Kinetics of loop formation in polymer chains

We investigate the kinetics of loop formation in ideal flexible polymer chains (the Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the time scale for cyclization is tau(c) approximately tau(0)N(2) (where tau(0) is a microscopic time scale and N is the number of monomers), provided the coupling between the relaxation dynamics of the end-to-end vector and the looping dynamics is taken into account. The resulting analytic expression fits the simulation results accurately when a, the capture radius for contact formation, exceeds b, the average distance between two connected beads. Simulations also show that when a < b, tau(c) approximately N(alpha)(tau), where 1.5 < alpha(tau) < or = 2 in the range 7 < N < 200 used in the simulations. By using a diffusion coefficient that is dependent on the length scales a and b (with a < b), which captures the two-stage mechanism by which looping occurs when a < b, we obtain an analytic expression for tauc that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly effected when interactions between monomers are taken into account. Remarkably, for N < 100, the values of tau(c) decrease by more than 2 orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for tau(c) to a power law in N (tau(c) approximately N(alpha)(tau)) show that alpha(tau) varies from about 2.4 in a good solvent to about 1.0 in poor solvents. The effective exponent alpha(tau) decreases as the strength of the attractive monomer-monomer interactions increases. Loop formation in poor solvents, in which the polymer adopts dense, compact globular conformations, occurs by a reptation-like mechanism of the ends of the chain. The time for contact formation between beads that are interior to the chain in good solvents changes nonmonotonically as the loop length varies. In contrast, the variation in interior loop closure time is monotonic in poor solvents. The implications of our results for contact formation in polypeptide chains, RNA, and single-stranded DNA are briefly outlined.     

Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism

In order to clarify the mechanism of denaturant-induced unfolding of proteins we have calculated the interactions between hydrophobic and ionic species in aqueous guanidinium chloride and urea solutions using molecular dynamics simulations. Hydrophobic association is not significantly changed in urea or guanidinium chloride solutions. The strength of interaction between ion pairs is greatly diminished by the guanidinium ion. Although the changes in electrostatic interactions in urea are small, examination of structures, using appropriate pair functions, of urea and water around the solutes show strong hydrogen bonding between urea's carbonyl oxygen and the positively charged solute. Our results strongly suggest protein denaturation occurs by the direct interaction model according to which the most commonly used denaturants unfold proteins by altering electrostatic interactions either by solvating the charged residues or by engaging in hydrogen bonds with the protein backbone. To further validate the direct interaction model we show that, in urea and guanidinium chloride solutions, unfolding of an unusually stable helix (H1) from mouse PrPC (residues 144-153) occurs by hydrogen bonding of denaturants to charged side chains and backbone carbonyl groups.     

A new Hg(2+) -selective fluorescent sensor based on a 1,3-alternate thiacalix[4]arene anchored with four 8-quinolinoloxy groups

A new thiacalix [4]arene derivative in a 1,3-alternate conformation bearing four quinolinoloxy groups through propyl chains has been synthesized, and its metal ion-binding and fluorescence-sensing properties were investigated in both THF and 10% H2O-THF systems. The designed ligand exhibited pronounced Hg2+ -selective on-off type fluoroionophoric properties among the representative transition and heavy metal ions including Cu2+. The detection limit for Hg2+ was found to be 2.0 x 10(-6) M in the mixed H2O-THF system. Detailed spectral studies including 1H NMR and MALDI-TOF mass spectroscopy reveal the unusual formation of a tetramercury complex with the ligand, in which the four propyl arms containing the quinolinoloxy groups adopt a "tetrapodand" conformation enclosing one Hg2+ ion each in the four cavities thus formed.     

Porous,hollow Li<Subscript>1.2</Subscript>Mn<Subscript>0.53</Subscript>Ni<Subscript>0.13</Subscript>Co<Subscript>0.13</Subscript>O<Subscript>2</Subscript> microspheres as a positive electrode material for Li-ion batteries

A porous, hollow, microspherical composite of Li₂MnO₃ and LiMn_1/3Co_1/3Ni_1/3O₂ (composition: Li_1.2Mn_0.53Ni_0.13Co_0.13O₂) was prepared using hollow MnO₂ as the sacrificial template. The resulting composite was found to be mesoporous; its pores were about 20 nm in diameter. It also delivered a reversible discharge capacity value of 220 mAh g^?1 at a specific current of 25 mA g^?1 with excellent cycling stability and a high rate capability. A discharge capacity of 100 mAh g^?1 was obtained for this composite at a specific current of 1000 mA g^?1. The high rate capability of this hollow microspherical composite can be attributed to its porous nature.

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Effects of crowding and confinement on the structures of the transition state ensemble in proteins

Characterization of the structures of the transition state ensemble is a key step in describing the folding reaction. Using two variants of a coarse-grained model of the three-stranded beta-sheet WW domain and a fully automated progress variable clustering (PVC) algorithm, we have dissected the effect of macromolecular crowding and confinement on the changes in the transition state structures in comparison to bulk. Each amino acid is represented using a Calpha atom and a side chain. The distance between the Calpha atom and center of mass of the side chain is taken to be its effective van der Waals radius. For the bulk case, we predict using the PVC algorithm, which does not assume knowledge of the underlying folding reaction coordinate, that there are two classes of structures in the transition state ensemble (TSE). The structures in both of the classes are compact. The dominant cluster is more structured than the structures in the less populated class. In accord with bulk experiments, the residues in strands beta2 and beta3 and the interactions at the beta2-beta3 interface are structured. When only excluded volume interactions between the crowding particles and the WW domain are taken into account or when the protein is confined to an inert spherical pore, the overall structure of the TSE does not change dramatically. However, in this entropy dominated regime, the width of the TSE decreases and the structures become more oblate and less spherical as the volume fraction of crowding particle increases or when the pore radius decreases. It suggests that the shape changes, which are computed using the moment of inertia tensor, may represent the slow degrees of freedom during the folding process. When non-native interactions between side chains and interactions with the cavity of the pores are taken into account, the TSE becomes considerably broader. Although the topology in the transition has a fold similar to the native state, the structures are far more plastic than in the bulk. The TSE is sensitive to the size of the pore as well as interactions between the pore and the protein. The differences between the two cases (confinement in an inert pore and when pore-protein interactions are considered) arise due to the increased importance of enthalpic interactions in the transition state as the strength of the protein-pore interaction increases.     

