Biochemistry, Genetics and Molecular Biology › Molecular Biology

ATP Synthase and ATPases Research

Works Count: 28460

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Description

This cluster of papers focuses on the function, regulation, and mechanisms of ATP synthase, including vacuolar ATPases, proton pump inhibitors, mitochondrial ATP synthase, V-ATPases, rotary mechanism, F1-ATPase, proton transport, and vacuolar H+-ATPase. The papers explore the molecular structure, physiological roles, pathophysiology, and interactions of ATP synthases in various cellular processes.

Keywords

ATP Synthase; Vacuolar ATPases; Proton Pump Inhibitors; Mitochondrial ATP Synthase; V-ATPases; Rotary Mechanism; F1-ATPase; Proton Transport; Vacuolar H+-ATPase; Mechanochemistry

Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold.

1982-08-01

John E. Walker , M Saraste , M J Runswick +1 more

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Timetables of neurogenesis in the human brain based on experimentally determined patterns in the rat.

1993-01-01

Shirley A. Bayer , Joseph Altman , Raymond J. Russo +1 more

Cellular pH gradient in tumor versus normal tissue: potential exploitation for the treatment of cancer.

1996-03-15

L.E. Gerweck , Koushik Seetharaman

Although limited data exist, electrode-measured pH values of human tumors and adjacent normal tissues, which are concurrently obtained by the same investigator in the same patient, consistently show that the … Although limited data exist, electrode-measured pH values of human tumors and adjacent normal tissues, which are concurrently obtained by the same investigator in the same patient, consistently show that the electrode pH (believed to primarily represent tissue extracellular pH) is substantially and consistently lower in the tumor than in normal tissue. In contrast, the 31P-magnetic resonance spectroscopy estimated that intracellular pH is essentially identical or slightly more basic in tumor compared to normal tissue. As a consequence, the cellular pH gradient is substantially reduced or reversed in tumor compared to normal tissue: in normal tissue the extracellular pH is relatively basic, and in tumor tissue the magnitude of the pH gradient is reduced or reversed. The difference provides an exploitable avenue for the treatment of cancer. The extent to which drugs exhibiting weakly acid or basic properties are ionized is strongly dependent on the pH of their milieu. Weakly acidic drugs which are relatively lipid soluble in their nonionized state may diffuse freely across the cell membrane and, upon entering a relatively basic intracellular compartment, become trapped and accumulate within a cell, leading to substantial differences in the intracellular/extracellular drug distribution between tumor and normal tissue for drugs exhibiting appropriate pKas.

ATP synthase — a marvellous rotary engine of the cell

2001-09-01

Masasuke Yoshida , Eiro Muneyuki , Toru Hisabori

Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy.

2000-09-01

Shimon Weiss

Vanadate is a potent (Na,K)-ATPase inhibitor found in ATP derived from muscle.

1977-11-01

Lewis C. Cantley , Lee Josephson , Ronald K. Warner +3 more

A potent (Na,K)-ATPase inhibitor purified from Sigma Grade* ATP has been identified as vanadium using electron probe microanalysis and confirmed by microwave-induced emission spectroscopy and electron paramagnetic resonance spectroscopy. Sodium … A potent (Na,K)-ATPase inhibitor purified from Sigma Grade* ATP has been identified as vanadium using electron probe microanalysis and confirmed by microwave-induced emission spectroscopy and electron paramagnetic resonance spectroscopy. Sodium orthovanadate (Na3 VO4) is identical with the purified inhibitor with respect to ultraviolet absorbance, migration on thin layer chromatography, and inhibition of (Na,K)-ATPase. The (Na,K)-ATPase is in-inhibited 50% by 40 nM Na3 VO4 under optimal conditions (28 mM Mg2+) and the inhibition is 100% reversible by millimolar concentrations of norepinephrine. The physiological significance of this inhibition is discussed in relation to vanadium concentrations in vivo.

Mutations in the gene encoding B1 subunit of H+-ATPase cause renal tubular acidosis with sensorineural deafness

1999-01-01

Fiona E. Karet , Karin E. Finberg , Raoul D. Nelson +7 more

Partial Resolution of the Enzymes Catalyzing Oxidative Phosphorylation

1971-09-01

Yasuo Kagawa , Efraim Racker

1. Amorphous membrane fragments depleted in P-lipids and cytochrome oxidase were isolated from bovine heart mitochondria and were reconstituted with P-lipids and coupling factors to yield vesicular structures. These vesicles … 1. Amorphous membrane fragments depleted in P-lipids and cytochrome oxidase were isolated from bovine heart mitochondria and were reconstituted with P-lipids and coupling factors to yield vesicular structures. These vesicles catalyzed a 32Pi—ATP exchange and showed an induced enhancement of anilinonaphthalene sulfonate fluorescence on addition of ATP 2. 32Pi—ATP exchange and fluorescence enhancement were abolished by uncouplers of oxidative phosphorylation and by energy transfer inhibitors. The ATPase activity was inhibited by energy transfer inhibitors, but stimulated by uncouplers or by the combined action of nigericin and valinomycin in the presence of K+. Both ATPase activity and 32Pi—ATP exchange were inhibited by a specific antibody against coupling factor 1. 3. It was shown that the reconstitution of vesicular structures with functional activity required several hours. Rapid reconstitution resulted in inactive vesicles. Evidence for the formation of new vesicles from solubilized P-lipids was obtained by demonstrating inclusion of macromolecules such as 14C-labeled inulin or ferritin which could not be removed by washing.

Reversible binding of Pi by beef heart mitochondrial adenosine triphosphatase.

1977-05-01

Harvey S. Penefsky

Beef heart mitochondrialATPase (F,) exhibited a single binding site for Pi.The interaction with P, was reversible, partially dependent on the presence of divalent metal ions, and characterized by a dissociation … Beef heart mitochondrialATPase (F,) exhibited a single binding site for Pi.The interaction with P, was reversible, partially dependent on the presence of divalent metal ions, and characterized by a dissociation constant at pH 7.5 of 80 pm.

Unidirectional rotary motion in a molecular system

1999-09-01

T. Ross Kelly , Harshani De Silva , Richard A. Silva

Molecular Architecture of the Rotary Motor in ATP Synthase

1999-11-26

Daniela Stock , Andrew G. W. Leslie , John E. Walker

Adenosine triphosphate (ATP) synthase contains a rotary motor involved in biological energy conversion. Its membrane-embedded F 0 sector has a rotation generator fueled by the proton-motive force, which provides the … Adenosine triphosphate (ATP) synthase contains a rotary motor involved in biological energy conversion. Its membrane-embedded F 0 sector has a rotation generator fueled by the proton-motive force, which provides the energy required for the synthesis of ATP by the F 1 domain. An electron density map obtained from crystals of a subcomplex of yeast mitochondrial ATP synthase shows a ring of 10 c subunits. Each c subunit forms an α-helical hairpin. The interhelical loops of six to seven of the c subunits are in close contact with the γ and δ subunits of the central stalk. The extensive contact between the c ring and the stalk suggests that they may rotate as an ensemble during catalysis.

THE ATP SYNTHASE—A SPLENDID MOLECULAR MACHINE

1997-06-01

Paul D. Boyer

An X-ray structure of the F 1 portion of the mitochondrial ATP synthase shows asymmetry and differences in nucleotide binding of the catalytic β subunits that support the binding change … An X-ray structure of the F 1 portion of the mitochondrial ATP synthase shows asymmetry and differences in nucleotide binding of the catalytic β subunits that support the binding change mechanism with an internal rotation of the γ subunit. Other structural and mutational probes of the F 1 and F 0 portions of the ATP synthase are reviewed, together with kinetic and other evaluations of catalytic site occupancy and behavior during hydrolysis or synthesis of ATP. Subunit function as related to proton translocation and rotational catalysis is considered. Physical demonstrations of the γ subunit rotation have been achieved. The findings have implications for other enzymatic catalyses.

The binding change mechanism for ATP synthase — Some probabilities and possibilities

1993-01-01

Paul D. Boyer

Distinct BH3 domains either sensitize or activate mitochondrial apoptosis, serving as prototype cancer therapeutics

2002-09-01

Anthony Letai , Michael C. Bassik , Loren D. Walensky +3 more

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Adenosinetriphosphatase activity and the active movements of alkali metal ions

1961-04-01

E. T. Dunham , I. M. Glynn

Doxil® — The first FDA-approved nano-drug: Lessons learned

2012-03-29

Yechezkel Barenholz

Osteoclastic Bone Resorption by a Polarized Vacuolar Proton Pump

1989-08-25

Harry C. Blair , Steven L. Teitelbaum , Robert W. Ghiselli +1 more

Bone resorption depends on the formation, by osteoclasts, of an acidic extracellular compartment wherein matrix is degraded. The mechanism by which osteoclasts transport protons into that resorptive microenvironment was identified … Bone resorption depends on the formation, by osteoclasts, of an acidic extracellular compartment wherein matrix is degraded. The mechanism by which osteoclasts transport protons into that resorptive microenvironment was identified by means of adenosine triphosphate-dependent weak base accumulation in isolated osteoclast membrane vesicles, which exhibited substrate and inhibition properties characteristic of the vacuolar, electrogenic H + -transporting adenosine triphosphatase (H + -ATPase). Identify of the proton pump was confirmed by immunoblot of osteoclast membrane proteins probed with antibody to vacuolar H + -ATPase isolated from bovine kidney. The osteoclast's H + -ATPase was immunocytochemically localized to the cell-bone attachment site. Immunoelectron microscopy showed that the H + -ATPase was present in the ruffled membrane, the resorptive organ of the cell.

