Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide

Longitudinal relaxation due to cross-correlation between dipolar ((HN-1H alpha)-H-1) and amide-proton chemical shift anisotropy (H-1(N) CSA) has been measured in a model tripeptide Piv-(L)Pro-(L)Pro-(L)Phe-OMe. The peptide bond across diproline segment is known to undergo cis/trans isomerization and only in the cis form does the lone Phe amide-proton become involved in intramolecular hydrogen bonding. The strength of the cross correlated relaxation interference is found to be significantly different between cis and trans forms, and this difference is shown as an influence of intramolecular hydrogen bonding on the amide-proton CSA. (C) 2015 Elsevier B.V. All rights reserved.

Negative hyperconjugation and red-, blue- or zero-shift in X-Z center dot center dot center dot Y complexes

A generalized explanation is provided for the existence of the red-and blue-shifting nature of X-Z bonds (Z = H, halogens, chalcogens, pnicogens, etc.) in X-Z center dot center dot center dot Y complexes based on computational studies on a selected set of weakly bonded complexes and analysis of existing literature data. The additional electrons and orbitals available on Z in comparison to H make for dramatic differences between the H-bond and the rest of the Z-bonds. The nature of the X-group and its influence on the X-Z bond length in the parent X-Z molecule largely controls the change in the X-Z bond length on X-Z center dot center dot center dot Y bond formation; the Y-group usually influences only the magnitude of the effects controlled by X. The major factors which control the X-Z bond length change are: (a) negative hyperconjugative donation of electron density from X-group to X-Z sigma* antibonding molecular orbital (ABMO) in the parent X-Z, (b) induced negative hyperconjugation from the lone pair of electrons on Z to the antibonding orbitals of the X-group, and (c) charge transfer (CT) from the Y-group to the X-Z sigma* orbital. The exchange repulsion from the Y-group that shifts partial electron density at the X-Z sigma* ABMO back to X leads to blue-shifting and the CT from the Y-group to the sigma* ABMO of X-Z leads to red-shifting. The balance between these two opposing forces decides red-, zero- or blue-shifting. A continuum of behaviour of X-Z bond length variation is inevitable in X-Z center dot center dot center dot Y complexes.

Structural characterization of folded and extended conformations in peptides containing gamma amino acids with proteinogenic side chains: crystal structures of gamma(n), (alpha gamma)(n) and gamma gamma delta gamma sequences

The crystal structures of nine peptides containing gamma(4)Val and gamma(4)Leu are described. The short sequences Boc-gamma(4)(R)Val](2)-OMe 1, Boc-gamma(4)(R)Val](3)-NHMe 2 and Boc-gamma(4)(S)Val-gamma(4)(R)Val-OMe 3 adopt extended apolar, sheet like structures. The tetrapeptide Boc-gamma(4)(R)Val](4)-OMe 4 adopts an extended conformation, in contrast to the folded C-14 helical structure determined previously for Boc-gamma(4)(R)Leu](4)-OMe. The hybrid alpha gamma sequence Boc-Ala-gamma(4)(R)Leu](2)-OMe 5 adopts an S-shaped structure devoid of intramolecular hydrogen bonds, with both alpha residues adopting local helical conformations. In sharp contrast, the tetrapeptides Boc-Aib-gamma(4)(S)Leu](2)-OMe 6 and Boc-Leu-gamma(4)(R)Leu](2)-OMe 7 adopt folded structures stabilized by two successive C-12 hydrogen bonds. gamma(4)Val residues have also been incorporated into the strand segments of a crystalline octapeptide, Boc-Leu-gamma(4)(R)Val-Val-(D)Pro-Gly-Leu-gamma(4)(R)Val-Val-OMe 8. The gamma gamma delta gamma tetrapeptide containing gamma(4)Val and delta(5)Leu residues adopts an extended sheet like structure. The hydrogen bonding pattern at gamma residues corresponds to an apolar sheet, while a polar sheet is observed at the lone delta residue. The transition between folded and extended structures at gamma residues involves a change of the torsion angle from the gauche to the trans conformation about the C-beta-C-alpha bond.

Protein Structure and Function: Looking through the Network of Side-Chain Interactions

Network theory has become an excellent method of choice through which biological data are smoothly integrated to gain insights into complex biological problems. Understanding protein structure, folding, and function has been an important problem, which is being extensively investigated by the network approach. Since the sequence uniquely determines the structure, this review focuses on the networks of non-covalently connected amino acid side chains in proteins. Questions in structural biology are addressed within the framework of such a formalism. While general applications are mentioned in this review, challenging problems which have demanded the attention of scientific community for a long time, such as allostery and protein folding, are considered in greater detail. Our aim has been to explore these important problems through the eyes of networks. Various methods of constructing protein structure networks (PSN) are consolidated. They include the methods based on geometry, edges weighted by different schemes, and also bipartite network of protein-nucleic acid complexes. A number of network metrics that elegantly capture the general features as well as specific features related to phenomena, such as allostery and protein model validation, are described. Additionally, an integration of network theory with ensembles of equilibrium structures of a single protein or that of a large number of structures from the data bank has been presented to perceive complex phenomena from network perspective. Finally, we discuss briefly the capabilities, limitations, and the scope for further explorations of protein structure networks.

