scholarly journals ATP hydrolysis coordinates the activities of two motors in a dimeric chromatin remodeling enzyme

2020 ◽  
Author(s):  
Stephanie L. Johnson ◽  
Geeta Narlikar
Keyword(s):  
Chromatin Remodeling ◽  
Single Molecule ◽  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Oligomeric State ◽  
Chromatin Remodelers ◽  
Chromatin Dynamics ◽  
A Cell ◽  
Conventional Methods ◽  
Eukaryotic Genomes

AbstractATP-dependent chromatin remodelers are essential enzymes that restructure eukaryotic genomes to enable all DNA-based processes. The diversity and complexity of these processes are matched by the complexity of the enzymes that carry them out, making remodelers a challenging class of molecular motors to study by conventional methods. Here we use a single molecule biophysical assay to overcome some of these challenges, enabling a detailed mechanistic dissection of a paradigmatic remodeler reaction, that of sliding a nucleosome towards the longer DNA linker. We focus on how two motors of a dimeric remodeler coordinate to accomplish such directional sliding. We find that ATP hydrolysis by both motors promotes coordination, suggesting a role for ATP in resolving the competition for directional commitment. Furthermore, we show an artificially constitutive dimer is no more or less coordinated, but is more processive, suggesting a cell could modulate a remodeler’s oligomeric state to modulate local chromatin dynamics.

scholarly journals A Generalized Kinetic Model for Coupling between Stepping and ATP Hydrolysis of Kinesin Molecular Motors

2019 ◽  
Vol 20 (19) ◽  
pp. 4911 ◽  
Author(s):  
Xie ◽  
Guo ◽  
Chen
Keyword(s):  
Kinetic Model ◽  
Atpase Activity ◽  
Single Molecule ◽  
Rate Constants ◽  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Power Production ◽  
Wild Type ◽  
Chemomechanical Coupling ◽  
Generalized Kinetic Model

A general kinetic model is presented for the chemomechanical coupling of dimeric kinesin molecular motors with and without extension of their neck linkers (NLs). A peculiar feature of the model is that the rate constants of ATPase activity of a kinesin head are independent of the strain on its NL, implying that the heads of the wild-type kinesin dimer and the mutant with extension of its NLs have the same force-independent rate constants of the ATPase activity. Based on the model, an analytical theory is presented on the force dependence of the dynamics of kinesin dimers with and without extension of their NLs at saturating ATP. With only a few adjustable parameters, diverse available single molecule data on the dynamics of various kinesin dimers, such as wild-type kinesin-1, kinesin-1 with mutated residues in the NLs, kinesin-1 with extension of the NLs and wild-type kinesin-2, under varying force and ATP concentration, can be reproduced very well. Additionally, we compare the power production among different kinesin dimers, showing that the mutation in the NLs reduces the power production and the extension of the NLs further reduces the power production.

scholarly journals Insights into the mechanisms of myosin and kinesin molecular motors from the single-molecule unbinding force measurements

2010 ◽  
Vol 7 (suppl_3) ◽  
Author(s):  
Sergey V. Mikhailenko ◽  
Yusuke Oguchi ◽  
Shin'ichi Ishiwata
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Force Measurements ◽  
Cellular Functions ◽  
Mechanochemical Cycle ◽  
The Individual ◽  
Experimental Geometry ◽  
External Loads ◽  
Individual Motor

In cells, ATP (adenosine triphosphate)-driven motor proteins, both cytoskeletal and nucleic acid-based, operate on their corresponding ‘tracks’, that is, actin, microtubules or nucleic acids, by converting the chemical energy of ATP hydrolysis into mechanical work. During each mechanochemical cycle, a motor proceeds via several nucleotide states, characterized by different affinities for the ‘track’ filament and different nucleotide (ATP or ADP) binding kinetics, which is crucial for a motor to efficiently perform its cellular functions. The measurements of the rupture force between the motor and the track by applying external loads to the individual motor–substrate bonds in various nucleotide states have proved to be an important tool to obtain valuable insights into the mechanism of the motors' performance. We review the application of this technique to various linear molecular motors, both processive and non-processive, giving special attention to the importance of the experimental geometry.

