Common recognition principles across diverse sequence and structural families of sialic acid binding proteins

Sialic acids form a large family of 9-carbon monosaccharides and are integral components of glycoconjugates. They are known to bind to a wide range of receptors belonging to diverse sequence families and fold classes and are key mediators in a plethora of cellular processes. Thus, it is of great interest to understand the features that give rise to such a recognition capability. Structural analyses using a non-redundant data set of known sialic acid binding proteins was carried out, which included exhaustive binding site comparisons and site alignments using in-house algorithms, followed by clustering and tree computation, which has led to derivation of sialic acid recognition principles. Although the proteins in the data set belong to several sequence and structure families, their binding sites could be grouped into only six types. Structural comparison of the binding sites indicates that all sites contain one or more different combinations of key structural features over a common scaffold. The six binding site types thus serve as structural motifs for recognizing sialic acid. Scanning the motifs against a non-redundant set of binding sites from PDB indicated the motifs to be specific for sialic acid recognition. Knowledge of determinants obtained from this study will be useful for detecting function in unknown proteins. As an example analysis, a genome-wide scan for the motifs in structures of Mycobacterium tuberculosis proteome identified 17 hits that contain combinations of the features, suggesting a possible function of sialic acid binding by these proteins.

Electric current induced flow of liquid metals: Mechanism and substrate-surface effects

Long range, continuous flow of liquid metals occurs upon application of an electric current. Here, we report experimental results elucidating the mechanism of current-induced liquid metal flow, and its dependence on substrate surface condition. It is shown that the observed flow is diffusion-controlled, with the flow-rate depending linearly on applied current density, indicating that it is driven by electromigration. The effective charge number for liquid electromigration, Z*, of several pure metals, such as Al, Bi, Ga, Sn, and Pb, were deduced from the experimental results and were found to be close to the elemental valency. With the exception of liquid Pb, Z* for all liquid metals tested in this study were positive, indicating that: (i) electron wind contributes much less to Z* in liquid metals than in solids, and (ii) with a few exceptions, liquid metals generally flow in the direction of the electric current. On smooth substrates which are wetted well by the liquid metal, flow occurs in a thin, continuous stream. On rough surfaces which are poorly wetted, on the other hand, discrete beads of liquid form, with mass transport between adjacent beads occurring by surface diffusion on the substrate. A rationale for the role of substrate roughness in fostering this observed transition in flow mechanism is presented. (C) 2014 AIP Publishing LLC.

Triarylborane-dipyrromethane conjugates bearing dual receptor sites: the synthesis and evaluation of the anion binding site preference

The synthesis and optical properties of four new triarylborane-dipyrromethane (TAB-DPM) conjugates (3a-d) containing dual binding sites (hydrogen bond donor and Lewis acid) have been reported. The new compounds exhibit a selective fluorogenic response towards the F-ion. The NMR titrations show that the anions bind to the TAB-DPM conjugates via the Lewis acidic triarylborane centre in preference to the hydrogen bond donor (dipyrromethane) units.

Beyond the ``Coffee Ring'': Re-entrant Ordering in an Evaporation-Driven Self-Assembly in a Colloidal Suspension on a Substrate

We study the phenomenon of evaporation-driven self-assembly of a colloid suspension of silica microspheres in the interior region and away from the rim of the droplet on a glass plate. In view of the importance of achieving a large-area, monolayer assembly, we first realize a suitable choice of experimental conditions, minimizing the influence of many other competing phenomena that usually complicate the understanding of fundamental concepts of such self-assembly processes in the interior region of a drying droplet. Under these simplifying conditions to bring out essential aspects, our experiments unveil an interesting competition between ordering and compaction in such drying systems in analogy to an impending glass transition. We establish a re-entrant behavior in the order disorder phase diagram as a function of the particle density, such that there is an optimal range of the particle density to realize the long-range ordering. The results are explained with the help of simulations and phenomenological theory.

