scholarly journals Concentration-dependent swelling and structure of ionic microgels: simulation and theory of a coarse-grained model

Soft Matter ◽  
2018 ◽  
Vol 14 (22) ◽  
pp. 4530-4540 ◽  
Author(s):  
Tyler J. Weyer ◽  
Alan R. Denton
Keyword(s):  
Structural Properties ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Coarse Grained Model

Swelling and structural properties of ionic microgel suspensions are described by a coarse-grained model that includes elastic and electrostatic interactions.

scholarly journals Adsorption of Lysozyme Into a Charged Confining Pore

2021 ◽  
Author(s):  
Sidney Carvalho ◽  
Ralf Metzler ◽  
Andrey Cherstvy ◽  
Daniel Caetano
Keyword(s):  
Electrostatic Interactions ◽  
Active Sites ◽  
Coarse Grained ◽  
Pore Surface ◽  
Solution Ph ◽  
Coarse Grained Model ◽  
Egg White Lysozyme ◽  
Constant Ph ◽  
Pka Shift ◽  
Effects Of Ph

Several applications arise from the confinement of proteins on surfaces since their stability and biological activity are enhanced. It is also known that the way a protein adsorbs on the surface is important for its biological function since its active sites should not be obstructed. In this study, the adsorption properties of hen egg-white Lysozyme, HEWL, into a negatively charged silica pore is examined employing a coarse-grained model and constant-pH Monte Carlo simulations. The role of electrostatic interactions is taken into account when including the Debye-Hueckel potentials into the Ca structure-based model. We evaluate the effects of pH, salt concentration, and pore radius on the protein preferential orientation and spatial distribution of its residues regarding the pore surface. By mapping the residues that stay closer to the pore surface, we find the increase of pH leads to orientational changes of the adsorbed protein when the solution pH gets closer to the HEWL isoelectric point. At these conditions, the pKa shift of these important residues caused by the adsorption into the charged confining surface results in a HEWL charge distribution that stabilizes the adsorption in the observed protein orientation. We compare our observations to the results of pKa shift for HEWL available in the literature and to some experimental data.

scholarly journals Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

2018 ◽  
Author(s):  
Debayan Chakraborty ◽  
Naoto Hori ◽  
D. Thirumalai
Keyword(s):  
Electrostatic Interactions ◽  
Persistence Length ◽  
Data Bank ◽  
Coarse Grained ◽  
Force Extension ◽  
Sequence Dependence ◽  
Coarse Grained Model ◽  
Interaction Sites ◽  
Double Stranded Dna ◽  
Centers Of Mass

AbstractWe develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduces the experimentally measured salt and sequence dependence of the size of single stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon application of mechanical force the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of poly(dT) is entropic in origin, and could be described by a standard polymer model. We also show that the persistence length of double stranded DNA, formed from two complementary ssDNAs with one hundred and thirty base pairs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.

scholarly journals Coarse-grained dynamic RNA titration simulations

2019 ◽  
Vol 9 (3) ◽  
pp. 20180066 ◽  
Author(s):  
S. Pasquali ◽  
E. Frezza ◽  
F. L. Barroso da Silva
Keyword(s):  
Electrostatic Interactions ◽  
Molecular Organization ◽  
Coarse Grained ◽  
Solution Ph ◽  
Dynamic Simulations ◽  
Rna Molecules ◽  
Coarse Grained Model ◽  
Constant Ph ◽  
Conformational Plasticity ◽  
And Function

Electrostatic interactions play a pivotal role in many biomolecular processes. The molecular organization and function in biological systems are largely determined by these interactions. Owing to the highly negative charge of RNA, the effect is expected to be more pronounced in this system. Moreover, RNA base pairing is dependent on the charge of the base, giving rise to alternative secondary and tertiary structures. The equilibrium between uncharged and charged bases is regulated by the solution pH, which is therefore a key environmental condition influencing the molecule’s structure and behaviour. By means of constant-pH Monte Carlo simulations based on a fast proton titration scheme, coupled with the coarse-grained model HiRE-RNA, molecular dynamic simulations of RNA molecules at constant pH enable us to explore the RNA conformational plasticity at different pH values as well as to compute electrostatic properties as local p K a values for each nucleotide.

scholarly journals Quantitative Prediction of pH-Controlled Ionization of Oligopeptides

2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Weak Acid ◽  
Coarse Grained ◽  
Quantitative Prediction ◽  
Bottom Up ◽  
Coarse Grained Model ◽  
Flexible Polymer ◽  
Acid And Base ◽  
Base Side ◽  
Capillary Zone

