Coherent two-dimensional infrared spectroscopy: quantitative analysis of protein secondary structure in solution

We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent two-dimensional infrared (2DIR) spectroscopy of backbone amide I vibrations (1550-1720 cm(-1)). Sixteen proteins with known crystal structures were used to construct a library of 2DIR spectra, and the fraction of residues in α-helix, β-sheet, and unassigned conformations was determined by singular value decomposition (SVD) of the measured two-dimensional spectra. The method was benchmarked by removing each individual protein from the set and comparing the composition extracted from 2DIR against the composition determined from the crystal structures. To highlight the increased structural content extracted from 2DIR spectra a similar analysis was also carried out using conventional infrared absorption of the proteins in the library.     

A space-indexed formulation of packing boxes into a larger box

Current integer programming solvers fail to decide whether 12 unit cubes can be packed into a 1×1×11 box within an hour using the natural relaxation of Chen/Padberg. We present an alternative relaxation of the problem of packing boxes into a larger box, which makes it possible to solve much larger instances.     

Non-extinction of a Fleming-Viot particle model

We consider a branching particle model in which particles move inside a Euclidean domain according to the following rules. The particles move as independent Brownian motions until one of them hits the boundary. This particle is killed but another randomly chosen particle branches into two particles, to keep the population size constant. We prove that the particle population does not approach the boundary simultaneously in a finite time in some Lipschitz domains. This is used to prove a limit theorem for the empirical distribution of the particle family.     

Can the replacement of a single atom in the enzyme horseradish peroxidase convert it into a monoxygenase? A density functional study

Density functional calculations on horseradish peroxidase mutants are presented, whereby one or two of the nitrogen atoms of the axial histidine ligand have been replaced by phosphorus atoms. Our calculations show that phosphorus entices a push effect on the oxoiron group, whereas a histidine side chain withdraws electrons. As a result, we predict that a phosphorus-substituted histidine ligand will convert the active form of a peroxidase into a monoxygenase. This subsitution may be useful for the bioengineering of commercially exploitable enzymes.     

Comparison of linear and 2D IR spectra in the presence of fast exchange

The few picosecond time scale H-bond making and breaking in the system acetonitrile-methanol dominates the mechanism of vibrational coherence transfer that is evident in the shapes of both the linear and nonlinear IR spectra of the CN group.     

What external perturbations influence the electronic properties of catalase compound I?

We have performed density functional theory calculations on an active-site model of catalase compound I and studied the responses of the catalytic center to external perturbations. Thus, in the gas phase, compound I has close-lying doublet and quartet spin states with three unpaired electrons: two residing in pi(FeO) orbitals and the third on the heme. The addition of a dielectric constant to the model changes the doublet-quartet energy ordering but keeps the same electronic configuration. By contrast, the addition of an external electric field along one of the principal axes of the system can change the doublet-quartet energy splitting by as much as 6 kcal mol(-1) in favor of either the quartet or the doublet spin state. This sensitivity is much stronger than the effect obtained for iron heme models with thiolate or imidazole axial ligands. Moreover, an external electric field is able to change the electronic system from a heme-based radical [Fe=O(Por*+)OTyr-] to a tyrosinate radical [Fe=O(Por)OTyr*]. This again shows that oxo-iron heme systems are chameleonic species that are influenced by external perturbations and change their character and catalytic properties depending on the local environment.     

Propene activation by the oxo-iron active species of taurine/alpha-ketoglutarate dioxygenase (TauD) enzyme. How does the catalysis compare to heme-enzymes?

