DEFINING alpha-HELIX GEOMETRY BY C-alpha ATOM TRACE vs (phi-psi) TORSION ANGLES: A COMPARATIVE ANALYSIS

A regular secondary structure is described by a well defined set of values for the backbone dihedral angles (phi,psi and omega) in a polypeptide chain. However in real protein structures small local variations give rise to distortions from the ideal structures, which can lead to considerable variation in higher order organization. Protein structure analysis and accurate assignment of various structural elements, especially their terminii, are important first step in protein structure prediction and design. Various algorithms are available for assigning secondary structure elements in proteins but some lacunae still exist. In this study, results of a recently developed in-house program ASSP have been compared with those from STRIDE, in identification of alpha-helical regions in both globular and membrane proteins. It is found that, while a combination of hydrogen bond patterns and backbone torsional angles (phi-psi) are generally used to define secondary structure elements, the geometry of the C-alpha atom trace by itself is sufficient to define the parameters of helical structures in proteins. It is also possible to differentiate the various helical structures by their C-alpha trace and identify the deviations occurring both at mid-positions as well as at the terminii of alpha-helices, which often lead to occurrence of 3(10) and pi-helical fragments in both globular and membrane proteins.

Emergent properties of the interferon-signalling network may underlie the success of hepatitis C treatment

Current interferon alpha-based treatment of hepatitis C virus (HCV) infection fails to cure a sizeable fraction of patients treated. The cause of this treatment failure remains unknown. Here using mathematical modelling, we predict treatment failure to be a consequence of the emergent properties of the interferon-signalling network. HCV induces bistability in the network, creating a new steady state where it can persist. Cells that admit the new steady state alone are refractory to interferon. Using a model of viral kinetics, we show that when the fraction of cells refractory to interferon in a patient exceeds a critical value, treatment fails. Direct-acting antivirals that suppress HCV replication can eliminate the new steady state, restoring interferon sensitivity and improving treatment response. Our study thus presents a new conceptual basis of HCV persistence and treatment response, elucidates the origin of the synergy between interferon and direct-acting antivirals, and facilitates rational treatment optimization.

Mono- and Dialkyne Insertion Reactions of Cyclopalladated N,N `,N `'-Triarylguanidines kappa(2)(C,N)Pd(mu-Br)](2) and cis-/trans-kappa(2)(C,N)Pd(Lewis Base)Br]. Scaffolds for Enlarged, Rearranged, and Zwitterionic Palladacycles through Ring Contraction cum Amine-Imine Tautomerization

Insertion reactions of six-membered cyclopalladated N,N',N''-triarylguanidines, kappa(2)(C,N)Pd(mu-Br)](2) with various alkynes in CH2Cl2 under ambient conditions afforded diinserted eight-membered palladacycles, (kappa(2)(C,N):eta(2)(C=C)-PdBr] (1-11), in high yield (76-96%), while insertion reactions of six-membered cyclopalladated N,N',N''-triarylguanidines, kappa(2)(C,N)Pd(Lewis base)Br] (VI-XI), with various alkynes under the aforementioned conditions afforded monoinserted six-membered palladacycles, kappa(2)(C,N)-Pd(Lewis base)Br] (12-21), in high yield (81-91%) except for 14 (23%). The insertion reaction of VI with 2 equiv of dimethyl acetylenedicarboxylate (DMAD) and the insertion reaction of 12 with 1 equiv of DMAD in CH2Cl2 under ambient conditions resulted in the formation of a diinserted zwitterionic five-membered palladacycle, kappa(2)(C,C)Pd(2,6-lutidine)Br] (22), in 76% and 70% yields, respectively. Palladacycle 22 upon reaction with AgOTf in wet MeCN afforded the ionic palladacycle kappa(2)(C,C)Pd(2,6-lutidine)(H2O)]OTf] (23) in 78% yield. The ring size of the ``kappa(2)(C,N)Pd]'' unit in the structurally characterized diinserted palladacycles (1 center dot 2CH(2)Cl(2)center dot H2O, 2, 5, and 7), and monoinserted palladacycles (17, 18, and 20 center dot C7H8 H2O) is smaller than that anticipated for mono- and diinserted palladacycles, and this feature is mainly ascribed to the proclivity of III-XI to undergo ring contraction cum amine-imine tautomerization upon alkyne insertion. Palladacycle 22 represents the first diinserted product obtained in alkyne insertion reactions of kappa(2)(C,N)Pd(Lewis base)X] type palladarycles. The molecular structure of 22 center dot H2O determined by X-ray diffraction indicates that the positive charge on the guanidinium moiety is balanced by the negative charge on the palladium atom and thus represents the first structurally characterized zwitterionic palladacycle to be reported in alkyne insertion chemistry. Plausible mechanisms of formation of 12-21 and 22 have been outlined. The presence of more than one species in solution for some of the palladacycles in the series 1-7 and 12-21 was explained by invoking the C-N single-bond rotation of the CN3 unit of the guanidine moiety, while this process in conjunction with Pd-N(lutidine) bond rotation was invoked to explain the presence of four isomers of 15, as studied with the aid of variable-concentration H-1 NMR experiments carried out for 14 and 15.

