Luffa acutangula agglutinin: Primary structure determination and identification of a tryptophan residue involved in its carbohydrate-binding activity using mass spectrometry

A lectin from phloem exudates of Luffa acutangula (ridge gourd) was purified on chitin affinity chromatography and characterized for its amino acid sequence and to study the role of tryptophan in its activity. The purified lectin was subjected to various proteolytic digestions, and the resulting peptides were analyzed by liquid chromatography coupled electrospray ionization ion trap mass spectrometer. The peptide precursor ions were fragmented by collision-induced dissociation or electron transfer dissociation experiments, and a manual interpretation of MS/MS was performed to deduce amino acid sequence. This gave rise to almost complete sequence coverage of the lectin which showed high-sequence similarity with deduced sequences of phloem lectins present in the database. Chemical modification of lysine, tyrosine, histidine, arginine, aspartic acid, and glutamic acid residues did not inhibit the hemagglutinating activity. However, the modification of tryptophan residues using N-bromosuccinimide showed the loss of hemagglutinating activity. Additionally, the mapping of tryptophan residues was performed to determine the extent and number of residues modified, which revealed that six residues per molecule were oxidized suggesting their accessibility. The retention of the lectin activity was seen when the modifications were performed in the presence of chitooligosaccharides due to protection of a tryptophan residue (W-102) in the protein. These studies taken together have led to the identification of a particular tryptophan residue (W-102) in the activity of the lectin. (c) 2015 IUBMB Life, 67(12):943-953, 2015

Electron transfer amongst flavo- and hemo-proteins: diffusible species effect the relay processes, not protein-protein binding

Hitherto, electron transfer (ET) between redox proteins has been deemed to occur via donor-acceptor binding, and diffusible reactive species are considered as deleterious side-products in such systems. Herein, ET from cytochrome P450 reductase (CPR, an animal membrane flavoprotein) and horseradish peroxidase (HRP, a plant hemoprotein) to cytochrome c (Cyt c, a soluble animal hemoprotein) was probed under diverse conditions, using standard assays. ET in the CPR-Cyt c system was critically inhibited by cyanide and sub-equivalent levels of polar one-electron cyclers like copper ions, vitamin C/Trolox and superoxide dismutase. In the presence of lipids, inhibition was also afforded by amphipathic molecules vitamin E, palmitoyl-vitamin C and the membrane hemoprotein, cytochrome b(5). Such nonspecific inhibition (by diverse agents in both aqueous and lipid phases) indicated that electron transfer/relay was effected by small diffusible agents, whose lifetimes are shortened by the diverse radical scavengers. When CPR was retained in a dialysis membrane and Cyt c presented outside in free solution, ET was still observed. Further, HRP (taken at nM levels) catalyzed oxidation of a phenolic substrate was significantly inhibited upon the incorporation of sub-nM levels of Cyt c. The findings imply that CPR-Cyt c or HRP-Cyt c binding is not crucial for ET. Further, fundamental quantitative arguments (based on diffusion/collision) challenge the erstwhile protein-protein binding-assisted ET hypothesis. It is proven beyond reasonable doubt that mobile and diffusible electron carriers (ions and radicals) serve as ``redox-relay agents'' in the biological ET models/setup studied.

The mechanism of PEO process on Al–Si alloys with the bulk primary silicon

This study focuses on mechanism of ceramic coating on Al-Si alloys with bulk primary Si using plasma electrolytic oxidation (PEO) technology. Al-Si alloys with 27-32% Si in weight were used as substrates. The morphologies, composition and microstructure of PEO coatings were investigated by scanning electron microscopy (SEM) with energy dispersive X-ray system (EDX). Results showed that the PEO process had four different stages. The effect of bulk Si is greatly on the morphology and composition of coatings at first three stages. Anodic oxide films formed on Al and Si phases, respectively. When the voltage exceeded 40 V, glow appeared and concentrated on the localized zone of interface of Al and Si phase. Al-Si-O compounds formed and covered on the dendrite Si phase surface, and the coating on bulk Si, which was silicon oxide, was rougher than that on other phase. If the treatment time was long enough, the coatings with uniform surface morphologies and elements distribution will be obtained but the microstructure of inner layer is looser due to the bulk Si.