Sensors and regulators of intracellular pH

2009-12-09

Joseph R. Casey , Sergio Grinstein , John Orlowski

Coiled coils: new structures and new functions

1996-10-01

Andrei N. Lupas

The vacuolar (H+)-ATPases — nature's most versatile proton pumps

2002-02-01

Tsuyoshi Nishi , Michael Forgac

F1-ATPase Is a Highly Efficient Molecular Motor that Rotates with Discrete 120° Steps

1998-06-01

Ryohei Yasuda , Hiroyuki Noji , Kazuhiko Kinosita +1 more

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Peptide growth factors are multifunctional

1988-03-01

Michael B. Sporn , Anita B. Roberts

Molecular dynamics and protein function

2005-05-03

Martin Karplus , John Kuriyan

A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to … A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F 1 ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems.

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Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology

2007-10-03

Michael Forgac

Dysregulated pH: a perfect storm for cancer progression

2011-08-11

Bradley A. Webb , Michael S. Chimenti , Matthew P. Jacobson +1 more

ROS-Generating Mitochondrial DNA Mutations Can Regulate Tumor Cell Metastasis

2008-04-04

Kaori Ishikawa , Keizo Takenaga , Miho Akimoto +6 more

Mutations in mitochondrial DNA (mtDNA) occur at high frequency in human tumors, but whether these mutations alter tumor cell behavior has been unclear. We used cytoplasmic hybrid (cybrid) technology to … Mutations in mitochondrial DNA (mtDNA) occur at high frequency in human tumors, but whether these mutations alter tumor cell behavior has been unclear. We used cytoplasmic hybrid (cybrid) technology to replace the endogenous mtDNA in a mouse tumor cell line that was poorly metastatic with mtDNA from a cell line that was highly metastatic, and vice versa. Using assays of metastasis in mice, we found that the recipient tumor cells acquired the metastatic potential of the transferred mtDNA. The mtDNA conferring high metastatic potential contained G13997A and 13885insC mutations in the gene encoding NADH (reduced form of nicotinamide adenine dinucleotide) dehydrogenase subunit 6 ( ND6 ). These mutations produced a deficiency in respiratory complex I activity and were associated with overproduction of reactive oxygen species (ROS). Pretreatment of the highly metastatic tumor cells with ROS scavengers suppressed their metastatic potential in mice. These results indicate that mtDNA mutations can contribute to tumor progression by enhancing the metastatic potential of tumor cells.

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Structure at 2.8 Â resolution of F1-ATPase from bovine heart mitochondria

1994-08-01

Jan Pieter Abrahams , Andrew G. W. Leslie , René Lutter +1 more

Direct observation of the rotation of F1-ATPase

1997-03-01

Hiroyuki Noji , Ryohei Yasuda , Masasuke Yoshida +1 more

Powering an Inorganic Nanodevice with a Biomolecular Motor

2000-11-24

Ricky Soong , George D. Bachand , Herc P. Neves +3 more

Biomolecular motors such as F 1 –adenosine triphosphate synthase (F 1 -ATPase) and myosin are similar in size, and they generate forces compatible with currently producible nanoengineered structures. We have … Biomolecular motors such as F 1 –adenosine triphosphate synthase (F 1 -ATPase) and myosin are similar in size, and they generate forces compatible with currently producible nanoengineered structures. We have engineered individual biomolecular motors and nanoscale inorganic systems, and we describe their integration in a hybrid nanomechanical device powered by a biomolecular motor. The device consisted of three components: an engineered substrate, an F 1 -ATPase biomolecular motor, and fabricated nanopropellers. Rotation of the nanopropeller was initiated with 2 mM adenosine triphosphate and inhibited by sodium azide.

Oxidative Phosphorylation at the fin de siècle

1999-03-05

Matti Saraste

Mitochondria produce most of the energy in animal cells by a process called oxidative phosphorylation. Electrons are passed along a series of respiratory enzyme complexes located in the inner mitochondrial … Mitochondria produce most of the energy in animal cells by a process called oxidative phosphorylation. Electrons are passed along a series of respiratory enzyme complexes located in the inner mitochondrial membrane, and the energy released by this electron transfer is used to pump protons across the membrane. The resultant electrochemical gradient enables another complex, adenosine 5'-triphosphate (ATP) synthase, to synthesize the energy carrier ATP. Important new mechanistic insights into oxidative phosphorylation have emerged from recent three-dimensional structural analyses of ATP synthase and two of the respiratory enzyme complexes, cytochrome bc1 and cytochrome c oxidase. This work, and new enzymological studies of ATP synthase's unusual catalytic mechanism, are reviewed here.

A direct colorimetric assay for Ca2+-stimulated ATPase activity

1986-09-01

Kwok‐Ming Chan , Dennis M. Delfert , Kurt D Junger

Antibiotics as tools for metabolic studies. I. A survey of toxic antibiotics in respiratory, phosphorylative and glycolytic systems

1958-12-01

Henry A. Lardy , Diane Johnson , W. C. McMurray

Structural organization, ion transport, and energy transduction of P-type ATPases

1996-05-01

Jesper V. Møller , Birte Juul , Marc le Maire

Dimer ribbons of ATP synthase shape the inner mitochondrial membrane

2008-03-06

Mike Strauss , Götz Hofhaus , Rasmus R. Schröder +1 more

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H+-Translocating ATPases: Advances Using Membrane Vesicles

1985-06-01

Heven Sze

In this paper, two primary active transport systems (H/sup +/ -ATPases) in plant cells are examined using membrane vesicles as a simple experimental tool. One electrogenic, H/sup +/ -translocating ATPase … In this paper, two primary active transport systems (H/sup +/ -ATPases) in plant cells are examined using membrane vesicles as a simple experimental tool. One electrogenic, H/sup +/ -translocating ATPase is vanadate-sensitive and associated with the plasma membrane. Another electrogenic, H/sup +/ -translocating ATPases is anion-sensitive, and localized on the tonoplast (and perhaps other membranes). According to the working model, the plasma membrane and tonoplast-type H/sup +/ -ATPases are detectable in inside-out plasma membrane and right-side-out tonoplast vesicles. The direction of H/sup +/ pumping into these vesicles would be consistent with the results from intact cells where H/sup +/ are extruded from the cell across the plasma membrane and pumped into the vacuole from the cytoplasm. Understanding the properties of H/sup +/ -pumping ATPases using membrane vesicles has paved the way for studies to identify secondary active transport systems coupled to the proton electrochemical gradient. Redox-driven transport systems can also be studied directly using the isolated vesicles. As transport proteins are identified, the functional activities can be specifically studied after reconstitution of the purified protein(s) into phospholipid membrane vesicles. 154 references.

Methods used in the structure determination of bovine mitochondrial F1 ATPase

1996-01-01

Jan Pieter Abrahams , Andrew G. W. Leslie

With a size of 372 kDa, the F(1) ATPase particle is the largest asymmetric structure solved to date. Isomorphous differences arising from reacting the crystals with methyl-mercury nitrate at two … With a size of 372 kDa, the F(1) ATPase particle is the largest asymmetric structure solved to date. Isomorphous differences arising from reacting the crystals with methyl-mercury nitrate at two concentrations allowed the structure determination. Careful data collection and data processing were essential in this process as well as a new form of electron-density modification, 'solvent flipping'. The most important feature of this new procedure is that the electron density in the solvent region is inverted rather than set to a constant value, as in conventional solvent flattening. All non-standard techniques and variations on new techniques which were employed in the structure determination are described.

