Preprocessing of rotamers for protein design calculations

We have developed a process that significantly reduces the number of rotamers in computational protein design calculations. This process, which we call Vegas, results in dramatic computational performance increases when used with algorithms based on the dead-end elimination (DEE) theorem. Vegas estimates the energy of each rotamer at each position by fixing each rotamer in turn and utilizing various search algorithms to optimize the remaining positions. Algorithms used for this context specific optimization can include Monte Carlo, self-consistent mean field, and the evaluation of an expression that generates a lower bound energy for the fixed rotamer. Rotamers with energies above a user-defined cutoff value are eliminated. We found that using Vegas to preprocess rotamers significantly reduced the calculation time of subsequent DEE-based algorithms while retaining the global minimum energy conformation. For a full boundary design of a 51 amino acid fragment of engrailed homeodomain, the total calculation time was reduced by 12-fold.     

Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.     

Phage-display selection of a human single-chain fv antibody highly specific for melanoma and breast cancer cells using a chemoenzymatically synthesized G(M3)-carbohydrate antigen

Overexpression of the cell-surface glycosphingolipid G(M3) is associated with a number of different cancers, including those of the skin, colon, breast, and lung. Antibodies against the G(M3) epitope have potential application as therapeutic agents in the treatment of these cancers. We describe the chemoenzymatic synthesis of two G(M3)-derived reagents and their use in the panning of a phage-displayed human single-chain Fv (scFv) antibody library derived from the blood of cancer patients. Three scFv-phage clones, GM3A6, GM3A8, and GM3A15, were selected for recombinant expression and were characterized using BIAcore and flow cytometry. BIAcore measurements using the purified, soluble scFvs yielded dissociation constants (K(d)) ranging from 4.2 x 10(-7) to 2.1 x 10(-5) M. Flow cytometry was used to evaluate the ability of each scFv to discriminate between normal human cells (human dermal fibroblast, HDFa), melanoma cells (HMV-1, M21, and C-8161), and breast cancer cells (BCM-1, BCM-2, and BMS). GM3A6 displayed cross-reactivity with normal cells, as well as tumor cells, and GM3A15 possessed little or no binding activity toward any of the cell lines tested. However, GM3A8 bound to five of the six tumor cell lines and showed no measurable reactivity against the HDFa cells. Hence, we have demonstrated that a synthetic G(M3) panning reagent can be used to isolate a fully human scFv that is highly specific for native G(M3) on the surface of tumor cells. The result is a significant step toward effective immunotherapies for the treatment of cancer.     

Molar extinction coefficients of some carbohydrates in aqueous solutions

Molar extinction coefficients of some carbohydrates viz. l-arabinose (C₅H₁₀O₅), d-glucose (C₆H₁₂O₆), d-mannose (C₆H₁₂O₆), d-galactose (C₆H₁₂O₆), d(-) fructose (C₆H₁₂O₆) and maltose (C₁₂H₂₄O₁₂) in aqueous solutions have been determined at 81, 356, 511, 662, 1173 and 1332 keV by gamma ray transmission method in a narrow beam good geometry set-up. These coefficients have been found to depend upon the photon energy following a 4-parameter polynomial. These extinction coefficients for different sugars having the same molecular formula have same values varying within experimental uncertainty. Within concentration ranges studied, Beer-Lambert law is obeyed very well.     

Comparative study on different carbon nanotube materials in terms of transparent conductive coatings

We compared conductive transparent carbon nanotube coatings on glass substrates made of differently produced single-wall (SWNT), double-wall, and multiwall carbon nanotubes. The airbrushing approach and the vacuum filtration method were utilized for the fabrication of carbon nanotube films. The optoelectronic performance of the carbon nanotube film was found to strongly depend on many effects including the ratio of metallic-to-semiconducting tubes, dispersion, length, diameter, chirality, wall number, structural defects, and the properties of substrates. The electronic transportability and optical properties of the SWNT network can be significantly altered by chemical doping with thionyl chloride. Hall effect measurements revealed that all of these thin carbon nanotube films are of p-type probably due to the acid reflux-based purification and atmospheric impurities. The competition between variable-range hoping and fluctuation-assisted tunneling in the functionized carbon nanotube system could lead to a crossover behavior in the temperature dependence of the network resistance.     

