Replica Exchange Monte Carlo Simulation of Human Serum Albumin–Catechin Complexes

Replica exchange Monte Carlo simulation equipped with an orientation-enhanced hydrophobic interaction was utilized to study the impacts of molar ratio and ionic strength on the complex formation of human serum albumin (HSA) and catechin. Only a small amount of catechins was found to act as bridges in the formation of HSA–catechin complexes. Selective binding behavior was observed at low catechin to HSA molar ratio (<i>R</i>). Increase of catechin amount can suppress HSA self-aggregation and diminish the selectivity of protein binding sites. Strong saturation binding with short-range interactions was found to level off at around 4.6 catechins per HSA on average, while this number slowly increased with <i>R</i> when long-range interactions were taken into account. Meanwhile, among the three rings of catechin, the 3,4-dihydroxyphenyl (B-ring) shows the strongest preference to bind HSA. Neither the aggregation nor the binding sites of the HSA–catechin complex was sensitive to ionic strength, suggesting that the electrostatic interaction is not a dominant force in such complexes. These results provide a further molecular level understanding of protein–polyphenol binding, and the strategy employed in this work shows a way to bridge phase behaviors at macroscale and the distribution of binding sites at residue level

Monte Carlo Simulation on Complex Formation of Proteins and Polysaccharides

In protein–polysaccharide complex systems, how nonspecific interactions such as electrostatic and van der Waals interactions affect complex formation has not been clearly understood. On the basis of a coarse-grained model with the specificity of a target system, we have applied Monte Carlo (MC) simulation to illustrate the process of complex coacervate formation from the association of proteins and polysaccharides. The coarse-grained model is based on serum albumin and a polycation system, and the MC simulation of pH impact on complex coacervation has been carried out. We found that complex coacervates could form three ways, but the conventional association through electrostatic attraction between the protein and polysaccharide still dominated the complex coacervation in such systems. We also observed that the depletion potential always participated in protein crowding and was weakened in the presence of strong electrostatic interactions. Furthermore, we observed that the sizes of polysaccharide chains nonmonotonically increased with the number of bound proteins. Our approach provides a new way to understand the details during protein–polysaccharide complex coacervation at multiple length scales, from interaction and conformation to aggregation

Evolution of Chain Conformation and Entanglements during Startup Shear

Using Brownian dynamics simulation, we determine chain dimensions in an entangled polymer melt undergoing startup shear at a rate lower than the reciprocal of the Rouse time yet higher than the reciprocal reptation time. Here the tube model expects negligible chain stretching. In contrast, our simulation shows the deformed coil to conform closely to affine deformation. We find that the total number of entanglements decreases with increasing shear. Remarkably, up to many Rouse time, the decline in the number of initial entanglements is slower than that under the quiescent condition. These results point to fundamental deficiencies in the molecular picture of the tube model for startup shear

Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers

How polymers with different architectures respond to shear stress is a key issue to develop a fundamental understanding of their dynamical behaviors. We investigate the conformation, orientation, dynamics, and rheology of individual star polymers in a simple shear flow by multiparticle collision dynamics integrated with molecular dynamics simulations. Our studies reveal that star polymers present a linear transformation from tumbling to tank-treading-like motions as the number of arms increases. In the transformation region, the flow-induced deformation, orientation, frequency of motions, and rheological properties show universal scaling relationships against the reduced Weissenberg number, independent of the number and the length of arms. Further, we make a comprehensive comparison on the flow-induced behaviors between linear, ring, and star polymers. The results indicate that distinct from linear polymers, star and ring polymers present weaker deformation, orientation change, and shear thinning, either contributed by a dense center or without ends

Monte Carlo Study of Polyelectrolyte Adsorption on Mixed Lipid Membrane

Monte Carlo simulations are employed to investigate the adsorption of a flexible linear cationic polyelectrolyte onto a fluid mixed membrane containing neutral (phosphatidyl-choline, PC), multivalent (phosphatidylinositol, PIP₂), and monovalent (phosphatidylserine, PS) anionic lipids. We systematically study the effect of chain length and charge density of the polyelectrolyte, the solution ionic strength, as well as the membrane compositions on the conformational and interfacial properties of the model system. In particular, we explore (i) the adsorption/desorption limit, (ii) the interfacial structure variations of the adsorbing polyelectrolyte and the lipid membrane, and (iii) the overcharging of the membrane. Polyelectrolyte adsorbs on the membrane when anionic lipid demixing entropy loss and polyelectrolyte flexibility loss due to adsorption are dominated by electrostatic attraction between polyelectrolyte and anionic lipids on the membrane. Polyelectrolytes with longer chain length and higher charge density can adsorb on the membrane with increased anionic lipid density under a higher critical ionic concentration. Below the critical ionic concentration, the adsorption extent increases with the charge density and chain length of the polyelectrolyte and decreases with the ionic strength of the solution. The diffusing anionic lipids prohibit the polyelectrolyte chain from forming too long tails. The adsorbing polyelectrolyte with long chain length and high charge density can overcharge a membrane with low charge density, and conversely, the membrane charge inversion forces the polyelectrolyte chain to form extended loops and tails in the solution

Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers

How polymers with different architectures respond to shear stress is a key issue to develop a fundamental understanding of their dynamical behaviors. We investigate the conformation, orientation, dynamics, and rheology of individual star polymers in a simple shear flow by multiparticle collision dynamics integrated with molecular dynamics simulations. Our studies reveal that star polymers present a linear transformation from tumbling to tank-treading-like motions as the number of arms increases. In the transformation region, the flow-induced deformation, orientation, frequency of motions, and rheological properties show universal scaling relationships against the reduced Weissenberg number, independent of the number and the length of arms. Further, we make a comprehensive comparison on the flow-induced behaviors between linear, ring, and star polymers. The results indicate that distinct from linear polymers, star and ring polymers present weaker deformation, orientation change, and shear thinning, either contributed by a dense center or without ends

Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers

How polymers with different architectures respond to shear stress is a key issue to develop a fundamental understanding of their dynamical behaviors. We investigate the conformation, orientation, dynamics, and rheology of individual star polymers in a simple shear flow by multiparticle collision dynamics integrated with molecular dynamics simulations. Our studies reveal that star polymers present a linear transformation from tumbling to tank-treading-like motions as the number of arms increases. In the transformation region, the flow-induced deformation, orientation, frequency of motions, and rheological properties show universal scaling relationships against the reduced Weissenberg number, independent of the number and the length of arms. Further, we make a comprehensive comparison on the flow-induced behaviors between linear, ring, and star polymers. The results indicate that distinct from linear polymers, star and ring polymers present weaker deformation, orientation change, and shear thinning, either contributed by a dense center or without ends

Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers

How polymers with different architectures respond to shear stress is a key issue to develop a fundamental understanding of their dynamical behaviors. We investigate the conformation, orientation, dynamics, and rheology of individual star polymers in a simple shear flow by multiparticle collision dynamics integrated with molecular dynamics simulations. Our studies reveal that star polymers present a linear transformation from tumbling to tank-treading-like motions as the number of arms increases. In the transformation region, the flow-induced deformation, orientation, frequency of motions, and rheological properties show universal scaling relationships against the reduced Weissenberg number, independent of the number and the length of arms. Further, we make a comprehensive comparison on the flow-induced behaviors between linear, ring, and star polymers. The results indicate that distinct from linear polymers, star and ring polymers present weaker deformation, orientation change, and shear thinning, either contributed by a dense center or without ends

Genetic Characterization of a Novel Iflavirus Associated with Vomiting Disease in the Chinese Oak Silkmoth <i>Antheraea pernyi</i>

<div><p>Larvae of the Chinese oak silkmoth (<i>Antheraea pernyi</i>) are often affected by AVD (<i>A. pernyi</i> vomiting disease), whose causative agent has long been suspected to be a virus. In an unrelated project we discovered a novel positive sense single-stranded RNA virus that could reproduce AVD symptoms upon injection into healthy <i>A. pernyi</i> larvae. The genome of this virus is 10,163 nucleotides long, has a natural poly-A tail, and contains a single, large open reading frame flanked at the 5′ and 3′ ends by untranslated regions containing putative structural elements for replication and translation of the virus genome. The open reading frame is predicted to encode a 3036 amino acid polyprotein with four viral structural proteins (VP1-VP4) located in the N-terminal end and the non-structural proteins, including a helicase, RNA-dependent RNA polymerase and 3C-protease, located in the C-terminal end of the polyprotein. Putative 3C-protease and autolytic cleavage sites were identified for processing the polyprotein into functional units. The genome organization, amino acid sequence and phylogenetic analyses suggest that the virus is a novel species of the genus <i>Iflavirus</i>, with the proposed name of <i>Antheraea pernyi</i> Iflavirus (ApIV).</p></div