scholarly journals Unfolding of the chromatin fiber driven by overexpression of bridging factors

2020 ◽  
Author(s):  
Isha Malhotra ◽  
Bernardo Oyarzún ◽  
Bortolo Matteo Mognetti
Keyword(s):  
Microphase Separation ◽  
Single Step ◽  
Chromatin Fiber ◽  
Coarse Grained ◽  
Morphological Properties ◽  
Cross Link ◽  
Simulation Methodology ◽  
Coarse Grained Model ◽  
Nuclear Molecules ◽  
The One

AbstractNuclear molecules control the functional properties of the chromatin fiber by shaping its morphological properties. The biophysical mechanisms controlling how bridging molecules compactify the chromatin are a matter of debate. On the one side, bridging molecules could cross-link faraway sites and fold the fiber through the formation of loops. Interacting bridging molecules could also mediate long-range attractions by first tagging different locations of the fiber and then undergoing microphase separation. Using a coarse-grained model and Monte Carlo simulations, we study the conditions leading to compact configurations both for interacting and non-interacting bridging molecules. In the second case, we report on an unfolding transition at high densities of the bridging molecules. We clarify how this transition, which disappears for interacting bridging molecules, is universal and controlled by entropic terms. In general, chains are more compact in the case of interacting bridging molecules since, in this case, interactions are not valence-limited. However, this result is conditional on the ability of our simulation methodology to relax the system towards its ground state. In particular, we clarify how, unless using reaction dynamics that change the length of a loop in a single step, the system is prone to remain trapped in metastable, compact configurations featuring long loops.

scholarly journals Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA

2021 ◽  
Author(s):  
Salvatore Assenza ◽  
Rubén Pérez
Keyword(s):  
Persistence Length ◽  
Independent Set ◽  
Single Step ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Sequence Dependence ◽  
Cellular Processes ◽  
Coarse Grained Model ◽  
Double Stranded Dna ◽  
Sequence Dependent

AbstractWe introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar and base moieties, and at the phosphate group. The sequence dependence is included by considering a step-dependent parameterization of the bonded interactions, which are tuned in order to reproduce the values of key observables obtained from exhaustive atomistic simulations from literature. The predictions of the model are benchmarked against an independent set of all-atom simulations, showing that it captures with high fidelity the sequence dependence of conformational and elastic features beyond the single step considered in its formulation. A remarkably good agreement with experiments is found for both sequence-averaged and sequence-dependent conformational and elastic features, including the stretching and torsion moduli, the twist-stretch and twist-bend couplings, the persistence length and the helical pitch. Overall, for the inspected quantities, the model has a precision comparable to atomistic simulations, hence providing a reliable coarse-grained description for the rationalization of singlemolecule experiments and the study of cellular processes involving dsDNA. Owing to the simplicity of its formulation, MADna can be straightforwardly included in common simulation engines.

scholarly journals On the Importance of Hydrodynamic Interactions in the Stepping Kinetics of Kinesin

2016 ◽  
Author(s):  
Dave Thirumalai ◽  
Yonathan Goldtzvik ◽  
Zhechun Zhang
Keyword(s):  
Coiled Coil ◽  
Quantitative Agreement ◽  
Single Step ◽  
Hydrodynamic Interactions ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Target Binding ◽  
Conventional Kinesin ◽  
Kinetics Of ◽  
Target Binding Site

Conventional kinesin walks by a hand-over-hand mechanism on the microtubule (MT) by taking ∼ 8nmdiscrete steps, and consumes one ATP molecule per step. The time needed to complete a single step is on the order of twenty microseconds. We show, using simulations of a coarse-grained model of the complex containing the two motor heads, the MT, and the coiled coil that in order to obtain quantitative agreement with experiments for the stepping kinetics hydrodynamic interactions (HI) have to be included. In simulations without hydrodynamic interactions spanning nearly twenty microseconds not a single step was completed in hundred trajectories. In sharp contrast, nearly 14% of the steps reached the target binding site within 6 microseconds when HI were included. Somewhat surprisingly, there are qualitative differences in the diffusion pathways in simulations with and without HI. The extent of movement of the trailing head of kinesin on the MT during the diffusion stage of stepping is considerably greater in simulations with HI than in those without HI. Our results suggest that inclusion of HI is crucial in the accurate description of motility of other motors as well.

scholarly journals Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin

2017 ◽  
Vol 114 (46) ◽  
pp. E9838-E9845 ◽  
Author(s):  
Zhechun Zhang ◽  
Yonathan Goldtzvik ◽  
D. Thirumalai
Keyword(s):  
Single Step ◽  
Coarse Grained ◽  
Power Stroke ◽  
Stochastic Motion ◽  
Coarse Grained Model ◽  
Correct Orientation ◽  
Stall Force ◽  
Target Binding ◽  
The Individual ◽  
Motor Head

