The Persistence Length of Semiflexible Polymers in Lattice Monte Carlo Simulations

Complementary Peptide Interactions Support the Ultra-Rigidity of Polymers of De Novo Designed Click-Functionalized Bundlemers

Computationally designed 29-residue peptides yield tetra-α-helical bundles with D2 symmetry. The "bundlemers" can be bifunctionally linked via thiol-maleimide cross-links at their N-termini, yielding supramolecular polymers with unusually large, micrometer-scale persistence lengths. To provide a molecularly resolved understanding of these systems, all-atom molecular modeling and simulations of linked bundlemers in explicit solvent are presented. A search over relative orientations of the bundlemers identifies a structure, wherein at the bundlemer-bundlemer interface, interior hydrophobic residues are in contact, and α-helices are aligned with a pseudocontiguous α-helix that spans the interface. Calculation of a potential of mean force confirms that the structure in which the bundlemers are in contact and colinearly aligned is a stable minimum. Analyses of hydrogen bonds and hydrophobic complementarity highlight the complementary interactions at the interface. The molecular insight provided reveals the molecular origins of bundlemer alignment within the supramolecular polymers.

Coarse-Grain Model of Ultrarigid Polymer Rods Comprising Bifunctionally Linked Peptide Bundlemers

Computationally designed homotetrameric helical peptide bundles have been functionalized at their N-termini to achieve supramolecular polymers, wherein individual bundles ("bundlemers") are the monomeric units. Adjacent bundles are linked via two covalent cross-links. The polymers exhibit a range of conformational properties, including formation of rigid-rods with micrometer-scale persistence lengths. Herein, a coarse-grained model is used to illuminate how molecular features affect the rod-like behavior of the polymers. With increasing affinity between bundlemer ends, a sharp transition in the persistence length is observed. Doubly linked chains exhibit larger persistence lengths and more robust formation of rigid-rod structures than singly linked chains. Chain stiffness increases with decreasing temperatures. Increasing the length of the cross-linker results in more flexible chains. This model provides insights into how molecular features control the structural properties of chains comprising doubly linked rigid bundlemers.

Structural and rheological properties of diluted alkali soluble pectin from apple and carrot

Pectin, a complex polysaccharide found in plant cell walls, plays a crucial role in various industries due to its functional properties. The diluted alkali-soluble pectin (DASP) fractions that result from the stepwise extraction of apples and carrots were studied to evaluate their structural and rheological properties. Homogalacturonan and rhamnogalacturonan I, in different proportions, were the main pectin domains that composed DASP from both materials. Atomic force microscopy revealed that the molecules of apple DASP were longer and more branched. A persistence length greater than 40 nm indicated that the pectin molecules deposited on mica behaved as stiff molecules. The weight-averaged molar mass was similar for both samples. Intrinsic viscosity values of 194.91 mL·g-1 and 186.79 mL·g-1 were obtained for apple and carrot DASP, respectively. Rheological measurements showed greater structural strength for apple-extracted pectin, whereas carrot pectin was characterized by a higher linear viscoelasticity limit. This comparison showed that the pectin fractions extracted by diluted alkali are structurally different and have different rheological properties depending on their botanical origin. The acquired insights can enhance the customized use of pectin residue and support further investigations in industries relying on pectin applications.

Genome wide nucleosome landscape shapes 3D chromatin organization

The hierarchical chromatin organization begins with formation of nucleosomes, which fold into chromatin domains punctuated by boundaries and ultimately chromosomes. In a hierarchal organization, lower levels shape higher levels. However, the dependence of higher-order 3D chromatin organization on the nucleosome-level organization has not been studied in cells. We investigated the relationship between nucleosome-level organization and higher-order chromatin organization by perturbing nucleosomes across the genome by deleting Imitation SWItch (ISWI) and Chromodomain Helicase DNA-binding (CHD1) chromatin remodeling factors in budding yeast. We find that changes in nucleosome-level properties are accompanied by changes in 3D chromatin organization. Short-range chromatin contacts up to a few kilo-base pairs decrease, chromatin domains weaken, and boundary strength decreases. Boundary strength scales with accessibility and moderately with width of nucleosome-depleted region. Change in nucleosome positioning seems to alter the stiffness of chromatin, which can affect formation of chromatin contacts. Our results suggest a biomechanical "bottom-up" mechanism by which nucleosome distribution across genome shapes 3D chromatin organization.

