bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding interactions of gastric inhibitory polypeptide (GIP) with its G‐protein coupled receptor through NMR and molecular modeling
Authors: Malde Alpeshkumar K. , Srivastava Sudha S. , Coutinho Evans C. 
Published: April 2007

AbstractGastric inhibitory polypeptide (GIP, or glucose‐dependent insulinotropic polypeptide) is a 42‐amino acid incretin hormone moderating glucose‐induced insulin secretion. Antidiabetic therapy based on GIP holds great promise because of the fact that its insulinotropic action is highly dependent on the level of glucose, overcoming the sideeffects of hypoglycemia associated with the current therapy of Type 2 diabetes. The truncated peptide, GIP(1–30)NH2, has the same activity as the full length native peptide. We have studied the structure of GIP(1–30)NH2 and built a model of its G‐protein coupled receptor (GPCR). The structure of GIP(1–30)NH2 in DMSO‐d6 and H2O has been studied using 2D NMR (total correlation spectroscopy (TOCSY), nuclear overhauser effect spectroscopy (NOESY), double quantum filtered‐COSY (DQF‐COSY), 13C‐heteronuclear single quantum correlation (HSQC) experiments, and its conformation built by MD simulations with the NMR data as constraints. The peptide in DMSO‐d6 exhibits an α‐helix between residues Ile12 and Lys30 with a discontinuity at residues Gln19 and Gln20. In H2O, the α‐helix starts at Ile7, breaks off at Gln19, and then continues right through to Lys30. GIP(1–30)NH2 has all the structural features of peptides belonging to family B1 GPCRs, which are characterized by a coil at the N‐terminal and a long C‐terminal α‐helix with or without a break. A model of the seven transmembrane (TM) helices of the GIP receptor (GIPR) has been built on the principles of comparative protein modeling, using the crystal structure of bovine rhodopsin as a template. The N‐terminal domain of GIPR has been constructed from the NMR structure of the N‐terminal of corticoptropin releasing factor receptor (CRFR), a family B1 GCPR. The intra and extra cellular loops and the C‐terminal have been modeled from fragments retrieved from the PDB. On the basis of the experimental data available for some members of family B1 GPCRs, four pairs of constraints between GIP(1–30)NH2 and its receptor were used in the FTDOCK program, to build the complete model of the GIP(1–30)NH2 : GIPR complex. The model can rationalize the various experimental observations including the potency of the truncated GIP peptide. This work is the first complete model at the atomic level of GIP(1–30)NH2 and of the complex with its GPCR. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
The sequence TGAAKAVALVL from glyceraldehyde‐3‐phosphate dehydrogenase displays structural ambivalence and interconverts between α‐helical and β‐hairpin conformations mediated by collapsed conformational states
Authors: Patel Sunita , Balaji Petety V. , Sasidhar Yellamraju U. 
Published: April 2007

AbstractThe peptide TGAAKAVALVL from glyceraldehyde‐3‐phosphate dehydrogenase adopts a helical conformation in the crystal structure and is a site for two hydrated helical segments, which are thought to be helical folding intermediates. Overlapping sequences of four to five residues from the peptide, sample both helical and strand conformations in known protein structures, which are dissimilar to glyceraldehyde‐3‐phosphate dehydrogenase suggesting that the peptide may have a structural ambivalence. Molecular dynamics simulations of the peptide sequence performed for a total simulation time of 1.2 µs, starting from the various initial conformations using GROMOS96 force field under NVT conditions, show that the peptide samples a large number of conformational forms with transitions from α‐helix to β‐hairpin and vice versa. The peptide, therefore, displays a structural ambivalence. The mechanism from α‐helix to β‐hairpin transition and vice versa reveals that the compact bends and turns conformational forms mediate such conformational transitions. These compact structures including helices and hairpins have similar hydrophobic radius of gyration (Rgh) values suggesting that similar hydrophobic interactions govern these conformational forms. The distribution of conformational energies is Gaussian with helix sampling lowest energy followed by the hairpins and coil. The lowest potential energy of the full helix may enable the peptide to take up helical conformation in the crystal structure of the glyceraldehyde‐3‐phosphate dehydrogenase, even though the peptide has a preference for hairpin too. The relevance of folding and unfolding events observed in our simulations to hydrophobic collapse model of protein folding are discussed. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Conformational solution studies of the anti‐microbial temporin A retro‐analogues by using NMR spectroscopy
Authors: Kamysz Wojciech , Mickiewicz Beata , Greber Katarzyna , Rodziewicz‐MotowidŁo Sylwia 
Published: April 2007

