Ca-Mediated Synthetic Biosystems Offer Protein Design Versatility, Signal Specificity, and Pathway Rewiring

Synthetic biosystems have been engineered that enable control of metazoan cell morphology, migration, and death. These systems possess signal specificity, but lack flexibility of input signal. To exploit the potential of Ca²⁺ signaling, we designed RhoA chimeras for reversible, Ca²⁺-dependent control over RhoA morphology and migration. First, we inserted a calmodulin-binding peptide into a RhoA loop that activates or deactivates RhoA in response to Ca²⁺ signals depending on the chosen peptide. Second, we localized the Ca²⁺-activated RhoA chimera to the plasma membrane, where it responded specifically to local Ca²⁺ signals. Third, input control of RhoA morphology was rewired by coexpressing the Ca²⁺-activated RhoA chimera with Ca²⁺-transport proteins using acetylcholine, store-operated Ca²⁺ entry, and blue light. Engineering synthetic biological systems with input versatility and tunable spatiotemporal responses motivates further application of Ca²⁺ signaling in this field.     

Electronic structures, vibrational and thermochemical properties of neutral and charged niobium clusters Nb(n), n = 7-12

Geometric and electronic structures, vibrational properties, and relative stabilities of niobium clusters Nb(n), n = 7-12, are studied using both DFT (BPW91 and M06 functionals) and CCSD(T) calculations with the cc-pVnZ-PP basis set. In each cluster, various lower-lying states are very close in energy in such a way that the ground state cannot be unambiguously established by DFT computations. Nb clusters tend to prefer the lowest possible spin state as the ground state, except for Nb(12) ((3)A(g)). The optimal structure of the cluster at a certain size does not simply grow from that of the smaller one by adding an atom randomly. Instead, the Nb clusters prefer a close-packed growth behavior. Nb(10) has a spherically aromatic character, high chemical hardness and large HOMO-LUMO gap. Electron affinities, ionization energies, binding energy per atom, and the stepwise dissociation energies are evaluated. Energetic properties exhibit odd-even oscillations. Comparison with experimental values shows that both BPW91 and M06 functionals are reliable in predicting the EA and IE values, but the BPW91 is deficient in predicting the binding and dissociation energies. We re-examine in particular the experimental far IR spectra previously recorded using the IR-MPD and free electron laser spectrometric techniques and propose novel assignments for Nb(7) and Nb(9) systems. The IR spectra of the anions are also predicted.     

Multi‐Species Multi‐Channel (MSMC): An Ab Initio‐based Parallel Thermodynamic and Kinetic Code for Complex Chemical Systems

Multi‐Species Multi‐Channel (MSMC) is an ab initio parallel program to calculate thermodynamic quantities (e.g., , , , and , time‐dependent species profiles, and rate coefficients as functions of temperature and pressure for complex chemical reaction systems, which consist of multiple stable species and multiple reaction channels interconnecting them. Thermodynamic properties of the species involved are calculated using statistical mechanics with molecular information from electronic structure calculations. Temperature‐ and pressure‐dependent behaviors are rigorously characterized within the eigenpair master equation/Rice–Ramsperger–Kassel–Marcus (ME/RRKM) framework. Corrections, e.g., for hindered internal rotation and tunneling treatment, are included. With the implementation of an ultra‐high precision package and rigorous matrix setup, MSMC is able to correctly mimic real behaviors of different types of chemical systems. Different eigenpair‐based approaches to extract phenomenological/macroscopic rate coefficients are implemented for different applications. Moreover, a friendly and platform‐independent graphical‐user‐interface (GUI) is provided to facilitate the use of MSMC and the pre‐/postcalculation data visualization/analysis on the fly. The program can be freely downloaded at https://sites.google.com/site/msmccode/ .     

