Rakwoo Chang

Nanochannel confinement: DNA stretch approaching full contour length

Fully stretched DNA molecules are becoming a fundamental component of new systems for comprehensive genome analysis. Among a number of approaches for elongating DNA molecules, nanofluidic molecular confinement has received enormous attentions from physical and biological communities for the last several years. Here we demonstrate a well-optimized condition that a DNA molecule can stretch almost to its full contour length: the average stretch is 19.1 µm ± 1.1 µm for YOYO-1 stained λ DNA (21.8 µm contour length) in 250 nm × 400 nm channel, which is the longest stretch value ever reported in any nanochannels or nanoslits. In addition, based on Odijks polymer physics theory, we interpret our experimental findings as a function of channel dimensions and ionic strengths. Furthermore, we develop a Monte Carlo simulation approach using a primitive model for the rigorous understanding of DNA confinement effects. Collectively, we present a more complete understanding of nanochannel confined DNA stretching via the comparisons to computer simulation results and Odijks polymer physics theory.

Solvent effects on the collapse dynamics of polymers

The effect of solvent on the collapse dynamics of polymers is studied using computer simulation. Two cases are investigated, one where the solvent is incorporated through a pairwise additive attraction between the polymer beads and a random force on each polymer bead, and another where the solvent is incorporated in an explicit fashion as a second component. Brownian dynamics and molecular dynamics simulations are used in the former and latter model, respectively, with intermolecular interactions chosen so that the equilibrium size of the polymer is similar in both models at similar conditions. In the Brownian dynamics simulations, at short times local blobs of monomers are found separated by linear segments. With time the blobs grow in size and coalesce to form sausage like shapes. These sausages gradually become thicker and shorter until the final shape of a spherical globule is reached. The first stage is rapid whereas the second sausage-sphere stage is slow. In this stage the polymer often gets trappe...

Molecular Dynamics Simulation Study of a Pulmonary Surfactant Film Interacting with a Carbonaceous Nanoparticle

This article reports an all-atom molecular dynamics simulation to study a model pulmonary surfactant film interacting with a carbonaceous nanoparticle. The pulmonary surfactant is modeled as a dipalmitoylphosphatidylcholine monolayer with a peptide consisting of the first 25 residues from surfactant protein B. The nanoparticle model with a chemical formula C188H53 was generated using a computational code for combustion conditions. The nanoparticle has a carbon cage structure reminiscent of the buckyballs with open ends. A series of molecular-scale structural and dynamical properties of the surfactant film in the absence and presence of nanoparticle are analyzed, including radial distribution functions, mean-square displacements of lipids and nanoparticle, chain tilt angle, and the surfactant protein B peptide helix tilt angle. The results show that the nanoparticle affects the structure and packing of the lipids and peptide in the film, and it appears that the nanoparticle and peptide repel each other. The ability of the nanoparticle to translocate the surfactant film is one of the most important predictions of this study. The potential of mean force for dragging the particle through the film provides such information. The reported potential of mean force suggests that the nanoparticle can easily penetrate the monolayer but further translocation to the water phase is energetically prohibitive. The implication is that nanoparticles can interact with the lung surfactant, as supported by recent experimental data by Bakshi et al.

Strongly charged flexible polyelectrolytes in poor solvents: Molecular dynamics simulations with explicit solvent

The behavior of salt-free solutions of charged flexible polymer molecules in poor solvents is studied using molecular dynamics simulations. The polymer molecules are modeled as chains of charged spheres, the counterions as charged spheres, and the solvent molecules are incorporated explicitly and modeled as uncharged spheres. The equilibrium static and dynamic properties are studied as a function of solvent quality. In many-chain systems, for slightly poor solvents, no peak is observed in the static structure factor at low semidilute concentrations, but a peak appears at higher concentrations. In this regime, chains form bead–necklace structures, and the counterions are strongly correlated with the polyions. When the solvent quality is decreased further, at nonzero but low polymer concentrations, the solution becomes unstable towards phase separation. The dense phase takes on spherical, cylindrical, or lamellar structures depending on the polymer concentration. The mass and charge density profiles of poly...

