4.5 Article

Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Structures of the free and capped ends of the actin filament

Peter J. Carman et al.

Summary: This study describes the structures of the free and capped ends of F-actin using cryo-electron microscopy. The terminal subunits at the free barbed end adopt a flat F-actin conformation, while the CapZ protein undergoes major changes when binding to the barbed end. In contrast, subunits at the free pointed end adopt a twisted monomeric actin conformation, and tropomodulin binding forces the second subunit into an F-actin conformation. These structures reveal the differences between the ends and middle of F-actin and how these differences control various interactions.

SCIENCE (2023)

Review Cell Biology

Biochemical and mechanical regulation of actin dynamics

Pekka Lappalainen et al.

Summary: Actin cytoskeleton plays a crucial role in cellular processes and its aberrant dynamics are associated with various diseases. Understanding the mechanisms of actin filament assembly, disassembly, and force production is essential for studying cellular, developmental, and pathological processes.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Accelerated 2D Classification With ISAC Using GPUs

Fabian Schoeenfeld et al.

Summary: This paper presents GPU ISAC, a newly developed algorithm that uses GPU-acceleration to analyze single particles in electron microscopy data. Compared to existing methods, GPU ISAC can process large data sets and generate high quality class averages on a single desktop machine equipped with affordable GPUs.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

Article Multidisciplinary Sciences

Bending forces and nucleotide state jointly regulate F-actin structure

Matthew J. Reynolds et al.

Summary: ATP-hydrolysis-coupled actin polymerization is a fundamental mechanism of cellular force generation. This study reveals that the nucleotide state of actin can modulate the structural transitions of F-actin induced by bending forces, which further affects the mechanical regulation of actin.

NATURE (2022)

Article Multidisciplinary Sciences

Structural basis of actin filament assembly and aging

Wout Oosterheert et al.

Summary: The structures of F-actin in different nucleotide states were determined using cryo-electron microscopy, revealing the role of water molecules and their impact on polymerization rates. These findings provide important insights into the assembly and aging mechanisms of F-actin filaments, as well as the design of drugs and small molecules for imaging and therapeutic applications.

NATURE (2022)

Article Multidisciplinary Sciences

Structures and mechanisms of actin ATP hydrolysis

Yusuke Kanematsu et al.

Summary: This study reveals the reaction mechanism of ATP hydrolysis by actin. Through structural analysis and calculations, the researchers have identified a specific reaction path, explaining the slow rate and irreversibility of actin ATP hydrolysis.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Multidisciplinary Sciences

A barbed end interference mechanism reveals how capping protein promotes nucleation in branched actin networks

Johanna Funk et al.

Summary: Heterodimeric capping protein (CP/CapZ) is crucial for the assembly of branched actin networks by both preventing filament elongation and promoting nucleation. Structural features of CP, particularly the C-terminal tentacle extension, play a key role in indirectly stimulating the activity of Arp2/3 activating nucleation promoting factors (NPFs) by preventing their association with filament barbed ends. Deletion of the beta tentacle modestly impairs capping, but strongly inhibits nucleation promoting factors' function in growing branched actin networks, revealing a mechanism by which CP balances capping and nucleation processes.

NATURE COMMUNICATIONS (2021)

Article Cell Biology

The non-muscle ADF/cofilin-1 controls sarcomeric actin filament integrity and force production in striated muscle laminopathies

Nicolas Vignier et al.

Summary: Cofilins play a crucial role in regulating the actin cytoskeleton and muscle function, while mutations in the LMNA gene cause increased expression of cofilin-1 in muscle cells, leading to impaired sarcomere structure and force generation. This finding provides insight into the molecular pathogenesis of muscular dystrophies caused by LMNA mutations.

CELL REPORTS (2021)

Article Multidisciplinary Sciences

Mechanism of actin-dependent activation of nucleotidyl cyclase toxins from bacterial human pathogens

Alexander Belyy et al.

