scholarly journals Coordinated conformational changes in the V1 complex during V-ATPase reversible dissociation

2021 ◽  
Author(s):  
Thamiya Vasanthakumar ◽  
Kristine A Keon ◽  
Stephanie A Bueler ◽  
Michael C Jaskolka ◽  
John L Rubinstein
Keyword(s):  
Atpase Activity ◽  
Conformational Changes ◽  
Rotational State ◽  
Eukaryotic Cells ◽  
Subunit C ◽  
Unknown Mechanism ◽  
Conformational Rearrangement ◽  
Reversible Dissociation ◽  
Intracellular Compartments

Vacuolar-type ATPases (V-ATPases) are rotary enzymes that acidify intracellular compartments in eukaryotic cells. These multi-subunit complexes consist of a cytoplasmic V1 region that hydrolyzes ATP and a membrane-embedded VO region that transports protons. V-ATPase activity is regulated by reversible dissociation of the two regions, with the isolated V1 and VO complexes becoming autoinhibited upon disassembly and subunit C subsequently detaching from V1. In yeast, assembly of the V1 and VO regions is mediated by the RAVE complex through an unknown mechanism. We used cryoEM of yeast V-ATPase to determine structures of the intact enzyme, the dissociated but complete V1 complex, and the V1 complex lacking subunit C. Upon separation, V1 undergoes a dramatic conformational rearrangement, with its rotational state becoming incompatible for reassembly with VO. Loss of subunit C allows V1 to match the rotational state of VO, suggesting how RAVE could reassemble V1 and VO by recruiting subunit C.

Structural features and nucleotide-binding capability of the C subunit are integral to the regulation of the eukaryotic V1Vo ATPases

2005 ◽  
Vol 33 (4) ◽  
pp. 883-885 ◽  
Author(s):  
G. Grüber
Keyword(s):  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Structural Features ◽  
Subunit C ◽  
Reversible Dissociation ◽  
Intracellular Compartments ◽  
C Subunit ◽  
Vacuolar Atpases ◽  
Made In

V-ATPases (vacuolar ATPases) are responsible for acidification of intracellular compartments and, in certain cases, proton transport across the plasma membrane of eukaryotic cells. They are composed of a catalytic V1 sector, in which ATP hydrolysis takes place, and the Vo sector, which functions in proton conduction. The best established mechanism for regulating the V-ATPase activity in vivo involves reversible dissociation of the V1 and Vo domains, in which subunit C is intimately involved. In the last year, impressive progress has been made in elucidating the structure of the C subunit and its arrangement inside the V-ATPase. Nucleotide occupancy by subunit C, followed by conformational changes of this subunit has shed light on the mechanism of V-ATPase regulation.

scholarly journals Inhibition of acanthamoeba actomyosin-II ATPase activity and mechanochemical function by specific monoclonal antibodies.

1984 ◽  
Vol 99 (3) ◽  
pp. 1024-1033 ◽  
Author(s):  
D P Kiehart ◽  
T D Pollard
Keyword(s):  
Monoclonal Antibodies ◽  
Atpase Activity ◽  
Conformational Changes ◽  
Binding Sites ◽  
Polyclonal Antibodies ◽  
Myosin Ii ◽  
Antigenic Site ◽  
Actin Binding ◽  
Filamentous Form ◽  
Antibody Effects

Monoclonal and polyclonal antibodies that bind to myosin-II were tested for their ability to inhibit myosin ATPase activity, actomyosin ATPase activity, and contraction of cytoplasmic extracts. Numerous antibodies specifically inhibit the actin activated Mg++-ATPase activity of myosin-II in a dose-dependent fashion, but none blocked the ATPase activity of myosin alone. Control antibodies that do not bind to myosin-II and several specific antibodies that do bind have no effect on the actomyosin-II ATPase activity. In most cases, the saturation of a single antigenic site on the myosin-II heavy chain is sufficient for maximal inhibition of function. Numerous monoclonal antibodies also block the contraction of gelled extracts of Acanthamoeba cytoplasm. No polyclonal antibodies tested inhibited ATPase activity or gel contraction. As expected, most antibodies that block actin-activated ATPase activity also block gel contraction. Exceptions were three antibodies M2.2, -15, and -17, that appear to uncouple the ATPase activity from gel contraction: they block gel contraction without influencing ATPase activity. The mechanisms of inhibition of myosin function depends on the location of the antibody-binding sites. Those inhibitory antibodies that bind to the myosin-II heads presumably block actin binding or essential conformational changes in the myosin heads. A subset of the antibodies that bind to the proximal end of the myosin-II tail inhibit actomyosin-II ATPase activity and gel contraction. Although this part of the molecule is presumably some distance from the ATP and actin-binding sites, these antibody effects suggest that structural domains in this region are directly involved with or coupled to catalysis and energy transduction. A subset of the antibodies that bind to the tip of the myosin-II tail appear to inhibit ATPase activity and contraction through their inhibition of filament formation. They provide strong evidence for a substantial enhancement of the ATPase activity of myosin molecules in filamentous form and suggest that the myosin filaments may be required for cell motility.

