Dynamic spatial and structural organization in artificial cells regulates signal processing by protein scaffolding

Structural and spatial organization are fundamental properties of biological systems that allow cells to regulate a wide range of biochemical processes. This organization is often transient and governed by external cues that initiate dynamic self-assembly processes. The construction of synthetic cell-like materials with similar properties requires the hierarchical and reversible organization of selected functional components on molecular scaffolds to dynamically regulate signaling pathways. The realization of such transient molecular programs in synthetic cells, however, remains underexplored due to the associated complexity of such hierarchical platforms. In this contribution, we effectuate dynamic spatial organization of effector protein subunits in a synthetic biomimetic compartment, a giant unilamellar vesicle (GUV), by associating in a reversible manner two fragments of a split luciferase to the membrane. This induces their structural dimerization, which consequently leads to the activation of enzymatic signaling. Importantly, such organization and activation are dynamic processes, and can be autonomously regulated – thus opening up avenues toward continuous spatiotemporal control over supramolecular organization and signaling in an artificial cell.

Engineered artificial cells respond to environmental cues through a pre-programmed enzymatic machinery that induces spatio-structural organization and activation of effector proteins at the lipid membrane.     

Quantum and classical studies of vibrational motion of CH5+ on a global potential energy surface obtained from a novel ab initio direct dynamics approach

We report a full dimensional, ab initio based potential energy surface for CH(5) (+). The ab initio electronic energies and gradients are obtained in direct-dynamics calculations using second-order M?ller-Plesset perturbation theory with the correlation consistent polarized valence triple zeta basis. The potential energy and the dipole moment surfaces are fit using novel procedures that ensure the full permutational symmetry of the system. The fitted potential energy surface is tested by comparing it against additional electronic energy calculations and by comparing normal mode frequencies at the three lowest-lying stationary points obtained from the fit against ab initio ones. Well-converged diffusion Monte Carlo zero-point energies, rotational constants, and projections along the CH and HH bond lengths and the tunneling coordinates are presented and compared with the corresponding harmonic oscillator and standard classical molecular dynamics ones. The delocalization of the wave function is analyzed through comparison of the CH(5) (+) distributions with those obtained when all of the hydrogen atoms are replaced by (2)H and (3)H. The classical dipole correlation function is examined as a function of the total energy. This provides a further probe of the delocalization of CH(5) (+).     

Potential energy surface and quantum dynamics study of rovibrational states for HO(3) (X (2)A')

An analytic potential energy surface has been constructed by fitting to about 28 thousand energy points for the electronic ground-state (X (2)A') of HO(3). The energy points are calculated using a hybrid density functional HCTH and a large basis set aug-cc-pVTZ, i.e., a HCTH/aug-cc-pVTZ density functional theory (DFT) method. The DFT calculations show that the trans-HO(3) isomer is the global minimum with a potential well depth of 9.94 kcal mol(-1) with respect to the OH + O(2) asymptote. The equilibrium geometry of the cis-HO(3) conformer is located 1.08 kcal mol(-1) above that of the trans-HO(3) one with an isomerization barrier of 2.41 kcal mol(-1) from trans- to cis-HO(3). By using this surface, a rigorous quantum dynamics (QD) study has been carried out for computing the rovibrational energy levels of HO(3). The calculated results determine a dissociation energy of 6.15 kcal mol(-1), which is in excellent agreement with the experimental value of Lester et al. [J. Phys. Chem. A, 2007, 111, 4727.].     

The theoretical prediction of infrared spectra of trans- and cis-hydroxycarbene calculated using full dimensional ab initio potential energy and dipole moment surfaces

Accurate infrared spectra of the two hydroxycarbene isomers are computed by diagonalizing the Watson Hamiltonian including up to four mode couplings using full dimensional potential energy and dipole moment surfaces calculated at the CCSD(T)/cc-pVTZ (frozen core) and CCSD6-311G(**) (all electrons correlated) levels, respectively. Anharmonic corrections are found to be very important for these elusive higher-energy isomers of formaldehyde. Both the energy levels and intensities of stretching fundamentals and all overtone transitions are strongly affected by anharmonic couplings between the modes. The results for trans-HCOHHCOD are in excellent agreement with the recently reported IR spectra, which validates our predictions for the cis-isomers.     