Engineering multi-step electron tunneling systems in proteins

Multi-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.

The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.

The theory of long distance electron transfer reactions

The rate of electron transport between distant sites was studied. The rate depends crucially on the chemical details of the donor, acceptor, and surrounding medium. These reactions involve electron tunneling through the intervening medium and are, therefore, profoundly influenced by the geometry and energetics of the intervening molecules. The dependence of rate on distance was considered for several rigid donor-acceptor "linkers" of experimental importance. Interpretation of existing experiments and predictions for new experiments were made.

The electronic and nuclear motion in molecules is correlated. A Born-Oppenheimer separation is usually employed in quantum chemistry to separate this motion. Long distance electron transfer rate calculations require the total donor wave function when the electron is very far from its binding nuclei. The Born-Oppenheimer wave functions at large electronic distance are shown to be qualitatively wrong. A model which correctly treats the coupling was proposed. The distance and energy dependence of the electron transfer rate was determined for such a model.

Electron tunneling in proteins and water

The subject of this thesis is electronic coupling in donor-bridge-acceptor systems. In Chapter 2, ET properties of cyanide-bridged dinuclear ruthenium complexes were investigated. The strong interaction between the mixed-valent ruthenium centers leads to intense metal-to-metal charge transfer bands (MMCT). Hush analysis of the MMCT absorption bands yields the electronic-coupling strength between the metal centers (H_(AB)) and the total reorganization energy (λ). Comparison of ET kinetics to calculated rates shows that classical ET models fail to account for the observed kinetics and nuclear tunneling must be considered.

In Chapter 3, ET rates were measured in four ruthenium-modified highpotential iron-sulfur proteins (HiPIP), which were modified at position His50, His81, His42 and His18, respectively. ET kinetics for the His50 and His81 mutants are a factor of 300 different, while the donor-acceptor separation is nearly identical. PATHWAY calculations corroborate these measurements and highlight the importance of structural detail of the intervening protein matrix.

In Chapter 4, the distance dependence of ET through water bridges was measured. Photoinduced ET measurements in aqueous glasses at 77 K show that water is a poor medium for ET. Luminescence decay and quantum yield data were analyzed in the context of a quenching model that accounts for the exponential distance dependence of ET, the distance distribution of donors and acceptors embedded in the glass and the excluded volumes generated by the finite sizes of the donors and acceptors.

In Chapter 5, the pH-dependent excited state dynamics of ruthenium-modified amino acids were measured. The [Ru(bpy)_(3)] ^(2+) chromophore was linked to amino acids via an amide linkage. Protonation of the amide oxygen effectively quenches the excited state. In addition. time-resolved and steady-state luminescence data reveal that nonradiative rates are very sensitive to the protonation state and the structure of the amino acid moiety.

Primary cosmic-ray positrons and negatrons in 1968 at energies between 11 and 204 MeV

The cosmic-ray positron and negatron spectra between 11 and 204 MeV have been measured in a series of 3 high-altitude balloon flights launched from Fort Churchill, Manitoba, on July 16, July 21, and July 29, 1968. The detector system consisted of a magnetic spectrometer utilizing a 1000-gauss permanent magnet, scintillation counters, and a lucite Čerenkov counter.

Launches were timed so that the ascent through the 100 g/cm² level of residual atmosphere occurred after the evening geomagnetic cutoff transition. Data gathered during ascent are used to correct for the contribution of atmospheric secondary electrons to the flux measured at float altitude. All flights floated near 2.4 g/cm².