Over-production of Proteins inEscherichia coli: Mutant Hosts that Allow Synthesis of some Membrane Proteins and Globular Proteins at High Levels

1996-07-01

Bruno Miroux , John E. Walker

mTORC1 Senses Lysosomal Amino Acids Through an Inside-Out Mechanism That Requires the Vacuolar H + -ATPase

2011-11-03

Roberto Zoncu , Liron Bar‐Peled , Alejo Efeyan +3 more

The mTOR complex 1 (mTORC1) protein kinase is a master growth regulator that is stimulated by amino acids. Amino acids activate the Rag guanosine triphosphatases (GTPases), which promote the translocation … The mTOR complex 1 (mTORC1) protein kinase is a master growth regulator that is stimulated by amino acids. Amino acids activate the Rag guanosine triphosphatases (GTPases), which promote the translocation of mTORC1 to the lysosomal surface, the site of mTORC1 activation. We found that the vacuolar H(+)-adenosine triphosphatase ATPase (v-ATPase) is necessary for amino acids to activate mTORC1. The v-ATPase engages in extensive amino acid-sensitive interactions with the Ragulator, a scaffolding complex that anchors the Rag GTPases to the lysosome. In a cell-free system, ATP hydrolysis by the v-ATPase was necessary for amino acids to regulate the v-ATPase-Ragulator interaction and promote mTORC1 translocation. Results obtained in vitro and in human cells suggest that amino acid signaling begins within the lysosomal lumen. These results identify the v-ATPase as a component of the mTOR pathway and delineate a lysosome-associated machinery for amino acid sensing.

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Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators

2009-09-01

Hiromi Imamura , Kim Phuong Huynh Nhat , Hiroko Togawa +5 more

Adenosine 5'-triphosphate (ATP) is the major energy currency of cells and is involved in many cellular processes. However, there is no method for real-time monitoring of ATP levels inside individual … Adenosine 5'-triphosphate (ATP) is the major energy currency of cells and is involved in many cellular processes. However, there is no method for real-time monitoring of ATP levels inside individual living cells. To visualize ATP levels, we generated a series of fluorescence resonance energy transfer (FRET)-based indicators for ATP that were composed of the epsilon subunit of the bacterial F(o)F(1)-ATP synthase sandwiched by the cyan- and yellow-fluorescent proteins. The indicators, named ATeams, had apparent dissociation constants for ATP ranging from 7.4 muM to 3.3 mM. By targeting ATeams to different subcellular compartments, we unexpectedly found that ATP levels in the mitochondrial matrix of HeLa cells are significantly lower than those of cytoplasm and nucleus. We also succeeded in measuring changes in the ATP level inside single HeLa cells after treatment with inhibitors of glycolysis and/or oxidative phosphorylation, revealing that glycolysis is the major ATP-generating pathway of the cells grown in glucose-rich medium. This was also confirmed by an experiment using oligomycin A, an inhibitor of F(o)F(1)-ATP synthase. In addition, it was demonstrated that HeLa cells change ATP-generating pathway in response to changes of nutrition in the environment.

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Dimers of mitochondrial ATP synthase form the permeability transition pore

2013-03-25

Valentina Giorgio , Sophia von Stockum , Manuela Antoniel +7 more

Here we define the molecular nature of the mitochondrial permeability transition pore (PTP), a key effector of cell death. The PTP is regulated by matrix cyclophilin D (CyPD), which also … Here we define the molecular nature of the mitochondrial permeability transition pore (PTP), a key effector of cell death. The PTP is regulated by matrix cyclophilin D (CyPD), which also binds the lateral stalk of the F O F 1 ATP synthase. We show that CyPD binds the oligomycin sensitivity-conferring protein subunit of the enzyme at the same site as the ATP synthase inhibitor benzodiazepine 423 (Bz-423), that Bz-423 sensitizes the PTP to Ca 2+ like CyPD itself, and that decreasing oligomycin sensitivity-conferring protein expression by RNAi increases the sensitivity of the PTP to Ca 2+ . Purified dimers of the ATP synthase, which did not contain voltage-dependent anion channel or adenine nucleotide translocator, were reconstituted into lipid bilayers. In the presence of Ca 2+ , addition of Bz-423 triggered opening of a channel with currents that were typical of the mitochondrial megachannel, which is the PTP electrophysiological equivalent. Channel openings were inhibited by the ATP synthase inhibitor AMP-PNP (γ-imino ATP, a nonhydrolyzable ATP analog) and Mg 2+ /ADP. These results indicate that the PTP forms from dimers of the ATP synthase.

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EVOLUTIONARY RELATIONSHIPS AND STRUCTURAL MECHANISMS OF AAA+ PROTEINS

2006-04-07

Jan P. Erzberger , James M. Berger

Complex cellular events commonly depend on the activity of molecular "machines" that efficiently couple enzymatic and regulatory functions within a multiprotein assembly. An essential and expanding subset of these assemblies … Complex cellular events commonly depend on the activity of molecular "machines" that efficiently couple enzymatic and regulatory functions within a multiprotein assembly. An essential and expanding subset of these assemblies comprises proteins of the ATPases associated with diverse cellular activities (AAA+) family. The defining feature of AAA+ proteins is a structurally conserved ATP-binding module that oligomerizes into active arrays. ATP binding and hydrolysis events at the interface of neighboring subunits drive conformational changes within the AAA+ assembly that direct translocation or remodeling of target substrates. In this review, we describe the critical features of the AAA+ domain, summarize our current knowledge of how this versatile element is incorporated into larger assemblies, and discuss specific adaptations of the AAA+ fold that allow complex molecular manipulations to be carried out for a highly diverse set of macromolecular targets.

Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase

2001-04-19

Ryohei Yasuda , Hiroyuki Noji , Masasuke Yoshida +2 more

Mechanical Processes in Biochemistry

2003-03-11

Carlos Bustamante , Yann R. Chemla , Nancy R. Forde +1 more

Mechanical processes are involved in nearly every facet of the cell cycle. Mechanical forces are generated in the cell during processes as diverse as chromosomal segregation, replication, transcription, translation, translocation … Mechanical processes are involved in nearly every facet of the cell cycle. Mechanical forces are generated in the cell during processes as diverse as chromosomal segregation, replication, transcription, translation, translocation of proteins across membranes, cell locomotion, and catalyzed protein and nucleic acid folding and unfolding, among others. Because force is a product of all these reactions, biochemists are beginning to directly apply external forces to these processes to alter the extent or even the fate of these reactions hoping to reveal their underlying molecular mechanisms. This review provides the conceptual framework to understand the role of mechanical force in biochemistry.

Vacuolar H+-ATPase Activity Is Required for Endocytic and Secretory Trafficking inArabidopsis

2006-02-03

Jan Dettmer , Anne Hong‐Hermesdorf , York‐Dieter Stierhof +1 more

Abstract In eukaryotic cells, compartments of the highly dynamic endomembrane system are acidified to varying degrees by the activity of vacuolar H+-ATPases (V-ATPases). In the Arabidopsis thaliana genome, most V-ATPase … Abstract In eukaryotic cells, compartments of the highly dynamic endomembrane system are acidified to varying degrees by the activity of vacuolar H+-ATPases (V-ATPases). In the Arabidopsis thaliana genome, most V-ATPase subunits are encoded by small gene families, thus offering potential for a multitude of enzyme complexes with different kinetic properties and localizations. We have determined the subcellular localization of the three Arabidopsis isoforms of the membrane-integral V-ATPase subunit VHA-a. Colocalization experiments as well as immunogold labeling showed that VHA-a1 is preferentially found in the trans-Golgi network (TGN), the main sorting compartment of the secretory pathway. Uptake experiments with the endocytic tracer FM4-64 revealed rapid colocalization with VHA-a1, indicating that the TGN may act as an early endosomal compartment. Concanamycin A, a specific V-ATPase inhibitor, blocks the endocytic transport of FM4-64 to the tonoplast, causes the accumulation of FM4-64 together with newly synthesized plasma membrane proteins, and interferes with the formation of brefeldin A compartments. Furthermore, nascent cell plates are rapidly stained by FM4-64, indicating that endocytosed material is redirected into the secretory flow after reaching the TGN. Together, our results suggest the convergence of the early endocytic and secretory trafficking pathways in the TGN.

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Toward Intelligent Molecular Machines: Directed Motions of Biological and Artificial Molecules and Assemblies

2005-03-23

Kazushi Kinbara , Takuzo Aida

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTToward Intelligent Molecular Machines: Directed Motions of Biological and Artificial Molecules and AssembliesKazushi Kinbara and Takuzo AidaView Author Information Department of Chemistry and Biotechnology, School of Engineering, … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTToward Intelligent Molecular Machines: Directed Motions of Biological and Artificial Molecules and AssembliesKazushi Kinbara and Takuzo AidaView Author Information Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan Cite this: Chem. Rev. 2005, 105, 4, 1377–1400Publication Date (Web):March 23, 2005Publication History Received13 September 2004Published online23 March 2005Published inissue 1 April 2005https://pubs.acs.org/doi/10.1021/cr030071rhttps://doi.org/10.1021/cr030071rresearch-articleACS PublicationsCopyright © 2005 American Chemical SocietyRequest reuse permissionsArticle Views9097Altmetric-Citations789LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Crystal structure,Filaments,Genetics,Molecules,Peptides and proteins Get e-Alerts

A novel response of cancer cells to radiation involves autophagy and formation of acidic vesicles.

