A carrier protein strategy yields the structure of dalbavancin

Many large natural product antibiotics act by specifically binding and sequestering target molecules found on bacterial cells. We have developed a new strategy to expedite the structural analysis of such antibiotic-target complexes, in which we covalently link the target molecules to carrier proteins, and then crystallize the entire carrier-target-antibiotic complex. Using native chemical ligation, we have linked the Lys-D-Ala-D-Ala binding epitope for glycopeptide antibiotics to three different carrier proteins. We show that recognition of this peptide by multiple antibiotics is not compromised by the presence of the carrier protein partner, and use this approach to determine the first-ever crystal structure for the new therapeutic dalbavancin. We also report the first crystal structure of an asymmetric ristocetin antibiotic dimer, as well as the structure of vancomycin bound to a carrier-target fusion. The dalbavancin structure reveals an antibiotic molecule that has closed around its binding partner; it also suggests mechanisms by which the drug can enhance its half-life by binding to serum proteins, and be targeted to bacterial membranes. Notably, the carrier protein approach is not limited to peptide ligands such as Lys-D-Ala-D-Ala, but is applicable to a diverse range of targets. This strategy is likely to yield structural insights that accelerate new therapeutic development.     

Investigation of two-dimensional acoustic resonant modes in a particle separator

Within an acoustic standing wave particles experience acoustic radiation forces, a phenomenon which is exploited in particle or cell manipulation devices. When developing such devices, one-dimensional acoustic characteristics corresponding to the transducer(s) are typically of most importance and determine the primary radiation forces acting on the particles. However, radiation forces have also been observed to act in the lateral direction, perpendicular to the primary radiation force, forming striated patterns. These lateral forces are due to lateral variations in the acoustic field influenced by the geometry and materials used in the resonator. The ability to control them would present an advantage where their effect is either detrimental or beneficial to the particle manipulation process. The two-dimensional characteristics of an ultrasonic separator device have been modelled within a finite element analysis (FEA) package. The fluid chamber of the device, within which the standing wave is produced, has a width to height ratio of approximately 30:1 and it is across the height that a half-wavelength standing wave is produced to control particle movement. Two-dimensional modal analyses have calculated resonant frequencies which agree well with both the one-dimensional modelling of the device and experimentally measured frequencies. However, these two-dimensional analyses also reveal that these modes exhibit distinctive periodic variations in the acoustic pressure field across the width of the fluid chamber. Such variations lead to lateral radiation forces forming particle bands (striations) and are indicative of enclosure modes. The striation spacings predicted by the FEA simulations for several modes compare well with those measured experimentally for the ultrasonic particle separator device. It is also shown that device geometry and materials control enclosure modes and therefore the strength and characteristics of lateral radiation forces, suggesting the potential use of FEA in designing for the control of enclosure modes in similar particle manipulator devices.     

The roaming atom pathway in formaldehyde decomposition

We present a detailed experimental and theoretical investigation of formaldehyde photodissociation to H(2) and CO following excitation to the 2(1)4(1) and 2(1)4(3) transitions in S(1). The CO velocity distributions were obtained using dc slice imaging of single CO rotational states (v=0, j(CO)=5-45). These high-resolution measurements reveal the correlated internal state distribution in the H(2) cofragments. The results show that rotationally hot CO (j(CO) approximately 45) is produced in conjunction with vibrationally "cold" H(2) fragments (v=0-5): these products are formed through the well-known skewed transition state and described in detail in the accompanying paper. After excitation of formaldehyde above the threshold for the radical channel (H(2)CO-->H+HCO) we also find formation of rotationally cold CO (j(CO)=5-28) correlated to highly vibrationally excited H(2) (v=6-8). These products are formed through a novel mechanism that involves near dissociation followed by intramolecular H abstraction [D. Townsend et al., Science 306, 1158 (2004)], and that avoids the region of the transition state entirely. The dynamics of this "roaming" mechanism are the focus of this paper. The correlations between the vibrational states of H(2) and rotational states of CO formed following excitation on the 2(1)4(3) transition allow us to determine the relative contribution to molecular products from the roaming atom channel versus the conventional molecular channel.     

1B2(1Sigma(u)+) excited state decay dynamics in CS2

The authors report time resolved photoelectron spectra of the (1)B(2)((1)Sigma(u) (+)) state of CS(2) at pump wavelengths in the region of 200 nm. In contrast to previous studies, the authors find that the predissociation dynamics is not well described by a single exponential decay. Biexponential modeling of the authors' data reveals a rapid decay pathway (tau<50 fs), in addition to a longer lived channel (tau approximately 350-650 fs) that displays a marked change in apparent lifetime when the polarization of the pump laser is rotated with respect to that of the probe. Since the initially populated (1)B(2)((1)Sigma(u) (+)) state may decay to form either S((1)D) or S((3)P) products (the latter produced via a spin-orbit induced crossing from a singlet to a triplet electronic surface), this lifetime observation may be rationalized in terms of changes in the relative ionization cross section of these singlet and triplet states of CS(2) as a function of laser polarization geometry. The experimentally observed lifetime of the longer lived channel is therefore a superposition of these two pathways, both of which decay on very similar time scales.     

A chemiluminescence study of madder lakes on paper

The photo degradation of watercolour drawings prepared with madder lake pigments on gelatine-sized paper was studied by chemiluminometry, viscometry, and colorimetry. A method of recto irradiation and verso measurement was developed to overcome absorption of the emitted photons by the paint layer. A complex relationship between paper substrate, applied chromophores and associated transition metals was observed with strong correlations between the presence of transition metals associated with the madder lakes and the degradation of the paper substrate and the applied paint layer as well as evidence of pro-oxidative activity by the chromophores in the applied paint layers. The pro-oxidant behaviour appears to be dependent on the type of transition metal present. This is the first in-depth research into the photodegradation of madder lake-based watercolours which attempts to understand the chemistry of the processes.     

Learning Elliptic Partial Differential Equations with Randomized Linear Algebra

Given input–output pairs of an elliptic partial differential equation (PDE) in three dimensions, we derive the first theoretically rigorous scheme for learning the associated Green’s function G. By exploiting the hierarchical low-rank structure of G, we show that one can construct an approximant to G that converges almost surely and achieves a relative error of \(\mathcal {O}(\varGamma _\epsilon ^{-1/2}\log ^3(1/\epsilon )\epsilon )\) using at most \(\mathcal {O}(\epsilon ^{-6}\log ^4(1/\epsilon ))\) input–output training pairs with high probability, for any \(0<\epsilon <1\). The quantity \(0<\varGamma _\epsilon \le 1\) characterizes the quality of the training dataset. Along the way, we extend the randomized singular value decomposition algorithm for learning matrices to Hilbert–Schmidt operators and characterize the quality of covariance kernels for PDE learning.