An antiparallel alpha-helical coiled-coil model system for rapid assessment of side-chain recognition at the hydrophobic interface

Both parallel and antiparallel alpha-helical coiled-coil dimers are common among proteins; however, biophysical scrutiny has focused almost entirely on parallel dimers. We describe the development of a model system that enables efficient and systematic analysis of hydrophobic packing between antiparallel alpha-helices. Our findings reveal significant differences in packing preferences between parallel and antiparallel coiled-coils.     

The problem of responses less than the reporting limit in unsupervised pattern recognition

The problem of the presence and of the treatment of values below the detection limit (or ‘less than’ values) is examined, for some real cases of unsupervised pattern recognition of samples. The experimental data refer to archaeological glass fragments of the seventh and eighth centuries AD and to ceramic shards of Roman epoch and of different provenances. Increasing amounts of less-thans are progressively introduced into the original data by a particular procedure and the less-thans treated each time with three different substitution methods (i.e. substitution with constant values, with randomly distributed values and with values obtained by principal component analysis). A subsequent multivariate classification of the samples by various techniques and an evaluation of the corresponding results, allows one to evaluate and to compare the effectiveness of the three methods of treatment of less-thans.     

The centrosomal localization of KM-HN-1 (MGC33607) depends on the leucine zipper motif and the C-terminal coiled-coil domain

KM-HN-1 is a C-terminal coiled-coil domain containing protein previously referred to as image clone MGC33607. This protein has been previously identified as a cancer/testis antigen and reported as nuclear and chromatin localizing protein. We raised polyclonal antisera with the GST fusion protein and identified them as a 105 kDa protein. Motif analysis showed that this protein harbors the leucine zipper motif in internal 1/3 region and the coiled-coil domain in the C-terminal region. Using the full length and various deletion mutants, we determined the motif that governs the subcellular localization of KM-HN-1. Immunofluorescence staining of the endogenous KM-HN-1 and various kinds of GFP-tagged KM-HN-1 revealed that KM-HN-1 localizes to the centrosomes as well as nucleus. The centrosomal localization-determining region of this protein is C-terminal coiled-coil domain in which the leucine zipper motif and the nuclear export signal (NES) harbor.     

Nanoswitches based on DNA base pairs: why adenine-thymine is less suitable than guanine-cytosine.

Substituted Watson–Crick guanine–cytosine (GC) base pairs were recently shown to yield robust three‐state nanoswitches. Here, we address the question: Can such supramolecular switches also be based on Watson–Crick adenine‐thymine (AT) base pairs? We have theoretically analyzed AT pairs in which purine‐C8 and/or pyrimidine‐C6 positions carry a substituent X=NH^?, NH₂, NH₃⁺ (N series), O^?, OH or OH₂⁺ (O series), using the generalized gradient approximation (GGA) of density functional theory at the BP86/TZ2P level. Thus, we explore the trend in geometrical shape and hydrogen bond strengths in AT pairs along a series of stepwise protonations of the substituents. Introducing a charge on the substituents leads to substantial and characteristic changes in the individual hydrogen bond lengths when compared to the neutral AT pair. However, the trends along the series of negative, neutral, and positive substituents are less systematic and less pronounced than for GC. In certain instances, internal proton transfer from thymine to adenine occurs. Our results suggest that AT is a less suitable candidate than GC in the quest for chemically controlled nanoswitches.     

Communication: The reason why +c ZnO surface is less stable than -c ZnO surface: first-principles calculation

It has been experimentally shown that an O(-c)-polar ZnO surface is more stable than a Zn(+c)-polar surface in H(2) ambient. We applied first-principles calculations to investigating the polarity dependence on the stability at the electronic level. The calculations revealed that the -c surface terminated with H atom was stable maintaining a wurtzite structure, whereas the +c surface was unstable due to the change of coordination numbers of Zn at the topmost surface from four (wurtzite) to six (rock salt). This causes the generation of O(2) molecules, resulting in instability at the +c surface.     