AbstractTemporin A (TA) is a small, basic and highly hydrophobic peptide, isolated from the skin of the European red frog, Rana temporaria. The TA (FLPLIGRVLSGIL‐NH2) displays a broad spectrum of anti‐microbial activity against Gram‐positive bacteria and fungi Candida albicans. In this study we investigate the solution structure of two TA retro‐analogues, (6‐1)(7–13)‐TA (GILPLFRVLSGIL‐NH2) and retro‐TA (LIGSLVRGILPLF‐NH2) by using nuclear magnetic resonance (NMR). The 3D solution structure of the analogues was established by using inter‐proton distances and vicinal coupling constants in the Simulated Annealing (SA) calculations (XPLOR program). The NMR conformational studies show the existence of the helical structure in the middle part of the (6‐1)(7–13)‐TA peptide and an unordered structure of the retro‐TA analogue under the D3‐TFE/H2O (3:7, v/v) conditions. Our investigations have shown that the hydrophobic cluster at N‐terminus with the Pro amino acid residue in position 3 or 4, the helical structure and the amphipathic character of the peptide are responsible for the anti‐microbial activity of the TA analogues. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Peptides and proteins in a confined environment: NMR spectra at natural isotopic abundance
Authors: Pastore Annalisa , Salvadori Severo , Temussi Piero Andrea 
Published: April 2007

AbstractConfinement of proteins and peptides in a small inert space mimics the natural environment of the cell, allowing structural studies in conditions that stabilize folded conformations. We have previously shown that confinement in polyacrylamide gels (PAGs) is sufficient to induce a change in the viscosity of the aqueous solution without changing the composition and temperature of the solvent. The main limitation of a PAG to run NMR experiments in a confined environment is the need for labelling the peptides. Here we report the use of the agarose gel to run the NMR spectra of proteins and peptides. We show that agarose gels are completely transparent in NMR experiments, relieving the need for labelling. Although it is necessary to expose biomolecules to fairly high temperatures during sample preparation, we believe that this is not generally an obstacle to the study of peptides, and found that the method is also compatible with temperature‐resistant proteins. The mesh of agarose gels is too wide for direct effects of confinement on the stability of proteins but confinement can be easily exploited to interact the proteins with other reagents, including crowding macromolecules that can eventually lead to fold stabilization. The use of these gels is ideally suited for low‐temperature studies; we show that a very flexible peptide at subzero temperatures is stabilized into a well‐folded conformation. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Application of gel‐phase 19F NMR spectroscopy for optimization of solid‐phase synthesis of a hydrophobic peptide from the signal sequence of the mucin MUC1
Authors: Pudelko Maciej , Kihlberg Jan , Elofsson Mikael 
Published: April 2007

AbstractThis paper describes the manual Fmoc/t‐Bu solid‐phase synthesis of a difficult nine‐residue hydrophobic peptide LLLLTVLTV from one of the signal sequences that flank the tandem repeat of the mucin MUC1. Gel‐phase 19F NMR spectroscopy was used as a straightforward method for optimization of the solid‐phase synthesis. Different approaches were applied for comparative studies. The strategy based on modified solid‐phase conditions using DIC/HOAt for coupling, DBU for Fmoc deprotection, and the incorporation of the pseudo proline dipeptide Fmoc‐Leu‐Thr(ψMe, Me pro)‐OH as a backbone‐protecting group was found to be superior according to gel‐phase 19F NMR spectroscopy. Implementation of the optimized Fmoc protocol enabled an effective synthesis of signal peptide LLLLTVLTV. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Spectra of differential gain and linewidth enhancement factor in InGaAsN/GaAs single quantum well structures
Authors: Wartak M. S. , Weetman P. 
Published: April 2007