scholarly journals Proteasomal conformation controls unfolding ability

2021 ◽  
Vol 118 (25) ◽  
pp. e2101004118
Author(s):  
Julianna R. Cresti ◽  
Abramo J. Manfredonia ◽  
Christopher E. Bragança ◽  
Joseph A. Boscia ◽  
Christina M. Hurley ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Fluorescent Proteins ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Conformational State ◽  
26S Proteasome ◽  
Eukaryotic Cells ◽  
Ubiquitinated Protein ◽  
Equilibrium Conditions ◽  
Substrate Processing

The 26S proteasome is the macromolecular machine responsible for the bulk of protein degradation in eukaryotic cells. As it degrades a ubiquitinated protein, the proteasome transitions from a substrate-accepting conformation (s1) to a set of substrate-processing conformations (s3 like), each stabilized by different intramolecular contacts. Tools to study these conformational changes remain limited, and although several interactions have been proposed to be important for stabilizing the proteasome’s various conformations, it has been difficult to test these directly under equilibrium conditions. Here, we describe a conformationally sensitive Förster resonance energy transfer assay, in which fluorescent proteins are fused to Sem1 and Rpn6, which are nearer each other in substrate-processing conformations than in the substrate-accepting conformation. Using this assay, we find that two sets of interactions, one involving Rpn5 and another involving Rpn2, are both important for stabilizing substrate-processing conformations. Mutations that disrupt these interactions both destabilize substrate-processing conformations relative to the substrate-accepting conformation and diminish the proteasome’s ability to successfully unfold and degrade hard-to-unfold substrates, providing a link between the proteasome’s conformational state and its unfolding ability.

scholarly journals Substrate recognition and ATPase activity of the E. coli cysteine/cystine ABC transporter YecSC-FliY

2020 ◽  
Vol 295 (16) ◽  
pp. 5245-5256 ◽  
Author(s):  
Siwar Sabrialabed ◽  
Janet G. Yang ◽  
Elon Yariv ◽  
Nir Ben-Tal ◽  
Oded Lewinson
Keyword(s):  
Atpase Activity ◽  
Abc Transporter ◽  
Conformational Changes ◽  
Binding Protein ◽  
Substrate Binding ◽  
Transporter Family ◽  
Wide Range ◽  
Substrate Binding Protein ◽  
Sulfur Containing ◽  
Sulfur Containing Compounds

Sulfur is essential for biological processes such as amino acid biogenesis, iron–sulfur cluster formation, and redox homeostasis. To acquire sulfur-containing compounds from the environment, bacteria have evolved high-affinity uptake systems, predominant among which is the ABC transporter family. Theses membrane-embedded enzymes use the energy of ATP hydrolysis for transmembrane transport of a wide range of biomolecules against concentration gradients. Three distinct bacterial ABC import systems of sulfur-containing compounds have been identified, but the molecular details of their transport mechanism remain poorly characterized. Here we provide results from a biochemical analysis of the purified Escherichia coli YecSC-FliY cysteine/cystine import system. We found that the substrate-binding protein FliY binds l-cystine, l-cysteine, and d-cysteine with micromolar affinities. However, binding of the l- and d-enantiomers induced different conformational changes of FliY, where the l- enantiomer–substrate-binding protein complex interacted more efficiently with the YecSC transporter. YecSC had low basal ATPase activity that was moderately stimulated by apo FliY, more strongly by d-cysteine–bound FliY, and maximally by l-cysteine– or l-cystine–bound FliY. However, at high FliY concentrations, YecSC reached maximal ATPase rates independent of the presence or nature of the substrate. These results suggest that FliY exists in a conformational equilibrium between an open, unliganded form that does not bind to the YecSC transporter and closed, unliganded and closed, liganded forms that bind this transporter with variable affinities but equally stimulate its ATPase activity. These findings differ from previous observations for similar ABC transporters, highlighting the extent of mechanistic diversity in this large protein family.

