SciCombinator

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Concept: Macromolecule

193

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology.

Concepts: Protein, Cell, Molecular biology, Metabolism, Enzyme, Nucleic acid, Biochemistry, Macromolecule

28

A model for the limiting surface tension of surfactant solutions (surface tension at and above the critical micelle concentration, cmc) was developed. This model takes advantage of the equilibrium between the surfactant molecules on the liquid/vacuum surface and in micelles in the bulk at the cmc. An approximate analytical equation for the surface tension at the cmc was obtained. The derived equation contains two parameters, which characterize the intermolecular interactions in the micelles, and the third parameter, which is the surface area per surfactant molecule at the interface. These parameters were calculated using a new atomistic modeling approach. The performed calculations of the limiting surface tension for four simple surfactants show good agreement with experimental data (∼30% accuracy). The developed model provides the guidance for design of surfactants with low surface tension values.

Concepts: Chemistry, Surface tension, Surfactant, Micelle, Quaternary ammonium cation, Solution, Macromolecule, Colloidal chemistry

28

Many biopolymers assume ordered structure in solution due to specific intermolecular interactions, and subsequently aggregate to form fibrous network structures, which play important structural and functional roles both in biomedical tissues and in biopolymeric applied materials. In this study, the pulsed-field-gradient stimulated echo (PGSTE) (1)H NMR method was utilized to elucidate the gelation mechanism and to determine the network structure of agarose. The echo signal intensity of agarose decreased with the formation of aggregated bundles, and therefore, it was used to determine the concentration of the solute agarose (c(sol)) in the gel. The diffusion coefficient of a dendrimer, added to the gel as a probe molecule, increased concomitantly with the formation of the network of aggregated bundles, suggesting apparent dilution of solute agarose in the network interspaces. The hydrodynamic mesh size (ξ) of the network was estimated from the degree of retardation of the diffusion. The dependence of ξ on c(sol) was interpreted using a simple model, where the hydrodynamic interaction of the probe molecule with a solute chain or an aggregated bundle of chains is same. Our theoretically predicted lines fitted well on the experimentally obtained plots, thus validating the use of this model.

Concepts: Matter, Structure, Concentration, Chemistry, Colloid, Physical chemistry, Solution, Macromolecule

27

Intermolecular interaction in the 1,2,5-chalcogenadiazole dimers was studied by ab initio molecular orbital calculations. Estimated CCSD(T) interaction energies for the thia-, selena- and tellura-diazole dimers are -3.14, -5.29 and -12.42 kcal/mol, respectively. The electrostatic and dispersion interactions are the major sources of the attraction in the dimers, although it was claimed that the orbital mixing (charge-transfer interaction) was the most prominent contribution to the stabilization. The induction (induced polarization) interaction also contributes largely to the attraction in the telluradiazole dimer. The large electrostatic and induction interactions are responsible for the strong attraction in the telluradiazole dimer. On the other hand, the short-range (orbital-orbital) interaction (sum of the exchange-repulsion and charge-transfer interactions) is repulsive. The directionality of the interactions increases in order of S < Se < Te. The electrostatic interaction is mainly responsible for the directionality. The strong directionality suggests that the chalcogen-nitrogen interaction plays important roles in controlling the orientation of molecules in those organic crystals. The nature of the chalcogen-nitrogen interaction in the chalcogenadiazole dimers is similar to that of the halogen bond, which is electrostatically-driven noncovalent interaction.

Concepts: Electron, Fundamental physics concepts, Maxwell's equations, Molecule, Chemistry, Van der Waals force, Chemical bonding, Macromolecule

27

A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.

Concepts: Cell nucleus, Cell, Cytosol, Organelle, Cell biology, Diffusion, Macromolecule, Random walk

27

In this paper, Small and Wide Angle X-ray Scattering (SWAXS) analysis of macromolecules is demonstrated through experimentation. SWAXS is a technique where X-rays are elastically scattered by an inhomogeneous sample in the nm-range at small angles (typically 0.1 - 5°) and wide angles (typically > 5°). This technique provides information about the shape, size, and distribution of macromolecules, characteristic distances of partially ordered materials, pore sizes, and surface-to-volume ratio. Small Angle X-ray Scattering (SAXS) is capable of delivering structural information of macromolecules between 1 and 200 nm, whereas Wide Angle X-ray Scattering (WAXS) can resolve even smaller Bragg spacing of samples between 0.33 nm and 0.49 nm based on the specific system setup and detector. The spacing is determined from Bragg’s law and is dependent on the wavelength and incident angle. In a SWAXS experiment, the materials can be solid or liquid and may contain solid, liquid or gaseous domains (so-called particles) of the same or another material in any combination. SWAXS applications are very broad and include colloids of all types: metals, composites, cement, oil, polymers, plastics, proteins, foods, and pharmaceuticals. For solid samples, the thickness is limited to approximately 5 mm. Usage of a lab-based SWAXS instrument is detailed in this paper. With the available software (e.g., GNOM-ATSAS 2.3 package by D. Svergun EMBL-Hamburg and EasySWAXS software) for the SWAXS system, an experiment can be conducted to determine certain parameters of interest for the given sample. One example of a biological macromolecule experiment is the analysis of 2 wt% lysozyme in a water-based aqueous buffer which can be chosen and prepared through numerous methods. The preparation of the sample follows the guidelines below in the Preparation of the Sample section. Through SWAXS experimentation, important structural parameters of lysozyme, e.g. the radius of gyration, can be analyzed.