Structural Properties of Neurofilament Sidearms: Sequence-Based Modeling of Neurofilament Architecture

Neurofilaments (NFs) are essential cytoskeletal filaments that impart mechanical integrity to nerve cells. They are assembled from three distinct molecular mass proteins that bind to each other to form a 10-nm-diameter filamentous rod with sidearm extensions. The sidearms are considered to play a critical role in modulating interfilament spacing and axonal caliber. However, the precise mechanism by which NF protrusions regulate axonal diameter remains to be well understood. In particular, the role played by individual NF protrusions in specifying interfilament distances is yet to be established. To gain insight into the role of individual proteins, we investigated the structural organization of NF architecture under different phosphorylation conditions. To this end, a physically motivated sequence-based coarse-grain model of NF brush has been developed based on the three-dimensional architecture of NFs. The model incorporates the charge distribution of sidearms, including charges from the phosphorylation sites corresponding to Lys-Ser-Pro repeat motifs. The model also incorporates the proper grafting of the real NF sidearms based on the stoichiometry of the three subunits. The equilibrium structure of the NF brush is then investigated under different phosphorylation conditions. The phosphorylation of NF modifies the structural organization of sidearms. Upon phosphorylation, a dramatic change involving a transformation from a compact conformation to an extended conformation is found in the heavy NF (NF-H) protein. However, in spite of extensive phosphorylation sites present in the NF-H subunit, the tails of the medium NF subunit are found to be more extended than the NF-H sidearms. This supports the notion that medium NF protrusions are critical in regulating NF spacings and, hence, axonal caliber.

Expansion of neurofilament medium C terminus increases axonal diameter independent of increases in conduction velocity or myelin thickness.

Maturation of the peripheral nervous system requires specification of axonal diameter, which, in turn, has a significant influence on nerve conduction velocity. Radial axonal growth initiates with myelination, and is dependent upon the C terminus of neurofilament medium (NF-M). Molecular phylogenetic analysis in mammals suggested that expanded NF-M C termini correlated with larger-diameter axons. We used gene targeting and computational modeling to test this new hypothesis. Increasing the length of NF-M C terminus in mice increased diameter of motor axons without altering neurofilament subunit stoichiometry. Computational modeling predicted that an expanded NF-M C terminus extended farther from the neurofilament core independent of lysine-serine-proline (KSP) phosphorylation. However, expansion of NF-M C terminus did not affect the distance between adjacent neurofilaments. Increased axonal diameter did not increase conduction velocity, possibly due to a failure to increase myelin thickness by the same proportion. Failure of myelin to compensate for larger axonal diameters suggested a lack of plasticity during the processes of myelination and radial axonal growth.

Brownian dynamics simulations of polyelectrolyte solutions with divalent counterions

Brownian dynamics simulations are performed for salt-free polyelectrolyte solutions with divalent counterions. The polymer molecules are modeled as freely jointed charged chains and the counterions are incorporated explicitly. The conformational properties, static structure, and dynamic properties of salt-free polyelectrolyte solutions show interesting behavior that can be attributed to the correlations induced by the counterions. The size of polyelectrolyte chains and the counterion self-diffusion coefficient show a nonmonotonic concentration dependence. There is a sharp peak in the polyion pair correlation functions at short distances and an upturn in the partial static structure factors at low wave vectors. In semidilute solutions, the polyions contract in the presence of divalent counterions, when compared to solutions with monovalent counterions. This contraction is accompanied by the peak in the static structure moving to lower wave vectors. The self-diffusion of polyions is faster with divalent cou...

