Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Structure and Dynamics of Coil-like Molecules by Residual Dipolar Couplings

Nuclear magnetic resonance (NMR) spectroscopy provides us with many means to study biological macromolecules in solution. Proteins in particular are the most intriguing targets for NMR studies. Protein functions are usually ascribed to specific three-dimensional structures but more recently tails, long loops and non-structural polypeptides have also been shown to be biologically active. Examples include prions, -synuclein, amylin and the NEF HIV-protein. However, conformational preferences in coil-like molecules are difficult to study by traditional methods. Residual dipolar couplings (RDCs) have opened up new opportunities; however their analysis is not trivial. Here we show how to interpret RDCs from these weakly structured molecules. The most notable residual dipolar couplings arise from steric obstruction effects. In dilute liquid crystalline media as well as in anisotropic gels polypeptides encounter nematogens. The shape of a polypeptide conformation limits the encounter with the nematogen. The most elongated conformations may come closest whereas the most compact remain furthest away. As a result there is slightly more room in the solution for the extended than for the compact conformations. This conformation-dependent concentration effect leads to a bias in the measured data. The measured values are not arithmetic averages but essentially weighted averages over conformations. The overall effect can be calculated for random flight chains and simulated for more realistic molecular models. Earlier there was an implicit thought that weakly structured or non-structural molecules would not yield to any observable residual dipolar couplings. However, in the pioneering study by Shortle and Ackerman RDCs were clearly observed. We repeated the study for urea-denatured protein at high temperature and also observed indisputably RDCs. This was very convincing to us but we could not possibly accept the proposed reason for the non-zero RDCs, namely that there would be some residual structure left in the protein that to our understanding was fully denatured. We proceeded to gain understanding via simulations and elementary experiments. In measurements we used simple homopolymers with only two labelled residues and we simulated the data to learn more about the origin of RDCs. We realized that RDCs depend on the position of the residue as well as on the length of the polypeptide. Investigations resulted in a theoretical model for RDCs from coil-like molecules. Later we extended the studies by molecular dynamics. Somewhat surprisingly the effects are small for non-structured molecules whereas the bias may be large for a small compact protein. All in all the work gave clear and unambiguous results on how to interpret RDCs as structural and dynamic parameters of weakly structured proteins.

Compact fiber Bragg grating dynamic strain sensor cum broadband thermometer for thermally unstable ambience

An instrument for simultaneous measurement of dynamic strain and temperature in a thermally unstable ambience has been proposed, based on fiber Bragg grating technology. The instrument can function as a compact and stand-alone broadband thermometer and a dynamic strain gauge. It employs a source wavelength tracking procedure for linear dependence of the output on the measurand, offering high dynamic range. Two schemes have been demonstrated with their relative merits. As a thermometer, the present instrumental configuration can offer a linear response in excess of 500 degrees C that can be easily extended by adding a suitable grating and source without any alteration in the procedure. Temperature sensitivity is about 0.06 degrees C for a bandwidth of 1 Hz. For the current grating, the upper limit of strain measurement is about 150 mu epsilon with a sensitivity of about 80 n epsilon Hz(-1/2). The major source of uncertainty associated with dynamic strain measurement is the laser source intensity noise, which is of broad spectral band. A low noise source device or the use of optical power regulators can offer improved performance. The total harmonic distortion is less than 0.5% up to about 50 mu epsilon, 1.2% at 100 mu epsilon and about 2.3% at 150 mu epsilon. Calibrated results of temperature and strain measurement with the instrument have been presented. Traces of ultrasound signals recorded by the system at 200 kHz, in an ambience of 100-200 degrees C temperature fluctuation, have been included. Also, the vibration spectrum and engine temperature of a running internal combustion engine has been recorded as a realistic application of the system.

Inhibition of Tyrosine Phosphorylation of Sperm Flagellar Proteins, Outer Dense Fiber Protein-2 and Tektin-2, Is Associated With Impaired Motility During Capacitation of Hamster Spermatozoa

In mammals, acquisition of fertilization competence of spermatozoa is dependent on the phenomenon of sperm capacitation. One of the critical molecular events of sperm capacitation is protein tyrosine phosphorylation. In a previous study, we demonstrated that a specific epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor, tyrphostin-A47, inhibited hamster sperm capacitation, accompanied by a reduced sperm protein tyrosine phosphorylation. Interestingly, a high percentage of tyrphostin-A47-treated spermatozoa exhibited circular motility, which was associated with a distinct hypo-tyrosine phosphorylation of flagellar proteins, predominantly of Mr 45,000-60,000. In this study, we provide evidence on the localization of capacitation-associated tyrosine-phosphorylated proteins to the nonmembranous, structural components of the sperm flagellum. Consistent with this, we show their ultrastructural localization in the outer dense fiber, axoneme, and fibrous sheath of spermatozoa. Among hypo-tyrosine phosphorylated major proteins of tyrphostin-A47-treated spermatozoa, we identified the 45 kDa protein as outer dense fiber protein-2 and the 51 kDa protein as tektin-2, components of the sperm outer dense fiber and axoneme, respectively. This study shows functional association of hypo-tyrosine-phosphorylation status of outer dense fiber protein-2 and tektin-2 with impaired flagellar bending of spermatozoa, following inhibition of EGFR-tyrosine kinase, thereby showing the critical importance of flagellar protein tyrosine phosphorylation during capacitation and hyperactivation of hamster spermatozoa.