Combinatorial functionalization with bisurea‐peptides and antifouling bisurea additives of a supramolecular elastomeric biomaterial

The bioactive additive toolbox to functionalize supramolecular elastomeric materials expands rapidly. Here we have set an explorative step toward screening of complex combinatorial functionalization with antifouling and three peptide‐containing additives in a bisurea‐based supramolecular system. Thorough investigation of surface properties of thin films with contact angle measurements, X‐ray photoelectron spectroscopy and atomic force microscopy, was correlated to cell‐adhesion of endothelial and smooth muscle cells to apprehend their respective predictive values for functional biomaterial development. Peptides were presented at the surface alone, and in combinatorial functionalization with the oligo(ethylene glycol)‐based non‐cell adhesive additive. The bisurea‐RGD additive was cell‐adhesive in all conditions, whereas the endothelial cell‐specific bisurea‐REDV showed limited bioactive properties in all chemical nano‐environments. Also, aspecific functionality was observed for a bisurea‐SDF1α peptide. These results emphasize that special care should be taken in changing the chemical nano‐environment with peptide functionalization. © 2019 The Authors. Journal of Polymer Science Part B: Polymer Physics published by Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1725–1735     

Synthesis and Reactivity of an Anionic Diazoolefin

Bent (hetero)allenes such as carbodicarbenes and carbodiphosphoranes can act as neutral C-donor ligands, and diverse applications in coordination chemistry have been reported. N-Heterocyclic diazoolefins are heterocumulenes, which can function in a similar fashion as L-type ligands. Herein, we describe the synthesis and the reactivity of an anionic diazoolefin. This compound displays distinct reactivity compared to neutral diazoolefins, as evidenced by the preparation of diazo compounds via protonation, alkylation, or silylation. The anionic diazoolefin can be employed as an ambidentate, X-type ligand in salt metathesis reactions with metal halide complexes. Extrusion of dinitrogen was observed in a reaction with PCl(NiPr₂)₂, resulting in a stable phosphinocarbene.     

Higher mass loadability in comprehensive two-dimensional gas chromatography-mass spectrometry for improved analytical performance in metabolomics analysis

A major challenge in metabolomics analysis is the accurate quantification of metabolites in the presence of (extremely) high abundant metabolites. Quantification of metabolites at low concentrations can be complicated by co-elution and/or peak distortion when these metabolites elute close to high abundant metabolites. To increase the separation efficiency a comprehensive two-dimensional gas chromatographic-mass spectrometric method (GC x GC-MS) was set up, in which a polar first dimension column and an apolar second dimension column were used to maximize the peak capacity. The feasibility of using wider bore, thicker film columns in the second dimension to improve the mass loadability and inertness of the analytical system was investigated. Several column combinations with varying second dimension column dimensions were compared with a setup with a narrow bore column (0.1mm I.D.) in the second dimension. With a wider bore column (0.32 mm I.D.) in the second dimension the mass loadability was improved 10-fold, and the more inert column surface of the thicker film second dimension column resulted in a more accurate (automated) quantification and improved linearity in the presence of high concentrations of matrix compounds or metabolites. These benefits amply compensated the observed decrease in peak capacity of 40% compared to the narrow bore (0.1mm I.D.) thin film second dimension column. Compared to GC-MS and conventional GC x GC-MS, better performance for quantification of metabolites for typical metabolomics samples was achieved.     

Accurate ab initio structure, dissociation energy, and vibrational spectroscopy of the F(-)-CH4 anion complex

Accurate equilibrium structure, dissociation energy, global potential energy surface (PES), dipole moment surface (DMS), and the infrared vibrational spectrum in the 0-3000 cm(-1) range of the F(-)-CH4 anion complex have been obtained. The equilibrium electronic structure calculations employed second-order M?ller-Plesset perturbation theory (MP2) and coupled-cluster (CC) method up to single, double, triple, and perturbative quadruple excitations using the aug-cc-p(C)VXZ [X = 2(D), 3(T), 4(Q), and 5] correlation-consistent basis sets. The best equilibrium geometry has been obtained at the all-electron CCSD(T)/aug-cc-pCVQZ level of theory. The dissociation energy has been determined based on basis set extrapolation techniques within the focal-point analysis (FPA) approach considering (a) electron correlation beyond the all-electron CCSD(T) level, (b) relativistic effects, (c) diagonal Born-Oppenheimer corrections (DBOC), and (d) variationally computed zero-point vibrational energies. The final D(e) and D0 values are 2398 +/- 12 and 2280 +/- 20 cm(-1), respectively. The global PES and DMS have been computed at the frozen-core CCSD(T)/aug-cc-pVTZ and MP2/aug-cc-pVTZ levels of theory, respectively. Variational vibrational calculations have been performed for CH4 and F(-)-CH4 employing the vibrational configuration interaction (VCI) method as implemented in Multimode.