Molecular Mechanics Investigation on Conformational Flexibility of 14β Steroids in Drug-Receptor Interactions

1986 ◽  
Vol 41 (3) ◽  
pp. 297-300 ◽  
Author(s):  
Martin Bohl ◽  
Manfred Wunderwald
Keyword(s):  
Atpase Activity ◽  
Molecular Mechanics ◽  
Receptor Binding ◽  
Conformational Changes ◽  
Conformational Flexibility ◽  
Receptor Binding Site ◽  
Receptor Interactions ◽  
Drug Receptor ◽  
Potential Inhibitors ◽  
Steroid Structure

The interaction between two 14 β steroids being still unsynthesized and a model receptor binding site is theoretically studied by a molecular mechanics scheme. Both com pounds containing seven-membered rings in the 17 β position are found to form stable hydrogen bonds to the receptor and can be attributed to be potential inhibitors of the Na +,K + -ATPase activity. Substantial steroid conformational changes necessary for an efficient receptor binding are calculated to reduce the interaction energy by only 10 kJ mol -1. Therefore, alterations in steroid structure should be generally taken into consideration in the investigation of steroid-receptor interactions.

Interaction of ethanol and catecholamines on rat brain (Na+ + K+)-ATPase

1979 ◽  
Vol 57 (10) ◽  
pp. 1098-1106 ◽  
Author(s):  
N. Rangaraj ◽  
H. Kalant
Keyword(s):  
Atpase Activity ◽  
Rat Brain ◽  
Unknown Mechanism ◽  
Dependent Inhibition

The (Na+ + K+)-ATPase activity in rat brain homogenates was stimulated by either d(+)- or l(−)-noradrenaline (NA) or by dopamine (DA) when vanadium-contaminated ATP was used as substrate, but not with vanadium-free ATP. Addition of 6.25–50 mM ethanol (EtOH) alone had no effect on the activity of dilute (1:2600) homogenates; however, in the presence of l-NA or DA, but not of d-NA, it produced a concentration-dependent reduction of activity below control values, regardless of which ATP was used. The minimum concentrations of catecholamine producing sensitization of ATPase to EtOH were 10−12 M l-NA and 10−7 M DA. With concentrated (1:65 or 1:78) homogenates, EtOH produced concentration-dependent inhibition without addition of exogenous catecholamines. The inhibition of ATPase by EtOH in the concentrated homogenate was decreased by elevation of K+ concentration, and was prevented in both dilute and concentrated homogenates by phentolamine but not by propranolol. The findings suggest that the action of NA or an α receptor may alter the enzyme microenvironment, by an as yet unknown mechanism, rendering it more susceptible to inhibition by EtOH.

scholarly journals Conformational heterogeneity of the AAA ATPase p97 characterized by single particle cryo-EM

2014 ◽  
Vol 70 (a1) ◽  
pp. C853-C853
Author(s):  
Driss Mountassif ◽  
Lucien Fabre ◽  
Kaustuv Basu ◽  
Mihnea Bostina ◽  
Slavica Jonic ◽  
...  
Keyword(s):  
Atpase Activity ◽  
Conformational Changes ◽  
Single Particle ◽  
Molecular Mechanisms ◽  
Protein Complexes ◽  
Normal Mode Analysis ◽  
Single Amino Acid ◽  
Mode Analysis ◽  
Conformational Heterogeneity ◽  
Aaa Atpase

p97, a member of the AAA (ATPase Associated with various Activities) ATPase family, is essential and centrally involved in a wide variety of cellular processes. Single amino-acid substitutions in p97 have been associated with the severe degenerative disorder of Inclusion Body Myopathy associated with Paget disease of bone and Frontotemporal Dementia (IBMPFD) as well as amytropic leteral sclerosis (ALS). Current models propose that p97 acts as a motor transmitting the energy from the ATPase cycle to conformational changes of substrate protein complexes causing segregation, remodeling or translocation. Mutations at the interface between the N and the D1 domains impact the ATPase activity and the conformation of D2 on the opposite side of the protein complex, suggesting intermolecular communication. Because of limited structural information, the molecular mechanisms on how p97 drives its activities and the molecular basis for transmission of information within the molecule remain elusive. Structural heterogeneity is observed in vitro and is likely relevant for the in vivo biological function of p97. Single particle cryo-EM is the method of choice to study a flexible complex. The technique allows study in solution and also deals with sample heterogeneity by image classification. We have set-up the characterization of the conformational heterogeneity in WT and disease relevant p97 mutant using multi-likelihood classification and Hybrid Electron Microscopy Normal Mode Analysis HEMNMA. The multi-likelihood analysis shows a link between the conformations of the N and D2 domains. HEMNMA allows the analysis of the asymmetry of the conformational changes. Together these studies describe the structural flexibility of p97 and the coupling of the ATPase activity with conformational changes in health and in disease. Study of this model system also allows the development of new methods to understand the conformational heterogeneity of other protein complexes.

scholarly journals The signaling lipid PI(3,5)P2 stabilizes V1–Vo sector interactions and activates the V-ATPase