Molecular Weight-Dependent Physiochemical Behaviors of Calcium Carbonate Chains

The regulation of physiochemical behaviors by changing molecular weights is an important cornerstone of polymer physics. However, similar correlations between molecular weights and properties have not been discovered in inorganic ionic compounds. In this work, we prepared a calcium carbonate specimen with a semiflexible chain topology analogous to those of polymers. The molecular weights of the calcium carbonate chains, which ranged from 3400 to 54 100 Da, were directly correlated to their physiochemical behaviors, including gel point, zero shear viscosity, and plateau modulus. The calcium carbonate chains showed similar polymeric characteristics, including shear thinning, thixotropy, entropic elasticity, and viscoelasticity. These features agreed with recent theories and formulas in polymer physics textbooks. On the basis of this understanding, the mechanical properties of calcium carbonate-based gels could be altered by changing their molecular weights. This study could represent a fusion of inorganic chemistry and polymer physics with similar molecular weight-dependent behaviors and material properties, establishing an alternative pathway for designing future inorganic materials.

Oligomer-assisted self-assembly of bisurea in organic solvent media

We report on molecular dynamics simulation evidence revealing that an oligomer additive can be used to greatly facilitate the self-assembly of a bisurea in organic solvent media, through the initial regular packing and the subsequent stiffening of the self-assembly filament. The underlying physics is attributed to the substantially reduced diffusivities of the solute and, in particular, solvent molecules, featuring a generally weakened (thermal) Brownian force under ambient conditions. Without such oligomer-induced molecular cooling-in contrast to the usual external cooling, the original solvent medium is noted to foster instead more stabilized and disordered aggregates and, in particular, it would require a temperature reduction that is practically inaccessible in order to sustain similar stiffness of the self-assembly filament. These features, in accord with recent experimental observations, highlight the open opportunity of promoting the self-assembly of small functional molecules in general solvent media without requiring substantial changes of the system temperature, as is crucial for many practical applications including the biological/biomedical ones.

Pulse EPR spectroscopy and molecular modeling reveal the origins of the local heterogeneity of dietary fibers

Optimizing human diet by including dietary fibers would be more efficient when the fibers' chain interactions with other molecules are understood in depth. Thereby, it is important to develop methods for characterizing the fiber chain to be able to monitor its structural alterations upon intermolecular interactions. Here, we demonstrate the utility of the electron paramagnetic resonance (EPR) spectroscopy, complemented by simulations in probing the atomistic details of the chain conformations for spin-labeled fibers. Barley β-glucan, a native polysaccharide with linear chain, was utilized as a test fiber system to demonstrate the technique's capabilities. Pulse dipolar EPR data show good agreement with results of the fiber chain modeling, revealing sinuous chain conformations and providing polymer shape descriptors: the gyration tensor, spin-spin distance distribution function, and information about proton density near the spin probe. Results from EPR measurements point to the fiber aggregation in aqueous solution, which agrees with the results of the dynamic light scattering. We propose that the combination of pulse EPR measurements with modeling can be a perfect experimental tool for in-depth structural investigation of dietary fibers and their interaction under such conditions, and that the presented methodology can be extended to other weakly ordered or disordered macromolecules.