Optimal configurations of active fiber composites based on asymptotic torsional analysis - art. no. 641413

Active Fiber Composites (AFC) possess desirable characteristics over a wide range of smart structure applications, such as vibration, shape and flow control as well as structural health monitoring. This type of material, capable of collocated actuation and sensing, call be used in smart structures with self-sensing circuits. This paper proposes four novel applications of AFC structures undergoing torsion: sensors and actuators shaped as strips and tubes; and concludes with a preliminary failure analysis. To enable this, a powerful mathematical technique, the Variational Asymptotic Method (VAM) was used to perform cross-sectional analyses of thin generally anisotropic AFC beams. The resulting closed form expressions have been utilized in the applications presented herein.

Macro fiber composite (MFC) as a delamination sensor in antisymmetric laminates

The change in extension-twist Coupling due to delamination in antisymmetric laminates is experimentally measured. Experimental results are compared with the results from analytical expression existing in literature and finite element analysis. The application of the Macro-Fiber Composite (MFC) developed at the NASA Langley Research Center for sensing the delamination in the laminates is investigated. While many applications have been reported in the literature using the MFC as an actuator, here its use as a twist sensor has been studied. The real-life application envisaged is structural health monitoring of laminated composite flexbeams taking advantage of the symmetry in the structure. Apart from the defect detection under symmetric conditions, other methods of health monitoring for the same structure are reported for further validation. Results show that MFC works well as a sensor.

Simulation of wavelength/time multiple-pulses-per-row fiber-optic CDMA network

Passive wavelength/time fiber-optic code division multiple access (WIT FO-CDMA) network is a viable option for highspeed access networks. Constructions of 2-D codes, suitable for incoherent WIT FO-CDMA, have been proposed to reduce the time spread of the 1-D sequences. The 2-D constructions can be broadly classified as 1) hybrid codes and 2) matrix codes. In our earlier work [141, we had proposed a new family of wavelength/time multiple-pulses-per-row (W/T MPR) matrix codes which have good cardinality, spectral efficiency and at the same time have the lowest off-peak autocorrelation and cross-correlation values equal to unity. In this paper we propose an architecture for a WIT MPR FO-CDAM network designed using the presently available devices and technology. A complete FO-CDMA network of ten users is simulated, for various number of simultaneous users and shown that 0 --> 1 errors can occur only when the number of interfering users is at least equal to the threshold value.

Strain-Temperature Discrimination Using a Single Fiber Bragg Grating

The out-diffusion of germanium from the core of a photosensitive fiber under elevated temperature is exploited to form a Fabry-Perot filter within a single fiber Bragg grating, by subjecting the diffused region to a single exposure using the standard phase-mask technique. A key aspect of our work is the measurement of the out-diffusion through energy dispersive X-ray analysis. Furthermore, we demonstrate the use of the above single-grating filter for discrimination and simultaneous measurement of strain and temperature. The proposed technique provides a significant advantage over other existing methods that require at least two gratings.

The Role of Interface Modification on Thermal Degradation and Crystallization Behavior of Composites from Commingled Polypropylene Fiber and Banana Fiber

The thermal degradation behavior of banana fiber and polypropylene/banana fiber composites has been studied by thermogravimetric analysis. Banana fiber was found to be decomposing in two stages, first one around 320 degrees C and the second one around 450 degrees C. For chemically treated banana fiber, the decomposition process has been at a higher temperature, indicating thermal stability for the treated fiber. Activation energies for thermal degradation were estimated using Coats and Redfern method. Calorific value of the banana fiber was measured using a constant volume isothermal bomb calorimeter. rystallization studies exhibited an increase in the crystallization temperature and crystallinity of polypropylene upon the addition of banana fiber. POLYM. COMPOS., 31:1113-1123, 2010. (C) 2009 Society of Plastics Engineers.

Dry sliding wear behavior of Al2O3 fiber reinforced aluminum composites

Dry sliding wear behavior of die-cast ADC12 aluminum alloy composites reinforced with short alumina fibers were investigated by using a pin-on-disk wear tester. The Al2O3 fibers were 4 mu m in diameter and were present in volume fractions (T-f)ranging from 0.03 to 0.26, The length of the fiber varied from 40 to 200 mu m. Disks of aluminum-alumina composites were rubbed against a pin of nitrided stainless steel SUS440B with a load of 10 N at a sliding velocity of 0.1 m/s. The unreinforced ADC 12 aluminum alloy and their composites containing low volume fractions of alumina (V-f approximate to 0.05) showed a sliding-distance-dependent transition from severe to mild wear. However, composites containing high volume fractions of alumina ( V-f > 0.05) exhibited only mild wear for all sliding distances. The duration of occurrence of the severe wear regime and the wear rate both decrease with increasing volume fraction. In MMCs the wear rate in the mild wear regime decreases with increase in volume fraction: reaching a minimum value at V-f = 0.09 Beyond V-f = 0.09 the wear rate increasesmarginally. On the other hand, the wear rate of the counterface (steel pin) was found to increase moderately with increase in V-f. From the analysis of wear data and detailed examination of (a) worn surfaces, (b) their cross-sections and (c) wear debris, two modes of wear mechanisms have been identified to be operative, in these materials and these are: (i) adhesive wear in the case of unreinforced matrix material and in MMCs with low Vf and (ii) abrasive wear in the case of MMCs with high V-f. (C) 2000 Elsevier Science Ltd. All rights reserved.

