations ◽  
Closed State ◽  
Gating Mechanism

The voltage-gated proton channel (Hv1) plays the important role in proton extrusion, pH homeostasis, sperm motility, and cancer progression. The closed-state structure of Hv1 was recently revealed by X-ray crystallography. However, the opened-state structure has not been captured yet. To investigate the mechanism of proton transfer in Hv1, molecular dynamics (MD) simulations were performed with the closed-state structure of Hv1 under electric field and pH conditions. The residues arrangement on the closed-state structure revealed that the selectivity filter (Asp108) which is located in the hydrophobic layer (consists of two Phe residues 146 and 179) might prevent water penetration. In molecular dynamics simulations, we observed that the channel opened by moving 3 Arg up on the S4 helix and a continuous hydrogen-bonded chain of water molecules (a “water wire”) went through the channel when it opened. During simulations, the open channel allowed water molecules to pass through the channel but excluded other ions. This indicates the Hv1 channel is highly selective for protons. Our results clearly showed the Hv1 channel is voltage-and pH-gradient sensing.

scholarly journals The ribosome quality control pathway can access nascent polypeptides stalled at the Sec61 translocon

2015 ◽  
Vol 26 (12) ◽  
pp. 2168-2180 ◽  
Author(s):  
Karina von der Malsburg ◽  
Sichen Shao ◽  
Ramanujan S. Hegde
Keyword(s):  
Quality Control ◽  
Cultured Cells ◽  
E3 Ligase ◽  
Cotranslational Translocation ◽  
Biochemical Analyses ◽  
Lateral Gate ◽  
Sec61 Channel ◽  
Cytosolic Ribosomes

Cytosolic ribosomes that stall during translation are split into subunits, and nascent polypeptides trapped in the 60S subunit are ubiquitinated by the ribosome quality control (RQC) pathway. Whether the RQC pathway can also target stalls during cotranslational translocation into the ER is not known. Here we report that listerin and NEMF, core RQC components, are bound to translocon-engaged 60S subunits on native ER membranes. RQC recruitment to the ER in cultured cells is stimulated by translation stalling. Biochemical analyses demonstrated that translocon-targeted nascent polypeptides that subsequently stall are polyubiquitinated in 60S complexes. Ubiquitination at the translocon requires cytosolic exposure of the polypeptide at the ribosome–Sec61 junction. This exposure can result from either failed insertion into the Sec61 channel or partial backsliding of translocating nascent chains. Only Sec61-engaged nascent chains early in their biogenesis were relatively refractory to ubiquitination. Modeling based on recent 60S–RQC and 80S–Sec61 structures suggests that the E3 ligase listerin accesses nascent polypeptides via a gap in the ribosome–translocon junction near the Sec61 lateral gate. Thus the RQC pathway can target stalled translocation intermediates for degradation from the Sec61 channel.

scholarly journals Interaction mapping of the Sec61 translocon identifies two Sec61α regions interacting with hydrophobic segments in translocating chains

2018 ◽  
Vol 293 (44) ◽  
pp. 17050-17060 ◽  
Author(s):  
Yuichiro Kida ◽  
Masao Sakaguchi
Keyword(s):  
Endoplasmic Reticulum ◽  
Lipid Bilayer ◽  
Secretory Pathway ◽  
Cross Linking ◽  
Secretory Proteins ◽  
Endoplasmic Reticulum Membrane ◽  
Conducting Channel ◽  
Nascent Chain ◽  
Biochemical Analyses ◽  
Lateral Gate

Many proteins in organelles of the secretory pathway, as well as secretory proteins, are translocated across and inserted into the endoplasmic reticulum membrane by the Sec61 translocon, a protein-conducting channel. The channel consists of 10 transmembrane (TM) segments of the Sec61α subunit and possesses an opening between TM2b and TM7, termed the lateral gate. Structural and biochemical analyses of complexes of Sec61 and its ortholog SecY have revealed that the lateral gate is the exit for signal sequences and TM segments of translocating polypeptides to the lipid bilayer and also involved in the recognition of such hydrophobic sequences. Moreover, even marginally hydrophobic (mH) segments insufficient for membrane integration can be transiently stalled in surrounding Sec61α regions and cross-linked to them, but how the Sec61 translocon accommodates these mH segments remains unclear. Here, we used Cys-scanned variants of human Sec61α expressed in cultured 293-H cells to examine which channel regions associate with mH segments. A TM segment in a ribosome-associated polypeptide was mainly cross-linked to positions at the lateral gate, whereas an mH segment in a nascent chain was cross-linked to the Sec61α pore-interior positions at TM5 and TM10, as well as the lateral gate. Of note, cross-linking at position 180 in TM5 of Sec61α was reduced by an I179A substitution. We therefore conclude that at least two Sec61α regions, the lateral gate and the pore-interior site around TM5, interact with mH segments and are involved in accommodating them.

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