A pronounced morning intensity increase was observed in each flight. We present daytime positron and negatron data which support the interpretation of the diurnal flux variation as a change in the local geomagnetic cutoff. A large diurnal variation was observed in the count rate of positrons and negatrons with magnetic rigidities less than 11 MV and is evidence that the nighttime cutoff was well below this value.

Using nighttime data we derive extraterrestrial positron and negatron spectra. The positron-to-total-electron ratio which we measure indicates that the interstellar secondary, or collision, source contributes ≾50 percent of the electron flux within this energy interval. By comparing our measured positron spectrum with the positron spectrum calculated for the collision source we derive the absolute solar modulation for positrons in 1968. Assuming negligible energy loss during modulation, we derive the total interstellar electron spectrum as well as the spectrum of directly accelerated, or primary, electrons. We examine the effect of adiabatic deceleration and find that many of the conclusions regarding the interstellar electron spectrum are not significantly altered for an assumed energy loss of up to 50 percent of the original energy.

A new strategy of enhancing two-photon absorption in benzothiazole-containing fluorene molecules: Introduction of auxiliary donor-acceptor effects

A series of benzothiazole-containing fluorene molecules have been designed and their one- and two-photon absorption properties have been investigated theoretically by using the ZINDO method. The effects of electron-excessive/deficient heterocyclic bridges as auxiliary donors (auxD)/acceptors (auxA) on TPA cross-sections were studied. The results show that the molecules with D-pi-auxA-A, D-aux D-pi-A, or D-auxD-pi-auxA-A structure types have large TPA cross-section, which can be a valuable strategy in the design of two-photon absorption materials. Also, a linear relationship between the first hyperpolarizability and the TPA cross-section is observed. (c) 2006 Elsevier B.V. All rights reserved.

Impact of donor traps on the 2DEG and electrical behavior of AlGaN/GaN MISFETs

As an important step in understanding trap-related mechanisms in AlGaN/GaN transistors, the physical properties of surface states have been analyzed through the study of the transfer characteristics of a MISFET. This letter focused initially on the relationship between donor parameters (concentration and energy level) and electron density in the channel in AlGaN/GaN heterostructures. This analysis was then correlated to dc and pulsed measurements of the transfer characteristics of a MISFET, where the gate bias was found to modulate either the channel density or the donor states. Traps-free and traps-frozen TCAD simulations were performed on an equivalent device to capture the donor behavior. A donor concentration of 1.14× 1013 ∼ cm-2 with an energy level located 0.2 eV below the conduction band edge gave the best fit to measurements. With the approach described here, we were able to analyze the region of the MISFET that corresponds to the drift region of a conventional HEMT. © 1980-2012 IEEE.

On the variation of the 2DEG charge density with the density of the surface donor traps in AiGaN/GaN transistors

Gallium nitride (GaN) has a bright future in high voltage device owing to its remarkable physical properties and the possibility of growing heterostructures on silicon substrates. GaN High Electron Mobility Transistors (HEMTs) are expected to make a strong impact in off line applications and LED drives. However, unlike in silicon-based power devices, the on-state resistance of HEMT devices is hugely influenced by donor and acceptor traps at interfaces and in the bulk. This study focuses on the influence of donor traps located at the top interface between the semiconductor layer and the silicon nitride on the 2DEG density. It is shown through TCAD simulations and analytical study that the 2DEG charge density has an 'S' shape variation with two distinctive 'flat' regions, wherein it is not affected by the donor concentration, and one linear region. wherein the channel density increases proportionally with the donor concentration. We also show that the upper threshold value of the donor concentration within this 'S' shape increases significantly with the AIGaN thickness and the Al mole fraction and is highly affected by the presence of a thin GaN cap layer. © 2013 IEEE.