2001-01-15

Shoshana Paglin , Timothy Hollister , Thomas Delohery +5 more

The mechanisms underlying neoplastic epithelial cell killing by ionizing radiation are largely unknown. We discovered a novel response to radiation manifested by autophagy and the development of acidic vesicular organelles … The mechanisms underlying neoplastic epithelial cell killing by ionizing radiation are largely unknown. We discovered a novel response to radiation manifested by autophagy and the development of acidic vesicular organelles (AVO). Acidification of AVO was mediated by the vacuolar H+-ATPase. Staining with the lysosomotropic agent acridine orange enabled us to quantify AVO accumulation and to demonstrate their time- and dose-dependent appearance. The appearance of AVO occurred in the presence of the pan-caspase inhibitor z-Val-Ala-Asp(Ome)-fluoromethyl ketone, but was inhibited by 3-methyladenine, an inhibitor of autophagy. The accretion of AVO in surviving progenies of irradiated cells, and the increased incidence of clonogenic death after inhibition of vacuolar H+-ATPase suggest that formation of acidic organelles represents a novel defense mechanism against radiation damage.

P<scp>LANT</scp>P<scp>LASMA</scp>M<scp>EMBRANE</scp>H+-ATPases: Powerhouses for Nutrient Uptake

2001-06-01

Michael Palmgren

Most transport proteins in plant cells are energized by electrochemical gradients of protons across the plasma membrane. The formation of these gradients is due to the action of plasma membrane … Most transport proteins in plant cells are energized by electrochemical gradients of protons across the plasma membrane. The formation of these gradients is due to the action of plasma membrane H+ pumps fuelled by ATP. The plasma membrane H+-ATPases share a membrane topography and general mechanism of action with other P-type ATPases, but differ in regulatory properties. Recent advances in the field include the identification of the complete H+-ATPase gene family in Arabidopsis, analysis of H+-ATPase function by the methods of reverse genetics, an improved understanding of the posttranslational regulation of pump activity by 14-3-3 proteins, novel insights into the H+ transport mechanism, and progress in structural biology. Furthermore, the elucidation of the three-dimensional structure of a related Ca2+ pump has implications for understanding of structure-function relationships for the plant plasma membrane H+-ATPase.

OPA1 processing controls mitochondrial fusion and is regulated by mRNA splicing, membrane potential, and Yme1L

2007-08-20

Zhiyin Song , Hsiuchen Chen , Maja Fiket +2 more

OPA1, a dynamin-related guanosine triphosphatase mutated in dominant optic atrophy, is required for the fusion of mitochondria. Proteolytic cleavage by the mitochondrial processing peptidase generates long isoforms from eight messenger … OPA1, a dynamin-related guanosine triphosphatase mutated in dominant optic atrophy, is required for the fusion of mitochondria. Proteolytic cleavage by the mitochondrial processing peptidase generates long isoforms from eight messenger RNA (mRNA) splice forms, whereas further cleavages at protease sites S1 and S2 generate short forms. Using OPA1-null cells, we developed a cellular system to study how individual OPA1 splice forms function in mitochondrial fusion. Only mRNA splice forms that generate a long isoform in addition to one or more short isoforms support substantial mitochondrial fusion activity. On their own, long and short OPA1 isoforms have little activity, but, when coexpressed, they functionally complement each other. Loss of mitochondrial membrane potential destabilizes the long isoforms and enhances the cleavage of OPA1 at S1 but not S2. Cleavage at S2 is regulated by the i-AAA protease Yme1L. Our results suggest that mammalian cells have multiple pathways to control mitochondrial fusion through regulation of the spectrum of OPA1 isoforms.

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Metabolism of Glycerolipids

1960-08-01

William E.M. Lands

In the course of W-tracer studies on the biological synthesis of lecithin in lung tissue slices, the ratio of fatty acid activity to glycerol activity in lecithin was higher than … In the course of W-tracer studies on the biological synthesis of lecithin in lung tissue slices, the ratio of fatty acid activity to glycerol activity in lecithin was higher than in the triglyceride fraction. It was suggested that the observed isotope distributions could be due to turnover of the fatty acid portion of lecithin without a corresponding synthesis and breakdown of the remainder of the molecule (1). Such a turnover of fatty acid might require the combined actions of a phospholipase, an enzyme activity found in many tissues (2-4), and also a lysophosphatide-acylating enzyme which has not been demonstrated before. Further studies of lecithin metabolism showed that the product of phospholipase action, lysolecithin, could be utilized for lecithin synthesis by rat liver microsomes. This result is in contrast to that obtained in the chemical acylation of lysolecithin, which has been unsuccessful with several different acyl derivatives (5, 6), although Tattrie and McArthur (7) recently obtained a 31% yield of lecithin by allowing an acid chloride to react with lysolecithin in anhydrous chloroform for 3 days. It is the purpose of this paper to describe the properties of the microsomal system which catalyzes the acylation of lysolecithin to form lecithin. This reaction requires ATP and CoA, and involves the formation of an acyl-CoA derivative.

A Naturally Occurring Inhibitor of Mitochondrial Adenosine Triphosphatase

1963-11-01

Maynard E. Pullman , G. Monroy

Publisher Correction: Analysis of R-loop forming regions identifies RNU2-2 and RNU5B-1 as neurodevelopmental disorder genes

2025-06-24

Adam Jackson , Nishi Thaker , Alexander J. M. Blakes +7 more | Nature Genetics

DDX3X/MAVS alleviates doxorubicin‑induced cardiotoxicity by regulating stress granules

2025-06-24

Kaixiang Zhao , Shaochen Wang , Dandan Feng +3 more | Molecular Medicine Reports

The specific mechanisms of doxorubicin (Dox)‑induced cardiotoxicity (DIC) remain unclear. In the present study, H9c2 cardiomyocytes were treated with Dox, and it was revealed that DEAD‑box RNA helicase 3 X‑linked … The specific mechanisms of doxorubicin (Dox)‑induced cardiotoxicity (DIC) remain unclear. In the present study, H9c2 cardiomyocytes were treated with Dox, and it was revealed that DEAD‑box RNA helicase 3 X‑linked (DDX3X), mitochondrial antiviral signaling (MAVS) and stress granules (SGs) were present at lower levels in the treated H9c2 cardiomyocytes compared with those in the control cells. The present study further investigated the mechanisms through which DIC occurs. Pretreatment with arsenite, which pharmacologically accelerates SGs, alleviated the myocardial injury caused by Dox. By contrast, anisomycin, an SG inhibitor, increased cardiomyocyte apoptosis induced by Dox. In addition, both DDX3X knockdown and pretreatment with RK‑33 (a DDX3X pharmacological inhibitor) decreased SG expression, whereas DDX3X overexpression promoted SG generation. These results indicated that DDX3X mitigated DIC through the regulation of SGs. In addition, MAVS knockdown inhibited SG assembly and reduced the expression of the anti‑apoptotic inhibitor Bcl2, and MAVS was influenced by DDX3X, thereby serving as a connector between DDX3X and SGs. The results from western blotting, reverse transcription‑quantitative PCR, immunofluorescence and flow cytometry analysis demonstrated that DDX3X, MAVS, and SGs may serve as key protective factors in DIC.

Repurposing Saroglitazar for neurodegenerative disorders: insight into molecular signalling pathways and neuroprotective modulations

2025-06-23

Shiv Kumar Kushawaha , Himanshu Kumar , Chetan Chauhan +2 more | Inflammopharmacology

Inhibition of the ATP synthase c subunit ameliorates HDM/LPS-induced inflammatory responses in asthmatic bronchial epithelial cells by blocking the mPTP-mtDNA-cGAS-STING axis

2025-06-21

Decai Wang , Chao Liu , Bao Chen +5 more | Respiratory Research

The ATP synthase c subunit (c subunit) constitutes the mitochondrial permeability transition pore (mPTP). The extended opening of the mPTP is crucial in the development of various human illnesses. Nevertheless, … The ATP synthase c subunit (c subunit) constitutes the mitochondrial permeability transition pore (mPTP). The extended opening of the mPTP is crucial in the development of various human illnesses. Nevertheless, it remains unclear whether the c subunit regulates the prolonged opening of the mPTP to attenuate inflammatory responses in asthma. This study sought to clarify the impact of the c subunit on inflammatory responses and to examine the therapeutic effects of 1,3,8-triazaspiro [4.5] decane derivatives (PP10), a c subunit inhibitor, in human bronchial epithelial (HBE) cells induced by house dust mite (HDM) and lipopolysaccharide (LPS), as well as in a mouse model. The findings indicated that the expression of the c subunit is elevated in asthmatic patients, HDM/LPS-induced HBE cells, and asthmatic mice. The inhibition of the c subunit by PP10 alleviated the prolonged opening of mPTP, then blocked the release of mitochondrial DNA (mtDNA) and cyclic GMP-AMP synthase (cGAS)-interferon response cGAMP interactor (STING) pathway activation in HDM/LPS-induced HBE cells. Furthermore, PP10 decreased the secretion of inflammatory cytokines and ameliorated airway inflammation in HDM/LPS-induced HBE cells and asthmatic animals, respectively. The data collectively suggest that the c subunit triggers an inflammatory response by promoting the sustained opening of mPTP, leading to the activation of the mtDNA-GAS-STING pathway in HDM/LPS-induced HBE cells. Inhibition of the c-subunit attenuates inflammatory responses in HDM/LPS-induced cells or mouse models. Clinical trial number Not applicable.

