scholarly journals ATP hydrolysis-coupled peptide translocation mechanism of Mycobacterium tuberculosis ClpB

2018 ◽  
Vol 115 (41) ◽  
pp. E9560-E9569 ◽  
Author(s):  
Hongjun Yu ◽  
Tania J. Lupoli ◽  
Amanda Kovach ◽  
Xing Meng ◽  
Gongpu Zhao ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Atp Hydrolysis ◽  
Asymmetric Distribution ◽  
High Affinity ◽  
Binding Domains ◽  
Closed Ring ◽  
Translocation Mechanism ◽  
One Step ◽  
Ring Conformations ◽  
Peptide Translocation

The protein disaggregase ClpB hexamer is conserved across evolution and has two AAA+-type nucleotide-binding domains, NBD1 and NBD2, in each protomer. In M. tuberculosis (Mtb), ClpB facilitates asymmetric distribution of protein aggregates during cell division to help the pathogen survive and persist within the host, but a mechanistic understanding has been lacking. Here we report cryo-EM structures at 3.8- to 3.9-Å resolution of Mtb ClpB bound to a model substrate, casein, in the presence of the weakly hydrolyzable ATP mimic adenosine 5′-[γ-thio]triphosphate. Mtb ClpB existed in solution in two closed-ring conformations, conformers 1 and 2. In both conformers, the 12 pore-loops on the 12 NTDs of the six protomers (P1–P6) were arranged similarly to a staircase around the bound peptide. Conformer 1 is a low-affinity state in which three of the 12 pore-loops (the protomer P1 NBD1 and NBD2 loops and the protomer P2 NBD1 loop) are not engaged with peptide. Conformer 2 is a high-affinity state because only one pore-loop (the protomer P2 NBD1 loop) is not engaged with the peptide. The resolution of the two conformations, along with their bound substrate peptides and nucleotides, enabled us to propose a nucleotide-driven peptide translocation mechanism of a bacterial ClpB that is largely consistent with several recent unfoldase structures, in particular with the eukaryotic Hsp104. However, whereas Hsp104’s two NBDs move in opposing directions during one step of peptide translocation, in Mtb ClpB the two NBDs move only in the direction of translocation.

Effect of Non-Solubilizing SDS Concentrations on High Affinity Ca2+ Binding and Steady State Phosphorylation by Inorganic Phosphate of the Sarcoplasmic Reticulum ATPase

1989 ◽  
Vol 44 (1-2) ◽  
pp. 139-152 ◽  
Author(s):  
Elisabeth Fassold ◽  
Wilhelm Hasselbach ◽  
Bernd Küchler
Keyword(s):  
Sarcoplasmic Reticulum ◽  
Inorganic Phosphate ◽  
Atp Hydrolysis ◽  
Mutual Exclusion ◽  
Chemical Properties ◽  
Cooperative Interaction ◽  
Hydrophobic Force ◽  
High Affinity ◽  
Binding Domains ◽  
Phosphorylation Domain

Abstract In this investigation low, non-solubilizing concentrations of the strong anionic detergent SDS were used to perturbate the interaction of Ca2+ and Pi with their respective binding domains on the sarcoplasmic reticulum Ca-transport ATPase. Rising SDS concentrations produce a two-step decline of Ca2+-dependent ATP hydrolysis. At pH 6.15, SDS differently affects high affinity Ca2+ binding and phosphorylation by inorganic phosphate and releases the “mutual exclusion” of these two ligand binding steps. The degree of uncoupling is considerably more pronounced in the presence of 20% Me2SO. The reduction of Ca2+ binding by SDS is demonstrated to be a result of decreased affinity of one of the two specific high affinity binding sites and of perturbation of their cooperative interaction. Higher SDS partially restores the original high Ca2+ affinity but not the cooperativity of binding. Phosphorylation exhibits a higher SDS sensitivity than Ca2+ binding: Increasing SDS competitively inhibits and then completely abolishes phosphoenzyme formation. Thus. SDS binds to the phosphorylation domain, evidently involving the Lys352 residue of the ATPase molecule; this is accompanied by a more unspecific concentration-dependent SDS effect, probably mediated by hydrophobic force, which, finally, suppresses phosphorylation. Me2SO does neither qualitatively affect the SDS-dependent chemical properties of the vesicular material nor the SDS-dependent perturbation of the investigated reaction steps.