Lysozyme stability in various deep eutectic solvents using molecular dynamics simulations

The ability of neat deep eutectic solvents (DESs) to influence protein structure and function has gained considerable interest due to the unstable nature of enzymes or therapeutic proteins, which are often exposed to thermal, chemical, or mechanical stresses when handled at an industrial scale. In this study, we simulated a model globular protein, lysozyme, in water and six choline chloride-based DES using molecular dynamics simulations, to investigate the structural changes in various solvent environments, giving insights into the overall stability of lysozyme. Root mean square deviation (RMSD) and root mean square fluctuations (RMSF) of the C-α backbone indicated that most DESs induced a less flexible and rigid lysozyme structure compared to water. The radius of gyration and end-to-end distance calculations pointed towards higher structural compactness in reline and levuline, while the structure of lysozyme considerably expanded in oxaline. Protein-solvent interactions were further analysed by hydrogen bonding interactions and radial distribution functions (RDF), which indicated a higher degree of lysozyme-hydrogen bond donor (HBD) interactions compared to lysozyme-choline hydrogen bonding. Surface area analysis revealed an overall % increase in total positive, negative, donor, and acceptor surface areas in malicine and oxaline compared to water and other DESs, indicating the exposure of a larger number of residues to interactions with the solvent. Reline, levuline, and polyol-based DESs comparatively stabilized lysozyme, even though changes in the secondary/tertiary structures were observed.Communicated by Ramaswamy H. Sarma.

Partition complex structure can arise from sliding and bridging of ParB dimers

In many bacteria, chromosome segregation requires the association of ParB to the parS-containing centromeric region to form the partition complex. However, the structure and formation of this complex have been unclear. Recently, studies have revealed that CTP binding enables ParB dimers to slide along DNA and condense the centromeric region through the formation of DNA bridges. Using semi-flexible polymer simulations, we demonstrate that these properties can explain partition complex formation. Transient ParB bridges organize DNA into globular states or hairpins and helical structures, depending on bridge lifetime, while separate simulations show that ParB sliding reproduces the multi-peaked binding profile observed in Caulobacter crescentus. Combining sliding and bridging into a unified model, we find that short-lived ParB bridges do not impede sliding and can reproduce both the binding profile and condensation of the nucleoprotein complex. Overall, our model elucidates the mechanism of partition complex formation and predicts its fine structure.

Probing the Effect of Aliphatic Ionic Liquids on Asphaltene Aggregation Using Classical Molecular Dynamics Simulations

One of the major constituents of heavy oil is asphaltenes. They are responsible for numerous problems in petroleum downstream and upstream processes, such as catalyst deactivation in heavy oil processing and blocking pipes while transporting crude oil. Probing the efficiency of new nonhazardous solvents in separating asphaltenes from crude oil is key to avoid conventional volatile and hazardous solvents by replacing these conventional solvents with new ones. In this work, we have investigated the efficiency of ionic liquids to separate asphaltenes from organic solvents (such as toluene and hexane) using molecular dynamics simulations. Triethylammonium-dihydrogen-phosphate and triethylammonium acetate ionic liquids are considered in this work. Various structural and dynamical properties are calculated, such as radial distribution function, end-to-end distance, trajectory density contour, and diffusivity of asphaltene in the ionic liquid-organic solvent mixture. Our results explain the role of anions, i.e., dihydrogen-phosphate and acetate ions, in separating asphaltene from toluene and hexane. Our study provides an important revelation about the dominant role played by the IL anion in intermolecular interactions which depends on the type of solvent (i.e., toluene or hexane) in which the asphaltene is present. The anion induces enhanced aggregation in the asphaltene-hexane mixture compared to the asphaltene-toluene mixture. The molecular insights obtained within this study on the role played by ionic liquid anion in asphaltene separation are key for the preparation of new ionic liquids for asphaltene precipitation applications.