The equilibrium between two quaternary assembly states determines the activity of SPOP and its cancer mutants

2025-06-20

M.J. Cuneo , Ömer Güllülü , Mohamed-Raafet Ammar +6 more | bioRxiv (Cold Spring Harbor Laboratory)

Abstract Proteostasis is critical for preventing oncogenesis. Both activating and inactivating mutations in the ubiquitin ligase subunit SPOP result in oncogenesis in different tissues. SPOP assembles into filaments that are … Abstract Proteostasis is critical for preventing oncogenesis. Both activating and inactivating mutations in the ubiquitin ligase subunit SPOP result in oncogenesis in different tissues. SPOP assembles into filaments that are multivalent for substrates, and substrates have multiple weak motifs for SPOP that are not activated via post-translational modifications. It is thus unclear how regulation is achieved. Here, we show that SPOP filaments circularize into rings that dimerize into up to 2.5 MDa-large, auto-inhibited double donuts. The equilibrium between double donuts and linear filaments determines SPOP activity. Activating and deactivating cancer mutations shift the equilibrium towards the filament or the double donut, respectively, and this influences substrate turnover and subcellular localization. This regulatory mechanism requires long filaments that can circularize into rings, likely explaining the presence of multiple weak SPOP-binding motifs in substrates. Activating and deactivating mutations combine to give rise to intermediate activities, suggesting new levers for cancer therapies. Highlights - SPOP assemblies exist in an equilibrium between circular double donuts and linear filaments. - Double donuts occlude access to the substrate binding site and are inactive. - Mutations in different cancers shift the equilibrium towards active or inactive states. - Regulation through these structural transitions requires large filamentous assemblies.

G4 Landscape Dynamics Underlies Neuroprotective Responses in Neonatal Hypoxic-Ischemic Brain Injury

2025-06-19

Magnar Bjørås , Adeel Manaf , Vidar Langseth Saasen +7 more | Research Square (Research Square)

<title>Abstract</title> Hypoxic Ischemic Encephalopathy (HIE) causes brain damage, ranging from mild to severe, in up to one million newborns worldwide every year. While HIE has been shown to modulate gene … <title>Abstract</title> Hypoxic Ischemic Encephalopathy (HIE) causes brain damage, ranging from mild to severe, in up to one million newborns worldwide every year. While HIE has been shown to modulate gene expression through epigenetic regulation, studies have primarily focused on limited loci, leaving a gap in genome-wide understanding. Using a neonatal mouse model that recapitulates human HIE pathology, we comprehensively profiled gene expression, DNA secondary structures, and histone modifications in the hippocampi of control, hypoxic, and hypoxic-ischemic mice. Our results demonstrate that both hypoxic and hypoxic-ischemic conditions reshape the hippocampal G-quadruplexes (G4s) landscape during the acute phase, following a strong transcriptional response in the hypoxic-ischemic hippocampi, whereas the hypoxic part displays a very moderate response. Substantial upregulation of stress-responsive genes in hypoxic-ischemic hippocampi correlated with G4 loss and the enrichment of active histone marks (H3K4me3 and H3K27ac) at promoters and CpG islands. Brain-specific enhancers also showed G4s depletion alongside asymmetric H3K27ac enrichment, suggesting a broader role for G4s in regulating mRNA expression and processing. Vulnerable hippocampal neurons (CA1/CA3) displayed pronounced G4 depletion following insult, while resilient neurons maintained low G4 occupancy. Together, these findings highlight the neuroprotective potential of G4s during acute neonatal hypoxia-ischemia, suggesting new directions for biomarker discovery and therapeutic development.

PDHA1 Orchestrates Hepatocellular Carcinoma Progression Through LINC00607-Mediated Regulation of Cuproptosis and Immune Evasion

2025-06-18

Libai Lu , Yufei Ma , Yuan Lu +4 more | Digestive Diseases and Sciences

Natural product library screening identifies Darutigenol for the treatment of myocardial infarction and ischemia/reperfusion injury

2025-06-18

Kun Liu , Li Zheng , Qian-Yu Huang +7 more | Chinese Medicine

Abstract Introduction Ischemic heart diseases are the leading cause of death worldwide due to the inability of regeneration of adult cardiomyocytes (CMs). Natural products from medical herbs are an important … Abstract Introduction Ischemic heart diseases are the leading cause of death worldwide due to the inability of regeneration of adult cardiomyocytes (CMs). Natural products from medical herbs are an important source of innovative drugs for many diseases including cardiovascular diseases. Objectives In this study, we set out to screen novel small-molecule therapies from natural products to protect heart against ischemic injury. Methods High-throughput screening was performed using a natural product library to identify the potential small molecules which can promote survival of CMs under ischemic and ischemic/reperfusion conditions. In addition, myocardial infarction (MI) and ischemia/reperfusion (I/R) mice models were used to evaluate the in vivo effects of the screened candidate. We also applied various analysis including cell viability, qPCR, Western blot, immunofluorescent staining, echocardiography, Masson’s staining, TTC staining, and network pharmacology. Results High-throughput screening showed that the small molecule compound Darutigenol (Dar), derived from the Chinese traditional herb Herba Siegesbeckiae , could significantly promote CM survival and proliferation under ischemic conditions. Moreover, I/R-induced CM apoptosis and ROS generation could be significantly reduced by Dar treatment. In addition, in vivo administration of Dar was able to attenuate MI- and I/R-induced cardiac injury in adult mice by decreasing fibrosis and apoptosis, thereby improving cardiac function. Network pharmacology analysis and molecule docking assay showed that Dar has the highest binding affinity with AKT1 protein. Western blotting assay further revealed that AKT1 activation was significantly enhanced by Dar administration in the infarcted hearts. Conclusions Our data revealed that the small molecule compound Dar, screened from the natural product library in this study, is capable of protecting heart against MI and I/R injury by activating AKT1 pathway. These findings enrich the natural product candidates for cardiovascular disease treatment and provide new insights into potential therapeutic agents for MI and I/R injury.

Overexpression of ATP1B2 promotes cancer cell migration and inhibits apoptosis in patients with esophageal squamous cell carcinoma

2025-06-17

Fangfei Liu , Hui Wen , Xiaobo Liu +4 more | Oncology Reports

The Role of V-ATPase ATP6V0D1 Subunit in Chemoresistance and Ellipticine-Induced Cytoplasmic Vacuolation in Neuroblastoma Cells

2025-06-17

Marie Rychlá , Jan Hraběta , Pavla Jenčová +2 more | Molecular & Cellular Oncology

Drug resistance remains a major obstacle in neuroblastoma treatment. Lysosomal sequestration, facilitated by the V-ATPase proton pump, is one of the mechanisms of chemoresistance. Overexpression of the ATP6V0D1 subunit of … Drug resistance remains a major obstacle in neuroblastoma treatment. Lysosomal sequestration, facilitated by the V-ATPase proton pump, is one of the mechanisms of chemoresistance. Overexpression of the ATP6V0D1 subunit of V-ATPase, previously reported in various cancers, was also observed in ellipticine-resistant neuroblastoma cells in our study. Neuroblastoma cells also exhibited increased lysosomal capacity and vacuolation after ellipticine treatment. Knockdown of ATP6V0D1, but not ATP6V1H, enhanced ellipticine sensitivity, suppressed proliferation and migration, decreased lysosomal uptake, and induced G2/M arrest in neuroblastoma cell lines. Notably, inhibiting another V-ATPase subunit, ATP6V1H, had no effect, highlighting the specific role of ATP6V0D1 in drug resistance. Ellipticine-induced vacuolation, identified as endoplasmic reticulum swelling, lacked evidence of paraptosis. ATP6V0D1 knockdown suppressed this phenomenon, whereas ATP6V1H silencing did not. Our findings underscore the importance of ATP6V0D1 in neuroblastoma and suggest potential therapeutic strategies targeting V-ATPase for overcoming drug resistance.

