Electron microscopy studies on DNA recognition by DNA-PK

Advances in transmission electron microscopy coupled to increasingly powerful biocomputing techniques are opening enormous possibilities to understand the structure and function of complex biological processes performed by large multi-protein assemblies. This is an exciting time for electron microscopists because we can combine our efforts with X-ray crystallographers and NMR spectroscopists to reach the prospect of studying the structure and dynamics of the so-called ‘molecular machines’. One of these fascinating systems is the macromolecular complex formed around double-stranded DNA breaks (DSBs). Non-homologous end-joining (NHEJ) is the main DSBs repair pathway in mammalian cells, where a collection of proteins interact to rejoin two broken DNA ends. During NHEJ, DNA-dependent protein kinase (DNA-PK) binds damaged DNA with high affinity and acts as the main scaffold for other repair factors. Several studies have made use of the electron microscope to reveal the three-dimensional architecture of DNA-PK and the structural basis for the recognition of damaged DNA and the activation of DNA-PK's kinase activity.     

High-speed horizontal-path atmospheric turbulence correction with a large-actuator-number microelectromechanical system spatial light modulator in an interferometric phase-conjugation engine

Results of atmospheric propagation for a high-speed, large-actuator-number adaptive optics system are presented. The system uses a microelectromechanical system- (MEMS-) based spatial light modulator correction device with 1024 actuators. Tests over a 1.35-km path achieved correction speeds in excess of 800 Hz and Strehl ratios close to 0.5. The wave-front sensor was based on a quadrature interferometer that directly measures phase. This technique does not require global wave-front reconstruction, making it relatively insensitive to scintillation and phase residues. The results demonstrate the potential of large-actuator-number MEMS-based spatial light modulators to replace conventional deformable mirrors.     

Glycopeptides by Linch-Pin C−H Activations for Peptide-Carbohydrate Conjugation by Manganese(I)-Catalysis

Late-stage C−H glycosylations of structurally complex amino acids and peptides were accomplished by means of racemization-free manganese(I)-catalyzed C−H activation. Thus, glycosylative modifications proved to be viable by a linch-pin approach, featuring chemo- and site-selective C−H transformations. The peptide–saccharide conjugation provided modular access to structurally complex glycopeptides, likewise enabling the assembly of fluorescent-labelled glycopeptides.     

Broadening the frequency bandwidth of a finite extensibility nonlinear vibration absorber by exploiting its internal resonances

Nonlinear Dynamics - In this paper, the dynamics response of a finite extensibility nonlinear elastic (FENE) absorber attached to a nonlinear primary system is investigated by writing the modal...     

Unravelling the Time Scale of Conformational Plasticity and Allostery in Glycan Recognition by Human Galectin-1

The interaction of human galectin-1 with a variety of oligosaccharides, from di-(N-acetyllactosamine) to tetra-saccharides (blood B type-II antigen) has been scrutinized by using a combined approach of different NMR experiments, molecular dynamics (MD) simulations, and isothermal titration calorimetry. Ligand- and receptor-based NMR experiments assisted by computational methods allowed proposing three-dimensional structures for the different complexes, which explained the lack of enthalpy gain when increasing the chemical complexity of the glycan. Interestingly, and independently of the glycan ligand, the entropy term does not oppose the binding event, a rather unusual feature for protein-sugar interactions. CLEANEX-PM and relaxation dispersion experiments revealed that sugar binding affected residues far from the binding site and described significant changes in the dynamics of the protein. In particular, motions in the microsecond-millisecond timescale in residues at the protein dimer interface were identified in the presence of high affinity ligands. The dynamic process was further explored by extensive MD simulations, which provided additional support for the existence of allostery in glycan recognition by human galectin-1.     

A Preorganized Hydrogen-Bonding Motif for the Molecular Recognition of Carbohydrates

The choice between adaptive and preorganized architectures, or of the most effective hydrogen bonding groups to be selected, are dilemmas that supramolecular chemists must address in designing synthetic receptors for such a challenging guest as carbohydrates. In this paper, structurally related architectures featuring two alternative hydrogen bonding motifs were compared to ascertain the structural and functional origin of their binding differences and the advantages that can be expected in monosaccharide recognition. A set of structurally related macrocyclic receptors were prepared, and their binding properties were measured by NMR and ITC techniques in chloroform vs a common saccharidic target, namely, the β-octyl glycoside of D-glucose. Results showed that the diaminocarbazolic motif, recently reported as the constituting unit of highly effective receptors for saccharides in water, is a superior hydrogen bonding motif compared to the previously described diaminopyrrolic motif, which was successfully employed in molecular recognition of carbohydrates in polar organic solvents, due to intrinsic structural and functional factors, rather than to hydrophobic contributions. In addition, the occurrence of a rare example of a thermodynamic template effect exerted by the beta-glucoside has been ascertained, enhancing the synthesis outcome of the otherwise low yielding preparation of the described macrocyclic receptors.     

Prescriptions for gravitational initial data as judged by a simple radiating model

Several methods of prescribing initial data for gravitational and matter fields, which are intended to eliminate extraneous radiation that is not produced by the matter source, are analysed in a simple exactly soluble radiating model. The model consists of an harmonic oscillator coupled to a scalar field along future light cones of Minkowski space time. In particular we analyze the asymptotic regime of the oscillator and find it is characterized essentially by two distinct decay modes. They differ in the way they behave both in the limit of small coupling constant and in a certain Newtonian limit. As a criterion to select initial data for the field with no extra radiation, we require that these initial data sets should put the oscillator from the start into the asymptotic regime. The underlying hypothesis here is that initial transients result from excitation of the oscillator by incoming radiation. We then see that the requirement of a uniform Newtonian limit leads to unique data for the scalar field for each arbitrary data set for the oscillator. We further find that this unique data set indeed satisfies our criterion.     

Quotient normed cones

Given a normed cone (X, p) and a subconeY, we construct and study the quotient normed cone (X/Y,p) generated byY. In particular we characterize the bicompleteness of (X/Y, ‖·‖ ^p ,p) in terms of the bicompleteness of (X, p), and prove that the dual quotient cone ((X/Y)^*, || · ‖·‖^p,p) can be identified as a distinguished subcone of the dual cone (X ^*, || · ||_{p, u}). Furthermore, some parts of the theory are presented in the general setting of the spaceCL(X, Y) of all continuous linear mappings from a normed cone (X, p) to a normed cone (Y, q), extending several well-known results related to open continuous linear mappings between normed linear spaces.     

Commutators of singular integrals on spaces of homogeneous type

In this work we prove some sharp weighted inequalities on spaces of homogeneous type for the higher order commutators of singular integrals introduced by R. Coifman, R. Rochberg and G. Weiss in Factorization theorems for Hardy spaces in several variables, Ann. Math. 103 (1976), 611–635. As a corollary, we obtain that these operators are bounded on L ^p (w) when w belongs to the Muckenhoupt’s class A _p , p > 1. In addition, as an important tool in order to get our main result, we prove a weighted Fefferman-Stein type inequality on spaces of homogeneous type, which we have not found previously in the literature.