AbstractThe differential gain and linewidth enhancement factor (α ‐factor) of a new material system InGaAsN/GaAs is studied using the 10‐band k · p Hamiltonian matrix. A self‐consistent scheme which involves simultaneous solution of the Schrödinger and Poisson equations is applied. It is shown that spectra of differential gain and α ‐factor have significant variation versus nitrogen composition and carrier density. The determined parameters and their variations play important role in designing practical structures based on InGaAsN/GaAs material system. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nanocrystalline MgB4O7:Dy for high dose measurement of gamma radiation
Authors: Lochab S. P. , Pandey A. , Sahare P. D. , Chauhan R. S. , Salah Numan , Ranjan Ranju 
Published: April 2007

AbstractMagnesium borate activated by dysprosium (MgB4O7:Dy) is a low‐Zeff, tissue‐equivalent material that is commonly used for medical dosimetry of ionizing radiations such as gamma and X‐rays using the thermoluminescence (TL) technique. Nanocrystals of the same material are produced and their TL characteristics are studied. It is found that the nanocrystalline MgB4O7:Dy with a dopant concentration of 1000 ppm is the most sensitive amongst varying dopant concentrations, with its sensitivity equal to 0.025 times that of the standard phosphor CaSO4:Dy. The glow curve has two peaks at 154 °C and 221 °C. The nanophosphor has very poor sensitivity for low doses up to 10 Gy but beyond this dose the phosphor exhibits a linear response up to 5000 Gy. On increasing the dose further the response first becomes supralinear and then sublinear, finally resulting into saturation. Considering also its low fading particularly under post‐irradiation annealing and excellent reusability features, this nanophosphor may be used for high dose (10–5000 Gy) measurements of ionizing radiations. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Lithium‐ion insertion in anodic TiO2 nanotubes resulting in high electrochromic contrast
Authors: Hahn Robert , Ghicov Andrei , Tsuchiya Hiroaki , Macak Jan M. , Muñoz Andres G. , Schmuki Patrik 
Published: April 2007

AbstractThe present work investigates lithium insertion into highly ordered nanotubular layers of TiO2 and its electrochromic effects. The nanotubes were formed by anodization of titanium in 1 M (H3PO4) + 1 M (NaOH) + 0.5wt% HF electrolyte at 20 V. This leads to nanotubular layers with a thickness of 1 ± 0.1 µm, individual tube diameter of 100 ± 10 nm and a tube wall thickness of 10 ± 2 nm. The cathodic behavior of tubes in the “as formed” amorphous phase and annealed to anatase were studied in a solution of 1 M LiClO4 in acetonitrile. Cyclic voltammograms and potential step experiments combined with reflectance measurements show for anatase nanotubes a well defined uptake potential for Li+ and a very strong and reversible electrochromic effect, while on the other investigated TiO2 structures the effects were much less pronounced. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Doping in silicon nanostructures
Authors: Iori F. , Ossicini S. , Degoli E. , Luppi E. , Poli R. , Magri R. , Cantele G. , Trani F. , Ninno D. 
Published: April 2007

AbstractWe report on an ab initio study of the structural, electronic and optical properties of boron and phosphorous doped silicon nanocrystals. The scaling with the Si‐nanocrystal size is investigated for both the neutral formation energies (FE) and the impurity activation energies. Both these energies scale with the nanocrystal inverse radius. The optical properties reveal the existence of new absorption peaks in the low energy region related to the presence of the impurity. The effects of B and P co‐doping show that the formation energies are always smaller than those of the corresponding single‐doped cases due to both carriers compensation and minor structural distortion. Moreover in the case of co‐doping the electronic and optical properties show a strong reduction of the band gap with respect to the pure silicon nanocrystals that makes possible to engineer the photoluminescence properties of silicon nanocrystals. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Macro porous silicon as pump media for electro‐osmotic pumps
Authors: Wallner J. Z. , Nagar N. , Friedrich C. R. , Bergstrom P. L. 
Published: April 2007

AbstractMicro pumps are a critical component in micro fluidic systems. Due to its ability to generate high flow‐rate/pressure without using any moving parts, electro‐osmotic (EO) pumps are an appealing candidate for micro applications. As part of the effort to produce miniaturized EO pumps, macro porous silicon (PS) with high aspect ratio pores has been investigated as the pump media. Initial tests in a meso‐scale pump body produced a maximum pressure of 5.2 kPa and a very large flow rate of 11.9 μl min–1 mm–2 at 60 V, demonstrating macro PS as a promising material for micro scale, high flow‐rate/pressure EO pumps. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Sum frequency generation from planar and porous silicon in contact with liquids
Authors: Kolasinski Kurt W. , DeWitt Kristy M. , Harrison Ian 
Published: April 2007

