The C-Terminal Domain of the MutL Homolog from Neisseria gonorrhoeae Forms an Inverted Homodimer

The mismatch repair (MMR) pathway serves to maintain the integrity of the genome by removing mispaired bases from the newly synthesized strand. In E. coli, MutS, MutL and MutH coordinate to discriminate the daughter strand through a mechanism involving lack of methylation on the new strand. This facilitates the creation of a nick by MutH in the daughter strand to initiate mismatch repair. Many bacteria and eukaryotes, including humans, do not possess a homolog of MutH. Although the exact strategy for strand discrimination in these organisms is yet to be ascertained, the required nicking endonuclease activity is resident in the C-terminal domain of MutL. This activity is dependent on the integrity of a conserved metal binding motif. Unlike their eukaryotic counterparts, MutL in bacteria like Neisseria exist in the form of a homodimer. Even though this homodimer would possess two active sites, it still acts a nicking endonuclease. Here, we present the crystal structure of the C-terminal domain (CTD) of the MutL homolog of Neisseria gonorrhoeae (NgoL) determined to a resolution of 2.4 A. The structure shows that the metal binding motif exists in a helical configuration and that four of the six conserved motifs in the MutL family, including the metal binding site, localize together to form a composite active site. NgoL-CTD exists in the form of an elongated inverted homodimer stabilized by a hydrophobic interface rich in leucines. The inverted arrangement places the two composite active sites in each subunit on opposite lateral sides of the homodimer. Such an arrangement raises the possibility that one of the active sites is occluded due to interaction of NgoL with other protein factors involved in MMR. The presentation of only one active site to substrate DNA will ensure that nicking of only one strand occurs to prevent inadvertent and deleterious double stranded cleavage.

Thermodynamics of water entry in hydrophobic channels of carbon nanotubes

Experiments and computer simulations demonstrate that water spontaneously fills the hydrophobic cavity of a carbon nanotube. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed two phase thermodynamics method to compute translational and rotational entropies of confined water molecules inside single-walled carbon nanotubes and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk water and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with that of bulk water shows significant shifts in the positions of the spectral peaks that are directly related to the tube radius. (C) 2011 American Institute of Physics.

Tribridged diruthenium complexes: A new structural motif

Dinuclear complexes containing a (mu-oxo)bis(mu-carboxylato) diruthenium (III) core have been prepared by a novel synthetic route using metal-metal bonded diruthenium(II,III) tetracarboxylates as precursors. The complexes have been structurally characterized and they are redox active. The terminal ligands play an important role in tuning the electronic structure of the core. The stability of the core is found to be dependent on the size and pi-acidic nature of the terminal ligand cis- to the mu-oxo ligand. The chemistry of such tribridged complexes is relatively new. The rapid growth of this chemistry is based on the discovery of similar core structures in several non-heme iron- and manganese-containing metalloproteins. The tribridged core presents a new structural motif in coordination chemistry. The chemistry of diruthenium complexes with a [Ru-2(mu-O) (mu-O(2)CR)(2)(2+)] core has been reviewed.

Preferential condensation of SAR-DNA by histone H1 and its SPKK containing octapeptide repeat motif

Linker histone H1 binds preferentially the scaffold associated region (SAR) DNA elements that contain characteristic oligo dA . dT tracts. In the present study, we have compared the condensation brought about by histone H1 of a SAR DNA fragment in the histone spacer region of Drosophila melanogaster with that of a random DNA (pBR322 EcoRI-SalI) fragment by circular dichroism spectroscopy. The condensation of the SAR DNA fragment by histone H1 is 3-4-fold higher than that of the random DNA fragment. A 16-mer peptide, ATPKKSTKKTPKKAKK, the sequence that is present in the C-terminus of histone H1d, which has recently been shown to possess DIVA and chromatin condensing properties, also condenses the SAR DNA fragment preferentially in a highly cooperative manner. We have proposed a model for the dynamics of chromatin structure involving histone H1-SAR DNA interaction through SPKK containing peptide motifs and its competition by AT-hook peptides present in the nonhistone chromosomal proteins like HMG-I and HMG-Y.