Aminobenzohydrazide based colorimetric and ‘turn-on’ fluorescence chemosensor for selective recognition of fluoride

Chemosensors based on aminobenzohydrazide Schiff bases bearing pyrene/anthracene as fluorophores have been designed and synthesized for F⁻ ion recognition. The addition of fluoride ions to the receptors causes a dramatically observable colour change from pale yellow to brown/red. ¹H NMR studies confirm that the F⁻ ion facilitates its recognition by forming hydrogen bond with hydrogens of amide and amine groups. Moreover these sensors have also been successfully applied to detection of fluoride ion in commercial tooth paste solution.     

An efficient heterogeneous iron oxide nanoparticle catalyst for the synthesis of 9-substituted xanthene-1,8-dione

Research on Chemical Intermediates - An efficient and simple method for the synthesis of xanthene derivatives by using iron oxide nanoparticles (NPs) as a catalyst has been investigated. Synthesis...     

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide

Understanding the influence of macromolecular crowding and nanoparticles on the formation of in-register β-sheets, the primary structural component of amyloid fibrils, is a first step towards describing in vivo protein aggregation and interactions between synthetic materials and proteins. Using all atom molecular simulations in implicit solvent we illustrate the effects of nanoparticle size, shape, and volume fraction on oligomer formation of an amyloidogenic peptide from the transthyretin protein. Surprisingly, we find that inert spherical crowding particles destabilize in-register β-sheets formed by dimers while stabilizing β-sheets comprised of trimers and tetramers. As the radius of the nanoparticle increases crowding effects decrease, implying smaller crowding particles have the largest influence on the earliest amyloid species. We explain these results using a theory based on the depletion effect. Finally, we show that spherocylindrical crowders destabilize the ordered β-sheet dimer to a greater extent than spherical crowders, which underscores the influence of nanoparticle shape on protein aggregation.     

Multiple barriers in forced rupture of protein complexes

Curvatures in the most probable rupture force (f(?)) versus log-loading rate (log?r(f)) observed in dynamic force spectroscopy (DFS) on biomolecular complexes are interpreted using a one-dimensional free energy profile with multiple barriers or a single barrier with force-dependent transition state. Here, we provide a criterion to select one scenario over another. If the rupture dynamics occurs by crossing a single barrier in a physical free energy profile describing unbinding, the exponent ν, from (1 - f(?)∕f(c))(1∕ν) ～ (log?r(f)) with f(c) being a critical force in the absence of force, is restricted to 0.5 ≤ ν ≤ 1. For biotin-ligand complexes and leukocyte-associated antigen-1 bound to intercellular adhesion molecules, which display large curvature in the DFS data, fits to experimental data yield ν < 0.5, suggesting that if ligand unbinding is assumed to proceed along one-dimensional pulling coordinate, the dynamics should occur in a energy landscape with multiple-barriers.     

A novel water soluble ligand bridged cobalt(II) coordination polymer of 2-oxo-1,2-dihydroquinoline-3-carbaldehyde (isonicotinic) hydrazone: evaluation of the DNA binding, protein interaction, radical scavenging and anticancer activity

A novel water soluble ligand-bridged cobalt(II) coordination polymer has been synthesized by reacting the new ligand, 2-oxo-1,2-dihydroquinoline-3-carbaldehyde (isonicotinic) hydrazone (H(2)L) with Co(NO(3))(2)·6H(2)O and characterized by spectral, analytical and structural methods. Single crystal X-ray diffraction studies revealed that the Co(II) complex, {[Co(H(2)L)(H(2)O)(2)](NO(3))(2)·3H(2)O}(n) has a slightly distorted octahedral geometry around the central Co(II) ion; the ligand is coordinated through the ONO donor atoms to one Co(II) metal center and bridged through the pyridine nitrogen atom to another similar Co(II) center so as to form a one-dimensional polymeric unit. The interaction of the ligand and the complex with calf thymus DNA (CT-DNA) has been explored by absorption and emission titration methods, which revealed that the compounds could interact with CT-DNA through intercalation. The interactions of the compounds with bovine serum albumin (BSA) were also investigated using UV-visible, fluorescence and synchronous fluorescence spectroscopic methods. The results indicated that the complex exhibited a strong binding to BSA over the ligand. Investigation of the antioxidative properties showed that the polymeric Co(II) complex has a strong radical scavenging potency against hydroxyl radicals, 2,2-diphenyl-1-picrylhydrazyl radicals, nitric oxide and superoxide anion radicals. Further, the cytotoxic effect of the compounds examined on cancerous cell lines, such as human cervical cancer cells (HeLa), human laryngeal epithelial carcinoma cells (HEp-2), human liver carcinoma cells (Hep G2), human skin cancer cells (A431) and non-cancerous NIH 3T3 mouse embryonic fibroblasts cell lines showed that the complex exhibited substantial anticancer activity.