Quenching of highly vibrationally excited pyrimidine by collisions with CO2

Relaxation of highly vibrationally excited pyrimidine (C(4)N(2)H(4)) by collisions with carbon dioxide has been investigated using diode laser transient absorption spectroscopy. Vibrationally hot pyrimidine (E(')=40 635 cm(-1)) was prepared by 248-nm excimer laser excitation, followed by rapid radiationless relaxation to the ground electronic state. The nascent rotational population distribution (J=58-80) of the 00(0)0 ground state of CO(2) resulting from collisions with hot pyrimidine was probed at short times following the excimer laser pulse. Doppler spectroscopy was used to measure the CO(2) recoil velocity distribution for J=58-80 of the 00(0)0 state. Rate constants and probabilities for collisions populating these CO(2) rotational states were determined. The measured energy transfer probabilities, indexed by final bath state, were resorted as a function of DeltaE to create the energy transfer distribution function, P(E,E(')), from E(')-E approximately 1300-7000 cm(-1). P(E,E(')) is fitted to a single exponential and a biexponential function to determine the average energy transferred in a single collision between pyrimidine and CO(2) and parameters that can be compared to previously studied systems using this technique, pyrazineCO(2), C(6)F(6)CO(2), and methylpyrazineCO(2). P(E,E(')) parameters for these four systems are also compared to various molecular properties of the donor molecules. Finally, P(E,E(')) is analyzed in the context of two models, one which suggests that the shape of P(E,E(')) is primarily determined by the low-frequency out-of-plane donor vibrational modes and one which suggests that the shape of P(E,E(')) can be determined by how the donor molecule final density of states changes with DeltaE.     

Fabrication and Mechanical Performance of Non-Crimp Unidirectional Jute-Yarn Preform-Based Composites

This work developed novel jute-yarn, non-crimp, unidirectional (UD) preforms and their composites, with three different types of warp jute yarns of varying linear densities and twists in the dry UD preforms, in order to present a possible solution to the detrimental effects of higher yarn twists and crimp at the warp–weft yarn interlacements of traditional, woven, preform-based composites on their mechanical properties. In the developed UD preforms, warp jute yarns were placed in parallel by using a wooden picture-frame pin board, with the minimal number of glass weft yarns to avoid crimp at the warp–weft yarns interlacements, which can significantly enhance the load-bearing ability of UD composites compared to traditional, woven, preform composites. It was found that an optimal combination of jute warp yarn linear densities and twists in the UD preforms is important to achieve the best possible mechanical properties of newly developed UD composites, because it encourages a proper polymer-matrix impregnation on jute fibres, leading to excellent fibre–matrix interface bonding. Composites made from the 25 lb/spindle jute warp yarn linear density (UD25) exhibited higher tensile and flexural properties than other UD composites (UD20, UD30). All the UD composites showed a much better performance compared to the traditional woven preform composites (W20), which were obviously related to the higher crimp and yarn interlacements, less load-carrying capacity, and poor fiber–matrix interfaces of W20 composites. UD25 composites exhibited a significant enhancement in tensile modulus by ~232% and strength by ~146%; flexural modulus by 138.5% and strength by 145% compared to W20 composites. This reveals that newly developed, non-crimp, UD preform composites can effectively replace the traditional woven composites in lightweight, load-bearing, complex-shaped composite applications, and hence, this warrants further investigations of the developed composites, especially on long-term and dynamic-loading mechanical characterizations.     

Ballistic Impact Behaviour of Glass/Epoxy Composite Laminates Embedded with Shape Memory Alloy (SMA) Wires

This paper aims to estimate the enhancement in the energy absorption characteristics of the glass fiber reinforced composites (GFRP) by embedding prestrained pseudo-elastic shape memory alloy (SMA) that was used as a secondary reinforcement. The pseudo-elastic SMA (PE-SMA) embedded were in the form of wires and have an equiatomic composition (i.e., 50%–50%) of nickel (Ni) and titanium (Ti). These specimens are fabricated using a vacuum-assisted resin infusion process. The estimation is done for the GFRP and SMA/GFRP specimens at four different impact velocities (65, 75, 85, and 103 m/s) using a gas-gun impact set-up. At all different impact velocities, the failure modes change as we switch from GFRP to SMA/GFRP specimen. In the SMA/GFRP specimen, the failure mode changed from delamination in the primary region to SMA-pull out and SMA deformation. This leads to an increase in the ballistic limit. It is observed that energy absorbed by SMA/GFRP specimens is higher than the GFRP specimens subjected to the same levels of impact energy. To understand the damping capabilities of SMA embedment, vibration signals are captured, and the damping ratio is calculated. SMA dampens the vibrations imparted by the projectile to the specimen. The damping ratio of the SMA/GFRP specimens is higher than the GFRP specimens. The damping effect is more prominent below the ballistic limit when the projectile got rebounded (65 m/s).     

Synthesis and Characterization of a Novel Diels–Alder Adduct of Codeine

The Diels–Alder reaction was applied to 4,5‐epoxymorphinan opioids to generate a novel aromatic cycloadduct at C(7) C(8): Thermolytic cleavage of sultine 8 produced the reactive diene o‐quinodimethane 7 which condensed favorably with codeine ( 11 ), but not with codeinone ( 9 ) or 14‐hydroxycodeinone ( 10 ), producing the desired tetrahydronaphtho adduct 12 with (7R,8R) geometry (Scheme). The configuration of the cycloadduct was determined by 1D‐ and 2D‐NMR experiments. The unanticipated reactivity of these codeine derivatives was investigated by quantum‐mechanical calculations, and it was determined that steric effects of the 6‐keto and 14‐hydroxy group likely precluded condensation by raising the molecular energy of their respective transition states.