Exact Phase Retrieval in Principal Shift-Invariant Spaces

We address the problem of phase retrieval from Fourier transform magnitude spectrum for continuous-time signals that lie in a shift-invariant space spanned by integer shifts of a generator kernel. The phase retrieval problem for such signals is formulated as one of reconstructing the combining coefficients in the shift-invariant basis expansion. We develop sufficient conditions on the coefficients and the bases to guarantee exact phase retrieval, by which we mean reconstruction up to a global phase factor. We present a new class of discrete-domain signals that are not necessarily minimum-phase, but allow for exact phase retrieval from their Fourier magnitude spectra. We also establish Hilbert transform relations between log-magnitude and phase spectra for this class of discrete signals. It turns out that the corresponding continuous-domain counterparts need not satisfy a Hilbert transform relation; notwithstanding, the continuous-domain signals can be reconstructed from their Fourier magnitude spectra. We validate the reconstruction guarantees through simulations for some important classes of signals such as bandlimited signals and piecewise-smooth signals. We also present an application of the proposed phase retrieval technique for artifact-free signal reconstruction in frequency-domain optical-coherence tomography (FDOCT).

Error Correcting Functional Source Coding with Decoder Side Information using Row-Latin Rectangles

The functional source coding problem in which the receiver side information (Has-set) and demands (Want-set) include functions of source messages is studied using row-Latin rectangle. The source transmits encoded messages, called the functional source code, in order to satisfy the receiver's demands. We obtain a minimum length using the row-Latin rectangle. Next, we consider the case of transmission errors and provide a necessary and sufficient condition that a functional source code must satisfy so that the receiver can correctly decode the values of the functions in its Want-set.

Wireless Network-Coded Accumulate-Compute-and-Forward Two-Way Relaying

For the physical-layer network-coded wireless two-way relaying, it was observed by Koike-Akino et al. that adaptively changing the network coding map used at the relay according to channel conditions greatly reduces the impact of multiple-access interference, which occurs at the relay, and all these network coding maps should satisfy a requirement called exclusive law. We extend this approach to an accumulate-compute-and-forward protocol, which employs two phases: a multiple access (MA) phase consisting of two channel uses with independent messages in each channel use and a broadcast (BC) phase having one channel use. Assuming that the two users transmit points from the same 4-phase-shift keying (PSK) constellation, every such network coding map that satisfies the exclusive law can be represented by a Latin square of side 16, and conversely, this relationship can be used to get the network coding maps satisfying the exclusive law. Two methods of obtaining this network coding map to be used at the relay are discussed. Using the structural properties of the Latin squares for a given set of parameters, the problem of finding all the required maps is reduced to finding a small set of maps for the case. Having obtained all the Latin squares, a criterion is provided to select a Latin square for a given realization of fade state. This criterion turns out to be the same as the one used byMuralidharan et al. for two-stage bidirectional relaying.

Evidence of quantum lateral confinement in side-gated resonant tunnelling diodes formed by patterned substrate regrowth

MBE regrowth on patterned np-GaAs wafers has been used to fabricate GaAs/AlGaAs double barrier resonant tunnel diodes with a side-gate in the plane of the quantum well. The physical diameters vary from 1 to 20 μm. For a nominally 1 μm diameter diode the peak current is reduced by more than 95% at a side-gate voltage of -2 V at 1.5 K, which we estimate corresponds to an active tunnel region diameter of 75 nm ± 10 nm. At high gate biases additional structure appears in the conductance data. Differential I-V measurements show a linear dependence of the spacing of subsidiary peaks on gate bias indicating lateral quantum confinement. © 1996 American Institute of Physics.

The convection during NaClO3 crystal growth observed by the phase shift interferometer

An optical diagnostic system consisting of the Mach-Zehnder interferometer with the phase shift device and an image processor has been developed for the study of the kinetics of the crystal growing process. The dissolution and crystallization process of NaClO3 crystal has been investigated. The concentration distributions around a growing and dissolving crystal have been obtained by using phase-shift of four-steps theory for the interpretation of the interferograms. The convection (a plume flow) has been visualized and analyzed in the process of the crystal growth. The experiment demonstrates that the buoyancy convection dominates the growth rate of the crystal growing face on the ground-based experiment.

High temperature direct double side cooled inverter module for hybrid electric vehicle application

In this paper a novel approach to the design and fabrication of a high temperature inverter module for hybrid electrical vehicles is presented. Firstly, SiC power electronic devices are considered in place of the conventional Si devices. Use of SiC raises the maximum practical operating junction temperature to well over 200°C, giving much greater thermal headroom between the chips and the coolant. In the first fabrication, a SiC Schottky barrier diode (SBD) replaces the Si pin diode and is paired with a Si-IGBT. Secondly, double-sided cooling is employed, in which the semiconductor chips are sandwiched between two substrate tiles. The tiles provide electrical connections to the top and the bottom of the chips, thus replacing the conventional wire bonded interconnect. Each tile assembly supports two IGBTs and two SBDs in a half-bridge configuration. Both sides of the assembly are cooled directly using a high-performance liquid impingement system. Specific features of the design ensure that thermo-mechanical stresses are controlled so as to achieve long thermal cycling life. A prototype 10 kW inverter module is described incorporating three half-bridge sandwich assemblies, gate drives, dc-link capacitance and two heat-exchangers. This achieves a volumetric power density of 30W/cm3.

Fabrication of self-aligned side gates to carbon nanotubes

We have fabricated self-aligned, side-gated suspended multi-walled carbon nanotubes (MWCNTs), with nanotube-to-gate spacing of less than 10 nm. Evaporated metal forms an island on a suspended MWCNT, the island and the nanotube act as a mask shielding the substrate, and lift-off then removes the metal island, leaving a set of self-aligned side gates. Al, Cr, Au, and Ti were investigated and the best results were obtained with Cr, at a yield of over 90%.