AbstractSum frequency generation (SFG) involving an ultrafast infrared pulse and a 787 nm up‐conversion pulse mixed at the surface of planar or porous Si as well as planar GaAs has been studied. We demonstrate that SFG data can be obtained while porous silicon is in contact either with an aqueous solution or ethanol. The nonresonant SFG signal responds to the chemical composition of the interface. It is also found that ultrafast 787 nm pulses can induce photochemistry between hydrogen‐terminated porous silicon and either aqueous HCl, ethanoic HF, or ethanol. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical properties of delta poly‐type quasiregular dielectric structures made of porous silicon
Authors: Agarwal V. , Escorcia‐Garcia J. , Mora‐Ramos Miguel E. 
Published: April 2007

AbstractTo investigate the reflection of light in quasi‐regular dielectrics, we study here the optical properties of porous‐silicon‐based Fibonacci, Thue‐Morse and Period Doubling heterostructures. The multilayered systems are fabricated in such a way that each element in the two‐block substitutional sequence has a poly‐type structure. Both delta‐like and traditional configurations are considered. The results for the optical transmittance are analyzed and compared with the classical periodic structure. Numerical simulation for the transmittance along the lines of the transfer matrix approach is also presented. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Porous silicon‐based polymer replicas formed by bead patterning
Authors: Park Jennifer S. , Meade Shawn O. , Segal Ester , Sailor Michael J. 
Published: April 2007

AbstractMonodisperse, micrometer‐sized polymer beads can be imparted with a porous nanostructure by softening them into a porous silicon photonic crystal template. Infiltration of the polymer and replication of the photonic spectral properties is verified by optical reflectivity measurements of the beads as they infuse into the nanostructure. The polymer beads can be removed from the porous Si template by dissolution of the template with a basic solution. This treatment destroys the photonic properties, although scanning electron microscopy (SEM) reveals that some nanotexturing remains in the polymer beads. This simple, solvent‐free process provides a means to produce nanotextured particles of controllable size and shape. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Porous silicon‐based potentiometric biosensor for triglycerides
Authors: Setzu S. , Salis S. , Demontis V. , Salis A. , Monduzzi M. , Mula Guido 
Published: April 2007

AbstractIn this paper we report on the fabrication and characterization of a potentiometric biosensor for the detection of triglycerides. This is constituted by a lipase immobilized on a mesoporous Si matrix. Prototypes, realized on 1 × 1 cm n+‐type silicon wafers, show a very high enzymatic activity. Moreover the properties of these biosensors have been shown to be stable in a several months time interval, clearly showing their advantages with respect to traditional triglycerides detection systems. The Michaelis Menten curve is obtained to demonstrate the absence of diffusion problems. Potentiometric measurements are also shown. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Using a porous silicon photonic crystal for bacterial cell‐based biosensing
Authors: Alvarez Sara D. , Schwartz Michael P. , Migliori Ben , Rang Camilla U. , Chao Lin , Sailor Michael J. 
Published: April 2007

AbstractThis work demonstrates a method for non‐invasively monitoring the growth and Φ6 virus infection of Pseudomonas syringae bacteria using a 1‐D porous silicon photonic crystal and a white‐light source coupled to a CCD spectrometer. Bacteria growth on porous Si leads to increased scattering efficiency that can be measured as a change in intensity of light reflected from a 1‐D porous Si photonic crystal. A linear relationship between bacteria concentration and intensity of light at the photonic resonance is observed, and detection limits are similar to those obtained from optical density measurements. Upon infection with virus, decreases in scattered light intensity are observed at times that correlate with cell lysis caused by viral replication and subsequent bursting of bacteria cells. It is shown that measurements can be performed in real‐time and in an incubator where cells remain in their ideal environment throughout the experiment. This method is well‐suited for cell‐based biosensing, because bacteria cells can be monitored remotely without the need for sampling cells for plating or optical density measurements. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Using an oxidized porous silicon interferometer for determination of relative protein binding affinity through non‐covalent capture probe immobilization
Authors: Schwartz Michael P. , Yu Christine , Alvarez Sara D. , Migliori Benjamin , Godin Denis , Chao Lin , Sailor Michael J. 
Published: April 2007