Extracellular matrix physical properties govern the diffusion of nanoparticles in tumor microenvironment

Nanoparticles (NPs) are confronted with limited and disappointing delivery efficiency in tumors clinically. The tumor extracellular matrix (ECM), whose physical traits have recently been recognized as new hallmarks of cancer, forms a main steric obstacle for NP diffusion, yet the role of tumor ECM physical traits in NP diffusion remains largely unexplored. Here, we characterized the physical properties of clinical gastric tumor samples and observed limited distribution of NPs in decellularized tumor tissues. We also performed molecular dynamics simulations and in vitro hydrogel experiments through single-particle tracking to investigate the diffusion mechanism of NPs and understand the influence of tumor ECM physical properties on NP diffusion both individually and collectively. Furthermore, we developed an estimation matrix model with evaluation scores of NP diffusion efficiency through comprehensive analyses of the data. Thus, beyond finding that loose and soft ECM with aligned structure contribute to efficient diffusion, we now have a systemic model to predict NP diffusion efficiency based on ECM physical traits and provide critical guidance for personalized tumor diagnosis and treatment.

What Is the Force-per-Molecule Inside a Biomaterial Having Randomly Oriented Units?

Both synthetic and natural protein-based materials are made of randomly oriented cross-linked molecules. Here we introduce a coarse-grained approach to estimate the average force-per-molecule for materials made from globular proteins. Our approach has three steps: placement of molecules inside a unit volume, cross-linking, and trimming to remove the protein domains that do not participate to the force response. Following this procedure, we estimate the number of active domains per cross-section area, that allows for a direct calculation of the force-per-domain. Among the variables considered, we found that concentration was the most sensitive parameter. We then synthesized protein hydrogels made from BSA and polyprotein L and measured the stresses that these materials can withstand. We found that forces-per-molecules of up to 17 pN per domain can be obtained experimentally using protein hydrogels. Our approach represents an important step toward understanding the scaling of tension in biomaterials.

Polyimide Hybrid Nanocomposites with Controlled Polymer Filling and Polymer-Matrix Interaction

Polyimide hybrid nanocomposites with the polyimide confined at molecular length scales exhibit enhanced fracture resistance with excellent thermal-oxidative stability at low density. Previously, polyimide nanocomposites were fabricated by infiltration of a polyimide precursor into a nanoporous matrix followed by sequential thermally induced imidization and cross-linking of the polyimide under nanometer-scale confinement. However, byproducts formed during imidization became volatile at the cross-linking temperature, limiting the polymer fill level and degrading the nanocomposite fracture resistance. This is solved in the present work with an easier approach where the nanoporous matrix is filled with shorter preimidized polyimide chains that are cross-linked while in the pores to eliminate the need for confined imidization reactions, which produces better results compared to the previous study. In addition, we selected a preimidized polyimide that has a higher chain mobility and a stronger interaction with the matrix pore surface. Consequently, the toughness achieved with un-cross-linked preimidized polyimide chains in this work is equivalent to that achieved with the cross-linking of the previously used polyimide chains and is doubled when preimidized polyimide chains are cross-linked. The increased chain mobility enables more efficient polymer filling and higher polymer fill levels. The higher polymer-pore surface interaction increases the energy dissipation during polyimide molecular bridging, increasing the nanocomposite fracture resistance. The combination of the higher polymer fill and the stronger polymer-surface interaction is shown to provide significant improvements to the nanocomposite fracture resistance and is validated with a molecular bridging model.