A new dimeric alkylresorcinol from the stem barks of Swintonia floribunda (Anacardiaceae)

From an EtOAc-soluble fraction of the stem barks of Swintonia floribunda (Anacardiaceae), one new dimeric alkylresorcinol named integracin E (1), together with 4 known compounds (2–5) were isolated. Their chemical structures were elucidated based on the spectroscopic data interpretation. The absolute configuration of 1 was determined by the specific rotation analysis of its acid-catalyzed hydrolysis product. Compound 1 showed potent tyrosinase inhibitory activity with an IC₅₀ value of 48.2?μM.     

Long‐Lived Spin States for Low‐Field Hyperpolarized Gas MRI

Parahydrogen induced polarization was employed to prepare a relatively long‐lived correlated nuclear spin state between methylene and methyl protons in propane gas. Conventionally, such states are converted into a strong NMR signal enhancement by transferring the reaction product to a high magnetic field in an adiabatic longitudinal transport after dissociation engenders net alignment (ALTADENA) experiment. However, the relaxation time T₁ of ～0.6 s of the resulting hyperpolarized propane is too short for potential biomedical applications. The presented alternative approach employs low‐field MRI to preserve the initial correlated state with a much longer decay time T_LLSS=(4.7±0.5) s. While the direct detection at low‐magnetic fields (e.g. 0.0475 T) is challenging, we demonstrate here that spin‐lock induced crossing (SLIC) at this low magnetic field transforms the long‐lived correlated state into an observable nuclear magnetization suitable for MRI with sub‐millimeter and sub‐second spatial and temporal resolution, respectively. Propane is a non‐toxic gas, and therefore, these results potentially enable low‐cost high‐resolution high‐speed MRI of gases for functional imaging of lungs and other applications.     

New method for determining size of critical nucleus of fibril formation of polypeptide chains

A new method for determining the size of critical nucleus of fibril formation of polypeptide chains is proposed. Based on the hypothesis that the fibril grows by addition of a nascent peptide to the preformed template, the nucleus size N(c) is defined as the number of forming template peptides above which the time to add a new monomer becomes independent of the template size. Using lattice models one can show that our method and the standard method which is based on calculation of the free energy, provide the same result for N(c).     

Unexpected formation of dinaphthoaza-17-crown-5 ether containing γ-aminopiperidine subunit

1. Download : Download high-res image (90KB)
2. Download : Download full-size image

     

On the position of the upper limit temperature of homogeneous nucleation of precipitates in low concentrated Al?Zn alloys

The upper limit temperature T_hn of the onset of homogeneous nucleation of Guinier-Preston (GP) zones was determined for three Al Zn alloys with xZn = 4.5, 6.0 and 8.0 at.% by SAXS investigations (cooling from the range of homogeneity to various temperatures T_a and ageing at T_a). The results are T_hn = (95 ± 3) °C for xZn = 4.5 at.%, (118 ± 3) °C (6.0 at.%) and (154 ± 3) °C (8.0 at.%), respectively. The obtained results fit well the data known for the alloys with higher contents of Zn. It is stressed that one has to distinguish between T_hn, determined by isothermal measurements after a direct quench or cooling to the respective T_a, and the upper limit temperature T_rhn of the onset of the rapid homogeneous nucleation of GP zones (continuous cooling).     

An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide

We present an application of our recently proposed coupled reference interaction site model (RISM) molecular dynamics (MD) solvation free energy methodology [Freedman and Truong, Chem. Phys. Lett. 381, 362 (2003); J. Chem. Phys. 121, 2187 (2004)] to study the conformational stability of alanine dipeptide in aqueous solution. In this methodology, radial distribution functions obtained from a single MD simulation are substituted into a RISM expression for solvation free energy. Consequently, iterative solution of the RISM equation is not needed. The relative solvation free energies of seven different conformations of the alanine dipeptide in aqueous solution are calculated. Results from the coupled RISM/MD methodology are in good agreement with those from earlier simulations using the accurate free energy perturbation approach, showing that the alphaR conformation is most stabilized by solution. This study establishes a framework for applying this coupled RISM/MD method to larger biological systems.