Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network.

The ubiquitin pathway required for most proteins' targeted degradation involves three classes of enzymes: E1-activating enzyme, E2-conjugating enzyme, and E3-ligases. The human Ark2C is the single known E3 ligase that adopts an alternative, Ub-dependent mechanism for the activation of Ub transfer in the pathway. Its RING domain binds both E2-Ub and free Ub with high affinity, resulting in a catalytic active UbR-RING-E2-UbD complex formation. We examined potential changes in the conformational plasticity of the Ark2C RING domain and its ligands in their complexed form within the ubiquitin pathway through molecular dynamics (MD). Three molecular mechanics force fields compared to previous NMR relaxation studies of RING domain of Arkadia were used for effective and accurate assessment of MDs. Our results suggest the Ark2C Ub-RING docking site has a substantial impact on maintaining the conformational rigidity of E2-E3 assembly, necessary for the E3's catalytic activity. In the UbR-RING-E2-UbD catalytic complex, the UbR molecule was found to have greater mobility than the other Ub, bound to E2. Furthermore, network-based bioinformatics helped us identify E3 RING ligase candidates which potentially exhibit similar structural modules as Ark2C, along with predicted substrates targeted by the Ub-binding RING Ark2C. Our findings could trigger a further exploration of related unrevealed functions of various other E3 RING ligases.

Mikto-Arm Stars as Soft-Patchy Particles: From Building Blocks to Mesoscopic Structures.

We present an atomistic molecular dynamics study of self-assembled mikto-arm stars, which resemble patchy-like particles. By increasing the number of stars in the system, we propose a systematic way of examining the mutual orientation of these fully penetrable patchy-like objects. The individual stars maintain their patchy-like morphology when creating a mesoscopic (macromolecular) self-assembled object of more than three stars. The self-assembly of mikto-arm stars does not lead to a deformation of the stars, and their shape remains spherical. We identified characteristic sub-units in the self-assembled structure, differing by the mutual orientation of the nearest neighbor stars. The current work aims to elucidate the possible arrangements of the realistic, fully penetrable patchy particles in polymer matrix and to serve as a model system for further studies of nanostructured materials or all-polymer nanocomposites using the mikto-arm stars as building blocks.

Effect of pH and Molecular Length on the Structure and Dynamics of Linear and Short-Chain Branched Poly(ethylene imine) in Dilute Solution: Scaling Laws from Detailed Molecular Dynamics Simulations.

Atomistic molecular dynamics (MD) simulations are carried out to examine the effect of molecular weight Mw (= 0.6, 0.86, 1.12, and 2.15 kDa) and pH (or equivalently, degree of ionization, α+ = 0, 50, and 100%) on the structure, state of hydration, and dynamics of linear and branched poly(ethylene imine) (PEI) chains in infinitely dilute salt-free aqueous solutions. It is found that the degree of ionization is the key factor determining the type of molecular conformation adopted by PEI, regardless of molecular architecture and chain length, resulting in a stable trans conformation for fully ionized solutions and in a stable gauche+/gauche- state for neutral or alternate ionized ones; in the latter case, a strong electrolyte behavior is verified for both linear and branched PEI. Linear PEI is observed to be significantly stiffer than branched PEI of the same molecular weight at 100% degree of ionization, but the effect subsides as the degree of ionization decreases. Also, linear PEI diffuses markedly slower than branched PEI of the same Mw. From the MD results, scaling exponents are deduced and reported for the conformation, solvent-accessible surface area, and dynamics of the two different PEI structures with Mw.

Effect of Polymer Concentration on the Structure and Dynamics of Short Poly(N,N-dimethylaminoethyl methacrylate) in Aqueous Solution: A Combined Experimental and Molecular Dynamics Study.

