The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage

The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial alpha-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.     

Rapid synthesis of the N-methylwelwitindolinone skeleton

An efficient, convergent synthesis of the core bicyclo[4.3.1]decane ring system of welwitindolinones is described. Key steps in the synthesis include an intramolecular palladium-catalyzed enolate arylation reaction to create the desired bicyclic skeleton and a Curtius rearrangement to install the bridgehead isocyanate unit. [reaction: see text]     

Lewis adducts of the side-on end-on dinitrogen-bridged complex [{(NPN)Ta}2(mu-H)2(mu-eta 1:eta 2-N2)] with AlMe3, GaMe3, and B(C6F5)3: synthesis, structure, and spectroscopic properties

Reaction of the side-on end-on dinitrogen complex [{(NPN)Ta}(2)(mu-H)(2)(mu-eta(1):eta(2)-N(2))] (1; in which NPN=(PhNSiMe(2)CH(2))(2)PPh), with the Lewis acids XR(3) results in the adducts [{(NPN)Ta}(2)(mu-H)(2)(mu-eta(1):eta(2)-NNXR(3))], XR(3)=GaMe(3) (2), AlMe(3) (3), and B(C(6)F(5))(3) (4). The solid-state molecular structures of 2, 3, and 4 demonstrate that the N-N bond length increases relative to those found in 1 by 0.036, 0.043, and 0.073 A, respectively. In solution complexes 2-4 are fluxional as evidenced by variable-temperature (1)H NMR spectroscopy. The (15)N{(1)H} NMR spectra of 2-4 are reported; furthermore, their vibrational properties and electronic structures are evaluated. The vibrational structures are found to be closely related to that of the parent complex 1. Detailed spectroscopic analysis on 2-4 leads to the identification of the theoretically expected six normal modes of the Ta(2)N(2) core. On the basis of experimental frequencies and the QCB-NCA procedure, the force constants are determined. Importantly, the N-N force constant decreases from 2.430 mdyn A(-1) in 1 to 1.876 (2), 1.729 (3), and 1.515 mdyn A(-1) (4), in line with the sequence of N-N bond lengths determined crystallographically. DFT calculations on a generic model of the Lewis acid adducts 2-4 reveal that the major donor interaction between the terminal nitrogen atom and the Lewis acid is mediated by a sigma/pi hybrid molecular orbital of N(2), corresponding to a sigma bond. Charge analysis performed for the adducts indicates that the negative charge on the terminal nitrogen atom of the dinitrogen ligand increases with respect to 1. The lengthening of the N-N bond observed for the Lewis adducts is therefore explained by the fact that charge donation from the complex fragment into the pi* orbitals of dinitrogen is increased, while electron density from the N-N bonding orbitals p(sigma) and pi(h) is withdrawn due to the sigma interaction with the Lewis acid.     

Experimental and Computational Study of the Thermal Decomposition of 3‐Methyl‐3‐buten‐1‐ol in m‐Xylene Solution

An experimental study of the thermal decomposition of a β‐hydroxy alkene, 3‐methyl‐3‐buten‐1‐ol, in m‐xylene solution, has been carried out at five different temperatures in the range of 513.15–563.15 K. The temperature dependence of the rate constants for the decomposition of this compound in the corresponding Arrhenius equation is given by ln k (s^?1) = (25.65 ± 1.52) ? (17,944 ± 814) (kJ·mol^?1)·T^?1. A computational study has been carried out at the M05–2X/6–31+G(d,p) level of theory to calculate the rate constants and the activation parameters by the classical transition state theory. There is a good agreement between the experimental and calculated rate constants and activation Gibbs energies. The bonding characteristics of reactant, transition state, and products have been investigated by the natural bond orbital analysis, which provides the natural atomic charges and the Wiberg bond indices. Based on the results obtained, the mechanism proposed is a one‐step process proceeding through a six‐membered cyclic transition state, being a concerted and slightly asynchronous process. The results have been compared with those obtained previously by us (Struct Chem 2013, 24, 1811–1816) for the thermal decomposition of 3‐buten‐1‐ol, in m‐xylene solution. We can conclude that in the compound studied in this work, 3‐methyl‐3‐buten‐1‐ol, the effect of substitution at position 3 by a weakly activating CH₃ group is the stabilization of the transition state formed in the reaction and therefore a small increase in the rate of thermal decomposition.     

Structural and Kinetic Aspects of Blood Plasma Protein Adsorption on the Surface of Hydrophobic Polymers

Abstract

Due to the wide use of polymers in medicine, researchers are required to solve a very important problem–to understand the interaction between materials of nonphysiological origin and the surrounding biological liquids, and tissues, particularly blood.     

Extended Peptide Nucleic Acid Nucleobases Based on Isoorotic Acid for the Recognition of A–U Base Pairs in Double-Stranded RNA

Peptide nucleic acids (PNA) with extended isoorotamide containing nucleobases ( I _o ) were designed for binding A–U base pairs in double-stranded RNA. Isothermal titration calorimetry and UV thermal melting experiments revealed improved affinity for A–U using the Io scaffold in PNA. PNAs having four sequential Io extended nucleobases maintained high binding affinity.