Structural Stability in Dimer and Tetramer Clusters of l-Alanine in the Gas Phase and the Feasibility of Peptide Bond Formation.

Stability in low-energy structures of the dimer and tetramer clusters of l-alanine in the gas phase is studied by accurate quantum chemical computations at the DLPNO2013-CCSD(T) level. It is found that the dispersion interaction energies in the dimer (-0.3 to -0.6 kcal/mol) and in the tetramer (-1.3 to -2.5 kcal/mol) have a small role in the stability of the clusters as compared to the hydrogen bond (HB) energies -4.1 to -14.2 and -32.2 to -40.1 kcal/mol, respectively. The HB energy in the alanine cluster is obtained from the binding energy (BE) of DLPNO2013-CCSD(T)//B2PLYP/def2-TZVP by subtracting the dispersion interaction energy. Local HB energies deduced from the dimer structures are found to be suitable to estimate total HB energies in similar environments. The BEs of OH···NH and OH···OC bonds are -9.5 and -7.1 kcal/mol, respectively. This suggests that the higher clusters are formed through OH···NH bonds as they confer more stability. Analysis of bonding in the tetramer shows that the low-energy tetramer and higher clusters are formed through the OH···NH mode of hydrogen bonding, unlike the dimer which is formed through the OH···OC bond. Feasibility of the amino acid cluster to function as a precursor for polypeptide formation is examined because the orientation of the OH···NH mode of hydrogen bonding is suitable for chemical condensation. The propensity of forming coiled structures in higher clusters and thus in the polypeptides is examined based on the conformational stability in the tetramer of alanine.

l-Alanine capping of ZnO nanorods: increased carrier concentration in ZnO/CuI heterojunction diode.

ZnO nanorods were capped with a simple amino acid, viz., l-alanine to increase the carrier concentration and improve the performance of ZnO/CuI heterojunction diodes. The effect of l-alanine capping on the morphology, structural, optical, electrochemical and electrical properties of ZnO nanorods had been studied in detail. The stable structure with two equally strong Zn-O coordinate bonds predicted by density functional theory was in agreement with the experimental results of FTIR spectroscopy. Due to the presence of electron-releasing (+I effect) moieties in l-Alanine, the carrier concentration of capped ZnO nanorods was two orders of magnitude higher and the ZnO/CuI heterojunction device showed more than a two-fold increase in the photovoltaic power conversion efficiency.

A novel approach for detection and classification of mammographic microcalcifications using wavelet analysis and extreme learning machine.

The objective of this paper is to reveal the effectiveness of wavelet based tissue texture analysis for microcalcification detection in digitized mammograms using Extreme Learning Machine (ELM). Microcalcifications are tiny deposits of calcium in the breast tissue which are potential indicators for early detection of breast cancer. The dense nature of the breast tissue and the poor contrast of the mammogram image prohibit the effectiveness in identifying microcalcifications. Hence, a new approach to discriminate the microcalcifications from the normal tissue is done using wavelet features and is compared with different feature vectors extracted using Gray Level Spatial Dependence Matrix (GLSDM) and Gabor filter based techniques. A total of 120 Region of Interests (ROIs) extracted from 55 mammogram images of mini-Mias database, including normal and microcalcification images are used in the current research. The network is trained with the above mentioned features and the results denote that ELM produces relatively better classification accuracy (94%) with a significant reduction in training time than the other artificial neural networks like Bayesnet classifier, Naivebayes classifier, and Support Vector Machine. ELM also avoids problems like local minima, improper learning rate, and over fitting.

Highly selective, sensitive and quantitative detection of Hg2+ in aqueous medium under broad pH range.

Amidothiourea linked acridinedione derivatives selectively detect Hg(2+) in unbuffered aqueous solution under broad pH range with both single- and two-photon excitation. The observed linear fluorescence intensity change allows the quantitative detection of Hg(2+) in the concentration range of 22 nM-0.33 µM with the lower detection limit of 2 nM.

Lipid-induced conformational transition of amyloid beta peptide fragments.

Conformational transition of soluble monomeric amyloid beta-peptide (Abeta) into oligomeric and protofibrillar aggregates plays a key role in the pathogenesis of Alzheimer's disease (AD). One of the central questions surrounding the molecular pathophysiology of AD is how the soluble Abeta is converted into its aggregated toxic form. A more detailed understanding of the conformational transitions involved in the self-assembly of Abeta may facilitate the design of inhibitors of aggregation. In this study, we evaluated the wild-type (WT) Abeta 16-28 peptide (KLVFFAEDVGSNK) and its associated mutants, including A21G (Flemish), E22K (Italian), E22Q (Dutch), and E22G (Arctic) mutants, by examining, in particular, their aggregation kinetics in the presence and in the absence of negatively charged and zwitterionic lipids. Circular dichroic and thioflavin T fluorescence studies indicated that the WT peptide undergoes a rapid conformational transition into beta-sheet structure in solution, whereas the Arctic and Dutch variants show a markedly rapid transition into beta-sheet structure in the presence of negatively charged lipids. These results provide strong evidence suggesting that the reduction in net charge, with a concurrent increase in the net hydrophobicity of the peptide alone or when complexed with lipid in solution, determines the rate of aggregate formation.