Concepts: Diffraction, Chemistry, Polymer, X-ray crystallography, Macromolecule, William Lawrence Bragg, X-rays, Small-angle X-ray scattering

27

Presently, there are no effective treatments for several diseases involving the CNS, which is protected by the blood-brain, blood-CSF and blood-arachnoid barriers. Traversing any of these barriers is difficult, especially for macromolecular drugs and particulates. However, there is significant experimental evidence that large molecules can be delivered to the CNS through the cerebro-spinal fluid (CSF). The flux of the interstitial fluid in the CNS parenchyma, as well as the macro flux of CSF in the leptomeningeal space, are believed to be generally opposite to the desirable direction of CNS-targeted drug delivery. On the other hand, the available data suggest that the layer of pia mater lining the CNS surface is not continuous, and the continuity of the leptomeningeal space (LMS) with the perivascular spaces penetrating into the parenchyma provides an unexplored avenue for drug transport deep into the brain via CSF. The published data generally do not support the view that macromolecule transport from the LMS to CNS is hindered by the interstitial and CSF fluxes. The data strongly suggest that leptomeningeal transport depends on the location and volume of the administered bolus and consists of four processes: (i) pulsation-assisted convectional transport of the solutes with CSF, (ii) active “pumping” of CSF into the periarterial spaces, (iii) solute transport from the latter to and within the parenchyma, and (iv) neuronal uptake and axonal transport. The final outcome will depend on the drug molecule behavior in each of these processes, which have not been studied systematically. The data available to date suggest that many macromolecules and nanoparticles can be delivered to CNS in biologically significant amounts (>1% of the administered dose); mechanistic investigation of macromolecule and particle behavior in CSF may result in a significantly more efficient leptomeningeal drug delivery than previously thought.

Concepts: Central nervous system, Brain, Molecule, Cerebrospinal fluid, Macromolecule, Meninges, Arachnoid mater, Pia mater

26

Abstract This study is aimed to investigate the applicability of poloxamer 407 (P407) and 188 (P188)-based temperature-sensitive in situ hydrogel (TSHG) in sustained delivery of hydrophilic macromolecules following intramuscular administration. Polyethylene glycols (PEGs) with molecular weight of 5-, 20-, and 40-kDa were used as model drugs, which can represent the common size range of hydrophilic macromolecular drugs using TSHG. The correlation between the level of poloxamers and thermogelling transition temperatures (Tsol-gel) was established and two formulations “20% P407/10% P188” and “24% P407/10% P188” were chosen for further study. The results showed that the release kinetics of PEGs was close to zero order. Sustained in vivo behaviors were achieved by both of the two formulations for all the PEGs though variations were seen. Lower molecular weight PEG showed more remarkable pharmacokinetic improvements. No significant differences in pharmacokinetics were observed between the two formulations for the same PEG. This suggested that 20-24% P407/10% P188 formulations, with accordingly Tsol-gel in the range of 24.6 °C-31.7 °C, might be freely chosen to achieve comparable pharmacokinetics for hydrophilic macromolecular drugs after intramuscular injection.

Concepts: Pharmacology, Molecule, In vivo, Route of administration, In situ, Macromolecule, Poloxamer, Poloxamer 407

22

The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies.

Concepts: Protein, Cell, Enzyme, Cytosol, Cytoskeleton, Macromolecule

19

Molecular self-assembly refers to the spontaneous assembly of molecules into larger structures. In order to exploit molecular self-assembly for the bottom-up synthesis of nanomaterials, the effects of chemical control (strength of the directionality in the intermolecular interaction) and entropic control (temperature) on the self-assembly process should be clarified. Here we present a theoretical methodology that unambiguously distinguishes the effects of chemical and entropic control on the self-assembly of molecules adsorbed to metal surfaces. While chemical control simply increases the formation probability of ordered structures, entropic control induces a variety of effects. These effects range from fine structure modulation of ordered structures, through to degrading large, amorphous structures into short, chain-shaped structures. Counterintuitively, the latter effect shows that entropic control can improve molecular ordering. By identifying appropriate levels of chemical and entropic control, our methodology can, therefore, identify strategies for optimizing the yield of desired nanostructures from the molecular self-assembly process.

Concepts: DNA, Molecule, Chemistry, Thermodynamics, Nanotechnology, Self-organization, Systems theory, Macromolecule