Spin-orbit splitting of a hydrogenic donor impurity in GaAs/GaAlAs quantum wells

The electronic states of a hydrogenic donor impurity in GaAs/GaAlAs quantum wells are investigated theoretically in the framework of effective-mass envelope function theory, including the effect of Rashba spin-orbit coupling. The splits of electron energy levels are calculated. The results show that (1) the split energy of the excited state is larger than that of the ground state; (2) the split energy peak appears as the GaAs well width increases from zero; and (3) the maximum split energy reaches about 1.6 meV. Our results are useful for the application of Rashba spin-orbit coupling to photoelectric devices. (c) 2008 American Institute of Physics.

Interplay between partial incoherence, partial inelasticity, resonance, and heterogeneity in long-range electron transfer and transport

A generalized scattering matrix formalism is constructed to elucidate the interplay of electron resonance, coherence, dephasing, inelastic scattering, and heterogeneity, which play important roles in the physics of long-range electron transfer/transport. The theory consists of an extension of the standard Buttiker phase-breaking model and an analytical expression of the electron transmission coefficient for donor-bridge-acceptor systems with arbitrary length and sequence. The theory incorporates the following features: Dephasing-assisted off-resonance enhancement, inelasticity-induced turnover, resonance enhancement and its dephasing-induced suppression, dephasing-induced smooth superexchange-hopping transition, and heterogeneity effects. (C) 2002 American Institute of Physics.

Shallow donor defect formation and its influence on semi-insulating indium phosphide after high temperature annealing with long duration

Fe-doped semi-insulating (SI) InP has become semi-conducting (SC) material completely after annealing at 900 V for 10 hours. Defects in the SC and SI InP materials have been studied by deep level transient spectroscopy (DLTS) and thermally stimulated current spectroscopy (TSC) respectively. The DLTS only detected Fe acceptor related deep level defect with significant concentration, suggesting the formation of a high concentration of shallow donor in the SC-InP TSC results confirmed the nonexistence of deep level defects in the annealed SI-InP. The results demonstrate a significant influence of the thermally induced defects on the electrical properties of SI-InP. The formation mechanism and the nature of the shallow donor defect have been discussed based on the results.

Self-consistent analysis of AlSb/InAs high electron mobility transistor structures

The influences of channel layer width, spacer layer width, and delta-doping density on the electron density and its distribution in the AlSb/InAs high electron mobility transistors (HEMTs) have been studied based on the self-consistent calculation of the Schrodinger and Poisson equations with both the strain and nonparabolicity effects being taken into account. The results show that, having little influence on the total two dimensional electron gas (2DEG) concentration in the channel, the HEMT's channel layer width has some influence on the electron mobility, with a channel as narrow as 100-130 angstrom being more beneficial. For the AlSb/InAs HEMT with a Te delta-doped layer, the 2DEG concentration as high as 9.1 X 10(12) cm(-2) can be achieved in the channel by enhancing the delta-doping concentration without the occurrence of the parallel conduction. When utilizing a Si delta-doped InAs layer as the electron-supplying layer of the AlSb/InAs HEMT, the effect of the InAs donor layer thickness is studied on the 2DEG concentration. To obtain a higher 2DEG concentration in the channel, it is necessary to use an InAs donor layer as thin as 4 monolayer. To test the validity of our calculation, we have compared our theoretical results (2DEG concentration and its distribution in different sub-bands of the channel) with the experimental ones done by other groups and show that our theoretical calculation is consistent with the experimental results.

EFFECTS OF AN EXTERNAL MAGNETIC-FIELD ON SHALLOW DONOR LEVELS IN SEMICONDUCTORS

An extension of Faulkner's method for the energy levels of the shallow donor in silicon and germanium at zero field is made in order to investigate the effects of a magnetic field upon the excited states. The effective-mass Hamiltonian matrix elements of an electron bound to a donor center and subjected to a magnetic field B, which involves both the linear and quadratic terms of magnetic field, are expressed analytically and matrices are solved numerically. The photothermal ionization spectroscopy of phosphorus in ultrapure silicon for magnetic fields parallel to the [1,0,0] and [1,1,1] directions and up to 10 T is explained successfully.