Unprecedented formation of an N-benzamidobisthiourea derivative and its role in the formation of a new CT state specific towards fluoride ion.

A novel N-benzamidobisthiourea derivative (1) was synthesized. Tuning of its emission from the locally excited (LE) state to the charge transfer (CT) state was observed specifically for fluoride ion.

Photophysical studies on the interaction of acridinedione dyes with universal protein denaturant: guanidine hydrochloride.

Photophysical studies of photoinduced electron transfer (PET) and non-PET based acridinedione dyes with guanidine hydrochloride (GuHCl) were carried out in water and methanol. Addition of GuHCl to photoinduced electron transfer (PET) based acridinedione dye (ADR 1) results in a fluorescence enhancement, whereas a non-PET based dye (ADR 2) shows no significant change in the fluorescence intensity and lifetime. Addition of GuHCl to ADR 1 dye in methanol results in single exponential decay behaviour, on the contrary a biexponential decay pattern was observed on the addition of GuHCl in water. Absorption and emission spectral studies of ADR 1 dye interaction with GuHCl reveals that the dye molecule is not in the protonated form in aqueous GuHCl solution, and the dye is confined to two distinguishable microenvironment in the aqueous phase. A large variation in the microenvironment around the dye molecule is created on the addition of GuHCl and this was ascertained by time-resolved area normalized emission spectroscopy (TRANES) and time-resolved emission spectroscopy (TRES). The dye molecule prefers to reside in the hydrophobic microenvironment, rather in the hydrophilic aqueous phase is well emphasized by time-resolved fluorescence lifetime studies. The mechanism of fluorescence enhancement of ADR 1 dye by GuHCl is attributed to the suppression of the PET process occurring through space.

Density functional theory analysis and spectral studies on amyloid peptide Abeta(28-35) and its mutants A30G and A30I.

Folding and self-assembly of amyloid beta (Abeta) peptide are linked to Alzheimer's disease. To understand the initial stage of amyloid-beta peptide aggregation, conformational characteristics of monomers of wild-type (WT) Abeta(28-35) and its mutant peptides A30G and A30I were investigated using density functional theory calculations and experimental studies. Monomeric structures and their relative stabilities were obtained on the basis of systematic structural optimization in the gas-phase and in the aqueous medium. Computations were performed by hybrid Hartree-Fock-Density Functional Theory (HF-DFT) at B3LYP/6-31G * level. Experimentally, the conformational transitions in the early stages of the octapeptide Abeta(28-35) and its mutants A30G and A30I in solution were characterized by CD, Thioflavin assay and FRET spectroscopy. Examination of the secondary structures revealed that Abeta(28-35) and its mutant monomers exist in random coil conformation in the aqueous medium in agreement with the theoretical predictions, which upon aging is transformed to sheet with different kinetics. This study deals with the structurally important intermediates and it may help to understand the mechanism of amyloid fibril aggregation leading to the onset of Alzheimer's disease.

Conformational polymorphism and cellular toxicity of IAPP and beta AP domains.

The principal component of the amyloid deposits in Alzheimer's disease is the beta-amyloid polypeptide, while in type II diabetes the deposits consist primarily of Islet amyloid polypeptide. These amyloid forming polypeptides consist of highly polymorphic domains, which take different conformations including random coil, helical and beta strand depending upon the microenvironment. We have studied major fibril-forming components of IAPP and beta AP and demonstrated that conformational polymorphism of these peptides in different microenvironments correlate with cellular toxicity and proteasomal inhibitory activity. On treating with trifluoroethanol (TFE) the peptide fragments undergo structural transition from a random coil to a helical conformation. Even though these domains share the same gross amyloid structural characteristic, their proteasomal activities differ. We found that even the tetrapeptides have significant proteasomal inhibitory activity indicating that the amyloid formation is involved in the enhanced life of the smaller aggregates of full-length and fragment peptides, which could explain the toxicity of these sequences.

Preparation, physiochemical characterization, and oral immunogenicity of Abeta(1-12), Abeta(29-40), and Abeta(1-42) loaded PLG microparticles formulations.