Systems-level modeling with molecular resolution elucidates the rate-limiting mechanisms of cellulose decomposition by cellobiohydrolases

Background: Cellobiohydrolase enzymes processively degrade crystalline cellulose into free sugar molecules. Results: A spatially resolved kinetic model has been developed to understand the effects of interfacial confinement on cellobiohydrolase activity. Conclusion: Cellobiohydrolase activity is limited by slow rates of complexation with cellulose and traffic jamming among enzymes on the substrate. Significance: Identifying kinetic effects imposed by interfacial confinement is crucial for understanding and engineering cellulose bioconversion. Interprotein and enzyme-substrate couplings in interfacial biocatalysis induce spatial correlations beyond the capabilities of classical mass-action principles in modeling reaction kinetics. To understand the impact of spatial constraints on enzyme kinetics, we developed a computational scheme to simulate the reaction network of enzymes with the structures of individual proteins and substrate molecules explicitly resolved in the three-dimensional space. This methodology was applied to elucidate the rate-limiting mechanisms of crystalline cellulose decomposition by cellobiohydrolases. We illustrate that the primary bottlenecks are slow complexation of glucan chains into the enzyme active site and excessive enzyme jamming along the crowded substrate. Jamming could be alleviated by increasing the decomplexation rate constant but at the expense of reduced processivity. We demonstrate that enhancing the apparent reaction rate required a subtle balance between accelerating the complexation driving force and simultaneously avoiding enzyme jamming. Via a spatiotemporal systems analysis, we developed a unified mechanistic framework that delineates the experimental conditions under which different sets of rate-limiting behaviors emerge. We found that optimization of the complexation-exchange kinetics is critical for overcoming the barriers imposed by interfacial confinement and accelerating the apparent rate of enzymatic cellulose decomposition.

Adsorption and Dynamics of a Single Polyelectrolyte Chain near a Planar Charged Surface: Molecular Dynamics Simulations with Explicit Solvent.

The effect of solvent quality on the behavior of a polyelectrolyte chain near a charged surface is studied using molecular dynamics simulation with explicit solvent. The polyion adsorbs completely on the surface for a high enough surface charge density, and the surface charge required for complete adsorption becomes lower as the solvent quality is decreased. Several static and dynamic properties display a nonmonotonic dependence on surface charge density and solvent quality. For a given value of solvent quality the component of the radius of gyration (Rg) parallel to the surface is a nonmonotonic function of the surface charge density, and for a given surface charge density the component of Rg perpendicular to the surface is a nonmonotonic function of the solvent quality. The center-of-mass diffusion coefficient and rotational relaxation time are nonmonotonic functions of the surface charge density. Translational diffusion coefficient increases, and the rotational relaxation time decreases as solvent quality is decreased for a fixed surface charge density.

Phosphorylation-mediated conformational changes in the mouse neurofilament architecture: Insight from a neurofilament brush model

Neurofilaments (NFs) are important cytoskeletal filaments that consist of long flexible C-terminal tails that are abundant with charges. The tails attain additional negative charges through serine phosphorylation of Lys-Ser-Pro (KSP) repeat motifs that are particularly found in neurofilament heavy (NF-H) and neurofilament medium (NF-M) proteins. These side-arm protrusions mediate the interaction between neighboring filaments and maintain axonal diameter. However, the precise role of NF proteins and their phosphorylation in regulating interfilament distances and axonal diameter still remains unclear. In this regard, a recent gene replacement study revealed that the phosphorylation of mouse NF-M KSP repeats does not affect axonal cytoarchitecture, challenging the conventional viewpoint on the role of NF phosphorylation. To better understand the effect of phosphorylation, particularly NF-M phosphorylation, we applied a computational method to reveal phosphorylation-mediated conformational changes in mouse NF architecture. We employed a three-dimensional sequence-based coarse-grained NF brush model to perform Monte Carlo simulations of mouse NF by using the sequence and stoichiometry of mouse NF proteins. Our result shows that the phosphorylation of mouse NF-M does not change the radial extension of NF-M side arms under a salt-free condition and in ionic solution, highlighting a structural factor that supports the notion that NF-M KSP phosphorylation has no effect on the axonal diameter of mouse. On the other hand, significant phosphorylation-mediated conformational changes were found in NF-H side arms under the salt-free condition, while the changes in ionic solution are not significant. However, NF-H side arms are found at the periphery of mouse NF architecture, implying a role in linking neighboring filaments.