scholarly journals Cryo-EM structures of outer-arm dynein array bound to microtubule doublet reveal a mechanism for motor coordination

2020 ◽  
Author(s):  
Kai Zhang ◽  
Qinhui Rao ◽  
Yue Wang ◽  
Pengxin Chai ◽  
Yin-Wei Kuo ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Conformational Changes ◽  
Motor Coordination ◽  
Atp Hydrolysis ◽  
Specific Pattern ◽  
Atp Turnover ◽  
Binding Domains ◽  
Dynein Motor ◽  
One Step ◽  
Microtubule Doublet

Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Using electron microscopy, we determined the structure of OAD array bound to microtubule doublets (MTDs) in near-atomic details and illuminate how OADs coordinate with each other to move one step forward. OAD prefers a specific pattern of MTD protofilaments for its distinct microtubule-binding domains. Upon MTD binding, free OADs are induced to adopt a stable parallel conformation, primed for array formation. Extensive tail-to-head (TTH) interactions between OADs are observed, which need to be broken for ATP turnover by the dynein motor. ATP-hydrolysis in turn relaxes the TTH interfaces to sequentially effectuate free nucleotide cycle of downstream OADs. These findings lead to a model for how conformational changes of OADs produce coordinated actions.

scholarly journals Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jakob M. Silberberg ◽  
Robin A. Corey ◽  
Lisa Hielkema ◽  
Charlott Stock ◽  
Phillip J. Stansfeld ◽  
...  
Keyword(s):  
Binding Site ◽  
Common Ancestor ◽  
Atp Hydrolysis ◽  
Md Simulations ◽  
High Affinity ◽  
Ion Translocation ◽  
Biochemical Assays ◽  
Subunit Interface ◽  
Translocation Mechanism ◽  
P Type

AbstractKdpFABC, a high-affinity K+ pump, combines the ion channel KdpA and the P-type ATPase KdpB to secure survival at K+ limitation. Here, we apply a combination of cryo-EM, biochemical assays, and MD simulations to illuminate the mechanisms underlying transport and the coupling to ATP hydrolysis. We show that ions are transported via an intersubunit tunnel through KdpA and KdpB. At the subunit interface, the tunnel is constricted by a phenylalanine, which, by polarized cation-π stacking, controls K+ entry into the canonical substrate binding site (CBS) of KdpB. Within the CBS, ATPase coupling is mediated by the charge distribution between an aspartate and a lysine. Interestingly, individual elements of the ion translocation mechanism of KdpFABC identified here are conserved among a wide variety of P-type ATPases from different families. This leads us to the hypothesis that KdpB might represent an early descendant of a common ancestor of cation pumps.

scholarly journals Structural basis for substrate gripping and translocation by the ClpB AAA+ disaggregase

2018 ◽  
Author(s):  
Alexandrea N. Rizo ◽  
JiaBei Lin ◽  
Stephanie N. Gates ◽  
Eric Tse ◽  
Stephen M. Bart ◽  
...  
Keyword(s):  
Atp Hydrolysis ◽  
Protein Aggregates ◽  
Nucleotide Binding ◽  
Structural Basis ◽  
Central Channel ◽  
Channel Entrance ◽  
Binding Domains ◽  
Translocation Mechanism ◽  
Terminal Domains

ABSTRACTBacterial ClpB and yeast Hsp104 are homologous Hsp100 protein disaggregases that serve critical functions in proteostasis by solubilizing protein aggregates. Two AAA+ nucleotide binding domains (NBDs) power polypeptide translocation through a central channel comprised of a hexameric spiral of protomers that contact substrate via conserved pore-loop interactions. To elucidate the translocation mechanism, we determined the cryo-EM structure of a hyperactive ClpB variant to 2.9 Å resolution bound to the model substrate, casein in the presence of slowly hydrolysable ATPγS. Distinct substrate-gripping mechanisms are identified for NBD1 and NBD2 pore loops. A trimer of N-terminal domains define a channel entrance that binds the polypeptide substrate adjacent the topmost NBD1 contact. NBD conformations at the spiral seam reveal how ATP hydrolysis and substrate engagement or disengagement are precisely tuned to drive a stepwise translocation cycle.

