Use of engineered unique cysteine residues to facilitate oriented coupling of proteins directly to a gold substrate

A prerequisite for any "lab on a chip" device that utilizes an electrical signal from the sensor protein is the ability to attach the protein in a specific orientation onto a conducting substrate. Here, we demonstrate the covalent attachment to a gold surface of light-harvesting membrane proteins, from Rhodobacter sphaeroides, via cysteine (Cys) residues engineered on either the cytoplasmic or periplasmic face. This simple directed attachment is superior in its ability to retain light-harvesting complex (LHC) function, when compared to a similar attachment procedure utilizing a self-assembled monolayer on gold. LH 1 has previously been observed to have superior photostability over LH 2 (Magis et al. [2010] Biochim. Biophys. Acta, 1798, 637-645); this characteristic is maintained even with the introduction of Cys residues.     

In vitro evolution of ligands to the membrane protein caveolin

Membrane proteins comprise a third of the human genome, yet present challenging targets for reverse chemical genetics. For example, although implicated in numerous diseases including multiple myeloma, the membrane protein caveolin-1 appears to offer a poor target for the discovery of synthetic ligands due to its largely unknown structure and insolubility. To break this impasse and identify new classes of caveolae controlling lead compounds, we applied phage-based, reverse chemical genetics for the discovery of caveolin-1 ligands derived from the anti-HIV therapeutic T20. Substitution of homologous residues into the T20 sequence used a process analogous to medicinal chemistry for the affinity maturation to bind caveolin. The resultant caveolin-1 ligands bound with >1000-fold higher affinity than wild-type T20. Two types of ELISAs and isothermal titration calorimetry (ITC) measurements demonstrated high affinity binding to caveolin by the T20 variants with K(d) values in the 150 nM range. Microscopy experiments with the highest affinity caveolin ligands confirmed colocalization of the ligands with endogenous caveolin in NIH 3T3 cells. The results establish the foundation for targeting caveolin and caveolae formation in living cells.     

A neutral redox-switchable [2]rotaxane

A limited range of redox-active, rotaxane-based, molecular switches exist, despite numerous potential applications for them as components of nanoscale devices. We have designed and synthesised a neutral, redox-active [2]rotaxane, which incorporates an electron-deficient pyromellitic diimide (PmI)-containing ring encircling two electron-rich recognition sites in the form of dioxynaphthalene (DNP) and tetrathiafulvalene (TTF) units positioned along the rod section of its dumbbell component. Molecular modeling using MacroModel guided the design of the mechanically interlocked molecular switch. The binding affinities in CH(2)Cl(2) at 298 K between the free ring and two electron-rich guests--one (K(a) = 5.8 × 10(2) M(-1)) containing a DNP unit and the other (K(a) = 6.3 × 10(3) M(-1)) containing a TTF unit--are strong: the one order of magnitude difference in their affinities favouring the TTF unit suggested to us the feasibility of integrating these three building blocks into a bistable [2]rotaxane switch. The [2]rotaxane was obtained in 34% yield by relying on neutral donor-acceptor templation and a double copper-catalysed azide-alkyne cycloaddition (CuAAC). Cyclic voltammetry (CV) and spectroelectrochemistry (SEC) were employed to stimulate and observe switching by this neutral bistable rotaxane in solution at 298 K, while (1)H NMR spectroscopy was enlisted to investigate switching upon chemical oxidation. The neutral [2]rotaxane is a chemically robust and functional switch with potential for applications in device settings.     

Random self-affine multifractal Sierpinski sponges in $${\mathbb{R}^d}$$

In this paper we study the Hausdorff and packing dimensions and the Rényi dimensions of random self-affine multifractal Sierpinski sponges in \({\mathbb{R}^{d}}\).     

Six-dimensional quasiclassical and quantum dynamics of H2 dissociation on the c(2 × 2)-Ti/Al(100) surface

Based on a slab model of H(2) dissociation on a c(2 × 2) structure with Ti atoms in the first and third layers of Al(100), a six-dimensional (6D) potential energy surface (PES) has been built. In this PES, a molecular adsorption well with a depth of 0.45 eV is present in front of a barrier of height 0.13 eV. Using this PES, H(2) dissociation probabilities are calculated by the classical trajectory (CT), the quasiclassical trajectory (QCT), and the time-dependent wave-packet (TDWP) method. The QCT study shows that trajectories can be trapped by the molecular adsorption well. Higher incident energy can lead to direct H(2) dissociation. Vibrational pre-excitation is the most efficient way to promote direct dissociation without trapping. We find that both rotational and vibrational excitation have efficacies close to 1.0 in the entire range of incident energies investigated, which supports the randomization in the initial conditions making the reaction rate solely dependent on the total (internal and translational) energy. The H(2) dissociation probabilities from quantum dynamics are in reasonable agreement with the QCT results in the energy range 50-200 meV, except for some fluctuations. However, the TDWP results considerably exceed the QCT results in the energy range 200-850 meV. The CT reaction probabilities are too low compared with the quantum dynamical results.     