Summary: The study presents the structures of ExoY from Pseudomonas aeruginosa and Vibrio vulnificus bound to their corresponding activators F-actin and profilin-G-actin, revealing insights into the activation mechanism of the bacterial cyclase toxins. Activation involves stabilization of specific regions resulting in activation of enzyme activity, with differences in actin-binding regions responsible for selective binding. Other cyclase toxins that bind to calmodulin show similar activation mechanism through stabilization, indicating conservation of allosteric activation-by-stabilization mechanism in these enzymes.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

SciPy 1.0: fundamental algorithms for scientific computing in Python

Pauli Virtanen et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

Structures of cofilin-induced structural changes reveal local and asymmetric perturbations of actin filaments

Andrew R. Huehn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Cell Biology

Towards a structural understanding of the remodeling of the actin cytoskeleton

Felipe Merino et al.

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2020)

Article Biochemical Research Methods

Two particle-picking procedures for filamentous proteins:SPHIRE-crYOLOfilament mode andSPHIRE-STRIPER

Thorsten Wagner et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state

Mohammed Shaaban et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Structure of the Lifeact-F-actin complex

Alexander Belyy et al.

PLOS BIOLOGY (2020)

Article Multidisciplinary Sciences

TranSPHIRE: automated and feedback-optimized on-the-fly processing for cryo-EM

Markus Stabrin et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Mechanism of actin polymerization revealed by cryo-EM structures of actin filaments with three different bound nucleotides

Steven Z. Chou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and fragmentation

Esa-Pekka Kumpula et al.

PLOS BIOLOGY (2019)

Article Chemistry, Multidisciplinary

A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis

Jasenko Zivanov et al.

Article Biology

SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM

Thorsten Wagner et al.

COMMUNICATIONS BIOLOGY (2019)

Article Biochemistry & Molecular Biology

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

Thomas D. Goddard et al.

PROTEIN SCIENCE (2018)

Article Biochemistry & Molecular Biology

Structural transitions of F-actin upon ATP hydrolysis at near-atomic resolution revealed by cryo-EM

Felipe Merino et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

Article Cell Biology

The Actin Cytoskeleton and Actin-Based Motility

Tatyana Svitkina

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2018)

Article Multidisciplinary Sciences

Structural basis for cofilin binding and actin filament disassembly

Kotaro Tanaka et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

Structural transitions of F-actin upon ATP hydrolysis at near-atomic resolution revealed by cryo-EM

Felipe Merino et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

Article Biochemical Research Methods

Real-space refinement in PHENIX for cryo-EM and crystallography

Pavel V. Afonine et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Latrunculin A Accelerates Actin Filament Depolymerization in Addition to Sequestering Actin Monomers

Ikuko Fujiwara et al.

CURRENT BIOLOGY (2018)

Article Biochemistry & Molecular Biology

WH2 and proline-rich domains of WASP-family proteins collaborate to accelerate actin filament elongation

Peter Bieling et al.

EMBO JOURNAL (2018)

Article Biochemical Research Methods

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Jing Huang et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

TrackMate: An open and extensible platform for single-particle tracking

Jean-Yves Tinevez et al.

METHODS (2017)

Letter Biochemical Research Methods

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

Shawn Q. Zheng et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

Ali Punjani et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

Alexis Rohou et al.

JOURNAL OF STRUCTURAL BIOLOGY (2015)

Article Multidisciplinary Sciences

Single-molecule imaging of a three-component ordered actin disassembly mechanism

Silvia Jansen et al.

NATURE COMMUNICATIONS (2015)

Article Multidisciplinary Sciences

Structure of the F-actin-tropomyosin complex

Julian von der Ecken et al.

NATURE (2015)

Article Cell Biology

Cofilin-2 Controls Actin Filament Length in Muscle Sarcomeres

Elena Kremneva et al.

DEVELOPMENTAL CELL (2014)

Article Biochemistry & Molecular Biology

Molecular mechanisms of disease-related human beta-actin mutations p.R183W and p.E364K

Nikolas Hundt et al.

FEBS JOURNAL (2014)

Article Biochemistry & Molecular Biology

Cryo-EM reveals different coronin binding modes for ADP- and ADP-BeFx actin filaments

Peng Ge et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)

Editorial Material Biophysics

On Phosphate Release in Actin Filaments

Antoine Jegou et al.

BIOPHYSICAL JOURNAL (2013)

Article Chemistry, Physical

Using collective variables to drive molecular dynamics simulations

Giacomo Fiorin et al.

