On the Role of Magnesium Ions in the DNA-Scissoring Activity of the Restriction Endonuclease ApaI: Stochastic Kinetics from a Single Molecule to Mesoscopic Paradigm

2021 ◽  
Author(s):  
Biswajit Das ◽  
Kinshuk Banerjee ◽  
Gautam Gangopadhyay
Keyword(s):  
Restriction Endonuclease ◽  
Single Molecule ◽  
Magnesium Ions ◽  
Stochastic Kinetics

Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease

FEBS Letters ◽  
2011 ◽  
Vol 585 (17) ◽  
pp. 2739-2743 ◽  
Author(s):  
Mai Zahran ◽  
Tomasz Berezniak ◽  
Petra Imhof ◽  
Jeremy C. Smith
Keyword(s):  
Restriction Endonuclease ◽  
Dna Recognition ◽  
Magnesium Ions

The localized electron: magnetic properties

2018 ◽  
Author(s):  
Jean-Pierre Launay ◽  
Michel Verdaguer
Keyword(s):  
Single Molecule ◽  
Model Systems ◽  
Ferromagnetic Coupling ◽  
Single Chain ◽  
Single Molecule Magnets ◽  
Magnetic Systems ◽  
Orbital Interactions ◽  
Prussian Blue Analogues ◽  
Mononuclear Complexes

After preliminaries about electron properties, and definitions in magnetism, one treats the magnetism of mononuclear complexes, in particular spin cross-over, showing the role of cooperativity and the sensitivity to external perturbations. Orbital interactions and exchange interaction are explained in binuclear model systems, using orbital overlap and orthogonality concepts to explain antiferromagnetic or ferromagnetic coupling. The phenomenologically useful Spin Hamiltonian is defined. The concepts are then applied to extended molecular magnetic systems, leading to molecular magnetic materials of various dimensionalities exhibiting bulk ferro- or ferrimagnetism. An illustration is provided by Prussian Blue analogues. Magnetic anisotropy is introduced. It is shown that in some cases, a slow relaxation of magnetization arises and gives rise to appealing single-ion magnets, single-molecule magnets or single-chain magnets, a route to store information at the molecular level.

scholarly journals Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

2021 ◽  
Vol 22 (3) ◽  
pp. 1018
Author(s):  
Hiroaki Yokota
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Underlying Mechanism ◽  
Amino Acid Sequences ◽  
E Coli ◽  
X Ray Crystallography ◽  
Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

scholarly journals Role of the ribosomal protein L27 revealed by single-molecule FRET study

2012 ◽  
Vol 21 (11) ◽  
pp. 1696-1704 ◽  
Author(s):  
Yuhong Wang ◽  
Ming Xiao
Keyword(s):  
Ribosomal Protein ◽  
Single Molecule ◽  
Single Molecule Fret

The Role of Calcium and Magnesium Ions in Uptake of β-Amyloid Peptides by Microglial Cells

2006 ◽  
Vol 19 (3) ◽  
pp. 683-696 ◽  
Author(s):  
N. Choucair ◽  
V. Laporte ◽  
R. Levy ◽  
C. Tranchant ◽  
J.-P. Gies ◽  
...  
Keyword(s):  
Microglial Cells ◽  
Magnesium Ions ◽  
Amyloid Peptides ◽  
Β Amyloid ◽  
Calcium And Magnesium ◽  
Calcium And Magnesium Ions

scholarly journals Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER

2021 ◽  
Vol 7 (21) ◽  
pp. eabg0942
Author(s):  
Jae Ho Lee ◽  
Ahmad Jomaa ◽  
SangYoon Chung ◽  
Yu-Hsien Hwang Fu ◽  
Ruilin Qian ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Translocation ◽  
Molecular Model ◽  
Genetic Diseases ◽  
Signal Recognition Particle ◽  
Biological Regulation ◽  
Single Molecule Studies ◽  
Guanosine Triphosphatase ◽  
Gtpase Cycle

The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP transitions from cargo recognition in the cytosol to protein translocation at the ER is not understood. Here, structural, biochemical, and single-molecule studies show that this transition requires multiple sequential conformational rearrangements in the targeting complex initiated by guanosine triphosphatase (GTPase)–driven compaction of the SRP receptor (SR). Disruption of these rearrangements, particularly in mutant SRP54G226E linked to severe congenital neutropenia, uncouples the SRP/SR GTPase cycle from protein translocation. Structures of targeting intermediates reveal the molecular basis of early SRP-SR recognition and emphasize the role of eukaryote-specific elements in regulating targeting. Our results provide a molecular model for the structural and functional transitions of SRP throughout the targeting cycle and show that these transitions provide important points for biological regulation that can be perturbed in genetic diseases.

