Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a ``spatial motif'' and several ``fold specific hot spots'' that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.

Molecular Marriage through Partner Preferences in Covalent Cage Formation and Cage-to-Cage Transformation

Unprecedented self-sorting of three-dimensional purely organic cages driven by dynamic covalent bonds is described. Four different cages were first synthesized by condensation of two triamines and two dialdehydes separately. When a mixture of all the components was allowed to react, only two cages were formed, which suggests a high-fidelity self-recognition. The issue of the preference of one triamine for a particular dialdehyde was further probed by transforming a non-preferred combination to either of the two preferred combinations by reacting it with the appropriate triamine or dialdehyde.

Self-Adapting Peripherally Heterofunctionalized Hyperbranched Polymers: Formation of Janus and Tripodal Structures

A peripherally clickable hyperbranched polyester carrying numerous propargyl terminal groups was prepared by a simple melt transesterification polycondensation of a suitably designed AB(2) monomer; this clickable hyperscaffold was then transformed into a variety of different derivatives by using the Cu-catalyzed azide-yne click reaction. Functionalization of the periphery with equimolar quantities of mutually immiscible segments, such as hydrocarbon, fluorocarbon, and PEG, yielded frustrated molecular systems that readapt and form structures wherein the immiscible segments appear to self-segregate to generate either Janus structures (when two immiscible segments are present) or tripodal structures (when three immiscible segments are present). Evidence for such self-segregation was obtained from a variety of studies, such as differential scanning calorimetry, Langmuir isotherms, AFM imaging, and small-angle X-ray scattering measurements. Crystallization of one or more of the peripheral segments reinforced this self-segregation; the weight-fraction-normalized enthalpies of melting associated with the different domains revealed a competition between the segments to optimize their crystalline organization. When one or more of the segments are amorphous, the remaining segments crystallize more effectively and consequently exhibit a higher melting enthalpy. AFM images of monolayers, transferred from the Langmuir trough, revealed that the thickness matches the expected values; furthermore, contact angle measurements clearly demonstrated that the monolayer films are fairly hydrophobic, and in the case of the tripodal hybramers, the presence of domains of hydrocarbon and fluorocarbon appears to impart nanoscale chemical heterogeneity that is reflected in the strong hysteresis in the advancing and receding contact angles.

Study of the Formation of Nano-Networks in Colloidal Particles

The authors studied the formation of a wafer-scale network of connected colloidal beads by reactive ion etching. The dimensions of the connections have been studied as a function of etching time for colloidal beads of different sizes, and could be well controlled. The authors have found that the nano-network forms and disappears for the same time of etching independent of the diameter of the polystyrene beads. With recent interest of connected colloidal networks in various optical sensing applications, such as photonic crystals, as surface-enhanced Raman scattering substrates, the studies have potential uses in the development of wafer-scale nanophotonic sensors.

Regulation of lipid biosynthesis, sliding motility, and biofilm formation by a membrane-anchored nucleoid-associated protein of mycobacterium tuberculosis

Bacteria use a number of small basic proteins for organization and compaction of their genomes. By their interaction with DNA, these nucleoid-associated proteins (NAPs) also influence gene expression. Rv3852, a NAP of Mycobacterium tuberculosis, is conserved among the pathogenic and slow-growing species of mycobacteria. Here, we show that the protein predominantly localizes in the cell membrane and that the carboxy-terminal region with the propensity to form a transmembrane helix is necessary for its membrane localization. The protein is involved in genome organization, and its ectopic expression in Mycobacterium smegmatis resulted in altered nucleoid morphology, defects in biofilm formation, sliding motility, and change in apolar lipid profile. We demonstrate its crucial role in regulating the expression of KasA, KasB, and GroEL1 proteins, which are in turn involved in controlling the surface phenotypes in mycobacteria.

Towards the understanding of formation of micro/nano holes of Ge/GeO2 through phase mapping

Here, we report for the first time a simple thermal oxidation strategy for the large area synthesis of Ge/GeO2 nanoholes from Ge and studied the luminescence of Ge/GeO2 and hole formation mechanism through phase and luminescence mapping. Photoluminescence mapping reveals that the emission in the visible range is only from the hole region, which provokes the necessity of the nanoholes. Such materials can also be used to convert ultraviolet to visible radiation for detection by conventional phototubes and to coat blue or ultraviolet diodes to obtain white light.

Spontaneous formation of branched nanochains from room temperature molten amides: visible and near-IR active, SERS substrates for non-fluorescent and fluorescent analytes

Highly stable, branched gold nanoworms are formed spontaneously in an acetamide-based room temperature molten solvent without any additional external stabilizing or aggregating agent. The nanoworms can be anchored onto solid substrates such as indium tin oxide (ITO) without any change in morphology. The anchored nanoworms are explored as substrates for surface enhanced Raman scattering (SERS) studies using non-fluorescent 4-mercaptobenzoic acid (4-MBA) and fluorescent rhodamine 6G (R6G) as probe molecules. The anchored nanostructured particles respond to near IR (1064 nm) as well as visible (785, 632.8 and 514 nm) excitation lasers and yield good surface enhancement in Raman signals. Enhancement factors of the order 10(6)-10(7) are determined for the analytes using a 1064 nm excitation source. Minimum detection limits based on adsorption from ethanolic solutions of 1028 M 4-MBA and aqueous solutions of 1027 M R6G are achieved. Experimental Raman frequencies and frequencies estimated by DFT calculations are in fairly good agreement. SERS imaging of the nanostructures suggests that the substrates comprising of three dimensional, highly interlinked particles are more suited than particles fused in one dimension. The high SERS activity of the branched nanoworms may be attributed to both electromagnetic and charge transfer effects.