Role of hydrophobic effect and surface charge in surfactant-DNA association

Ethidium bromide is one of the best known DNA intercalator. Upon intercalation inside DNA, the fluorescence due to ethidium bromide gets enhanced by many orders of magnitude. In this paper, we employed ethidium bromide as a probe for studying surfactant-DNA complexation using fluorescence spectroscopy and agarose gel electrophoresis. Surfactants of different charge types and chain lengths were used and the results were compared with that of the related small organic cations or salts under comparable conditions. The cationic surfactants induced destabilization of the ethidium bromide-DNA complex at concentrations in orders of magnitude lower than that of the small organic cations or salts. In contrast however, the anionic surfactants failed to promote any such destabilization of probe-DNA complex. DNA loses its ethidium bromide stainability in the presence of high concentration of cationic surfactant aggregates as revealed from agarose gel electrophoresis experiments. Inclusion of surfactants and other additives into the DNA generally enhanced the DNA double-strand to single strand transition melting temperatures by a few degrees, in a concentration-dependent manner and at high surfactant concentration melting profiles got broadened.

A C-H center dot center dot center dot O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins

The serendipitous observation of a C-H...O hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been examined. The C-H...O interaction between the T - 4 (CH)-H-alpha and T + 1 C=O group (C...O 3.5 Angstrom) becomes possible only when the T + 1 residue adopts an extended beta conformation (T is defined as the helix terminating residue adopting an alpha(L) conformation). In all, 111 examples of this chain reversal motif have been identified and the compositional and conformational. preferences at positions T - 4, T, and T + 1 determined. A marked preference for residues like Set, Glu and Gln is observed at T - 4 position with the motif being further stabilized by the formation of a side-chain-backbone O...H-N hydrogen bond involving the side-chain of residue T - 4 and the N-H group of residue T + 3. In as many as 57 examples, the segment following the helix was extended with three to four successive residues in beta conformation. In a majority of these cases, the succeeding beta strand lies approximately antiparallel with the helix, suggesting that the backbone C-H...O interactions may provide a means of registering helices and strands in an antiparallel orientation. Two examples were identified in which extended registry was detected with two sets of C-H...O hydrogen bonds between (T - 4) (CH)-H-alpha...C=O (T + 1) and (T - 8) (CH)-H-alpha...C=O (T + 3). 0 2002 Published by Elsevier Science Ltd.

Entrapment of a Water Wire in a Hydrophobic Peptide Channel with an Aromatic Lining

A one-dimensional water wire has been characterized by X-ray diffraction in single crystals of the tripeptide Ac-Phe-Pro-Trp-OMe. Crystals in the hexagonal space group P6(5) reveal a central hydrophobic channel lined by aromatic residues which entraps an approximately linear array of hydrogen bonded water molecules. The absence of any significant van der Waals contact with the channel walls suggests that the dominant interaction between the ``water wire'' and ``peptide nanotube'' is electrostatic in origin. An energy difference of 16 KJmol(-1) is estimated for the distinct orientations of the water wire dipole with respect to the macrodipole of the peptide nanotube. The structural model suggests that Grotthuss type proton conduction may, through constricted hydrophobic channels, be facilitated by concerted, rotational reorientation of water molecules.

Fluctuation quench and hydrophobic collapse of polymers and biopolymers in water-DMSO binary mixture at low DMSO concentration