MOLECULAR PHYSICS (2013)

Article Multidisciplinary Sciences

Phosphate release coupled to rotary motion of F1-ATPase

Kei-ichi Okazaki et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemistry & Molecular Biology

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

Sjors H. W. Scheres

JOURNAL OF STRUCTURAL BIOLOGY (2012)

Article Multidisciplinary Sciences

Intermittent depolymerization of actin filaments is caused by photo-induced dimerization of actin protomers

Thomas Niedermayer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

Iterative Stable Alignment and Clustering of 2D Transmission Electron Microscope Images

Zhengfan Yang et al.

STRUCTURE (2012)

Article Biochemistry & Molecular Biology

Cofilin Tunes the Nucleotide State of Actin Filaments and Severs at Bare and Decorated Segment Boundaries

Cristian Suarez et al.

CURRENT BIOLOGY (2011)

Article Biophysics

The effect of toxins on inorganic phosphate release during actin polymerization

Andrea Vig et al.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2011)

Article Chemistry, Multidisciplinary

Software News and Updates MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations

Naveen Michaud-Agrawal et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Biophysics

Graphical analysis of pH-dependent properties of proteins predicted using PROPKA

Michal Rostkowski et al.

BMC STRUCTURAL BIOLOGY (2011)

Article Cell Biology

Segmentation and Tracking of Cytoskeletal Filaments Using Open Active Contours

Matthew B. Smith et al.

CYTOSKELETON (2010)

Article Biochemistry & Molecular Biology

Pi Release from Myosin: A Simulation Analysis of Possible Pathways

Marco Cecchini et al.

STRUCTURE (2010)

Article Biochemistry & Molecular Biology

The Cofilin Activity Cycle in Lamellipodia and Invadopodia

Matthew Oser et al.

JOURNAL OF CELLULAR BIOCHEMISTRY (2009)

Review Chemistry, Multidisciplinary

CHARMM: The Biomolecular Simulation Program

B. R. Brooks et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Multidisciplinary Sciences

The nature of the globular-to fibrous-actin transition

Toshiro Oda et al.

NATURE (2009)

Article Physics, Multidisciplinary

Actin Polymerization and Depolymerization Coupled to Cooperative Hydrolysis

Xin Li et al.

PHYSICAL REVIEW LETTERS (2009)

Article Clinical Neurology

Histopathologic progression and a novel mutation in a child with nemaline myopathy

Shafeeq Ladha et al.

JOURNAL OF CHILD NEUROLOGY (2008)

Article Chemistry, Multidisciplinary

Software news and updates - CHARNIM-GUI: A web-based grraphical user interface for CHARMM

Sunhwan Jo et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

Review Physiology

Regulation of actin assembly associated with protrusion and adhesion in cell migration

Christophe Le Clainche et al.

PHYSIOLOGICAL REVIEWS (2008)

Review Biochemistry & Molecular Biology

Molecular and structural basis for redox regulation of β-actin

Ingrid Lassing et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Multidisciplinary Sciences

Polymerization kinetics of ADP- and ADP-Pi-actin determined by fluorescence microscopy

Ikuko Fujiwara et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Chemistry, Physical

From A to B in free energy space

Davide Branduardi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

Canonical sampling through velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Biochemistry & Molecular Biology

Inorganic phosphate regulates the binding of cofilin to actin filaments

A Muhlrad et al.

FEBS JOURNAL (2006)

Review Chemistry, Multidisciplinary

GROMACS: Fast, flexible, and free

D Van der Spoel et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Article Cell Biology

Actin-binding proteins

SJ Winder et al.

JOURNAL OF CELL SCIENCE (2005)

Article Biophysics

A mechanistic model of the actin cycle

M Bindschadler et al.

BIOPHYSICAL JOURNAL (2004)

Review Biochemistry & Molecular Biology

Cellular motility driven by assembly and disassembly of actin filaments

TD Pollard et al.

Article Multidisciplinary Sciences

Escaping free-energy minima

A Laio et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemistry & Molecular Biology

Hydrolysis of ATP by polymerized actin depends on the bound divalent cation but not profilin

L Blanchoin et al.

BIOCHEMISTRY (2002)

Article Genetics & Heredity

Nemaline myopathy caused by mutations in the muscle α-skeletal-actin gene

B Ilkovski et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2001)