Hydrophobic core repacking in a coiled-coil dimer via phage display: insights into plasticity and specificity at a protein-protein interface

The coiled-coil, which consists of two or more interwoven amphiphilic alpha-helices, is formed by sequences that have a characteristic heptad repeat (abcdefg) where a and d are hydrophobic residues. Most efforts to elucidate the origins of coiled-coil pairing selectivity have focused on electrostatic interactions among side chains that flank the core (positions e and g) and on polar side chains that occur occasionally at core positions. We have used phage display to explore another source of coiled-coil specificity: steric matching among nonpolar side chains in the core. We introduced a destabilizing Leu-->Ala mutation into the core of one helix in a known heterodimer and then screened a phage-based library of potential partner helices in search of compensating mutations. We identified a new heterodimer pair (30 residues/helix) that is comparable in stability to the GCN4-p1 homodimer (33 residues/helix). Furthermore, the Leu-->Ala mutant shows specificity for its phage-derived partner over the original partner despite their similar sequences. These results show that a phage-based approach can provide unique insights on coiled-coil pairing preferences that should facilitate both the analysis of natural sequences and the development of specific dimerization motifs that are orthogonal to one another.     

Theoretical investigation into the nature of the second vertical ionic state of the water dimer

Ab initio molecular orbital calculations have been carried out to resolve questions concerning the location of the second ionization in the water dimer. The results indicate that it is from the proton acceptor molecule of the water dimer.     

The AFM measured force required to rupture the dithiolate linkage of thioctic acid to gold is less than the rupture force of a simple gold-alkyl thiolate bond

We show with atomic force microscopy that thioctic acid, a spatially constrained system with two sulfur linkages to gold, is less stable to tensile stress than a thiolate with a single attachment to gold. The force required to remove the dithiolate-linked thioctic acid was 0.31+/-0.13 nN, whereas the force required to remove a simple thiolate from the gold substrate was 1.05+/-0.29 nN. These results suggest that SAMs of densely packed or polypodal thiols may be substantially less stable under tensile stress than previously recognized and that the additional thiolate linkages may not only fail to increase the overall strength of attachment but could actually reduce it.     

Proton conduction in materials comprising conducting domains with widths less than 6 nm

We review the literature on proton conductivity and water uptake of composite polymer electrolyte membranes comprising bicontinuous hydrophilic and hydrophobic domains with well-controlled geometries. Both quantities appear to be enhanced when the width of the hydrophilic channels is smaller than 6 nm.     

The structure of the carbon dioxide dimer

The structure of the carbon dioxide dimer is discussed theoretically in terms of two empirical potentials and using CNDO/2 and ab initio quantum mechanical calculations. All these methods support the conclusion that there are two structures of comparable energy, the lower one being non-polar.     

Grand European Chemical Conferences: The Whole is More than the Sum of the Parts

National chemical society conferences are major platforms for communication and the exchange of ideas among the various chemical communities. However, in light of increasing efforts to create a true European research area in chemistry, there is an obvious need to establish such a platform on the European level. The GDCh has recently come up with a concept for achieving this goal.     

The complex role of the triphenylmethyl motif in anticancer compounds

Compounds incorporating the triphenylmethyl motif constitute an emerging family of potent anticancer agents. Although several small molecules containing this pharmacophore have now been identified, the mechanism of cell death induction for some of these compounds is unknown. In an effort to define their mechanism of action, and to distinguish subtypes within the group of compounds containing the triphenylmethyl moiety, we have created novel triphenylmethyl-containing small molecules and have evaluated them in a battery of biological assays. Here we show that several phosphonate and phosphonochloridates possessing the triphenylmethyl motif potently induce death of multiple cancer cell lines in culture. Further assays evaluating the ability to cause cell cycle arrest, inhibit tubulin polymerization, dissociate mitochondrial-bound hexokinase in cancer cells, and inhibit calcium-dependent potassium ion channels indicate that triphenylmethyl-containing compounds can be placed into at least four distinct categories, each with a different mechanism of action.     