Binary mixtures have strong influence on activities of polymers and biopolymers even at low cosolvent concentration. Among the several aqueous binary mixtures studied, water-DMSO especially stands out for its unusual behavior at certain specific concentrations of DMSO. In the present work, we study the effect of water-DMSO binary mixture on polymers and biopolymers by taking a simple linear hydrocarbon chain of intermediate length (n = 30) and the protein lysozyme, respectively. We find that at a mole fraction of 0.05 of DMSO (x(DMSO) = 0.05) in aqueous solution, the hydrocarbon chain adopts the collapsed conformation as the most stable and rigid state. In this case of 0.05 mole fraction of DMSO in bulk, the DMSO concentration in the first hydration layer around the polymer is found to be as large as 17%. Formation of such hydrophobic environment around the polymer is the reason for the collapsed state gaining so much stability. Interestingly, similar quench of conformational fluctuation is also observed for the protein investigated. It is observed that in the case of alkane polymer chains, long wavelength fluctuation gets easily quenched, the polymer being purely hydrophobic. However, in case of the protein, quench of fluctuation is prominent only at the hydrophobic surface, and quench of long wavelength fluctuation becomes insignificant for the full protein. As protein contains both hydrophobic and hydrophilic moieties, the extent of quench of conformational fluctuation with respect to that in pure water is almost half for the biopolymer complex (16.83%) than the same for pure hydrophobic polymer chain (32.43%).

Interaction of guar gum with hydrophobic solids

The interaction of guar gum with the hydrophobic solids namely talc, mica and graphite has been investigated through adsorption, electrokinetic and flotation experiments. The adsorption densities of guar gum onto the above hydrophobic minerals show that they are more or less independent of pH. The adsorption isotherms of guar gum onto talc, mica and graphite indicate that the adsorption densities increase with increase in guar gum concentration and all the isotherms follow the as L1 type according to Giles classification. The magnitude of the adsorption density of guar gum onto the above minerals may be arranged in the following sequence: talc > graphite > mica The effect of particle size on the adsorption density of guar gum onto these minerals has indicated that higher adsorption takes place in the coarser size fraction, consequent to an increase in the surface face-to-edge ratio. In the case of the talc and mica samples pretreated with EDTA and the leached graphite sample, a decrease in the adsorption density of guar gum is observed, due to a reduction in the metallic adsorption sites. The adsorption densities of guar gum increase with decrease in sample weight for all the three minerals. Electrokinetic measurements have indicated that the isoelectric points (iep) of these minerals lie between pH 2-3, Addition of guar gum decreases the negative electrophoretic mobility values in proportion to the guar gum concentration without any observable shift in the iep values, resembling the influence of an indifferent electrolyte. The flotation recovery is diminished in the presence of guar gum for all the three minerals, The magnitude of depression follows the same sequence as observed in the adsorption studies. The floatability of EDTA treated talc and mica samples as well as the leached graphite sample is enhanced, complementing the adsorption data, Possible mechanisms of interaction between the hydrophobic minerals and guar gum are discussed.

Facile synthesis of large area porous Cu2O as super hydrophobic yellow-red phosphors

By employing a thermal oxidation strategy, we have grown large area porous Cu2O from Cu foil. CuO nanorods are grown by heating Cu which were in turn heated in an argon atmosphere to obtain a porous Cu2O layer. The porous Cu2O layer is superhydrophobic and exhibits red luminescence. In contrast, Cu2O obtained by direct heating, is hydrophobic and exhibits yellow luminescence. Two more luminescence bands are observed in addition to red and yellow luminescence, corresponding to the recombination of free and bound excitons. Over all, the porous Cu2O obtained from Cu via CuO nanorods, can serve as a superhydrophobic luminescence/phosphor material.

Nanocrystallization of TiO2 Anatase Phase in Hydrophobic BaO-TiO2-B2O3 Glass System

Transparent colorless glasses in the ternary BaOTiO2B2O3 system were fabricated via conventional melt-quenching technique. The glasses with certain molar concentrations of BaO and TiO2 on heat treatment at appropriate temperatures yielded nanocrystalline phase of TiO2 associated with the crystallite size in the 515 nm range. Nanocrystallized glasses exhibited high refractive index (n = 2.15) measured at lambda = 543 nm. These glasses were found to be hydrophobic in nature associated with the contact angle of 90 degrees. These high-index glass nanocrystal composites would be of potential interest for optical device applications.

Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg2+, presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg2+ accounts for 1/3 and all of the free energy gain in 50% and pure MgCl2 solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl2 compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg2+. In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg2+ may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.