Cardiac Glycosides: From Natural Defense Molecules to Emerging Therapeutic Agents

2025-06-17

Arturo Ponce , Catalina Flores-Maldonado , R. Contreras | Biomolecules

Cardiac glycosides (CGs), a class of plant- and animal-derived compounds historically used to treat heart failure, have garnered renewed interest for their diverse pharmacological properties beyond Na+/K+-ATPase (NKA) inhibition. Recent … Cardiac glycosides (CGs), a class of plant- and animal-derived compounds historically used to treat heart failure, have garnered renewed interest for their diverse pharmacological properties beyond Na+/K+-ATPase (NKA) inhibition. Recent studies reveal that CGs modulate key signaling pathways-such as NF-κB, PI3K/Akt, JAK/STAT, and MAPK-affecting processes central to cancer, viral infections, immune regulation, and neurodegeneration. In cancer, CGs induce multiple forms of regulated cell death, including apoptosis, ferroptosis, pyroptosis, and immunogenic cell death, while also inhibiting angiogenesis, epithelial-mesenchymal transition, and cell cycle progression. They demonstrate broad-spectrum antiviral activity by disrupting viral entry, replication, and mRNA processing in viruses such as HSV, HIV, influenza, and SARS-CoV-2. Immunologically, CGs regulate Th17 differentiation via RORγ signaling, although both inhibitory and agonistic effects have been reported. In the nervous system, CGs modulate neuroinflammation, support synaptic plasticity, and improve cognitive function in models of Alzheimer's disease, epilepsy, and multiple sclerosis. Despite their therapeutic potential, clinical translation is hindered by narrow therapeutic indices and systemic toxicity. Advances in drug design and nanocarrier-based delivery are critical to unlocking CGs' full potential as multi-target agents for complex diseases. This review synthesizes the current knowledge on the emerging roles of CGs and highlights strategies for their safe and effective repurposing.

Molecular mechanisms and intervention approaches of heart failure (Review)

2025-06-13

Shuang Guo , Y. Linda Hu , Li Ling +6 more | International Journal of Molecular Medicine

Heart failure is a major health issue that threatens life and health. Previous studies have shown that heart failure is the terminal stage of arrhythmia, dilated cardiomyopathy, hypertension, hypertrophic cardiomyopathy … Heart failure is a major health issue that threatens life and health. Previous studies have shown that heart failure is the terminal stage of arrhythmia, dilated cardiomyopathy, hypertension, hypertrophic cardiomyopathy and myocardial infarction. The pathological mechanisms through which cardiovascular diseases result in heart failure include myocardial fibrosis and hypertrophy, myocardial cell death, mitochondrial dysfunction, vascular remodeling and calcium dysregulation. However, the detailed molecular mechanisms of heart failure remain elusive because of its complexity, hindering the development of intervention approaches for heart failure. The present study reviewed recent research progress on heart failure and provided references and strategies for the prevention and treatment of heart failure.

Analysis of the regulation of undecaprenyl diphosphate dephosphorylation in Escherichia coli

2025-06-13

Tomotaka Jitsukawa , Yasushi Shigeri , Shingo Fujisaki | FEBS Open Bio

Undecaprenyl phosphate (C 55 P) is an essential sugar carrier for bacterial cell wall synthesis, which has gained importance in recent years as a promising target for new antibiotic development. … Undecaprenyl phosphate (C 55 P) is an essential sugar carrier for bacterial cell wall synthesis, which has gained importance in recent years as a promising target for new antibiotic development. In Escherichia coli , C 55 P is produced by dephosphorylation of undecaprenyl diphosphate (C 55 PP) by BacA and two type 2 phosphatidic acid phosphatase (PAP2) family enzymes, PgpB and YbjG, in the periplasmic space. To clarify the regulatory mechanism of C 55 PP dephosphorylation, we quantified C 55 P and C 55 PP using a new high‐performance liquid chromatography method, conducted susceptibility tests against bacitracin, and analyzed the gene expression of bacA , pgpB , and ybjG in E. coli single‐ and double‐disruption strains of those genes. C 55 P levels were similar in all strains, but C 55 PP levels increased only in the bacA, ybjG double‐disruption strain. The double‐disruption strains containing bacA disruption and the bacA single‐disruption strain were more susceptible to bacitracin than the other strains. In the double‐disruption strains containing bacA disruption, the expression of the remaining genes pgpB and ybjG increased. These results indicate that the transcription of the PAP2 family enzyme genes, pgpB and ybjG , was activated under conditions where C 55 PP dephosphorylation activity in cells was reduced. This transcriptional regulation might contribute to the maintenance of C 55 P levels in cells.

Abstract P1-01-04: EPLIN and EPLIN responsive protein APOC3 in breast cancer

2025-06-13

Wang Cai , Tracey A. Martin , Jimmy Jianyuan Zeng +4 more | Clinical Cancer Research

Abstract Introduction. EPLIN (Epithelial Protein Lost in Neoplasm, also known as LIMA1) is a cytoskeletal associated element and has been shown to act as a tumour suppressive molecule in breast … Abstract Introduction. EPLIN (Epithelial Protein Lost in Neoplasm, also known as LIMA1) is a cytoskeletal associated element and has been shown to act as a tumour suppressive molecule in breast cancer and a few other cancer types. Little is known about the regulatory and the responsive proteins for EPLIN. The present study has explored the potential EPLIN responsive proteins in cancer cells and the possible clinical connections in prognosis and treatment in breast cancer. Methods. EPLIN knockdown cell models were created by using lentiviral shRNA for EPLIN. The responsive proteins including phospho-proteins following EPLIN knockdown were systemically evaluated by MS based bioinformatics analysis. Clinical cohorts and tissue microarrays were used to evaluate the potential EPLIN interactive candidates at gene transcript and protein levels, respectively. The prognostic connection and therapeutic values were also explored. Results. Knockdown EPLIN resulted in active responses of a number of proteins, of which APOC3 (apolipoprotein C3) was amongst the top ones (both total level and phosphorylated proteins). In clinical cohort, APOC3 were found to be significantly correlated with EPLIN in breast tumour tissues (r=-0.218, p=0.042) but not in normal mammary tissues (p=0.555). APOC3 expression in breast tumour tissues was found to be higher in ER negative tumour (p=0.0058) and in PGR positive tumours (p=0.039), and also in those who died of breast cancer (p=0.016, versus those who remained disease free). The expression profile of the EPLIN related molecule identified patients with high survival risk in those who had PGR negative breast tumours (p=0.014, HR=1.374 (95%CI 1.007-1.875) and in triple negative breast tumours (TNBC) (p=0.045). Multivariate analysis revealed that the expression profile is an independent prognostic factor for PR negative patients (p=0.037) against other clinical factors. Finally, we explored the value of APOC3 and EPLIN in relation to patient’s response to drug treatments in a public database. It was clear that high levels of APOC3 in breast cancers rendered the patients with a significant chance of developing resistance to chemotherapies (p=0.000024) and this connection is independent on status of ER, ERBB2 and the molecular subtypes. Intriguingly, APOC3 was found to be a good indicator for sensitivity to anti-Her2 treatment (AUC=0.79, p=0.00076). Conclusion. The present study identifies a key EPLIN response protein, APOC3 which together with EPLIN forms an important prognostic factor for patients with breast cancer particularly in those with PR negative tumours. It also forms a theranostic indicator for patient’s response to drug treatment. Citation Format: Cai Wang,Tracey A. Martin, Jimmy J. Zeng, Amber X. Li, Eleri Davies, Fiona Ruge, Wen G. Jiang. EPLIN and EPLIN responsive protein APOC3 in breast cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P1-01-04.

SARS-CoV-2 envelope protein induces LC3 lipidation via the V-ATPase-ATG16L1 axis

2025-06-13

Carmen Figueras-Novoa , Lewis Timimi , Elena Marcassa +7 more | bioRxiv (Cold Spring Harbor Laboratory)

Coronaviruses encode envelope (E), a structural component of the virion that is important for assembly and egress. E has proton channel activity that prevents premature rearrangement of the spike glycoprotein … Coronaviruses encode envelope (E), a structural component of the virion that is important for assembly and egress. E has proton channel activity that prevents premature rearrangement of the spike glycoprotein as virions encounter acidic compartments as they exit the cell. How infected cells respond to this pH disruption during coronavirus infection is unknown. Here we show that SARS-CoV-2 E ion channel activity triggers the proton pump V-ATPases to recruit the ATG16L1 complex during infection. This results in ATG8 molecules such as LC3B decorating perturbed compartments. This recruitment of autophagy machinery does not inhibit viral replication, rather SARS-CoV-2 exploits this response. Inhibition of the V-ATPase/ATG16L1 interaction using the Salmonella effector SopF inhibits SARS-CoV-2 replication. Careful distinction between use of the autophagic machinery from canonical macroautophagy is required in order to better understand coronavirus replication and for rational targeting of any potential host-directed therapies.