scholarly journals The role of surface corrugation and tip oscillation in single-molecule manipulation with a non-contact atomic force microscope

2014 ◽  
Vol 5 ◽  
pp. 202-209 ◽  
Author(s):  
Christian Wagner ◽  
Norman Fournier ◽  
F Stefan Tautz ◽  
Ruslan Temirov
Keyword(s):  
Frequency Shift ◽  
Single Molecule ◽  
Oscillation Amplitude ◽  
Surface Corrugation ◽  
Atomic Force ◽  
Data Points ◽  
Atomic Surface ◽  
Tetracarboxylic Dianhydride ◽  
Single Molecule Manipulation

Scanning probe microscopy (SPM) plays an important role in the investigation of molecular adsorption. The possibility to probe the molecule–surface interaction while tuning its strength through SPM tip-induced single-molecule manipulation has particularly promising potential to yield new insights. We recently reported experiments, in which 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) molecules were lifted with a qPlus-sensor and analyzed these experiments by using force-field simulations. Irrespective of the good agreement between the experiment and those simulations, systematic inconsistencies remained that we attribute to effects omitted from the initial model. Here we develop a more realistic simulation of single-molecule manipulation by non-contact AFM that includes the atomic surface corrugation, the tip elasticity, and the tip oscillation amplitude. In short, we simulate a full tip oscillation cycle at each step of the manipulation process and calculate the frequency shift by solving the equation of motion of the tip. The new model correctly reproduces previously unexplained key features of the experiment, and facilitates a better understanding of the mechanics of single-molecular junctions. Our simulations reveal that the surface corrugation adds a positive frequency shift to the measurement that generates an apparent repulsive force. Furthermore, we demonstrate that the scatter observed in the experimental data points is related to the sliding of the molecule across the surface.

scholarly journals Human DNA2 possesses a cryptic DNA unwinding activity that functionally integrates with BLM or WRN helicases

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Cosimo Pinto ◽  
Kristina Kasaciunaite ◽  
Ralf Seidel ◽  
Petr Cejka
Keyword(s):  
Single Molecule ◽  
Nuclease Activity ◽  
Molecular Machine ◽  
Dna Unwinding ◽  
Metabolic Processes ◽  
Nuclease Domain

Human DNA2 (hDNA2) contains both a helicase and a nuclease domain within the same polypeptide. The nuclease of hDNA2 is involved in a variety of DNA metabolic processes. Little is known about the role of the hDNA2 helicase. Using bulk and single-molecule approaches, we show that hDNA2 is a processive helicase capable of unwinding kilobases of dsDNA in length. The nuclease activity prevents the engagement of the helicase by competing for the same substrate, hence prominent DNA unwinding by hDNA2 alone can only be observed using the nuclease-deficient variant. We show that the helicase of hDNA2 functionally integrates with BLM or WRN helicases to promote dsDNA degradation by forming a heterodimeric molecular machine. This collectively suggests that the hDNA2 motor promotes the enzyme's capacity to degrade dsDNA in conjunction with BLM or WRN and thus promote the repair of broken DNA.

scholarly journals TRPV channel OCR-2 is distributed along C. elegans chemosensory cilia by diffusion in a local interplay with intraflagellar transport

2020 ◽  
Author(s):  
Jaap van Krugten ◽  
Noémie Danné ◽  
Erwin J.G. Peterman
Keyword(s):  
Single Molecule ◽  
Transmembrane Proteins ◽  
Intraflagellar Transport ◽  
Single Molecule Tracking ◽  
C Elegans ◽  
Normal Diffusion ◽  
Cellular Signal ◽  
Underlying Mechanisms ◽  
And Function

AbstractSensing and reacting to the environment is essential for survival and procreation of most organisms. Caenorhabditis elegans senses soluble chemicals with transmembrane proteins (TPs) in the cilia of its chemosensory neurons. Development, maintenance and function of these cilia relies on intraflagellar transport (IFT), in which motor proteins transport cargo, including sensory TPs, back and forth along the ciliary axoneme. Here we use live fluorescence imaging to show that IFT machinery and the sensory TP OCR-2 reversibly redistribute along the cilium after exposure to repellant chemicals. To elucidate the underlying mechanisms, we performed single-molecule tracking experiments and found that OCR-2 distribution depends on an intricate interplay between IFT-driven transport, normal diffusion and subdiffusion that depends on the specific location in the cilium. These insights in the role of IFT on the dynamics of cellular signal transduction contribute to a deeper understanding of the regulation of sensory TPs and chemosensing.

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