Kinesin walks processively on microtubules (MTs) in an asymmetric hand-over-hand manner consuming one ATP molecule per 16-nm step. The individual contributions due to docking of the approximately 13-residue neck linker to the leading head (deemed to be the power stroke) and diffusion of the trailing head (TH) that contributes in propelling the motor by 16 nm have not been quantified. We use molecular simulations by creating a coarse-grained model of the MT–kinesin complex, which reproduces the measured stall force as well as the force required to dislodge the motor head from the MT, to show that nearly three-quarters of the step occurs by bidirectional stochastic motion of the TH. However, docking of the neck linker to the leading head constrains the extent of diffusion and minimizes the probability that kinesin takes side steps, implying that both the events are necessary in the motility of kinesin and for the maintenance of processivity. Surprisingly, we find that during a single step, the TH stochastically hops multiple times between the geometrically accessible neighboring sites on the MT before forming a stable interaction with the target binding site with correct orientation between the motor head and the α/β tubulin dimer.

A Short Synthesis of (+)-Brefeldin C via Enantioselective Radical Hydroalkynylation

2019 ◽  
Author(s):  
Lars Gnägi ◽  
Severin Vital Martz ◽  
Daniel Meyer ◽  
Robin Marc Schärer ◽  
Philippe Renaud
Keyword(s):  
Total Synthesis ◽  
Natural Product ◽  
Oxidation State ◽  
Single Step ◽  
Radical Process ◽  
Target Molecule ◽  
Short Synthesis ◽  
The One

<div><div><div><div><p>A very concise total synthesis of (+)-brefeldin C starting from 2-furanylcyclopentene is described. This approach is based on an unprecedented enantioselective radical hydroalkynylation process to introduce the two cyclopentane stereocenters in a single step. The use of a furan substituent allows to achieve a high trans diastereoselectivity during the radical process and it contains the four carbon atoms C1–C4 of the natural product in an oxidation state closely related to the one of the target molecule. The eight-step synthesis require six product purifications and it provides (+)-brefeldin C in 18% overall yield.</p></div></div></div></div>

scholarly journals Synthesis and Polymerization Kinetics of Rigid Tricyanate Ester

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1686
Author(s):  
Andrey Galukhin ◽  
Roman Nosov ◽  
Ilya Nikolaev ◽  
Elena Melnikova ◽  
Daut Islamov ◽  
...  
Keyword(s):  
Kinetic Analysis ◽  
Single Step ◽  
Polymerization Kinetics ◽  
Scanning Calorimetry ◽  
Modulated Differential Scanning Calorimetry ◽  
Diffusion Controlled ◽  
Polymerization Product ◽  
The One ◽  
Kinetics Of

A new rigid tricyanate ester consisting of seven conjugated aromatic units is synthesized, and its structure is confirmed by X-ray analysis. This ester undergoes thermally stimulated polymerization in a liquid state. Conventional and temperature-modulated differential scanning calorimetry techniques are employed to study the polymerization kinetics. A transition of polymerization from a kinetic- to a diffusion-controlled regime is detected. Kinetic analysis is performed by combining isoconversional and model-based computations. It demonstrates that polymerization in the kinetically controlled regime of the present monomer can be described as a quasi-single-step, auto-catalytic, process. The diffusion contribution is parameterized by the Fournier model. Kinetic analysis is complemented by characterization of thermal properties of the corresponding polymerization product by means of thermogravimetric and thermomechanical analyses. Overall, the obtained experimental results are consistent with our hypothesis about the relation between the rigidity and functionality of the cyanate ester monomer, on the one hand, and its reactivity and glass transition temperature of the corresponding polymer, on the other hand.

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model

2009 ◽  
Vol 131 (7) ◽  
Author(s):  
Vincent K. Shen ◽  
Jason K. Cheung ◽  
Jeffrey R. Errington ◽  
Thomas M. Truskett
Keyword(s):  
Protein Stability ◽  
Coarse Grained ◽  
Protein Solutions ◽  
Native State ◽  
High Concentration ◽  
Coarse Grained Model ◽  
Excluded Volume Effects ◽  
Thermodynamic Phase ◽  
Broad Interest ◽  
Liquid Liquid Phase Separation

Proteins aggregate and precipitate from high concentration solutions in a wide variety of problems of natural and technological interest. Consequently, there is a broad interest in developing new ways to model the thermodynamic and kinetic aspects of protein stability in these crowded cellular or solution environments. We use a coarse-grained modeling approach to study the effects of different crowding agents on the conformational equilibria of proteins and the thermodynamic phase behavior of their solutions. At low to moderate protein concentrations, we find that crowding species can either stabilize or destabilize the native state, depending on the strength of their attractive interaction with the proteins. At high protein concentrations, crowders tend to stabilize the native state due to excluded volume effects, irrespective of the strength of the crowder-protein attraction. Crowding agents reduce the tendency of protein solutions to undergo a liquid-liquid phase separation driven by strong protein-protein attractions. The aforementioned equilibrium trends represent, to our knowledge, the first simulation predictions for how the properties of crowding species impact the global thermodynamic stability of proteins and their solutions.

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