Viscoelasticity of Low-Molecular-Weight Polyelectrolytes

Shear-thickening fluids that absorb the impact energy of high-velocity projectiles are of great interest for aerospace and body-armor applications. In such a frame, we investigate transient states of neat and aqueous polyelectrolytes (PE) having low molecular weights and containing poly([2-(methacryloyloxy)ethyl]trimethylammonium) as polycations and poly(acrylamide-co-acrylic acid) as polyanions. We compare results with those of bulk water. We employ nonequilibrium molecular dynamics to simulate oscillatory shear, mainly in the linear viscoelastic regime. We find that neat PE exhibits properties of a viscoelastic solid, whereas water and the aqueous mixture of PE conform to viscoelastic liquids with Maxwellian behavior at low angular frequencies. Terminal relaxation times are ∼0.499 and ∼1.385 ps for water and the aqueous mixture of PE, respectively. At high angular frequencies, storage moduli show anomalous behaviors that correspond to transitions between shear thinning and shear thickening in complex shear viscosities. The change in potential energy with the increase of the angular frequency is mainly driven by intramolecular interactions for neat PE, whereas short-range Coulomb interactions are the major contributions for water and the aqueous mixture of PE. Upon observation of the molecular configurations, only the local polyionic structure in the aqueous mixture of PE shows improvement when increasing the angular frequency, whereas the rest remains barely affected. Thus, the water structure in the aqueous mixture of PE allows the storage of energy elastically through the hydrogen-bond network at large angular frequencies, whereas the mechanical contribution of polyions weakens and fully vanishes at the beginning of shear thinning, explaining the superimposed data with data of bulk water. Our method and findings set the path for future molecular simulations in the nonlinear viscoelastic regime with more complex underlying molecular mechanisms.

The Dynamic Behavior of Chromatin in Response to DNA Double-Strand Breaks

The primary functions of the eukaryotic nucleus as a site for the storage, retrieval, and replication of information require a highly dynamic chromatin organization, which can be affected by the presence of DNA damage. In response to double-strand breaks (DSBs), the mobility of chromatin at the break site is severely affected and, to a lesser extent, that of other chromosomes. The how and why of such movement has been widely studied over the last two decades, leading to different mechanistic models and proposed potential roles underlying both local and global mobility. Here, we review the state of the knowledge on current issues affecting chromatin mobility upon DSBs, and highlight its role as a crucial step in the DNA damage response (DDR).

Mechanical Properties of Flexible TPU-Based 3D Printed Lattice Structures: Role of Lattice Cut Direction and Architecture

This study addresses the mechanical behavior of lattice materials based on flexible thermoplastic polyurethane (TPU) with honeycomb and gyroid architecture fabricated by 3D printing. Tensile, compression, and three-point bending tests were chosen as mechanical testing methods. The honeycomb architecture was found to provide higher values of rigidity (by 30%), strength (by 25%), plasticity (by 18%), and energy absorption (by 42%) of the flexible TPU lattice compared to the gyroid architecture. The strain recovery is better in the case of gyroid architecture (residual strain of 46% vs. 31%). TPUs with honeycomb architecture are characterized by anisotropy of mechanical properties in tensile and three-point bending tests. The obtained results are explained by the peculiarities of the lattice structure at meso- and macroscopic level and by the role of the pore space.

Adsorption of semiflexible polymers in crowded environments

Macromolecular crowding is a feature of cellular and cell-free systems that, through depletion effects, can impact the interactions of semiflexible biopolymers with surfaces. In this work, we use computer simulations to study crowding-induced adsorption of semiflexible polymers on otherwise repulsive surfaces. Crowding particles are modeled explicitly, and we investigate the interplay between the bending stiffness of the polymer and the volume fraction and size of crowding particles. Adsorption to flat surfaces is promoted by stiffer polymers, smaller crowding particles, and larger volume fractions of crowders. We characterize transitions from non-adsorbed to partially and strongly adsorbed states as a function of bending stiffness. The crowding-induced transitions occur at smaller values of the bending stiffness as the volume fraction of crowders increases. Concomitant effects on the size and shape of the polymer are reflected by crowding- and stiffness-dependent changes to the radius of gyration. For various polymer lengths, we identify a critical crowding fraction for adsorption and analyze its scaling behavior in terms of polymer stiffness. We also consider crowding-induced adsorption in spherical confinement and identify a regime in which increasing the bending stiffness induces desorption. The results of our simulations shed light on the interplay of crowding and bending stiffness on the spatial organization of biopolymers in encapsulated cellular and cell-free systems.