Fiber Bragg grating magnetic field sensor

In this paper we demonstrate experimentally a magnetic field sensor using a fiber Bragg grating. The shift in the Bragg condition as a result of strain applied on the fiber mounted on a nickel base by the magnetic field gives an indirect measure of the field. The proposed method overcomes the need for long fiber lengths required in methods such as Faraday effect sensors.

Comparison of compressive properties of fiber-free and fiber-bearing syntactic foams

The comparative compressive properties of syntactic foam with and without the inclusion of E-glass fibers in the form of chopped strands are reported. The effort pointed to the fact that the fiber-free syntactic foam had a higher compressive strength than the fiber-bearing one whereas as regards the moduli values they did not differ much. The difference in strength is correlated with the amount of voids present in two foams. The scope of the work was further expanded by including scanning electron microscopy for examining: the surface features of samples prior to and after compression test.

Simultaneous Measurement of Strain and Temperature using Type I and Pre-strained Fiber Bragg Gratings

Strain and temperature sensitivities of a type I Bragg grating inscribed in a germania doped silica fiber, fabricated under normal conditions and zero strain, are compared with that of a Bragg grating inscribed under pre-strained condition. The results obtained reveal that the strain and temperature sensitivities of the two gratings are different. Based on these results, we demonstrate a technique which enables discrimination of strain and temperature in a Fiber Bragg Grating (FBG) with a linear response. The present technique allows for an easy implementation of the sensor by providing a direct access to the grating region in the fiber and demands only a simple interrogation system.

Detection of Tsunami Wave Generation and Propagation Using Fiber Bragg Grating Sensors

This paper describes the design and development of a Fiber Bragg Grating (FBG) sensor system for monitoring tsunami waves generated in the deep ocean. An experimental setup was designed and fabricated to simulate the generation and propagation of a tsunami wave. The characteristics and efficiency of the developed FBG sensor was evaluated with a standard commercial Digiquartz sensor. For real time monitoring of tsunami waves, FBG sensors bonded to a cantilever is used and the wavelength shifts (Delta lambda(B)) in the reflected spectra resulting from the strain/pressure imparted on the FBGs have been recorded using a high-speed Micron Optics FBG interrogation system. The parameters sensed are the signal burst during tsunami generation and pressure variations at different places as the tsunami wave propagates away from the source of generation. The results obtained were compared with the standard commercial sensor used in tsunami detection. The observations suggest that the FBG sensor was highly sensitive and free from many of the constraints associated with the commercial tsunameter.

A novel fiber-coated strong base-type anion exchanger with superfast kinetics. Removal and recovery of silver thiosulfate from aqueous solutions

A commercial acrylic fiber with 92% (w/w) acrylonitrile content was partially hydrolyzed converting a fraction of the nitrile (-CN) groups to carboxylic acid (-COOH) groups, to coat the fiber with polyethylenimine (PEI) resin, which was then crosslinked with glutaraldehyde and further quaternized with ethyl chloroacetate to produce a novel strong-base anionic exchanger in the form of fiber. Designated as PAN(QPEI.XG)(Cl-), the fibrous sorbent was compared with a commercial bead-form resin Amberlite IRA-458(Cl-) in respect of sorption capacity, selectivity, and kinetics for removal of silver thiosulfate complexes from aqueous solutions. Though the saturation level of [Ag(S2O3)(2)](3-) on PAN(QPEI.XG)(Cl-) is considerably less than that on IRA-458(Cl-), the gel-coated fibrous sorbent exhibits, as compared to the bead-form sorbent, a significantly higher sorption selectivity for the silver thiosulfate complex in the presence of excess of other anions Such as S2O32-, SO42-, and Cl-, and a remarkably faster rate of both sorption and stripping. The initial uptake of the sorbate by the fibrous sorbent is nearly instantaneous, reaching up to similar to 80% of the saturation capacity within 10 s, as compared to only similar to 12% on the bead-form sorbent. The high initial rate of uptake fits a shell-core kinetic model for sorption on fiber of cylindrical geometry. With 4M HCl, the stripping of the sorbed silver complex from the fibrous sorbent is clean and nearly instantaneous, while, in contrast, a much slower rate of stripping on the bead-form sorbent leads to its fouling due to a slow decomposition of the silver thiosulfate complex in the acidic medium.