AsCas12a Exhibits Intrinsic, DNA-Independent ATPase Activity

2025-06-06

Supreet Bhattacharya | bioRxiv (Cold Spring Harbor Laboratory)

Cas12a (Cpf1) is a class 2 CRISPR-Cas effector protein with RNA-guided DNA endonuclease activity widely used for genome editing. While its DNA cleavage and target recognition mechanisms have been studied … Cas12a (Cpf1) is a class 2 CRISPR-Cas effector protein with RNA-guided DNA endonuclease activity widely used for genome editing. While its DNA cleavage and target recognition mechanisms have been studied extensively, the possibility of auxiliary enzymatic functions remains underexplored. Here, I report that Acidaminococcus sp. Cas12a (AsCas12a) possesses intrinsic ATPase activity, despite lacking canonical nucleotide-binding or hydrolysis motifs. Using a radiometric thin-layer chromatography (TLC) assay, I demonstrate that AsCas12a hydrolyzes ATP in a concentration and time-dependent manner. Importantly, this activity occurs independently of DNA cofactors, as neither single-stranded nor double-stranded DNA influenced the rate or extent of ATP hydrolysis. Bioinformatic analyses using NsitePred and SwissDock identified potential ATP-binding residues with predicted favorable binding energies. This preliminary finding uncovers a previously unrecognized biochemical property of AsCas12a and raises questions regarding the physiological role of this ATPase activity in CRISPR function.

Local enrichment of cardiolipin to transient membrane undulations

2025-06-01

Christopher T. Lee , Kailash Venkatraman , Itay Budin +1 more | Biophysical Journal

CO1

2025-06-01

| Archivos de Bronconeumología

The OSCP subunit of ATP Synthase is a dimer in solution: strategy to induce the monomeric protein as a new tool for drug discovery

2025-06-01

Simone Fabbian , Laura Gabbatore , Laura Morbiato +6 more | Journal of Molecular Biology

Corrigendum to “F-53B disrupts energy metabolism by inhibiting the V-ATPase-AMPK axis in neuronal cells,” [ J. Hazard Mater. (487 (2025) 137111]

2025-06-01

Yue Zhang , Tingting Li , Xueman Ding +7 more | Journal of Hazardous Materials

Effect of Ionic Strength on Chloroplast ATP Synthase

2025-06-01

Andronika V. Minaeva , Stepan D. Osipov , A.V. Vlasov | Biochemistry (Moscow) Supplement Series A Membrane and Cell Biology

Naringenin exerts antiarrhythmic action in septic cardiomyopathy by downregulating the CaMKⅡ/Drp1/Bcl-2 pathway

2025-06-01

Yali Zhang , Yu Zhang , Hongmei Deng +7 more | Phytomedicine

CD36-Retinoic Acid- FABP5- PPARδ Signaling Axis Primes Neonatal Cardiomyocytes to Spontaneously Proliferate

2025-06-01

Abou Bakr M. Salama , Qinghui Ou , Riham Abouleisa +7 more | Journal of Molecular and Cellular Cardiology Plus

A Non-Canonical Interface of SNX9 PX Domain Selectively Sequesters PI(3,4)P2 Lipids, Protecting Them from Hydrolysis

2025-05-30

Feng‐Ching Tsai , Jeriann Beiter , Carl Sung +7 more | Research Square (Research Square)

<title>Abstract</title> Plasma membrane remodeling processes are tightly regulated by the spatiotemporal distribution and dynamic conversion of phosphoinositidyl lipids (PIPs). This regulation is controlled by the recruitment of proteins such as … <title>Abstract</title> Plasma membrane remodeling processes are tightly regulated by the spatiotemporal distribution and dynamic conversion of phosphoinositidyl lipids (PIPs). This regulation is controlled by the recruitment of proteins such as sorting nexin 9 (SNX9), a key mediator of late-stage endocytosis and macropinocytosis. Using live cell imaging, <italic>in vitro</italic> reconstitution assays, and molecular dynamics simulations, we investigated how SNX9 distinguishes between PI(3,4)P2 and PI(4,5)P2, and the physiological relevance of this selectivity. Our results revealed that during macropinocytic membrane ruffling, SNX9 is recruited in a spatiotemporally coordinated manner with PI(3,4)P2, but not with PI(4,5)P2. While SNX9 induces comparably weak mechanical remodeling on model membranes containing either PIP2 species, it exhibits a clear selective binding to PI(3,4)P2, mediated by a non-canonical interface. Through mutational analysis of key residues involved in this sequestration, we further demonstrated that SNX9 protects PI(3,4)P2 from hydrolysis. Together, these results reveal a previously unrecognized mechanism of SNX9-PIP2 lipid interaction that underscores the pivotal role of SNX9 in coordinating membrane remodeling processes.

The a subunit isoforms of V-ATPase are involved in glucose-dependent trafficking of insulin granules

2025-05-30

Mizuki Sekiya , Mayumi Nakanishi‐Matsui , Naomi Matsumoto +6 more | Scientific Reports

Abstract In pancreatic β cells, insulin granules move toward the plasma membrane to secrete insulin upon glucose stimulation, but the amount of secreted insulin is only a small portion of … Abstract In pancreatic β cells, insulin granules move toward the plasma membrane to secrete insulin upon glucose stimulation, but the amount of secreted insulin is only a small portion of the total, and many granules do not release insulin. Here, using MIN6 cells derived from mouse pancreatic β cells, we observed that granules that moved toward the plasma membrane returned to the inner area after the stimulation was removed. This back-and-forth trafficking is likely important for strict regulation of insulin secretion in response to the blood glucose level. However, the mechanism was largely unknown. We found that “back” (inward) and “forth” (outward) trafficking was reduced in cells with knockdown of the a2 and a3 subunit isoforms of the proton pump V-ATPase, respectively. Interestingly, the amount of secreted insulin was increased in a2 knockdown cells. Both a2 and a3 interacted with GDP-bound form Rab27A, a member of the Rab small GTPase family that regulates insulin secretion. These results indicate that a2 and a3 are involved in back-and-forth trafficking of insulin granules, respectively. The a subunit isoforms of V-ATPase seem to determine the direction of insulin granule trafficking dependent on the glucose level.

Oxr1 and Ncoa7 regulate V-ATPase to achieve optimal pH for glycosylation within the Golgi apparatus and trans-Golgi network

2025-05-30

Shin‐ichiro Yoshimura , Tomoaki Sobajima , Masataka Kunii +1 more | Proceedings of the National Academy of Sciences

Maintenance of pH within membranous organelles is crucial for cellular processes such as posttranslational modifications, ligand–receptor interactions, and proteostasis. The precise mechanisms that determine the luminal pH of each organelle … Maintenance of pH within membranous organelles is crucial for cellular processes such as posttranslational modifications, ligand–receptor interactions, and proteostasis. The precise mechanisms that determine the luminal pH of each organelle are not fully understood. This study investigated the mechanisms that regulate luminal pH to ensure optimal enzymatic activity. We identified Oxr1 and its paralog Ncoa7, which regulate the vacuolar-type proton pump ATPase (V-ATPase) at the Golgi apparatus and trans-Golgi network (TGN). Oxr1 and Ncoa7 were predominantly localized at the Golgi and TGN membranes, dependent on their binding to various GTP-bound Rab proteins. In vitro experiments using purified recombinant proteins indicated that Oxr1 and Ncoa7 directly bind to the catalytic subunit of V-ATPase, inhibiting its ATP hydrolytic activity via their TLDc domains. We observed significant acidification of the Golgi/TGN lumen in Oxr1- and Ncoa7-depleted cells. Lectin blot analysis demonstrated that depletion of Oxr1 and Ncoa7 led to a defect in protein glycosylation, a major enzymatic posttranslational modification in the Golgi and TGN. Furthermore, depletion of Oxr1 and Ncoa7, along with drug-induced inhibition of glycosylation, increased lysosomal pH and sensitivity to silicon dioxide-induced membrane damage. This apparent lysosomal dysfunction suggested that, in addition to the Golgi and TGN, Oxr1 and Ncoa7 also contribute to the integrity of other organelles. Our findings indicate that Oxr1 and Ncoa7 protect the Golgi and TGN lumen from excess acidification by inhibiting V-ATPase activity and providing an optimal environment for enzymatic activity in the Golgi and TGN.

Effect of BXQ-350, a novel sphingolipid metabolism modulator, on neuronal environments through modulation of gene pathways.