A combined experimental and molecular dynamics (MD) study is performed to investigate the effect of polymer concentration on the zero shear rate viscosity η0 of a salt-free aqueous solution of poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA), a flexible thermoresponsive weak polyelectrolyte with a bulky 3-methyl-1,1-diphenylpentyl unit as the terminal group. The study is carried out at room temperature (T = 298 K) with relatively short PDMAEMA chains (each containing N = 20 monomers or repeat units) at a fixed degree of ionization (α+ = 100%). For the MD simulations, a thorough validation of several molecular mechanics force fields is first undertaken for assessing their capability to accurately reproduce the experimental observations and established theoretical laws. The generalized Amber force field in combination with the restrained electrostatic potential charge fitting method is eventually adopted. Three characteristic concentration regimes are considered: the dilute (from 5 to 10 wt %), the semidilute (from 10 to 20 wt %), and the concentrated (from 20 to 29 wt %); the latter two are characterized by polymer concentrations cp higher than the characteristic overlap concentration cp*. The structural behavior of the PDMAEMA chains in the solution is assessed by calculating the square root of their mean-square radius of gyration ⟨Rg2⟩0.5, the square root of the average square chain end-to-end distance ⟨Ree2⟩0.5, the ratio ⟨Ree2⟩/⟨Rg2⟩, and the persistence length Lp. It is observed that at low polymer concentrations, PDMAEMA chains adopt a stiffer and slightly extended conformation because of excluded-volume effects (a good solvent is considered in this study) and electrostatic repulsions within the polymer chains. As the polymer concentration increases above 20 wt %, the PDMAEMA chains adopt more flexible conformations, as the excluded-volume effects seize and the charge repulsion within the polymer chains subsides. The effect of total polymer concentration on PDMAEMA chain dynamics in the solution is assessed by calculating the orientational relaxation time τc of the chain, the center-of-mass diffusion coefficient D, and the zero shear rate viscosity η0; the latter is also measured experimentally here and found to be in excellent agreement with the MD predictions.

Effect of pH and Molecular Length on the Structure and Dynamics of Short Poly(acrylic acid) in Dilute Solution: Detailed Molecular Dynamics Study.

Long MD simulations are carried out using a detailed all-atom force field to investigate the effect of pH or, equivalently, degree of ionization α- (= 0, 50, 100%) and degree of polymerization N (= 20, 23, 46, 70, and 110) on the structure and dynamics of poly(acrylic acid) (PAA) at infinite dilution. To ensure the validity and add to the reliability of our research conclusions, a systematic validation of several molecular mechanics force fields is performed. It is observed that the generalized AMBER force field in combination with the RESP charge fitting method best describes both the structural and dynamical behavior of PAA in comparison to experimentally obtained data. It is found that ⟨ Rg2⟩0.5changes with N as ⟨ Rg2⟩0.5 ∼ Nν, with ν = 0.27 at α- = 0% degree of ionization (acidic conditions), ν = 0.94 at α- = 50% degree of ionization (neutral conditions), and ν = 0.87 at α- = 100% degree of ionization (basic conditions), which is in perfect agreement with theory. The global shape of the PAA chain in the solution is quantified in terms of the three eigenvalues of the average radius-of-gyration tensor, the relative shape anisotropy κ2, and the asphericity parameter b. It is revealed that at α- = 0%, the chain adopts a spherelike conformation, while at α- = 50 and 100%, its conformation is flattened and flexible. In addition, it is revealed that as the degree of ionization increases, the persistence length Lp increases, which suggests that PAA chains become stiffer with increasing pH. The global and local conformational changes of the PAA chain with the degree of ionization are found to be highly related to the solvation of the polymer. Finally, it is revealed that the diffusion coefficient D of the center of mass of PAA also exhibits a power law scaling with N, D ∼ Nν, with ν = 0.25 at α- = 0% degree of ionization, ν = 0.46 at α- = 50% degree of ionization (neutral conditions), and ν = 0.44 at α- = 100% degree of ionization (basic conditions), in excellent agreement with recent experimental data and theoretical predictions.