Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions

Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs). The overestimation of protein-protein interactions tends to make IDPs more compact than those in experiments. Likewise, multiple proteins in crowded solutions are aggregated with each other too strongly. To optimize the balance, Lennard-Jones (LJ) interactions between protein and water are often increased about 10% (with a scaling parameter, λ = 1.1) from the existing force fields. Here, we explore the optimal scaling parameter of protein-water LJ interactions for CHARMM36m in conjunction with the modified TIP3P water model, by performing enhanced sampling MD simulations of several peptides in dilute solutions and conventional MD simulations of globular proteins in dilute and crowded solutions. In our simulations, 10% increase of protein-water LJ interaction for the CHARMM36m cannot maintain stability of a small helical peptide, (AAQAA)₃ in a dilute solution and only a small modification of protein-water LJ interaction up to the 3% increase (λ = 1.03) is allowed. The modified protein-water interactions are applicable to other peptides and globular proteins in dilute solutions without changing thermodynamic properties from the original CHARMM36m. However, it has a great impact on the diffusive properties of proteins in crowded solutions, avoiding the formation of too sticky protein-protein interactions.     

Efficient Transformation of Polymer Main Chain Catalyzed by Macrocycle Metal Complexes via Pseudorotaxane Intermediate

Post-synthesis modification of polymers streamlines the synthesis of functionalized polymers, but is often incomplete due to the negative polymer effects. Developing efficient polymer reactions in artificial systems thus represents a long-standing objective in the fields of polymer and material science. Here, we show unprecedented macrocycle-metal-complex-catalyzed systems for efficient polymer reaction that result in 100 % transformation of the main chain functional groups presumably via a processive mode reaction. The complete polymer reactions were confirmed in not only intramolecular reaction (hydroamination) but also intermolecular reaction (hydrosilylation) by using Pd- and Pt-macrocycle-catalyzed systems. The most fascinating feature of the both reactions is that higher-molecular-weight polymers reach completion faster. Various studies suggested that the reactions occur in the catalyst cavity via the formation of a supramolecular complex between the macrocycle catalyst and polymer substrate like pseudorotaxane, which should be of characteristic of the efficient polymer reactions progressing in a processive mode.     

ATP-Responsive Nanoparticles Covered with Biomolecular Machine “Chaperonin GroEL”

Herein, we report an ATP-responsive nanoparticle (^GroELNP) whose surface is fully covered with the biomolecular machine “chaperonin protein GroEL”. ^GroELNP was synthesized by DNA hybridization between a gold NP with DNA strands on its surface and GroEL carrying complementary DNA strands at its apical domains. The unique structure of ^GroELNP was visualized by transmission electron microscopy including under cryogenic conditions. The immobilized GroEL units retain their machine-like function and enable ^GroELNP to capture denatured green fluorescent protein and release it in response to ATP. Interestingly, the ATPase activity of ^GroELNP per GroEL was 4.8 and 4.0 times greater than those of precursor ^cysGroEL and its DNA-functionalized analogue, respectively. Finally, we confirmed that ^GroELNP could be iteratively extended to double-layered NP.     

Polymer design for thermally stable polyimides with low dielectric constant

We successfully prepared a series of thermally stable polyimides (PIs) with low dielectric constant (k) by introducing bulky diphenyl fluorenylidene moieties in backbone. The lowest k was found to be 2.77 among non-fluorinated PIs and 2.35 among fluorinated ones. In order to prove the lowest limit of k in PIs, we prepared soluble and thermally stable polyarylenes (PArs) without polar imide linkage with the same aromatic moieties by coupling polymerization. The lowest k was 2.7 without fluorine (F) and 2.2 with F atom, which showed also promising for low k materials. From these results, PIs we prepared were estimated to the lowest k values among PIs. On the basis of statistics on these results, we could express contour lines of k as a function of imide concentration and F content with high correlation factor (r= 0.96) in PIs and PArs.