scholarly journals Active liquid crystals powered by force-sensing DNA-motor clusters

2021 ◽  
Vol 118 (30) ◽  
pp. e2102873118
Author(s):  
Alexandra M. Tayar ◽  
Michael F. Hagan ◽  
Zvonimir Dogic
Keyword(s):  
Molecular Motors ◽  
Chemical Structure ◽  
Nonequilibrium Dynamics ◽  
Force Sensing ◽  
Critical Threshold ◽  
Nematic Order ◽  
Double Stranded Dna ◽  
Active Liquid ◽  
Energy Consuming ◽  
Insight Into

Cytoskeletal active nematics exhibit striking nonequilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which kinesin motors are linked by a double-stranded DNA linker. The efficiency by which DNA-based clusters power active nematics depends on both the stepping dynamics of the kinesin motors and the chemical structure of the polymeric linker. Fluorescence anisotropy measurements reveal that the motor clusters, like filamentous microtubules, exhibit local nematic order. The properties of the DNA linker enable the design of force-sensing clusters. When the load across the linker exceeds a critical threshold, the clusters fall apart, ceasing to generate active stresses and slowing the system dynamics. Fluorescence readout reveals the fraction of bound clusters that generate interfilament sliding. In turn, this yields the average load experienced by the kinesin motors as they step along the microtubules. DNA-motor clusters provide a foundation for understanding the molecular mechanism by which nanoscale molecular motors collectively generate mesoscopic active stresses, which in turn power macroscale nonequilibrium dynamics of active nematics.

scholarly journals NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors

2020 ◽  
Author(s):  
Bryon P. Mahler ◽  
Pawel J. Bujalowski ◽  
Huzhang Mao ◽  
Erik A. Dill ◽  
Paul J. Jardine ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Molecular Motors ◽  
Solution Structure ◽  
Nuclease Activity ◽  
Structural Basis ◽  
Binding Assays ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Fluorescence Binding ◽  
Insight Into

SummaryDouble-stranded DNA viruses use ATP-powered molecular motors to package their genomes. To do so, these motors must efficiently transition between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the bacteriophage phi29 ATPase (CTD) that suggest a structural basis for these functional transitions. Sedimentation experiments show that the inter-domain linker in the full-length protein promotes dimerization and thus may play a role in assembly of the functional motor. The NMR solution structure of the CTD indicates it is a vestigial nuclease domain that likely evolved from conserved nuclease domains in phage terminases. Despite the loss of nuclease activity, fluorescence binding assays confirm the CTD retains its DNA binding capabilities and fitting the CTD into cryoEM density of the phi29 motor shows that the CTD directly binds DNA. However, the interacting residues differ from those identified by NMR titration in solution, suggesting that packaging motors undergo conformational changes to transition between initiation, translocation, and termination.

scholarly journals NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors

2020 ◽  
Vol 48 (20) ◽  
pp. 11737-11749 ◽  
Author(s):  
Bryon P Mahler ◽  
Paul J Bujalowski ◽  
Huzhang Mao ◽  
Erik A Dill ◽  
Paul J Jardine ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Molecular Motors ◽  
Solution Structure ◽  
Nuclease Activity ◽  
Structural Basis ◽  
Binding Assays ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Fluorescence Binding ◽  
Insight Into

Abstract Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the bacteriophage phi29 ATPase (CTD) that suggest a structural basis for these functional transitions. Sedimentation experiments show that the inter-domain linker in the full-length protein promotes oligomerization and thus may play a role in assembly of the functional motor. The NMR solution structure of the CTD indicates it is a vestigial nuclease domain that likely evolved from conserved nuclease domains in phage terminases. Despite the loss of nuclease activity, fluorescence binding assays confirm the CTD retains its DNA binding capabilities and fitting the CTD into cryoEM density of the phi29 motor shows that the CTD directly binds DNA. However, the interacting residues differ from those identified by NMR titration in solution, suggesting that packaging motors undergo conformational changes to transition between initiation, translocation, and termination. Taken together, these results provide insight into the evolution of functional transitions in viral dsDNA packaging motors.