scholarly journals Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC

2021 ◽  
Author(s):  
Jakob M Silberberg ◽  
Robin A Corey ◽  
Lisa Hielkema ◽  
Charlott Stock ◽  
Phillip James Stansfeld ◽  
...  
Keyword(s):  
Binding Site ◽  
Common Ancestor ◽  
Atp Hydrolysis ◽  
Md Simulations ◽  
High Affinity ◽  
Ion Translocation ◽  
Biochemical Assays ◽  
Subunit Interface ◽  
Translocation Mechanism ◽  
P Type

KdpFABC, a high-affinity K+ pump, combines the ion channel KdpA and the P-type ATPase KdpB to secure survival at K+ limitation. Here, we apply a combination of cryo-EM, biochemical assays, and MD simulations to illuminate the mechanisms underlying transport and the coupling to ATP hydrolysis. We unambiguously show that ions are transported via an intersubunit tunnel through KdpA and KdpB. At the subunit interface, the tunnel is constricted by a phenylalanine, which, by polarized cation-π stacking, controls K+ entry into the canonical substrate binding site (CBS) of KdpB. Within the CBS, ATPase coupling is mediated by the charge distribution between an aspartate and a lysine. Interestingly, individual elements of the ion translocation mechanism of KdpFABC identified here are conserved among a wide variety of P-type ATPases from different families. This leads us to the hypothesis that KdpB might represent an early descendant of a common ancestor of cation pumps.

Combination of ribosome and phage display for fast selection of high affinity VHH antibody fragments

2019 ◽  
pp. 27-33
Author(s):  
YuE Kravchenko ◽  
SV Ivanov ◽  
DS Kravchenko ◽  
EI Frolova ◽  
SP Chumakov
Keyword(s):  
Phage Display ◽  
Selection Procedure ◽  
Free System ◽  
Phage Displays ◽  
High Affinity ◽  
Binding Domains ◽  
A Cell ◽  
Vhh Antibodies ◽  
Efficiency Of Selection ◽  
Selection Of

Selection of antibodies using phage display involves the preliminary cloning of the repertoire of sequences encoding antigen-binding domains into phagemid, which is considered the bottleneck of the method, limiting the resulting diversity of libraries and leading to the loss of poorly represented variants before the start of the selection procedure. Selection in cell-free conditions using a ribosomal display is devoid from this drawback, however is highly sensitive to PCR artifacts and the RNase contamination. The aim of the study was to test the efficiency of a combination of both methods, including pre-selection in a cell-free system to enrich the source library, followed by cloning and final selection using phage display. This approach may eliminate the shortcomings of each method and increase the efficiency of selection. For selection, alpaca VHH antibody sequences suitable for building an immune library were used due to the lack of VL domains. Analysis of immune libraries from the genes of the VH3, VHH3 and VH4 families showed that the VHH antibodies share in the VH3 and VH4 gene groups is insignificant, and selection from the combined library is less effective than from the VHH3 family of sequences. We found that the combination of ribosomal and phage displays leads to a higher enrichment of high-affinity fragments and avoids the loss of the original diversity during cloning. The combined method allowed us to obtain a greater number of different high-affinity sequences, and all the tested VHH fragments were able to specifically recognize the target, including the total protein extracts of cell cultures.

scholarly journals Tripodal, Squaramide-Based Ion Pair Receptor for Effective Extraction of Sulfate Salt

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2751
Author(s):  
Damian Jagleniec ◽  
Marcin Wilczek ◽  
Jan Romański
Keyword(s):  
Ion Pairs ◽  
Binding Mode ◽  
Selective Extraction ◽  
Ion Pair ◽  
Hofmeister Series ◽  
Sulfate Salt ◽  
Lower Affinity ◽  
High Affinity ◽  
Binding Domains ◽  
Hydrated Sulfate

Combining three features—the high affinity of squaramides toward anions, cooperation in ion pair binding and preorganization of the binding domains in the tripodal platform—led to the effective receptor 2. The lack of at least one of these key elements in the structures of reference receptors 3 and 4 caused a lower affinity towards ion pairs. Receptor 2 was found to form an intramolecular network in wet chloroform, which changed into inorganic–organic associates after contact with ions and allowed salts to be extracted from an aqueous to an organic phase. The disparity in the binding mode of 2 with sulfates and with other monovalent anions led to the selective extraction of extremely hydrated sulfate anions in the presence of more lipophilic salts, thus overcoming the Hofmeister series.

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