Dual Binding Site Assisted Chromogenic and Fluorogenic Recognition and Discrimination of Fluoride and Cyanide by a Peripherally Borylated Metalloporphyrin: Overcoming Anion Interference in Organoboron Based Sensors

Peripherally triarylborane decorated porphyrin (2) and its Zn(II) complex (3) have been synthesized. Compound 3 contains of two different Lewis acidic binding sites (Zn(II) and boron center). Unlike all previously known triarylborane based sensors, the optical responses of 3 toward fluoride and cyanide are distinctively different, thus enabling the discrimination of these two interfering anions. Metalloporphyrin 3 shows a multiple channel fluorogenic response toward fluoride and cyanide and also a selective visual colorimetric response toward cyanide. By comparison with model systems and from detailed photophysical studies on 2 and 3, we conclude that the preferential binding of fluoride occurs at the peripheral borane moieties resulting in the cessation of the EET (electronic energy transfer) process from borane to porphyrin core and with negligible negetive cooperative effects. On the other hand, cyanide binding occurs at the Zn(II) core leading to drastic changes in its absorption behavior which can be followed by the naked eye. Such changes are not observed when the boryl substituent is absent (e.g., Zn-TPP and TPP). Compounds 2 and 3 were also found to be capable of extracting fluoride from aqueous medium.

Formal Synthesis of Actin Binding Macrolide Rhizopodin

Formal synthesis, of an actin binding macrolide rhizopodin was achieved in 19 longest linear steps. The key features of the synthesis include a stereoselective Mukaiyama aldol reaction, dual role of a Nagao auxiliary (first, as a chiral auxiliary of choice for installing hydroxy centers and, later, as an acylating agent to form an amide bond with an amino alcohol), late stage oxazole formation, and Stille coupling reactions.

Identification of heat shock factor binding protein in Plasmodium falciparum

Background: Heat shock factor binding protein (HSBP) was originally discovered in a yeast two-hybrid screen as an interacting partner of heat shock factor (HSF). It appears to be conserved in all eukaryotes studied so far, with yeast being the only exception. Cell biological analysis of HSBP in mammals suggests its role as a negative regulator of heat shock response as it appears to interact with HSF only during the recovery phase following exposure to heat stress. While the identification of HSF in the malaria parasite is still eluding biologists, this study for the first time, reports the presence of a homologue of HSBP in Plasmodium falciparum. Methods: PfHSBP was cloned and purified as his-tag fusion protein. CD (Circular dichroism) spectroscopy was performed to predict the secondary structure. Immunoblots and immunofluorescence approaches were used to study expression and localization of HSBP in P. falciparum. Cellular fractionation was performed to examine subcellular distribution of PfHSBP. Immunoprecipitation was carried out to identify HSBP interacting partner in P. falciparum. Results: PfHSBP is a conserved protein with a high helical content and has a propensity to form homo-oligomers. PfHSBP was cloned, expressed and purified. The in vivo protein expression profile shows maximal expression in trophozoites. The protein was found to exist in oligomeric form as trimer and hexamer. PfHSBP is predominantly localized in the parasite cytosol, however, upon heat shock, it translocates to the nucleus. This study also reports the interaction of PfHSBP with PfHSP70-1 in the cytoplasm of the parasite. Conclusions: This study emphasizes the structural and biochemical conservation of PfHSBP with its mammalian counterpart and highlights its potential role in regulation of heat shock response in the malaria parasite. Analysis of HSBP may be an important step towards identification of the transcription factor regulating the heat shock response in P. falciparum.

Effect of Substrate Temperature on the Microstructure Variation in Sputter-deposited Hydrogenated Amorphous Silicon Thinfilms

Vacancy, void incorporation and Si-H-x configuration in hydrogenated amorphous silicon (a-Si:H) thin films was studied. Films were grown by Direct Current (DC), pulsed DC and Radio Frequency (RF) magnetron sputtering. Fourier Transform Infrared (FTIR) spectroscopic analysis has been carried out on the films and found that, the a-Si: H films grown by DC magnetron sputtering are of good quality compared to pulsed DC and RF deposited films. The effect of Substrate temperature (T-S) on the total hydrogen concentration (C-H), configuration of hydrogen bonding, density (decided by the vacancy and void incorporation) and the microstructure factor (R*) was studied. T-S is found to be an active parameter in affecting the above said properties of the films. The films contain both vacancies and voids. At low hydrogen dilutions the films are vacancy dominated and at high hydrogen dilutions they are void dominated. It is found that T-S favors monohydride (Si-H) bonding at the cost of dihydride (Si-H-2) bonding. This dividing line is at C-H=14 at.% H for DC sputter deposited films. The microstructure structure factor R* is found to be zero for as deposited DC films at T-S=773K. The threshold C-H for void dominated region is found to be C-H=23 at.% H for RF, C-H=18 at.% H for PDC and C-H similar to 14 at.%H for DC sputter deposited films.

PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites

Knowledge of protein-ligand interactions is essential to understand several biological processes and important for applications ranging from understanding protein function to drug discovery and protein engineering. Here, we describe an algorithm for the comparison of three-dimensional ligand-binding sites in protein structures. A previously described algorithm, PocketMatch (version 1.0) is optimised, expanded, and MPI-enabled for parallel execution. PocketMatch (version 2.0) rapidly quantifies binding-site similarity based on structural descriptors such as residue nature and interatomic distances. Atomic-scale alignments may also be obtained from amino acid residue pairings generated. It allows an end-user to compute database-wide, all-to-all comparisons in a matter of hours. The use of our algorithm on a sample dataset, performance-analysis, and annotated source code is also included.

Electronic band Structure and Photoemission Spectra of Graphene on Silicon Substrate

Synergizing graphene on silicon based nanostructures is pivotal in advancing nano-electronic device technology. A combination of molecular dynamics and density functional theory has been used to predict the electronic energy band structure and photo-emission spectrum for graphene-Si system with silicon as a substrate for graphene. The equilibrium geometry of the system after energy minimization is obtained from molecular dynamics simulations. For the stable geometry obtained, density functional theory calculations are employed to determine the energy band structure and dielectric constant of the system. Further the work function of the system which is a direct consequence of photoemission spectrum is calculated from the energy band structure using random phase approximations.

Colorimetric anion sensor based on receptor having indole- and thiourea-binding sites

A new colorimetric sensor L containing nitro-substituted indole and bisthiocarbonohydrazone units for selective fluoride and acetate ions is designed and synthesized. The receptor L shows well-defined color change in the visible region of the spectrum with an absorption band at similar to 515 nm and 506 nm, respectively, for the F- and CH3COO- ions in an acetonitrile solution. Job's plots indicated the formation of 1 : 1 (L with CH3COO-) and 1 : 2 (L with F-) complexes. The interaction of L with the F- ion undergoes a deprotonation process and release of HX2](-), whereas with the CH3COO- ion, it forms a stable LH2(...)X](-) complex. The relative affinities of the anions with L are rationalized using computational studies.

A Genetic Analysis of the Functional Interactions within Mycobacterium tuberculosis Single-Stranded DNA Binding Protein

Single-stranded DNA binding proteins (SSBs) are vital in all organisms. SSBs of Escherichia coli (EcoSSB) and Mycobacterium tuberculosis (MtuSSB) are homotetrameric. The N-terminal domains (NTD) of these SSBs (responsible for their tetramerization and DNA binding) are structurally well defined. However, their C-terminal domains (CTD) possess undefined structures. EcoSSB NTD consists of beta 1-beta 1'-beta 2-beta 3-alpha-beta 4-beta 45(1)-beta 45(2)-beta 5 secondary structure elements. MtuSSB NTD includes an additional beta-strand (beta 6) forming a novel hook-like structure. Recently, we observed that MtuSSB complemented an E. coli Delta ssb strain. However, a chimeric SSB (m beta 4-beta 5), wherein only the terminal part of NTD (beta 4-beta 5 region possessing L-45 loop) of EcoSSB was substituted with that from MtuSSB, failed to function in E. coli in spite of its normal DNA binding and oligomerization properties. Here, we designed new chimeras by transplanting selected regions of MtuSSB into EcoSSB to understand the functional significance of the various secondary structure elements within SSB. All chimeric SSBs formed homotetramers and showed normal DNA binding. The m beta 4-beta 6 construct obtained by substitution of the region downstream of beta 5 in m beta 4-beta 5 SSB with the corresponding region (beta 6) of MtuSSB complemented the E. coli strain indicating a functional interaction between the L-45 loop and the beta 6 strand of MtuSSB.

Antimicrobial and conducting polymer substrate derived from hybrid structures of silver nanoparticles and multiwall carbon nanotubes

Hybrid nanocomposites of polycaprolactone (PCL) with multiwall carbon nanotubes (MWNTs) and silver nanoparticles (nAg) were prepared by melt mixing. Synergetic effect of the two nanofillers (MWNT and nAg) in PCL matrix was evaluated for dielectric and antibacterial properties. Dielectric results showed that the addition of nAg as filler in PCL matrix (PCL/nAg) had no effect on conductivity, whereas addition of MWNT in PCL matrix (PCL/MWNT) caused a sharp increase in conductivity of PCL. Interestingly, the hybrid nanocomposite (PCL/MWNT/nAg) incorporating MWNT and nAg also exhibited high electrical conductivity. The hybrid composite was found to have antibacterial property similar to that of PCL/nAg composite for lower loading of nAg. This study demonstrates that the synergetic interaction of the nanofillers in the hybrid nanocomposite improves both electrical conductivity and antibacterial properties of PCL.