Determination of favorable inter-particle interactions for formation of substitutionally ordered solid phases from a binary mixture of oppositely charged colloidal suspensions

The solid phase formed by a binary mixture of oppositely charged colloidal particles can be either substitutionally ordered or substitutionally disordered depending on the nature and strength of interactions among the particles. In this work, we use Monte Carlo molecular simulations along with the Gibbs-Duhem integration technique to map out the favorable inter-particle interactions for the formation of substitutionally ordered crystalline phases from a fluid phase. The inter-particle interactions are modeled using the hard core Yukawa potential but the method can be easily extended to other systems of interest. The study obtains a map of interactions depicting regions indicating the type of the crystalline aggregate that forms upon phase transition.

Gibbs energy of formation of Ca7V4O17

Thermodynamic properties of Ca7V4O17 are measured for the first time using a solid-state electrochemical cell incorporating single crystal of CaF2 as the electrolyte over the temperature range from (900 to 1175) K. An equimolar mixture of CaO and CaF2 is used as the reference electrode and a mixture of Ca3V2O8, Ca7V4O17 and CaF2 as the measuring electrode. Both the electrodes are placed under flowing oxygen gas at ambient pressure. The standard Gibbs energy change for the reaction: 2Ca(3)V(2)O(8) + CaO -> Ca7V4O17; which is related to the chemical potential of CaO in the two-phase region (Ca3V2O8 + Ca7V4O17) of the pseudo-binary system CaO + V2O5, is obtained from the electromotive force of the cell as: Delta(r)G(o) +/- 127/(J . mol(-1)) = Delta mu(CaO) = -11453 + 8.273(T/K). The derived standard enthalpy of formation of Ca7V4O17 from elements in their normal standard states is ( 8208.97 +/- 8) kJ . mol (1) and its standard entropy is (560.05 +/- 7.5) J . K (1) . mol (1), both at T = 298.15 K. The results indicate that Ca7V4O17 decomposes into Ca3V2O8 and CaO at T = (1384 +/- 3) K.

Black hole formation at the correspondence point

We study the process of bound state formation in a D-brane collision. We consider two mechanisms for bound state formation. The first, operative at weak coupling in the worldvolume gauge theory, is pair creation of W-bosons. The second, operative at strong coupling, corresponds to formation of a large black hole in the dual supergravity. These two processes agree qualitatively at intermediate coupling, in accord with the correspondence principle of Horowitz and Polchinski. We show that the size of the bound state and time scale for formation of a bound state agree at the correspondence point. The time scale involves matching a parametric resonance in the gauge theory to a quasinormal mode in supergravity.

Unprecedented formation of a 14-membered dihydropyran macrocycle via sequential olefin cross metathesis-intramolecular hetero Diels-Alder reaction

Formation of a 2,3-dihydro-4H-pyran containing 14-membered macrocycle by sequential olefin cross metathesis and a highly regiospecific hetero Diels-Alder reaction was observed in the reaction of a hydroxydienone derived from tartaric acid with Grubbs' second generation catalyst. It was found that the free alcohol in the hydroxyenone led to the macrocycle formation, while protection of the hydroxy group formed the ring closing metathesis product. (C) 2013 Elsevier Ltd. All rights reserved.

Organogels from Dimeric Bile Acid Esters: In Situ Formation of Gold Nanoparticles

A new class of steroid dimers (bile acid derivatives) linked through ester functionalities were synthesized, which gelled various aromatic solvents. The organogels formed by the three dimeric ester molecules showed birefringent textures and fibrous nature by polarizing optical microscopy and scanning electron microscopy, respectively. A detailed rheological study was performed to estimate the mechanical strengths of two sets of organogels. In these systems, the storage modulus varied in the range of 0.8-3.5 X 10(4) at 1% w/v of the organogelators. The exponents of scaling of the storage modulus and yield stress of the two systems agreed well with those expected for viscoelastic soft colloidal gels with fibrillar flocs. The nanofibers in the organogel were utilized to engineer gold nanoparticles of different sizes and shapes and generate new gel-nanoparticle hybrid materials.

Black hole formation in fuzzy sphere collapse

We study the collapse of a fuzzy sphere, that is a spherical membrane built out of D0-branes, in the Banks-Fischler-Shenker-Susskind model. At weak coupling, as the sphere shrinks, open strings are produced. If the initial radius is large then open string production is not important and the sphere behaves classically. At intermediate initial radius the backreaction from open string production is important but the fuzzy sphere retains its identity. At small initial radius the sphere collapses to form a black hole. The crossover between the later two regimes is smooth and occurs at the correspondence point of Horowitz and Polchinski.

Note: Effect of fluid phase compositions on the formation of substitutionally ordered solid phases from a binary mixture of oppositely charged colloidal suspensions

A binary mixture of oppositely charged colloidal particles can self-assemble into either a substitutionally ordered or substitutionally disordered crystalline phase depending on the nature and strength of interactions among the particles. An earlier study had mapped out favorable inter-particle interactions for the formation of substitutionally ordered crystalline phases from a fluid phase using Monte Carlo molecular simulations along with the Gibbs-Duhem integration technique. In this paper, those studies are extended to determine the effect of fluid phase composition on formation of substitutionally ordered solid phases.