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their ionisation response and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Differences in ionisation response between oligopeptides and monomeric amino acids showed that electrostatic interactions between weak acid and base side chains play a key role in oligopeptide ionisation, as predicted by our model. Moreover, by comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the ionisation response and electrophoretic mobilities of various peptide sequences. Ultimately, our model is the first step towards using predictive bottom-up design of responsive ampholytes to tailor their properties as a function of charge and pH.<br>

A minimal coarse-grained model for the low-frequency normal mode analysis of icosahedral viral capsids

Soft Matter ◽  
2020 ◽  
Vol 16 (14) ◽  
pp. 3443-3455 ◽  
Author(s):  
M. Martín-Bravo ◽  
J. M. Gomez Llorente ◽  
J. Hernández-Rojas
Keyword(s):  
Structural Properties ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Low Frequency ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Viral Capsids ◽  
Mode Spectrum ◽  
Coarse Grained Model

A minimal coarse-grained model unveils relevant structural properties of icosahedral viral capsids when fitted to reproduce their low-frequency normal-mode spectrum.

scholarly journals Quantitative Prediction of pH-Controlled Ionization of Oligoampholytes

2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Weak Acid ◽  
Coarse Grained ◽  
Quantitative Prediction ◽  
Bottom Up ◽  
Coarse Grained Model ◽  
Flexible Polymer ◽  
Acid And Base ◽  
Base Side ◽  
Capillary Zone

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their ionisation response and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Differences in ionisation response between oligopeptides and monomeric amino acids showed that electrostatic interactions between weak acid and base side chains play a key role in oligopeptide ionisation, as predicted by our model. Moreover, by comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the ionisation response and electrophoretic mobilities of various peptide sequences. Ultimately, our model is the first step towards using predictive bottom-up design of responsive ampholytes to tailor their properties as a function of charge and pH.<br>

scholarly journals Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

2015 ◽  
Vol 142 (23) ◽  
pp. 234901 ◽  
Author(s):  
Benedict E. K. Snodin ◽  
Ferdinando Randisi ◽  
Majid Mosayebi ◽  
Petr Šulc ◽  
John S. Schreck ◽  
...  
Keyword(s):  
Structural Properties ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Salt Dependence

scholarly journals Entropic forces drive self-organization and membrane fusion by SNARE proteins

2017 ◽  
Vol 114 (21) ◽  
pp. 5455-5460 ◽  
Author(s):  
Hakhamanesh Mostafavi ◽  
Sathish Thiyagarajan ◽  
Benjamin S. Stratton ◽  
Erdem Karatekin ◽  
Jason M. Warner ◽  
...  
Keyword(s):  
Membrane Fusion ◽  
Electrostatic Interactions ◽  
Fusion Rate ◽  
Snare Proteins ◽  
Coarse Grained ◽  
Fusion Reactions ◽  
Coarse Grained Model ◽  
Fusion Site ◽  
Target Membrane ◽  
Long Timescales

SNARE proteins are the core of the cell’s fusion machinery and mediate virtually all known intracellular membrane fusion reactions on which exocytosis and trafficking depend. Fusion is catalyzed when vesicle-associated v-SNAREs form trans-SNARE complexes (“SNAREpins”) with target membrane-associated t-SNAREs, a zippering-like process releasing ∼65 kT per SNAREpin. Fusion requires several SNAREpins, but how they cooperate is unknown and reports of the number required vary widely. To capture the collective behavior on the long timescales of fusion, we developed a highly coarse-grained model that retains key biophysical SNARE properties such as the zippering energy landscape and the surface charge distribution. In simulations the ∼65-kT zippering energy was almost entirely dissipated, with fully assembled SNARE motifs but uncomplexed linker domains. The SNAREpins self-organized into a circular cluster at the fusion site, driven by entropic forces that originate in steric–electrostatic interactions among SNAREpins and membranes. Cooperative entropic forces expanded the cluster and pulled the membranes together at the center point with high force. We find that there is no critical number of SNAREs required for fusion, but instead the fusion rate increases rapidly with the number of SNAREpins due to increasing entropic forces. We hypothesize that this principle finds physiological use to boost fusion rates to meet the demanding timescales of neurotransmission, exploiting the large number of v-SNAREs available in synaptic vesicles. Once in an unfettered cluster, we estimate ≥15 SNAREpins are required for fusion within the ∼1-ms timescale of neurotransmitter release.

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