The primary step in the ultrafast photodissociation of the methyl iodide dimer

This paper shows the results of combined experimental and theoretical work that have unravelled the mechanism of ultrafast ejection of a methyl group from a cluster, the methyl iodide dimer (CH(3)I)(2). Ab initio calculations have produced optimized geometries for the dimer and energy values and oscillator strengths for the excited states of the A band of (CH(3)I)(2). These calculations have allowed us to describe the blue shift that had been observed in the past in this band. This blue shift has been experimentally determined with higher precision than in all previously reported experiments, since it has been measured through its effect upon the kinetic energy release of the fragments using femtosecond velocity map imaging. Observations of the reaction branching ratio and of the angular nature of the fragment distribution indicate that two main changes occur in A-band absorption in the dimer with respect to the monomer: a substantial change in the relative absorption to different states of the band, and, more importantly, a more efficient non-adiabatic crossing between two of those states. Additionally, time resolved experiments have been performed on the system, obtaining snapshots of the dissociation process. The apparent retardation of more than 100 fs in the dissociation process of the dimer relative to the monomer has been assigned to a delay in the opening of the optical detection window associated with the resonant multiphoton ionization detection of the methyl fragment.     

High-resolution continuous-wave-diode laser cavity ring-down spectroscopy of the hydrogen fluoride dimer in a pulsed slit jet expansion: two components of the N=2 triad near 1.3 microm

The near-infrared overtone spectra of the prototypical hydrogen-bond hydrogen fluoride dimer (HF)2 contain rich information on hydrogen bond dynamics. We report a study of the N=2 triad involving excitations with two quanta of HF stretching in (HF)2 around 1.3 microm (7500-7800 cm(-1)) by means of continuous-wave-diode laser cavity ring-down spectroscopy in a pulsed supersonic slit jet expansion. The analysis of the rotationally resolved overtone spectra allows the study of vibrational mode-selective kinetics, such as hydrogen bond predissociation with lifetimes tauPD and tunneling rearrangement (switching) processes with periods tausw obtained from the tunneling splitting DeltaT in highly excited vibrational states. The Ka=1<--0 transition of the Nj=22 band of (HF)2 has been reinvestigated by us in a supersonic jet expansion; the much improved data obtained here are in excellent agreement with several previous experimental results. Our analysis provides subband-level positions and properties 0(Ka=1(A+))=7711.37956(66) cm(-1), DeltaT=0.0936(10) cm(-1), and tauPD=1.3-1.9x10(-9) s, depending on the level symmetry A+ and B+. We have also analyzed spectra of the Nj=21 band, which we have observed for the first time in a supersonic jet with rotational resolution. For the Ka=0<--0 transition of this band, we find the band center at 0(A+)=7550.3555(26) cm(-1) and a tunneling splitting of DeltaT=0.0150(37) cm(-1). This level involves mostly excitation of the H-bonded HF stretching with two quanta. The mode-selective tunneling switching is in agreement with a simple picture of inhibited tunneling. These experimental values are close to those calculated on the "SO(-3)" potential energy hypersurface of Klopper, Quack, and Suhm. The N=2 triad also exhibits a strongly mode-selective predissociation dynamics, with a predissociation lifetime tauPD=4.99(84)x10(-11) s in the Nj=21 level, which is more than 20 times shorter than that for the Nj=22 level.     

Electron-counting procedures in clusters of the iron triad

Until recently all known high-nuclearity carbonyl clusters of the iron triad had metal core structures based on an octahedron with formulations corresponding to seven skeletal electron pairs (S = 7), in agreement with the predictions of polyhedral skeletal electron counting procedures. The isolation of the monoanion [HOs₈(CO)₂₂]^?, which also has S = 7, first broke this pattern, as it has a fused tetrahedral core geometry. The extension of skeletal electron counting procedures to include multiple “capping” of incomplete polyhedra permits a simple rationalisation of this structure as a tetra-capped arachno-octahedral. This approach has allowed the development of a matrix correlation for the main structural types observed in this triad. Structural relationships between the first members of a new class of high-nuclearity clusters based on the fusion of two are also discussed.     