2025-05-28

Michael Gazda , Tariq Arshad , Jim Beach +3 more | Journal of Clinical Oncology

e24058 Background: Chemotherapeutic Induced Neuropathy (CIPN) remains an obstacle for the successful completion of chemotherapeutic courses. Patients have had to stop first line treatment courses such as FOLFOX due to … e24058 Background: Chemotherapeutic Induced Neuropathy (CIPN) remains an obstacle for the successful completion of chemotherapeutic courses. Patients have had to stop first line treatment courses such as FOLFOX due to complications that arise from CIPN. Finding suitable treatments to allow for the progression of these courses has been a focus of the industry for some time. BXQ-350, a novel protein-lipid small molecule, is currently in Phase 2 clinical trials to determine its efficacy as an anti-CIPN and anti-cancer adjuvant for Oxaliplatin and FOLFOX treatment. Preclinical data shows BXQ-350 anti-CIPN effects. However, those effects do not appear to directly counteract Oxaliplatin treatment insults. Instead, BXQ-350 upregulates homeostatic neuronal genes of dorsal root ganglions (DRGs) in response to chemotherapeutic insults. Methods: The company Transpharmation treated 48 mice intro-peritoneally with 2mg/kg or 10mg/kg BXQ-350, 10mg/kg Oxaliplatin, and/or vehicle over 14 days. Dorsal root ganglia were isolated from 45 of the treated mice, 10 from the control group, 12 from the BXQ-350 and combo groups, and 11 from the Oxaliplatin group, and sent to Nanostring to run gene analysis on. A suite of genes deemed to be implicated in CIPN were investigated looking at the differences in RNA levels between mice DRGs from the BXQ-350 alone, BXQ-350/Oxaliplatin, Oxaliplatin alone, and vehicle alone groups. RNA differential analysis was performed using Nanostring’s nCounter3 and Rosalind, a bioinformatics platform. Results: BXQ-350 positively impacted several pathways known to promote healthy neurons that are affected by CIPN. Two pathways implicated are the axon guidance and synaptic plasticity which help regulate the neurotransmitter response to stimuli. Following BXQ-350 dosing, multiple genes were upregulated from homeostatic pathways that are shown to promote axon guidance and plasticity. CIPN has been known to cause reactive oxygen species build up in neurons leading to inflammation and cell death. BXQ-350 indirectly regulates genes from pathways responsible for ROS creation and alleviation. In response to inflammation, BXQ-350 downregulates several inflammatory pathways. Conclusions: CIPN is a dangerous side effect of chemotherapy that causes patients to discontinue treatment courses. BXQ-350 has been shown to reduce the burden of CIPN in vivo and in vitro . Instead of directly counteracting the effects of specific chemotherapeutics, BXQ-350 promotes several pathways that regulate neuronal health, cleaning up neurons and promoting homeostatic neuronal environments.

Feasibility of half-dose dual-targeted therapy in advanced solid tumors with NGS-proven actionable targets: A comparative analysis with OMCT.

2025-05-28

Anudeep Padakanti , Vidya Sagar Dusi , Suresh VS Attili +2 more | Journal of Clinical Oncology

e14659 Background: Inspired by the efficacy of low-dose combination therapies in overcoming resistance in EGFR inhibitor-resistant NSCLC (Nature Communications), this study explores a similar strategy in advanced solid tumors. Standard-dose … e14659 Background: Inspired by the efficacy of low-dose combination therapies in overcoming resistance in EGFR inhibitor-resistant NSCLC (Nature Communications), this study explores a similar strategy in advanced solid tumors. Standard-dose targeted therapies often face toxicity-related limitations in combinatory use. While metronomic chemotherapy (OMCT) reduces toxicity, it may not fully leverage molecular vulnerabilities .This feasibility study evaluates a novel approach using half-dose dual-targeted therapies, combining monoclonal antibodies (mAbs) or tyrosine kinase inhibitors (TKIs), to balance efficacy with reduced adverse effects. Methods: A multicentric, retrospective analysis was conducted on 48 patients with advanced solid tumors beyond the fourth line of therapy, all harboring at least two actionable targets via NGS. Patients were assigned to two arms: Intervention Arm: Half-dose dual-targeted therapy (n=24). Control Arm: Standard OMCT regimen (n=24). Results: NGS identified 376 non-silent mutations across 48 samples, with common mutations in CDK (46%), PIK3 (38%), RET (35%), EGFR (30%), and AR (25%). Most mutations were missense (84.3%). Efficacy: Median overall survival (OS) was longer in the intervention arm (11.4 ± 6.7 months) than the control arm (9.6 ± 3.8 months, p=0.02). Complete response (CR) was observed only in the intervention arm (n=2). Partial response (PR) was more frequent in the intervention arm (n=15 vs. 11, p=0.40), while stable disease (SD) was higher in the control arm (n=11 vs. 4, p=0.028). Safety: Grade III/IV adverse events (AEs) were more in interventional arm (n=3 vs. 11, p=0.001). Grade I/II AEs were comparable between arms (n=17 vs. 19, p=0.3). Quality of Life (QOL): QOL improvements were higher in the intervention arm (mean score 11.8 ± 3.6 vs. 7.6 ± 2.5, p=0.03). Time Without Symptoms or Toxicity (TWISTT): The intervention arm showed longer TWISTT durations (182 ± 51 days vs. 148 ± 36 days, p=0.01). Conclusions: This study highlights that half-dose dual-targeted therapy, leveraging mAbs and TKIs, offers a viable alternative to OMCT in advanced solid tumors with actionable targets. Targeting key mutations such as CDK , PIK3 , RET , EGFR , and AR showed promising results in improving efficacy, safety, and patient quality of life. Further prospective studies are needed to validate these . Demographic data. Characteristic Overall n=48 Doubket MAB/ TKI n=24 OMCT n=24 P-value Female : Male 7:5 7:5 1 Grade III/IV Adverse Events 14 11 3 0.001 Grade I/II Adverse Events 36 17 19 0.3 Complete response (CR) 2 2 0 0.317311 Partial Response (PR) 26 15 11 0.405381 Stable Disease (SD) 15 4 11 0.02846 Progressive Disease (PD) 5 3 2 1 Median OS (months) Mean+SD 11.4+6.7 9.6+3.8 0.02 QOL- improvement on scale of 50 (mean+SD) 7.6+2.5 11.8+3.6 0.03 TWISTT score- days (Mean+SD) 148+36 182+51 0.01

Comprehensive results of ESG401, a TROP2-targeting ADC: Updated phase 1 analysis in advanced solid tumors.

2025-05-28

Fei Ma , Fuming Qiu , Zhongsheng Tong +7 more | Journal of Clinical Oncology

1044 Background: ESG401 is a novel ADC comprising a humanized anti-TROP2 IgG1 monoclonal antibody conjugated to the Topoisomerase I inhibitor SN-38 via a stable cleavable linker. ESG401-101 is a phase … 1044 Background: ESG401 is a novel ADC comprising a humanized anti-TROP2 IgG1 monoclonal antibody conjugated to the Topoisomerase I inhibitor SN-38 via a stable cleavable linker. ESG401-101 is a phase 1, open-label, dose-escalation (1a) and dose-expansion(1b) study evaluating the safety and antitumor activity of ESG401 in advanced solid tumors. This report summarizes the comprehensive phase 1 results. Methods: Patients (pts) aged 18–75 years with locally advanced/metastatic solid tumors received ESG401 until unacceptable toxicity, progressive disease, or consent withdrawal. Phase 1a results (n = 40) have been reported previously. Phase Ib comprised three parallel cohorts: late-stage TNBC, late-stage HR+/HER2-, and first-line TNBC. Results: As of Oct 23, 2024, 156 pts were enrolled at 13 sites across China (40 in 1a; 116 in 1b). Most pts had metastatic HR+/HER2-BC (n = 65; median prior lines: 3; range: 1–10), followed by late-line TNBC (n = 47; median prior lines: 3; range: 1–12), first-line TNBC (n = 40), HER2+BC (n = 2), and one case each of endometrial cancer (EC) and adenoid cystic carcinoma (ACC). All pts had distant metastases at baseline; 13%, 57%, and 54% had brain, liver, and lung metastases, respectively. ESG401 demonstrated efficacy in pts with solid tumor(Table), including those with brain metastases. The safety profile remained consistent with no new or unexpected signals. The most common any-grade TEAEs were leukopenia, neutropenia, anemia, nausea, and vomiting. Grade ≥3 TRAEs were primarily neutropenia and leukopenia, none leading to permanent discontinuation. TRAEs led to delayed dosing, dose reduction, and discontinuation in 38.5%, 7.1%, and 2.6% of pts, respectively. Conclusions: ESG401 demonstrated favorable safety and efficacy benefits due to its enhanced linker, showing good safety and promising antitumor activity in advanced solid tumors across settings. These results warrant further clinical investigation. Clinical trial information: NCT04892342 . Late-line First-line HR+/HER2–BC TNBC HER2+BC EC ACC TNBC n 58 37 2 1 1 35 ORR% (95% CI) 34.5 (22.5, 48.1) 35.1 (20.2, 52.5) 0 0 0 83.0 (66.4, 93.4) DCR% (95% CI) 77.6 (64.7, 87.5) 62.2 (44.8, 77.5 100 100 100 100 (90.0, -) mPFS Mons (95% CI) 7.4 (4.0, 9.2) 3.7 (2.1, 4.9) 3.8, 21.3 a 8.3 b 3.7 b NR mDOR Mons (95% CI) 6.6 (4.6, 14.2) 4.5 (3.1, 13.6) NA NA NA NR a The actual value for these two patients is listed. b The actual value for one patient is listed. NA, not applicable. NR, not reached.