Wetting characteristics of polymer adhesives with different chain bending stiffness

Polymer adhesives are widely used in daily applications and in industry owing to their flexibility and overall non-toxicity, particularly in interfacial adhesion. The spreading of polymer adhesives on adherend is one of the essential considerations for the interfacial adhesion of polymer adhesives, which is strongly related to their wetting behaviors. While relationships between polymer microstructure and adhesion have been investigated in previous studies, it remains challenging to unveil the effect of polymer microstructure on wettability. To address this issue, here we utilize coarse-grained molecular dynamics (CGMD) simulations to systematically elucidate how the wettability of a polymer adhesive droplet on a surface depends on bending stiffness. The wetting dynamics and the contact angle are studied to show the evolution of morphology of droplets during the wetting process. The results indicate the wettability is weakened by the increase of bending stiffness of polymer chain. Detailed thermodynamic property analysis is further conducted, revealing that the adhesion between the polymer droplet and substrate deteriorates due to the decline of wettability. Interestingly, we observe such deterioration becomes more significant by both increasing the temperature and decreasing the bending stiffness. Our study sheds light on the dependence of chain bending stiffness and temperature on the wetting behavior of polymer adhesive droplets, and offers insights, which, upon experimental validation can then be used for the design of adhesives or hydrogels.

Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps

JCVI-syn3A is a genetically minimal bacterial cell, consisting of 493 genes and only a single 543 kbp circular chromosome. Syn3A’s genome and physical size are approximately one-tenth those of the model bacterial organism Escherichia coli’s, and the corresponding reduction in complexity and scale provides a unique opportunity for whole-cell modeling. Previous work established genome-scale gene essentiality and proteomics data along with its essential metabolic network and a kinetic model of genetic information processing. In addition to that information, whole-cell, spatially-resolved kinetic models require cellular architecture, including spatial distributions of ribosomes and the circular chromosome’s configuration. We reconstruct cellular architectures of Syn3A cells at the single-cell level directly from cryo-electron tomograms, including the ribosome distributions. We present a method of generating self-avoiding circular chromosome configurations in a lattice model with a resolution of 11.8 bp per monomer on a 4 nm cubic lattice. Realizations of the chromosome configurations are constrained by the ribosomes and geometry reconstructed from the tomograms and include DNA loops suggested by experimental chromosome conformation capture (3C) maps. Using ensembles of simulated chromosome configurations we predict chromosome contact maps for Syn3A cells at resolutions of 250 bp and greater and compare them to the experimental maps. Additionally, the spatial distributions of ribosomes and the DNA-crowding resulting from the individual chromosome configurations can be used to identify macromolecular structures formed from ribosomes and DNA, such as polysomes and expressomes.

The branching angle effect on the properties of rigid dendrimers studied by Monte Carlo simulation

We studied the properties of rigid dendrimers with different branching angles by means of Monte Carlo simulations on a coarse-grained level. It was found that the terminal groups of dendrimers with both rigid and flexible spacers could locate near the center of the molecule. In flexible dendrimers, the wide distribution is attributed to the back folding of flexible spacers, while in rigid dendrimers, it is caused by the branching angle effect that a branch will grow laterally due to the restriction of a non-zero branching angle. It has been established that the branching angle is a key parameter for rigid dendrimers, which can be applied to tune the properties of rigid dendrimers: decreasing branching angle is helpful to obtain dendrimers with a larger size, lower density, and more terminal groups locating at periphery.

3D Conformations of Thick Synthetic Polymer Chains Observed by Cryogenic Electron Microscopy

The backbone conformations of individual, unperturbed synthetic macromolecules have so far not been observed directly in spite of their fundamental importance to polymer physics. Here we report the dilute solution conformations of two types of linear dendronized polymers, obtained by cryogenic transmission electron stereography and tomography. The three-dimensional trajectories show that the wormlike chain model fails to adequately describe the scaling of these thick macromolecules already beyond a few nanometers in chain length, in spite of large apparent persistence lengths and long before a signature of self-avoidance appears. This insight is essential for understanding the limitations of polymer physical models, and it motivated us to discuss the advantages and disadvantages of this approach in comparison to the commonly applied scattering techniques.