Density functional calculations on the oxygenation reaction of propene by a model for taurine/alpha-ketoglutarate dioxygenase (TauD) enzyme are presented. The oxo-iron active species of TauD is shown to be a powerful and aggressive oxidant, which is able to hydroxylate C-H bonds and epoxidize C=C bonds with low barriers. In the case of propene oxygenation, the hydroxylation and epoxidation mechanisms are competitive on a dominant quintet spin state surface. We have compared the mechanism and thermodynamics of TauD with oxo-iron heme catalysts, such as the cytochromes P450, and found some critical differences. The TauD model is found to be much more reactive toward oxygenation of substrates than oxo-iron complexes in a heme environment with much lower reaction barriers. We have analyzed this and assigned this to the strength of the O-H bond formed after hydrogen abstraction from a substrate, which is at least 10 kcal mol(-)(1) stronger in five-coordinated oxo-iron nonheme complexes than in six-coordinated oxo-iron heme complexes. Since, the metal in TauD enzymes is five-coordinated, whereas in heme-enzymes it is six-coordinated there are some critical differences in the valence molecular orbitals. Thus, in oxo-iron heme catalysts one of the antibonding pi orbitals is replaced by a low-lying nonbonding delta orbital resulting in a lower overall spin state. Moreover, heme-enzymes have an extra oxidation equivalent located on the heme, which is missing in non-heme oxo-iron catalysts. As a result, the oxo-iron species of TauD reacts via single-state reactivity on a dominant quintet spin state surface, whereas oxo-iron heme catalysts react via two-state reactivity on competing doublet and quartet spin states.     

Vibrational dynamics of N-H, C-D, and C=O modes in formamide

By means of heterodyned two-dimensional IR photon echo experiments on liquid formamide and isotopomers the vibrational frequency dynamics of the N-H stretch mode, the C-D mode, and the C=O mode were obtained. In each case the vibrational frequency correlation function is fitted to three exponentials representing ultrafast (few femtoseconds), intermediate (hundreds of femtoseconds), and slow (many picoseconds) correlation times. In the case of N-H there is a significant underdamped contribution to the correlation decay that was not seen in previous experiments and is attributed to hydrogen-bond librational modes. This underdamped motion is not seen in the C-D or C=O correlation functions. The motions probed by the C-D bond are generally faster than those seen by N-H and C=O, indicating that the environment of C-D interchanges more rapidly, consistent with a weaker C-D...O=C bond. The correlation decays of N-H and C=O are similar, consistent with both being involved in strong H bonding.     

Were Chinchorros exposed to arsenic? Arsenic determination in Chinchorro mummies' hair by laser ablation inductively coupled plasma-mass spectrometry (LA-ICP-MS)

Chinchorros, a fishermen culture, who lived about 7000 years ago in the coastal region of the Atacama Desert in the northern outpost of present-day Chile, practiced an intricate system of mummification of their dead. The drinking water in this region is rich with arsenic, and the mummies were found in these arsenic endemic areas. Well preserved mummy hair samples provided a unique opportunity to explore the ancient arsenic exposure of the Chinchorros by laser ablation inductively coupled plasma-mass spectrometry (LA-ICP-MS) using a single hair strand without any elaborate sample preparation. Forty-six hair samples from mummies found in five burial sites around the Atacama Desert, Chile, were used for this study. After cleaning, hair strands were placed on mounting tape and ablated using a Nd-YAG UV laser coupled to ICP-MS. A suite of contemporary human hair from the same region with known arsenic concentrations was used for calibration of LA-ICP-MS. Satisfactory linear calibration functions were obtained for arsenic in hair. The method detection limit was 0.8 µg/g and the sample throughput for this method is ∼ 10 samples per hour. It appears that mummies from the Morro (Arica), Iquique and Camarones had the elevated concentration of arsenic in hair (AsH > 10 µg/g) in this sub-set of samples, where Morro had the broad distribution of As concentrations.     

Microwave-assisted synthesis of 4-chloro-N-(naphthalen-1-ylmethyl)-5-(3-(piperazin-1-yl)phenoxy)thiophene-2-sulfonamide (B-355252): a new potentiator of Nerve Growth Factor (NGF)-induced neurite outgrowth

The synthesis of 4-chloro-N-(naphthalen-1-ylmethyl)-5-(3-(piperazin-1-yl)phenoxy)thiophene-2-sulfonamide (B-355252) using an MW-assisted nucleophilic aromatic substitution (S_NAr) reaction will be discussed. Utilization of this method allowed for the rapid generation of B-355252 heteroaryl ether core structure in the presence of cesium carbonate in dimethylformamide or tripotassium phosphate in N-methyl-2-pyrrolidone in 94% yield. Evaluation of B-355252 enhancement of nerve growth factor’s ability to stimulate neurite outgrowths was determined using NS-1 cells.