Peptide internal motions on nanosecond time scale derived from direct fitting of (13)C and (15)N NMR spectral density functions

NMR relaxation-derived spectral densities provide information on molecular and internal motions occurring on the picosecond to nanosecond time scales. Using (13)C and (15)N NMR relaxation parameters [T(1), T(2), and NOE] acquired at four Larmor frequencies (for (13)C: 62.5, 125, 150, and 200 MHz), spectral densities J(0), J(omega(C)), J(omega(H)), J(omega(H) + omega(C)), J(omega(H) - omega(C)), J(omega(N)), J(omega(H) + omega(N)), and J(omega(H) - omega(N)) were derived as a function of frequency for (15)NH, (13)C(alpha)H, and (13)C(beta)H(3) groups of an alanine residue in an alpha-helix-forming peptide. This extensive relaxation data set has allowed derivation of highly defined (13)C and (15)N spectral density maps. Using Monte Carlo minimization, these maps were fit to a spectral density function of three Lorentzian terms having six motional parameters: tau(0), tau(1), tau(2), c(0), c(1), and c(2), where tau(0), tau(1) and tau(2) are correlation times for overall tumbling and for slower and faster internal motions, and c(0), c(1), and c(2) are their weighting coefficients. Analysis of the high-frequency portion of these maps was particularly informative, especially when deriving motional parameters of the side-chain methyl group for which the order parameter is very small and overall tumbling motions do not dominate the spectral density function. Overall correlation times, tau(0), are found to be in nanosecond range, consistent with values determined using the Lipari-Szabo model-free approach. Internal motional correlation times range from picoseconds for methyl group rotation to nanoseconds for backbone N-H, C(alpha)-H, and C(alpha)-C(beta) bond motions. General application of this approach will allow greater insight into the internal motions in peptides and proteins.     

Designing protein beta-sheet surfaces by Z-score optimization

Studies of lattice models of proteins have suggested that the appropriate energy expression for protein design may include nonthermodynamic terms to accommodate negative design concerns. One method, developed in lattice model studies, maximizes a quantity known as the " Z-score," which compares the lowest energy sequence whose ground state structure is the target structure to an ensemble of random sequences. Here we show that, in certain circumstances, the technique can be applied to real proteins. The resulting energy expression is used to design the beta-sheet surfaces of two real proteins. We find experimentally that the designed proteins are stable and well folded, and in one case is even more thermostable than the wild type.     

BIPHASIC PHOTOCHEMISTRY: THE FIRST ACTINOMETRIC REACTION ON A SOLID SUPPORT

Abstract Measurements were performed to determine the action spectrum and dose dependence for photoreactivation of E. coli B_s-1 cells after γ-irradiation. The similarities between photoreactivation after UV- and after γ-irradiation in action spectra, kinetics, and other characteristics indicate that the increased survival of γ-irradiated cells after illumination with photoreactivating light is the result of true photoenzymatic repair.     

Magnetism in gold-iron alloysbelow 14 at.% Fe

The dependence of the magnetization on temperature and on magnetic field for Au alloys with 5, 10 and 13·8 at.% Fe has been measured. The gradual freezing of the spin orientations on cooling, time dependence, and thermomagnetic history effects characteristic of mictomagnetism are found. This magnetic behavior, occurring in disordered alloys, can be described in terms of a “spin glass” matrix with magnetic clusters. Metallurgical treatment strongly affects the cluster sizes and concentrations and the magnetization. The “Curie temperatures” observed by earlier Mössbauer measurements apparently correspond to the freezing of the “spin glass” matrix.     

Adult-child differences in acoustic cue weighting are influenced by segmental context: children are not always perceptually biased toward transitions

It has been proposed that young children may have a perceptual preference for transitional cues [Nittrouer, S. (2002). J. Acoust. Soc. Am. 112, 711-719]. According to this proposal, this preference can manifest itself either as heavier weighting of transitional cues by children than by adults, or as heavier weighting of transitional cues than of other, more static, cues by children. This study tested this hypothesis by examining adults' and children's cue weighting for the contrasts /saI/-/integral of aI/, /de/-/be/, /ta/-/da/, and /ti/-/di/. Children were found to weight transitions more heavily than did adults for the fricative contrast /saI/-/integral aI/, and were found to weight transitional cues more heavily than nontransitional cues for the voice-onset-time contrast /ta/-/da/. However, these two patterns of cue weighting were not found to hold for the contrasts /de/-/be/ and /ti/-/di/. Consistent with several studies in the literature, results suggest that children do not always show a bias towards vowel-formant transitions, but that cue weighting can differ according to segmental context, and possibly the physical distinctiveness of available acoustic cues.     

Fabrication and performance of polymer–nanocomposite anti-reflective thin films deposited by RIR-MAPLE

Design of polymer anti-reflective (AR) optical coatings for plastic substrates is challenging because polymers exhibit a relatively narrow range of refractive indices. Here, we report synthesis of a four-layer AR stack using hybrid polymer:nanoparticle materials deposited by resonant infrared matrix-assisted pulsed laser evaporation. An Er:YAG laser ablated frozen solutions of a high-index composite containing TiO₂ nanoparticles and poly(methyl-methacrylate) (PMMA), alternating with a layer of PMMA. The optimized AR coatings, with thicknesses calculated using commercial software, yielded a coating for polycarbonate with transmission over 97 %, scattering <3 %, and a reflection coefficient below 0.5 % across the visible range, with a much smaller number of layers than would be predicted by a standard thin film calculation. The TiO₂ nanoparticles contribute more to the enhanced refractive index of the high-index layers than can be accounted for by an effective medium model of the nanocomposite.     

Influence and dynamic behavior in random boolean networks

We present a rigorous mathematical framework for analyzing dynamics of a broad class of boolean network models. We use this framework to provide the first formal proof of many of the standard critical transition results in boolean network analysis, and offer analogous characterizations for novel classes of random boolean networks. We show that some of the assumptions traditionally made in the more common mean-field analysis of boolean networks do not hold in general. For example, we offer evidence that imbalance (internal inhomogeneity) of transfer functions is a crucial feature that tends to drive quiescent behavior far more strongly than previously observed.