Mechanistic insight into the recognition of single-stranded and double-stranded DNA substrates by ABH2 and ABH3

2010 ◽  
Vol 6 (11) ◽  
pp. 2143 ◽  
Author(s):  
Baoen Chen ◽  
Hongchuan Liu ◽  
Xiaoxu Sun ◽  
Cai-Guang Yang
Keyword(s):  
Double Stranded Dna ◽  
Mechanistic Insight ◽  
Dna Substrates ◽  
Insight Into

scholarly journals Mechanism of riboregulation of p62 protein oligomerisation by vault RNA1-1 in selective autophagy

2021 ◽  
Author(s):  
Magdalena Buescher ◽  
Rastislav Horos ◽  
Kevin Haubrich ◽  
Nikolay Dobrev ◽  
Florence Baudin ◽  
...  
Keyword(s):  
Chemical Structure ◽  
Membrane Vesicles ◽  
Underlying Mechanism ◽  
Selective Autophagy ◽  
Ubiquitinated Proteins ◽  
Flexible Loop ◽  
Structure Probing ◽  
Molecular Determinants ◽  
Necessary And Sufficient ◽  
Insight Into

Macroautophagy ensures the clearance of intracellular substrates ranging from single ubiquitinated proteins to large proteotoxic aggregates and defective organelles. The selective autophagy receptor p62 binds these targets and recruits them to double-membrane vesicles, which fuse with lysosomes to degrade their content. We recently uncovered that p62 function is riboregulated by the small non-coding vault RNA1-1. Here, we present detailed insight into the underlying mechanism. We show that the PB1 domain and adjacent linker region of p62 (aa 1-122) are necessary and sufficient for specific vault RNA1-1 binding, and identify lysine 7 and arginine 21 as key hinges for p62 riboregulation. Chemical structure probing of vault RNA1-1 further reveals a central flexible loop within the RNA that mediates the specific p62 interaction. Our data define molecular determinants that govern mammalian autophagy via the p62-vault RNA1-1 riboregulatory pair.

BIOMIMETIC SYSTEMS SHED LIGHT ON ACTIN-BASED MOTILITY DOWN TO THE MOLECULAR SCALE

2009 ◽  
Vol 04 (01n02) ◽  
pp. 5-15 ◽  
Author(s):  
GUILLAUME ROMET-LEMONNE ◽  
EMMANUELE HELFER ◽  
VINCENT DELATOUR ◽  
BEATA BUGYI ◽  
MONTSERRAT BOSCH ◽  
...  
Keyword(s):  
Molecular Motors ◽  
Molecular Mechanisms ◽  
Directed Assembly ◽  
Cellular Processes ◽  
Self Organized ◽  
Filament Assembly ◽  
Physical Measurements ◽  
Minimum Number ◽  
Broad Variety ◽  
Insight Into

Cell motility, one of the modular activities of living cells, elicits the response of the cell to extra-cellular signals, to move directionally, feed, divide or transport materials. The combined actions of molecular motors and re-modeling of the cytoskeleton generate forces and movement. Here we describe mechanistic approaches of force and movement produced by site-directed assembly of actin filaments. The insight derived from a biochemical analysis of the protein machineries involved in "actin-based motile processes" like cell protrusions, invaginations, organelle propulsion, is used to build reconstituted assays that mimic cellular processes, using several protein machineries known to initiate filament assembly by different mechanisms. Reconstitution of complex self-organized systems presents a broad variety of interests. Reconstituting actin-based movement of a functionalized particle from a minimum number of pure proteins, first used to prove the general thermodynamic principles at work in motility, then was the basis for fully controlled physical measurements of forces produced by polymerization of actin against an obstacle and of the mechanical properties of the resulting polymer arrays. In addition, measurements at the mesoscopic scale (trajectories, velocity, polymer mechanics, fluorescence of specifically labeled components of the actin array, use of mutated proteins) can provide further insight into the molecular mechanisms underlying motility.

From Fundamental Properties to Applications of Surface Activity Investigations: The Kinetic and Thermodynamic Aspects

2020 ◽  
Vol 10 (1) ◽  
pp. 3-9
Author(s):  
Hary Razafindralambo
Keyword(s):  
Chemical Structure ◽  
Fundamental Property ◽  
Fluid Interfaces ◽  
Colloidal Systems ◽  
Fundamental Properties ◽  
Amphiphilic Molecules ◽  
Boundary Limits ◽  
Mixed Systems ◽  
Insight Into

Interfaces, or surfaces in particular (fluid-solid interfaces), are the boundary limits of two immiscible phases characterized by the surface free energy. Getting insight into their fundamental property is of great importance for both scientific and industrial activities. Such an approach enables us to control the formation and stabilization of colloidal systems, which consist of producing homogenous dispersions from at least two initially immiscible phases. In this mini-review, the kinetic and thermodynamic aspects of fluid surfaces are overviewed. Successively, the main phenomena occurring at the interfaces and the appropriate methodology of investigations, the role of amphiphilic molecules in modifying surface properties and generating various functionalities as a function of their chemical structure, size, and shape, and the current approaches for characterizing interactions as well as synergism or antagonism within mixed systems are treated. Relevant relationships of dynamic fundamental properties to macroscopic consequences at the solid and fluid interfaces of single and mixed amphiphile systems are illustrated.

