Collisional cooling enhances the ability to observe non-covalent interactions within the inducible nitric oxide synthase oxygenase domain: Dimerization,complexation, and dissociation

The investigation of protein quaternary structure, protein-cofactor, and protein-ligand interactions by mass spectrometry is often limited by the fragility of such interactions under experimental conditions. To develop more gentle conditions of perhaps general use, we used as a model for study the oxygenase domain of murine inducible nitric oxide synthase (iNOS), which is homodimeric, binds heme and tetrahydrobiopterin H(4)B cofactors, and the substrate L-arginine. The energetics of the collisions in q2 and in the lens region of the mass spectrometer were manipulated for varying the degree of solvation around the non-covalently bound ions. Furthermore, the number of low-energy collisions in the collision cell of the instrument was varied, focusing and dampening the ion beam. Under gentle source collision conditions, and using multiple low-energy collisions in the collision cell of the mass spectrometer, dimers of the iNOS oxygenase domain containing heme, H(4)B, and arginine were observed intact after electrospraying at pH values near neutrality; a mutant of this protein (Trp188 --> Phe) was monomeric and did not bind cofactors. The pH dependence of the iNOS oxygenase domain under acidic conditions was also studied; while heme remained bound to the protein between pH 2.5 and 4.0, the dimeric structure was disrupted. Our findings confirm that non-covalently bound macromolecular complexes are retained and observable using electrospray mass spectrometry under the appropriate experimental conditions.     

Thermal denaturation of some proteins and its effect on their electrospray mass spectrat

The effects of beat on the electrospray mass spectra of eight globular proteins in solution were studied. These ranged from hardly noticeable to a dramatic shift in the mass spectrometric profile and a concomitant increase in ion abundance. This change is believed to be the result of thermal denaturation of the protein species in solution resulting in a transition from a more compact to a less compact conformation. We accounted for this transition by means of a recently proposed model based on aqueous solution acid/base equilibria. For cytochrome c, profiles calculated by means of this model agree well with experimental data. The ΔH of the denaturation reaction of cytochrome c in aqueous solution containing 0.2% acetic acid was calculated from experimental data to be 103.8 ± 9.2 kJ mol^?1, in good agreement with previous measurements.     

Kurdyka–Łojasiewicz Exponent via Inf-projection

Foundations of Computational Mathematics - Kurdyka–Łojasiewicz (KL) exponent plays an important role in estimating the convergence rate of many contemporary first-order methods. In...     

A Construction of Partial Difference Sets in {\mathbb{Z}}_{p^{2 \times } } {\mathbb{Z}}_{p^{2 \times \cdot \cdot \cdot \times } } {\mathbb{Z}}_{p^2 }

In this paper, we give a construction of partial difference sets in _p ² x _p ² x ... x _p ²using some finite local rings.Dedicated to Hanfried Lenz on the occasion of his 80th birthdayThe work of this paper was done when the authors visited the University of Hong Kong.     

Vacuum ultraviolet 178.7 nm emission in sodium vapour under two-photon resonance excitation

We have observed a fixed wavelength emission at 178.7 nm in sodium vapour under 578.7 nm two-photon resonance excitation. The proposed non-linear wave mixing scheme is described by _{178.7 nm} = 2_L + _{465.7 nm}; where _178.7 is the 178.7 nm photon frequency, _L is the laser-photon frequency, and _465.7 is the 465.7 nm photon frequency. This 465.7 nm emission comes from another six-wave mixing process involving two hyper-electronic Raman scattering photons. The excitation spectrum of the 178.7 nm emission has a typical multiwave mixing pattern with a competing effect appearing at higher temperatures under two-photon resonance excitation. Numerical analysis indicates that this vacuum ultraviolet emission has a poor phase-match condition that will depress the emission intensity to a certain extent. This makes the observation more difficult compared with other reported four-wave mixing generated emissions. Fortunately, on the one hand, it is enhanced by quasi-auto-ionization resonance when the 3s–5s transition is coupled to the sodium continuum by a 330.2 nm photon. On the other hand, its wavelength sits so close to the sodium Cooper minimum that weak absorption will not suppress this vacuum ultraviolet emission further.     

Marine biological reference materials for methylmercury: analytical methodologies used in certification

Summary The methylmercury concentrations in three existing marine biological certified reference materials — TORT-1, DORM-1 and DOLT-1 — are determined by gas chromatography with electron capture detection, cold vapour atomic absorption spectrometry and inductively coupled plasma mass spectrometry after selective isolation of methylmercury. Two such procedures were used. These and the three analytical techniques are evaluated and compared. The certified methylmercury concentrations are: TORT-1, 0.128 ± 0.014; DORM-1, 0.731±0.060; and DOLT-1, 0.080 ± 0.011 g Hg/g dry weight.