scholarly journals Molecular motors: forty years of interdisciplinary research

2011 ◽  
Vol 22 (21) ◽  
pp. 3936-3939 ◽  
Author(s):  
James A. Spudich
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Molecular Motor ◽  
Single Molecule Level ◽  
In Vitro Motility ◽  
Nonmuscle Cell ◽  
Nonmuscle Cells ◽  
City Plan

A mere forty years ago it was unclear what motor molecules exist in cells that could be responsible for the variety of nonmuscle cell movements, including the “saltatory cytoplasmic particle movements” apparent by light microscopy. One wondered whether nonmuscle cells might have a myosin-like molecule, well known to investigators of muscle. Now we know that there are more than a hundred different molecular motors in eukaryotic cells that drive numerous biological processes and organize the cell's dynamic city plan. Furthermore, in vitro motility assays, taken to the single-molecule level using techniques of physics, have allowed detailed characterization of the processes by which motor molecules transduce the chemical energy of ATP hydrolysis into mechanical movement. Molecular motor research is now at an exciting threshold of being able to enter into the realm of clinical applications.

scholarly journals Extreme parsimony in ATP consumption by 20S complexes in the global disassembly of single SNARE complexes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Changwon Kim ◽  
Min Ju Shon ◽  
Sung Hyun Kim ◽  
Gee Sung Eun ◽  
Je-Kyung Ryu ◽  
...  
Keyword(s):  
Energy Efficiency ◽  
Single Molecule ◽  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Snare Complex ◽  
Atp Binding ◽  
Attachment Protein ◽  
Receptor Complexes ◽  
Protein Receptor ◽  
Sensitive Factor

AbstractFueled by ATP hydrolysis in N-ethylmaleimide sensitive factor (NSF), the 20S complex disassembles rigid SNARE (soluble NSF attachment protein receptor) complexes in single unraveling step. This global disassembly distinguishes NSF from other molecular motors that make incremental and processive motions, but the molecular underpinnings of its remarkable energy efficiency remain largely unknown. Using multiple single-molecule methods, we found remarkable cooperativity in mechanical connection between NSF and the SNARE complex, which prevents dysfunctional 20S complexes that consume ATP without productive disassembly. We also constructed ATP hydrolysis cycle of the 20S complex, in which NSF largely shows randomness in ATP binding but switches to perfect ATP hydrolysis synchronization to induce global SNARE disassembly, minimizing ATP hydrolysis by non-20S complex-forming NSF molecules. These two mechanisms work in concert to concentrate ATP consumption into functional 20S complexes, suggesting evolutionary adaptations by the 20S complex to the energetically expensive mechanical task of SNARE complex disassembly.

scholarly journals A 2-dimensional ratchet model describes assembly initiation of a specialized bacterial cell surface

2019 ◽  
Vol 116 (43) ◽  
pp. 21789-21799 ◽  
Author(s):  
Emily A. Peluso ◽  
Taylor B. Updegrove ◽  
Jiji Chen ◽  
Hari Shroff ◽  
Kumaran S. Ramamurthi
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Bacterial Spores ◽  
Coat Proteins ◽  
Structural Protein ◽  
A Cell ◽  
Protein Shell ◽  
Ratchet Model