Two- and four-component relativistic generalized-active-space coupled cluster method: implementation and application to BiH

A string-based coupled-cluster method of general excitation rank and with optimal scaling which accounts for special relativity within the four-component framework is presented. The method opens the way for the treatment of multi-reference problems through an active-space inspired single-reference based state-selective expansion of the model space. The evaluation of the coupled-cluster vector function is implemented by considering contractions of elementary second-quantized operators without setting up the amplitude equations explicitly. The capabilities of the new method are demonstrated in application to the electronic ground state of the bismuth monohydride molecule. In these calculations simulated multi-reference expansions with both doubles and triples excitations into the external space as well as the regular coupled-cluster hierarchy up to full quadruples excitations are compared. The importance of atomic outer core-correlation for obtaining accurate results is shown. Comparison to the non-relativistic framework is performed throughout to illustrate the additional work of the transition to the four-component relativistic framework both in implementation and application. Furthermore, an evaluation of the highest order scaling for general-order expansions is presented.     

Bond alternation, polarizability, and resonance detuning in methine dyes

We derive structure-property relationships for methine ("Brooker") dyes relating the color of the dye and its symmetric parents to its bond alternation in the ground state and also to the dipole properties associated with its low-lying charge-resonance (or charge-transfer) transition. We calibrate and test these relationships on an array of different protonation states of the green fluorescent protein chromophore motif (an asymmetric halochromic methine dye) and its symmetric parent dyes. The relationships rely on the assumption that the diabatic states that define the Platt model for methine dye color [J. R. Platt, J. Chem. Phys. 25, 80 (1956)] can also be distinguished by their single-double bond alternation and by their charge localization character. These assumptions are independent of the primary constraint that defines the diabatic states in the Platt model--specifically, the Brooker deviation rule for methine dyes [L. G. S. Brooker, Rev. Mod. Phys. 14, 275 (1942)]. Taking these assumptions, we show that the Platt model offers an alternate route to known structure-property relationships between the bond length alternation and the quadratic nonlinear polarizability β. We show also that the Platt model can be parameterized without the need for synthesis of the symmetric parents of a given dye, using the dipole data obtained through spectroscopic measurements. This suggests that the Platt model parameters may be used as independent variables in free-energy relationships for chromophores whose symmetric parents cannot be synthesized or chromophores strongly bound to biomolecular environments. The latter category includes several recently characterized biomolecular probe constructs. We illustrate these concepts by an analysis of previously reported electroabsorption and second-harmonic generation experiments on green fluorescent proteins.     

A multifaceted approach to hydrogen storage

The widespread adoption of hydrogen as an energy carrier could bring significant benefits, but only if a number of currently intractable problems can be overcome. Not the least of these is the problem of storage, particularly when aimed at use onboard light-vehicles. The aim of this overview is to look in depth at a number of areas linked by the recently concluded HYDROGEN research network, representing an intentionally multi-faceted selection with the goal of advancing the field on a number of fronts simultaneously. For the general reader we provide a concise outline of the main approaches to storing hydrogen before moving on to detailed reviews of recent research in the solid chemical storage of hydrogen, and so provide an entry point for the interested reader on these diverse topics. The subjects covered include: the mechanisms of Ti catalysis in alanates; the kinetics of the borohydrides and the resulting limitations; novel transition metal catalysts for use with complex hydrides; less common borohydrides; protic-hydridic stores; metal ammines and novel approaches to nano-confined metal hydrides.     

Kernels by monochromatic paths in digraphs with covering number 2

We call the digraph D an k-colored digraph if the arcs of D are colored with k colors. A subdigraph H of D is called monochromatic if all of its arcs are colored alike. A set N⊆V(D) is said to be a kernel by monochromatic paths if it satisfies the following two conditions: (i) for every pair of different vertices u,v∈N, there is no monochromatic directed path between them, and (ii) for every vertex x∈(V(D)?N), there is a vertex y∈N such that there is an xy-monochromatic directed path. In this paper, we prove that if D is an k-colored digraph that can be partitioned into two vertex-disjoint transitive tournaments such that every directed cycle of length 3,4 or 5 is monochromatic, then D has a kernel by monochromatic paths. This result gives a positive answer (for this family of digraphs) of the following question, which has motivated many results in monochromatic kernel theory: Is there a natural numberlsuch that if a digraphDisk-colored so that every directed cycle of length at mostlis monochromatic, thenDhas a kernel by monochromatic paths?