2014 ◽  
Vol 25 (8) ◽  
pp. 1251-1262 ◽  
Author(s):  
Sheena Claire Li ◽  
Theodore T. Diakov ◽  
Tao Xu ◽  
Maureen Tarsio ◽  
Wandi Zhu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Atpase Activity ◽  
Human Disease ◽  
Proton Pumps ◽  
Disease Phenotypes ◽  
Reversible Dissociation ◽  
Signaling Mechanisms ◽  
Vacuolar Acidification ◽  
Direct Binding

Vacuolar proton-translocating ATPases (V-ATPases) are highly conserved, ATP-driven proton pumps regulated by reversible dissociation of its cytosolic, peripheral V1 domain from the integral membrane Vo domain. Multiple stresses induce changes in V1-Vo assembly, but the signaling mechanisms behind these changes are not understood. Here we show that certain stress-responsive changes in V-ATPase activity and assembly require the signaling lipid phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2). V-ATPase activation through V1-Vo assembly in response to salt stress is strongly dependent on PI(3,5)P2 synthesis. Purified Vo complexes preferentially bind to PI(3,5)P2 on lipid arrays, suggesting direct binding between the lipid and the membrane sector of the V-ATPase. Increasing PI(3,5)P2 levels in vivo recruits the N-terminal domain of Vo-sector subunit Vph1p from cytosol to membranes, independent of other subunits. This Vph1p domain is critical for V1-Vo interaction, suggesting that interaction of Vph1p with PI(3,5)P2-containing membranes stabilizes V1-Vo assembly and thus increases V-ATPase activity. These results help explain the previously described vacuolar acidification defect in yeast fab1∆ and vac14∆ mutants and suggest that human disease phenotypes associated with PI(3,5)P2 loss may arise from compromised V-ATPase stability and regulation.

scholarly journals Binding Dynamics of Structural Nucleoporins Govern Nuclear Pore Complex Permeability and May Mediate Channel Gating

2003 ◽  
Vol 23 (2) ◽  
pp. 534-542 ◽  
Author(s):  
Nataliya Shulga ◽  
David S. Goldfarb
Keyword(s):  
Nuclear Pore Complex ◽  
Size Range ◽  
Channel Gating ◽  
Aliphatic Alcohols ◽  
Complex Permeability ◽  
Nuclear Pore ◽  
Wild Type ◽  
Unknown Mechanism ◽  
Reversible Dissociation ◽  
Wide Size Range

ABSTRACT The nuclear pore complex (NPC) is a permeable sieve that can dilate to facilitate the bidirectional translocation of a wide size range of receptor-cargo complexes. The binding of receptors to FG nucleoporin docking sites triggers channel gating by an unknown mechanism. Previously, we used deoxyglucose and chilling treatments to implicate Nup170p and Nup188p in the control of NPC sieving in Saccharomyces cerevisiae. Here, we report that aliphatic alcohols increase the permeability of wild-type and nup170Δ NPCs. In conjunction with increases in permeability, aliphatic alcohols, deoxyglucose, and chilling trigger the reversible dissociation of several nucleoporins from nup170Δ NPCs. These results are consistent with the hypothesis that NPC gating occurs when molecular latches composed of FG repeats and structural nucleoporins dissociate.

scholarly journals The DNA damage-recognition problem in human and other eukaryotic cells: the XPA damage binding protein

1997 ◽  
Vol 328 (1) ◽  
pp. 1-12 ◽  
Author(s):  
E. James CLEAVER ◽  
J. Christopher STATES
Keyword(s):  
Zinc Finger ◽  
Conformational Changes ◽  
Binding Capacity ◽  
Binding Protein ◽  
Protein A ◽  
Eukaryotic Cells ◽  
Damage Recognition ◽  
Recognition Ability ◽  
Associated Proteins ◽  
Group A

The capacity of human and other eukaryotic cells to recognize a disparate variety of damaged sites in DNA, and selectively excise and repair them, resides in a deceptively small simple protein, a 38-42 kDa zinc-finger binding protein, XPA (xeroderma pigmentosum group A), that has no inherent catalytic properties. One key to its damage-recognition ability resides in a DNA-binding domain which combines a zinc finger and a single-strand binding region which may infiltrate small single-stranded regions caused by helix-destabilizing lesions. Another is the augmentation of its binding capacity by interactions with other single-stranded binding proteins and helicases which co-operate in the binding and are unloaded at the binding site to facilitate further unwinding of the DNA and subsequent catalysis. The properties of these reactions suggest there must be considerable conformational changes in XPA and associated proteins to provide a flexible fit to a wide variety of damaged structures in the DNA.

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