Bacterial spores are dormant cells that are encased in a thick protein shell, the “coat,” which participates in protecting the organism’s DNA from environmental insults. The coat is composed of dozens of proteins that assemble in an orchestrated fashion during sporulation. In Bacillus subtilis, 2 proteins initiate coat assembly: SpoVM, which preferentially binds to micron-scale convex membranes and marks the surface of the developing spore as the site for coat assembly; and SpoIVA, a structural protein recruited by SpoVM that uses ATP hydrolysis to drive its irreversible polymerization around the developing spore. Here, we describe the initiation of coat assembly by SpoVM and SpoIVA. Using single-molecule fluorescence microscopy in vivo in sporulating cells and in vitro on synthetic spores, we report that SpoVM’s localization is primarily driven by a lower off-rate on membranes of preferred curvature in the absence of other coat proteins. Recruitment and polymerization of SpoIVA results in the entrapment of SpoVM on the forespore surface. Using experimentally derived reaction parameters, we show that a 2-dimensional ratchet model can describe the interdependent localization dynamics of SpoVM and SpoIVA, wherein SpoVM displays a longer residence time on the forespore surface, which favors recruitment of SpoIVA to that location. Localized SpoIVA polymerization in turn prevents further sampling of other membranes by prelocalized SpoVM molecules. Our model therefore describes the dynamics of structural proteins as they localize and assemble at the correct place and time within a cell to form a supramolecular complex.

scholarly journals Single molecule measurements and molecular motors

2008 ◽  
Vol 363 (1500) ◽  
pp. 2123-2134 ◽  
Author(s):  
Toshio Yanagida ◽  
Mitsuhiro Iwaki ◽  
Yoshiharu Ishii
Keyword(s):  
Brownian Motion ◽  
Single Molecule ◽  
Molecular Motors ◽  
Dynamic Behaviour ◽  
Atp Hydrolysis ◽  
Thermal Fluctuation ◽  
Molecular Machines ◽  
Single Cycle ◽  
Step Movement ◽  
Directional Movement

Single molecule imaging and manipulation are powerful tools in describing the operations of molecular machines like molecular motors. The single molecule measurements allow a dynamic behaviour of individual biomolecules to be measured. In this paper, we describe how we have developed single molecule measurements to understand the mechanism of molecular motors. The step movement of molecular motors associated with a single cycle of ATP hydrolysis has been identified. The single molecule measurements that have sensitivity to monitor thermal fluctuation have revealed that thermal Brownian motion is involved in the step movement of molecular motors. Several mechanisms have been suggested in different motors to bias random thermal motion to directional movement.

scholarly journals FUS Oncofusion Protein Condensates Recruit mSWI/SNF Chromatin Remodelers via Heterotypic Interactions Between Prion-like Domains

2021 ◽  
Author(s):  
Richoo B. Davis ◽  
Taranpreet Kaur ◽  
Mahdi Muhammad Moosa ◽  
Priya R. Banerjee
Keyword(s):  
Transcription Factors ◽  
Chromatin Remodeling ◽  
Single Molecule ◽  
Fusion Proteins ◽  
Dna Binding Domain ◽  
Chromatin Remodelers ◽  
Transcriptional Reprogramming ◽  
Essential Components ◽  
Heterotypic Interactions ◽  
Transcription Regulators

AbstractFusion transcription factors generated by genomic translocations are common drivers of several types of cancers including sarcomas and leukemias. Oncofusions of the FET (FUS, EWSR1, and TAF15) family of proteins result from fusion of the prion-like domain (PLD) of FET proteins to the DNA-binding domain (DBD) of certain transcription regulators and are implicated in aberrant transcriptional programs through interactions with chromatin remodelers. Here, we show that FUS-DDIT3, a FET oncofusion protein, undergoes PLD-mediated phase separation into liquid-like condensates. Nuclear FUS-DDIT3 condensates can recruit essential components of the global transcriptional machinery such as the chromatin remodeler SWI/SNF. The recruitment of mammalian SWI/SNF is driven by heterotypic PLD-PLD interactions between FUS-DDIT3 and core subunits of SWI/SNF, such as the catalytic component BRG1. Further experiments with single-molecule correlative force-fluorescence microscopy support a model wherein the fusion protein forms condensates on DNA surface and enrich BRG1 to activate transcription by ectopic chromatin remodeling. Similar PLD-driven co-condensation of mSWI/SNF with transcription factors can be employed by other oncogenic fusion proteins with a generic PLD-DBD domain architecture for global transcriptional reprogramming.