Alzheimer's disease (AD) is caused by the deposition of beta-amyloid (Abeta) protein in brain. The current AD immunotherapy aims to prevent Abeta plaque deposition and enhance its degradation in the brain. In this work, the peptides B-cell epitope Abeta(1-12), T-cell epitope Abeta(29-40) and full-length Abeta(1-42) were loaded separately to the poly (D,L-lactide co-glycolide) (PLG) microparticles by using W/O/W double emulsion solvent evaporation method with entrapment efficacy of 70.46%, 60.93%, and 65.98%, respectively. The prepared Abeta PLG microparticles were smooth, spherical, individual, and nonporous in nature with diameters ranging from 2 to 12 microm. The cumulative in vitro release profiles of Abeta(1-12), Abeta(29-40), and Abeta(1-42) from PLG microparticles sustained for long periods and progressively reached to 73.89%, 69.29%, and 70.08% by week 15. In vitro degradation studies showed that the PLG microparticles maintained the surface integrity up to week 8 and eroded completely by week 16. Oral immunization of Abeta peptides loaded microparticles in mice elicited stronger immune response by inducing anti-Abeta antibodies for prolonged time (24 weeks). The physicochemical characterization and immunogenic potency of Abeta peptides incorporated PLG microparticles suggest that the microparticles formulation of Abeta can be a potential oral AD vaccine.

Synthesis, pharmacological screening, quantum chemical and in vitro permeability studies of N-Mannich bases of benzimidazoles through bovine cornea.

A novel series of N-Mannich bases of benzimidazole derivatives were synthesized and characterized by (1)H NMR, IR spectral studies and elemental analysis. The compounds were screened for analgesic and anti-inflammatory activity. 1-((Diethylamino)-methyl)-2-styryl benzimidazole 4 at 40mg/kg was found to be equipotent to paracetamol. 1-((Piperidin-1-yl) methyl)-2-styryl-benzimidazole 6 at 40mg/kg was found to be more potent than Diclofenac. Corneal permeability and quantum chemical calculations were performed to correlate the hydrogen bonding ability with permeability and activity. The energies of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) were correlated with pharmacological activity. The semi-empirical PM3 calculations (quantum chemical calculations) revealed that E(LUMO) and energy gap DeltaE were capable of accounting for the high in vitro bovine corneal permeability and activity of the compounds.

Aggregation and conformational studies on a pentapeptide derivative.

Most of the disease causing proteins such as beta amyloid, amylin, and huntingtin protein, which are natively disordered, readily form fibrils consisting of beta-sheet polymers. Though all amyloid fibrils are made up of beta-sheet polymers, not all peptides with predominant beta-sheet content in the native state develop into amyloid fibrils. We hypothesize that stable amyloid like fibril formation may require mixture of different conformational states in the peptide. We have tested this hypothesis on amyloid forming peptide namely HCl(Ile)(5)NH(CH(2)CH(2)O)(3)CH(3) (I). We show peptide I, has propensity to form self-assembled structures of beta-sheets in aqueous solutions. When incubated over a period of time in aqueous buffer, I self assembled into beta sheet like structures with diameters ranging from 30 to 60 A that bind with amyloidophilic dyes like Congo red and Thioflavin T. Interestingly peptide I developed into unstable fibrils after prolonged aging at higher concentration in contrast with the general mature fibril-forming propensity of various amyloid petides known to date.

Lipid-induced conformational transition of the amyloid core fragment Abeta(28-35) and its A30G and A30I mutants.

The interaction of the beta-amyloid peptide (Abeta) with neuronal membranes could play a key role in the pathogenesis of Alzheimer's disease. Recent studies have focused on the interactions of Abeta oligomers to explain the neuronal toxicity accompanying Alzheimer's disease. In our study, we have investigated the role of lipid interactions with soluble Abeta(28-35) (wild-type) and its mutants A30G and A30I in their aggregation and conformational preferences. CD and Trp fluorescence spectroscopic studies indicated that, immediately on dissolution, these peptides adopted a random coil structure. Upon addition of negatively charged 1,2-dipalmitoyl-syn-glycero-3-phospho-rac-(glycerol) sodium salt (PG) lipid, the wild-type and A30I mutant underwent reorganization into a predominant beta-sheet structure. However, no conformational changes were observed in the A30G mutant on interaction with PG. In contrast, the presence of zwitterionic 1,2-dipalmitoyl-syn-glycero-3-phosphatidylcholine (PC) lipid had no effect on the conformation of these three peptides. These observations were also confirmed with atomic force microscopy and the thioflavin-T assay. In the presence of PG vesicles, both the wild-type and A30I mutant formed fibrillar structures within 2 days of incubation in NaCl/P(i), but not in their absence. Again, no oligomerization was observed with PC vesicles. The Trp studies also revealed that both ends of the three peptides are not buried deep in the vesicle membrane. Furthermore, fluorescence spectroscopy using the environment-sensitive probe 1,6-diphenyl-1,3,5-hexatriene showed an increase in the membrane fluidity upon exposure of the vesicles to the peptides. The latter effect may result from the lipid head group interactions with the peptides. Fluorescence resonance energy transfer experiments revealed that these peptides undergo a random coil-to-sheet conversion in solution on aging and that this process is accelerated by negatively charged lipid vesicles. These results indicate that aggregation depends on hydrophobicity and propensity to form beta-sheets of the amyloid peptide, and thus offer new insights into the mechanism of amyloid neurodegenerative disease.