AbstractAn oxidized porous Si interferometer was used to measure binding of immunoglobulin G (IgG) to an immobilized protein A capture probe. Protein A was non‐covalently immobilized on a thermally oxidized porous Si (PSiO2) sample and exposed to IgG originating from different species. The resulting order of IgG affinity toward the protein A‐coated surface (human > rabbit ≫ sheep IgG) agrees with previous inhibition studies for protein A/IgG binding. No signal change was observed when a protein A coated sample was exposed to bovine serum albumin (BSA), demonstrating that the adsorbed sensing layer sufficiently coats the PSiO2 surface to prevent non‐specific binding. This strategy is excellent for qualitative measurements of protein binding affinity because it is label‐free, requires minimal sample preparation, and can be implemented using an inexpensive CCD‐based spectrometer coupled to a tungsten lamp. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An integrated vapor source with a porous silicon wick
Authors: Wallner J. Z. , Kunt K. S. , Obanionwu H. , Oborny M. C. , Bergstrom P. L. , Zellers E. T. 
Published: April 2007

AbstractA micro vapor source has been developed for calibrating micro gas chromatograph (μGC) systems. By utilizing a porous silicon wick in a micro diffusion system, vapor generation with excellent stability has been achieved. The source has shown uniform and repeatable vapor generation for n‐decane with less than a 0.1% variation in 9 hours, and less than a 0.5% variation in rate over 7 days. The evolution rate follows the diffusion model as expected, although the room temperature rate is higher than theoretically predicted. Equipped with a refillable reservoir, this vapor source is suitable for extended μGC field deployment. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A porous silicon based particle filter for microsystems
Authors: Wallner J. Z. , Bergstrom P. L. 
Published: April 2007

AbstractA porous silicon (PS) based particle filter has been fabricated and tested for integrated microsystems. By engineering the morphology of the porous silicon membrane, depth filtration with high collection efficiency in the submicron range (0.3∼1 μm), low pressure‐drop, and large filtration capacity (0.5 mg/cm2) has been demonstrated. With the PS particle filter, on‐board gas filtration can be achieved. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Rare earth ions in porous silicon: optical properties
Authors: Elhouichet H. , Oueslati M. 
Published: April 2007

AbstractPorous silicon (PS) is doped with rare earth (RE) ions (Er, Eu, Tb) by electrochemical anodisation. The penetration of RE into the PS layer is confirmed by Rutherford Backscattering Spectroscopy (RBS) and by Energy Dispersive X‐ray (EDX) measurements. Efficient visible and infrared emissions were observed at room temperature. The activation temperatures of Eu, Tb and Er in PS are determined from the effect of thermal annealing on the photoluminescence (PL) intensity. From the evolution of the PL intensity versus temperature, it was found that a RE related level defect can be involved on the excitation and emission processes. Pump intensity dependent PL studies revealed that for the electrochemical incorporation, most of the RE ions are localized inside the Si nanocrystallites and not in stochiometric SiO2. The optical cross section is close to that of erbium in Si nanocrystallites. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Betavoltaic and photovoltaic energy conversion in three‐dimensional macroporous silicon diodes
Authors: Clarkson J. P. , Sun W. , Hirschman K. D. , Gadeken L. L. , Fauchet P. M. 
Published: April 2007

AbstractA three‐dimensional p–n diode structure is presented for the generation of energy via photovoltaic and betavoltaic modes of operation. Macroporous Silicon (MPS) has a large degree of internal surface area and its vertically oriented pores, which extend deep into the bulk of the Si substrate, allow for the creation of three‐dimensional structures. In this device the MPS will not only serve as a means for creating 3D diode structures, it will also serve as a host matrix for a tritium isotope which emits energetic beta particles. By varying electrochemical etching conditions and using a prepatterning technique, 1.1 μm diameter pores with a spacing of 2.5 μm were achieved. The p–n junction was created using a rapid thermal process (RTP) which relies on the diffusion from an n‐type solid source into the MPS. To ensure the quality of the diode structure, devices were tested using a light source which resulted in a photovoltaic response. Finally, betavoltaic operation was demonstrated by exposing devices to a tritium gas source. The average energy conversion efficiency of the first generation 3D diode was one order of magnitude higher than that of a similar planar device. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)