Vibrational predissociation in the HCl dimer

We present results of a combined theoretical and experimental study on the vibrational predissociation of the HCl dimer. On the theoretical side, photodissociation linewidths and product-state distributions for monomer stretch excited states with total angular momentum J=0 were computed, using the Fermi golden rule approximation. The resonances investigated include excitation of the hydrogen bond donor and acceptor stretches, as well as combinations of one of these modes with the intermolecular stretch and geared bend modes, for both even and odd permutation symmetry. Line strengths for the transitions from the J=1, K=0 ground state to excited states with J=0 were computed using quasibound states. On the experimental side, the photofragment angular distribution method was employed to obtain complete final-state distributions for the monomer stretch excited states. Three different transitions were probed, all starting from the lower tunneling component of the ground state: the (R)Q(0)(1) transition for excitation of the acceptor stretch and the (Q)R(0)(0) transition and unresolved (R)Q(0) branch for the donor stretch excitation. We find that, in contrast to the HF dimer, the excited-state alignment of the HCl dimer, resulting from excitation using a polarized laser beam, is completely lost on the time scale of the dissociation. The agreement between theory and experiment for the product-state distributions and line strengths is reasonable. The computed lifetimes are 1-2 orders of magnitude too small, which is attributed to a deficiency in the potential energy surface.     

The electronic spectrum of the dimer of thiocarbonyl chloride

The electronic spectrum of the dimer of thiocarbonyl chloride has been measured and interpreted in terms of D_2h symmetry and with the aid of computer resolution and of CNDO molecular orbital calculations. Evidence is presented for sulphur—sulphur interactions.     

The electronic structure of the HCN dimer and trimer

The electronic structure and energy of dimerization and trimerization of HCN are computed with an STO-3G basis and the results found to be in good agreement with the experimental E. Unlike CNDO/2, this small ab initio basis predicts the correct geometry for the dimer of hydrogen cyanide. The charge redistribution effects found in this H-bond involving a C-H proton donor and sp hybridized acceptor are similar to those found in previous H-bonded studies.     

The 48 bp centromeric repeat is a functionally conserved motif in great apes and man showing protein-binding properties

The centromere-kinetochore complex is a chromosomal assembly site including repeat motifs and protein binding properties thus mediating chromosome motility and mitotic regulation. Next to the alpha-satellite DNA family as well as human satellite III DNA, contribution of other repetitive sequences has to be strongly considered in centromere function. Here, we report the identification of centromeric 48 bp motifs, isolated from chimpanzee and orang-utan using an orthologous human DNA probe. Applying Southern hybridization we show that these sequences are restricted to hominoid species. Diminishing hybrid formation in gibbons suggested that the 48 bp repeat originated approximately 25-20 million years ago. Consistently, both chimpanzee as well as human repeat probes failed to generate any hybridization signal with the monkey species Cercopithecus aethiops and Aotes trivirgatus. Sequence deviations from the consensus of human repeat monomers of 6% and 10.4% in chimpanzee and orang-utan, respectively, were found within a 16 bp region of the 48 bp repeat units. Gel mobility shift assays using chimpanzee repeat dimers as probes revealed peptide-binding properties with human and chimpanzee nuclear extracts. Species-specific DNA-protein complexes remained unaffected by competition studies and indicated the presence of at least one novel interacting protein consisting of two subunits with 90 and 95 kDa. Our data suggest that the 48 bp repeat, next to alpha-satellite DNA, provides essential sequence information for specific DNA-protein interaction and they imply phylogenetic conservation of these binding properties in primates. The complex is likely involved in the proper formation and/or function of mammalian centromeres.