A novel fluorophore with dual fluorescence: local excited state and photoinduced electron-transfer-promoted charge-transfer state.

Absorption and emission spectra of 9-N,N-dimethylaniline decahydroacridinedione (DMAADD) have been studied in different solvents. The fluorescence spectra of DMAADD are found to exhibit dual emission in aprotic solvents and single emission in protic solvents. The effect of solvent polarity and viscosity on the absorption and emission spectra has also been studied. The fluorescence excitation spectra of DMAADD monitored at both the emission bands are different. The presence of two different conformation of the same molecule in the ground state has lead to two close lying excited states, local excited (LE) and charge transfer (CT), and thereby results in the dual fluorescence of the dye. A CTstate involving the N,N-dimethylaniline group and the decahy droacridinedione chromophore as donor and acceptor, respectively, has been identified as the source of the long wavelength anomalous fluorescence. The experimental studies were supported by ab initio time dependent-density functional theory (TDDFT) calculations performed at the B3LYP/6-31G* level. The molecule possesses photoinduced electron transfer (PET) quenching in the LE state, which is confirmed by the fluorescence lifetime and fluorescent intensity enhancement in the presence of transition metal ions.

Do penta- and decaphospha analogues of lithocene anion and beryllocene exist? Analysis of stability, structure, and bonding by hybrid density functional study.

Stability in penta- and decaphospha analogues of lithocene anion and beryllocene is investigated by complete structural optimization at the B3LYP/6-31G level. Natural bond orbital analysis is carried out to examine the bonding between the metal and the ligands. The heterolytic dissociation energies of 667 and 608 kcal/mol predicted by B3LYP/6-311+G//B3LYP/6-31G calculations for CpBeP(5) and (P(5))(2)Be are comparable with the observed value of 635 +/- 15 kcal/mol in ferrocene. The high stability in CpBeP(5) and (P(5))(2)Be shows that these species are isolable under appropriate conditions. Lithocene anion and its phospha analogues possess lower stability toward dissociation into ionic fragments. A novel observation of the present study is that CpBeP(5) and (P(5))(2)Be have lowest energies when the two planar ligands are arranged perpendicular to each other such that one of the ligands, cyclo-P(5), is eta(1)-coordinated while the second ligand is eta(5)-coordinated to Be. The resulting structure having C(s)() point group (denoted as C(s)()(p)) is predicted to be 22 and 28 kcal/mol lower than the staggered sandwich geometry in CpBeP(5) and (P(5))(2)Be, respectively, at the B3LYP/6-311+G//B3LYP/6-31G level. In the analogous lithocene anions [CpLiP(5)](-) and [(P(5))(2)Li](-) also the C(s)()(p) structures are found to be the lowest energy structures, though their relative stabilities are small. We also characterized the geometry with both ligands eta(1)-coordinated to the metal in a linear arrangement having the D(2)(h)() point group in the decaphospha analogues [(P(5))(2)Li](-) and (P(5))(2)Be. This structure is found to be higher in energy than the C(s)()(p) structure. The D(2)(h)() structure could not be located as a potential minimum in the biscyclopentadienyl complexes and their pentaphospha analogues. Both the C(s)()(p) and D(2)(h)() structures are characterized for the first time in metallocenes. The D(2)(h)() structure seems to be a unique feature in the decaphospha metallocenes under consideration. Covalent bond formation between beryllium and phosphorus atom P(1) of eta(1)-(cyclo-P(5)) is more pronounced (bond orders 0.43-0.49) than that between Be and C(1) of eta(1)-Cp (bond orders 0.24-0.27). Though both eta(1)-coordinated cyclo-P(5) and Cp exhibit C(2)(v)() point groups, bond alternation is less pronounced in the former. The Wiberg P-P bond orders in the eta(1)-(cyclo-P(5)) of CpBeP(5) and (P(5))(2)Be having C(s)()(p) structures are in the range 1.29-1.47. These ring bond orders indicate that the P(5) ring retains aromaticity to a large extent in the eta(1)-mode of bonding with Be. Second-order perturbational energy analysis of the Fock matrix in the natural bond orbital basis reveals that there is a significant stabilizing interaction of approximately 123 kcal/mol between the lone pair orbital of P(1) and the 2s orbital of Be in the C(s)()(p) structures.