scholarly journals Temperature-Dependent Activity of Motor Proteins: Energetics and Their Implications for Collective Behavior

2021 ◽  
Vol 9 ◽  
Author(s):  
Saumya Yadav ◽  
Ambarish Kunwar
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Intracellular Transport ◽  
Motor Proteins ◽  
Atp Hydrolysis ◽  
Molecular Motor ◽  
Surrounding Medium ◽  
Biochemical Properties ◽  
Cellular Transport ◽  
Temperature Dependent

Molecular motor proteins are an extremely important component of the cellular transport system that harness chemical energy derived from ATP hydrolysis to carry out directed mechanical motion inside the cells. Transport properties of these motors such as processivity, velocity, and their load dependence have been well established through single-molecule experiments. Temperature dependent biophysical properties of molecular motors are now being probed using single-molecule experiments. Additionally, the temperature dependent biochemical properties of motors (ATPase activity) are probed to understand the underlying mechanisms and their possible implications on the enzymatic activity of motor proteins. These experiments in turn have revealed their activation energies and how they compare with the thermal energy available from the surrounding medium. In this review, we summarize such temperature dependent biophysical and biochemical properties of linear and rotary motor proteins and their implications for collective function during intracellular transport and cellular movement, respectively.

Single-molecule fluorescence to study molecular motors

2007 ◽  
Vol 40 (1) ◽  
pp. 87-111 ◽  
Author(s):  
Hyokeun Park ◽  
Erdal Toprak ◽  
Paul R. Selvin
Keyword(s):  
Fluorescence Imaging ◽  
Single Molecule ◽  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Imaging Techniques ◽  
Single Molecule Fluorescence ◽  
New Techniques ◽  
Single Molecule Level ◽  
Living Organisms ◽  
Run Lengths

AbstractMolecular motors, which use energy from ATP hydrolysis to take nanometer-scale steps with run-lengths on the order of micrometers, have important roles in areas such as transport and mitosis in living organisms. New techniques have recently been developed to measure these small movements at the single-molecule level. In particular, fluorescence imaging has contributed to the accurate measurement of this tiny movement. We introduce three single-molecule fluorescence imaging techniques which can find the position of a fluorophore with accuracy in the range of a few nanometers. These techniques are named after Hollywood animation characters: Fluorescence Imaging with One Nanometer Accuracy (FIONA), Single-molecule High-REsolution Colocalization (SHREC), and Defocused Orientation and Position Imaging (DOPI). We explain new understanding of molecular motors obtained from measurements using these techniques.

scholarly journals ATP-Dependent Chromatin Remodeling Complex in the Lineage Specification of Mesenchymal Stem Cells

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Wen Du ◽  
Daimo Guo ◽  
Wei Du
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Chromatin Remodeling ◽  
Cardiac Tissue ◽  
Gene Expression Regulation ◽  
Atp Hydrolysis ◽  
Transcriptional Level ◽  
Lineage Specification ◽  
Chromatin Remodelers ◽  
Chromatin Remodeling Complexes

Mesenchymal stem cells (MSCs) present in multiple tissues can self-renew and differentiate into multiple lineages including the bone, cartilage, muscle, cardiac tissue, and connective tissue. Key events, including cell proliferation, lineage commitment, and MSC differentiation, are ensured by precise gene expression regulation. ATP-dependent chromatin alteration is one form of epigenetic modifications that can regulate the transcriptional level of specific genes by utilizing the energy from ATP hydrolysis to reorganize chromatin structure. ATP-dependent chromatin remodeling complexes consist of a variety of subunits that together perform multiple functions in self-renewal and lineage specification. This review highlights the important role of ATP-dependent chromatin remodeling complexes and their different subunits in modulating MSC fate determination and discusses the proposed mechanisms by which ATP-dependent chromatin remodelers function.

Sign in / Sign up

Export Citation Format

Share Document