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Meeresbioligische Referenzmaterialien für Methylquecksilber: Analytische Methoden der Zertifizierung

     

Ab initio studies on Al(+)(H(2)O)(n), HAlOH(+)(H(2)O)(n-1), and the size-dependent H(2) elimination reaction

We report computational studies on Al(+)(H(2)O)(n), and HAlOH(+)(H(2)O)(n-1), n = 6-14, by the density functional theory based ab initio molecular dynamics method, employing a planewave basis set with pseudopotentials, and also by conventional methods with Gaussian basis sets. The mechanism for the intracluster H(2) elimination reaction is explored. First, a new size-dependent insertion reaction for the transformation of Al(+)(H(2)O)(n), into HAlOH(+)(H(2)O)(n-1) is discovered for n > or = 8. This is because of the presence of a fairly stable six-water-ring structure in Al(+)(H(2)O)(n) with 12 members, including the Al(+). This structure promotes acidic dissociation and, for n > or = 8, leads to the insertion reaction. Gaussian based BPW91 and MP2 calculations with 6-31G* and 6-31G** basis sets confirmed the existence of such structures and located the transition structures for the insertion reaction. The calculated transition barrier is 10.0 kcal/mol for n = 9 and 7.1 kcal/mol for n = 8 at the MP2/6-31G** level, with zero-point energy corrections. Second, the experimentally observed size-dependent H(2) elimination reaction is related to the conformation of HAlOH(+)(H(2)O)(n-1), instead of Al(+)(H(2)O)(n). As n increases from 6 to 14, the structure of the HAlOH(+)(H(2)O)(n-1) cluster changes into a caged structure, with the Al-H bond buried inside, and protons produced in acidic dissociation could then travel through the H(2)O network to the vicinity of the Al-H bond and react with the hydride H to produce H(2). The structural transformation is completed at n = 13, coincident approximately with the onset of the H(2) elimination reaction. From constrained ab initio MD simulations, we estimated the free energy barrier for the H(2) elimination reaction to be 0.7 eV (16 kcal/mol) at n = 13, 1.5 eV (35 kcal/mol) at n = 12, and 4.5 eV (100 kcal/mol) at n = 8. The existence of transition structures for the H(2) elimination has also been verified by ab initio calculations at the MP2/6-31G** level. Finally, the switch-off of the H(2) elimination for n > 24 is explored and attributed to the diffusion of protons through enlarged hydrogen bonded H(2)O networks, which reduces the probability of finding a proton near the Al-H bond.     

Photoionization dynamics of glycine adsorbed on a silicon cluster: "on-the-fly" simulations

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by "on-the-fly" molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering.     

Evaluation of the use of consensus values in proficiency testing programmes

Proficiency testing (PT) is an essential tool used by laboratory accreditation bodies to assess the competency of laboratories. Because of limited resources of PT providers or for other reasons, the assigned reference value used in the calculation of z-score values has usually been derived from some sort of consensus value obtained by central tendency estimators such as the arithmetic mean or robust mean. However, if the assigned reference value deviates significantly from the ‘true value’ of the analyte in the test material, laboratories’ performance will be evaluated incorrectly. This paper evaluates the use of consensus values in proficiency testing programmes using the Monte Carlo simulation technique. The results indicated that the deviation of the assigned value from the true value could be as large as 40%, depending on the parameters of the proficiency testing programmes under investigation such as sample homogeneity, number of participant laboratories, concentration level, method precision and laboratory bias. To study how these parameters affect the degree of discrepancy between the consensus value and the true value, a fractional factorial design was also applied. The findings indicate that the number of participating laboratories and the distribution of laboratory bias were the prime two factors affecting the deviation of the consensus value from the true value.     

Oral malodor,assessed by closed-loop,gas chromatography,and ion-trap technology

A method is described for the analysis of volatile organic compounds in saliva and tongue coating samples. The techniue is based on an off-line preconcentration step by means of a closed-loop trapping system followed by gas chromatography-ion trap detection. With the closed-loop technique, the volatile organic compounds(VOCs) are released from the matrix and trapped on an adsorbent without interference of water. The VOCs are released from the adsorbent into the gas chromatograph by thermdesorption. After separation, identification of the compounds is performed by ion trap technology. By this technique 82 compounds could be demonstrated in saliva and tongue coating samples. The technique is also used to demonstrate the formation of volatile bacterial fermentation compounds when a protein substrate is added to tongue coating samples. It is considered a very promising tool in further research on oral malodor.