The genome of Oryctes rhinoceros nudivirus provides novel insight into the evolution of nuclear arthropod-specific large circular double-stranded DNA viruses

Virus Genes ◽  
2011 ◽  
Vol 42 (3) ◽  
pp. 444-456 ◽  
Author(s):  
Yongjie Wang ◽  
Olaf R. P. Bininda-Emonds ◽  
Monique M. van Oers ◽  
Just M. Vlak ◽  
Johannes A. Jehle
Keyword(s):  
Dna Viruses ◽  
Oryctes Rhinoceros ◽  
Double Stranded Dna ◽  
Insight Into

LIGHT-INDUCED MODIFICATION OF KINETIC MOLECULAR PROPERTIES: ENHANCEMENT OF OPTICAL KERR EFFECT IN ABSORBING LIQUIDS, PHOTOINDUCED TORQUE AND MOLECULAR MOTORS IN DYE-DOPED NEMATICS

2000 ◽  
Vol 09 (02) ◽  
pp. 157-182 ◽  
Author(s):  
M. KREUZER ◽  
L. MARRUCCI ◽  
D. PAPARO
Keyword(s):  
Liquid Crystals ◽  
Molecular Motors ◽  
Kerr Effect ◽  
Optical Nonlinearity ◽  
Molecular Structures ◽  
Molecular Properties ◽  
Main Role ◽  
Theoretical Results ◽  
Insight Into ◽  
Dye Molecule

In this paper we review some experimental and theoretical results on the enhancement of orientational optical nonlinearities observed in dye-doped liquids and liquid crystals. We argue that this enhancement is derived from a photoinduced modification of kinetic molecular properties. Moreover we highlight an analogy between the mechanism of this effect in nematic liquid crystals and the working principles of "molecular motors". This analogy helps us to refine the understanding of this effect and to identify the molecular parameters which play the main role. Finally we review some recent experimental results about the dependence of the optical nonlinearity enhancement on the detailed dye and host molecular structures. These results provide some insight into the light-induced phenomena taking place inside a dye molecule.

scholarly journals Insight into DNA and Protein Transport in Double-Stranded DNA Viruses: The Structure of Bacteriophage N4

2008 ◽  
Vol 378 (3) ◽  
pp. 726-736 ◽  
Author(s):  
Kyung H. Choi ◽  
Jennifer McPartland ◽  
Irene Kaganman ◽  
Valorie D. Bowman ◽  
Lucia B. Rothman-Denes ◽  
...  
Keyword(s):  
Protein Transport ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Bacteriophage N4 ◽  
Insight Into

scholarly journals Mechanochemical tuning of myosin-I by the N-terminal region

2015 ◽  
Vol 112 (26) ◽  
pp. E3337-E3344 ◽  
Author(s):  
Michael J. Greenberg ◽  
Tianming Lin ◽  
Henry Shuman ◽  
E. Michael Ostap
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Critical Role ◽  
Terminal Region ◽  
Power Stroke ◽  
Force Sensing ◽  
Myosin Isoforms ◽  
Structural Elements ◽  
Structural Element ◽  
Myosin I

Myosins are molecular motors that generate force to power a wide array of motile cellular functions. Myosins have the inherent ability to change their ATPase kinetics and force-generating properties when they encounter mechanical loads; however, little is known about the structural elements in myosin responsible for force sensing. Recent structural and biophysical studies have shown that myosin-I isoforms, Myosin-Ib (Myo1b) and Myosin-Ic (Myo1c), have similar unloaded kinetics and sequences but substantially different responses to forces that resist their working strokes. Myo1b has the properties of a tension-sensing anchor, slowing its actin-detachment kinetics by two orders of magnitude with just 1 pN of resisting force, whereas Myo1c has the properties of a slow transporter, generating power without slowing under 1-pN loads that would stall Myo1b. To examine the structural elements that lead to differences in force sensing, we used single-molecule and ensemble kinetic techniques to show that the myosin-I N-terminal region (NTR) plays a critical role in tuning myosin-I mechanochemistry. We found that replacing the Myo1c NTR with the Myo1b NTR changes the identity of the primary force-sensitive transition of Myo1c, resulting in sensitivity to forces of <2 pN. Additionally, we found that the NTR plays an important role in stabilizing the post–power-stroke conformation. These results identify the NTR as an important structural element in myosin force sensing and suggest a mechanism for generating diversity of function among myosin isoforms.

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