Dense network of O-H ... O and C-H ... O interactions in the solid state structure of n-pentyl-2-chloro-2-deoxy-alpha-D-manno-sept 3-uloside

Single crystal X-ray structural analysis of a septanoside, namely, n-pentyl-2-chloro-2-deoxy sept-3-uloside (1) provides many finer details of the molecular structure, in addition to its preferred twist-chair conformation, namely, (TC3,4)-T-5,6 conformation. Structural analysis reveals a dense network of O-H...O, C-H...O and van der Waals interactions that stabilize interdigitized, planar bi-layer structure of the crystal lattice. (C) 2014 Elsevier Ltd. All rights reserved.

Groundnut Bud Necrosis Virus Encoded NSm Associates with Membranes via Its C-Terminal Domain

Groundnut Bud Necrosis Virus (GBNV) is a tripartite ambisense RNA plant virus that belongs to serogroup IV of Tospovirus genus. Non-Structural protein-m (NSm), which functions as movement protein in tospoviruses, is encoded by the M RNA. In this communication, we demonstrate that despite the absence of any putative transmembrane domain, GBNV NSm associates with membranes when expressed in E. coli as well as in N. benthamiana. Incubation of refolded NSm with liposomes ranging in size from 200-250 nm resulted in changes in the secondary and tertiary structure of NSm. A similar behaviour was observed in the presence of anionic and zwitterionic detergents. Furthermore, the morphology of the liposomes was found to be modified in the presence of NSm. Deletion of coiled coil domain resulted in the inability of in planta expressed NSm to interact with membranes. Further, when the C-terminal coiled coil domain alone was expressed, it was found to be associated with membrane. These results demonstrate that NSm associates with membranes via the C-terminal coiled coil domain and such an association may be important for movement of viral RNA from cell to cell.

Effect of adsorbate loading on selectivity during adsorption of C/C and C/C n-alkane binary mixtures in silicalite

Adsorption experiments of mixtures of long chain alkanes into silicalite under liquid phase conditions show selectivity inversion and azeotrope formation. These effects are due to the subtle interplay between the size of the adsorbed molecules and pore topology of the adsorbent. In this study, the selective uptake of lighter component during liquid phase adsorption of C/C and C/C n-alkane binary mixtures in the zeolite silicalite is understood through configurational bias grand-canonical Monte Carlo molecular simulation technique and a coarse-grained siting analysis. The simulations are conducted under conditions of low and intermediate levels of loading. The siting pattern of the adsorbates inside the zeolite pores explain the selectivity as seen in experiments.

High-Resolution Solid State C-13 NMR Studies of Bent-Core Mesogens of Benzene and Thiophene

Bent-core mesogens are an important class of thermotropic liquid crystals as they exhibit unusual properties as well as morphologies distinctly different from rodlike mesogens. Two bent-core mesogens with differing center rings namely benzene and thiophene are considered and investigated using high-resolution oriented solid state C-13 NMR method in their liquid crystalline phases. The mesogens exhibit different phase sequences with the benzene-based mesogen showing a B-1 phase, while the one based on thiophene showing nematic and smectic C phases. The 2-dimensional separated local field (2D-SLF) NMR method was used to obtain the C-13-H-1 dipolar couplings of carbons in the center ring as well as in the side-wing phenyl rings. Couplings, characteristic of the type of the center ring, that also provide orientational information on the molecule in the magnetic field were observed. Together with the dipolar couplings of the side-wing phenyl ring carbons from which the local order parameters of the different subunits of the core could be extracted, the bent angle of the mesogenic molecule could be obtained. Accordingly, for the benzene mesogen in its B-1 phase at 145 degrees C, the center ring methine C-13-H-1 dipolar couplings were found to be significantly larger (9.5-10.2 kHz) compared to those of the side-wing rings (1.6-2.1 kHz). From the local order parameter values of the center (0.68) as well as the side-wing rings (0.50), a bent-angle of 130.3 degrees for this mesogen was obtained. Interestingly, for the thiophene mesogen in its smectic C phase at 210 degrees C, the C-13-H-1 dipolar coupling of the center ring methine carbon (2.11 kHz) is smaller than those of the side-wing phenyl ring carbons (2.75-3.00 kHz) which is a consequence of the different structures of the thiophene and the benzene rings. These values correspond to local order parameters of 0.85 for the center thiophene ring and 0.76 for the first side-wing phenyl ring and a bent-angle of 149.2 degrees. Thus, the significant differences in the dipolar couplings and the order parameter values between different parts in the rigid core of the mesogens are a direct consequence of the nature of the center ring and the bent structure of the molecule. The present investigation thus highlights the ability of the C-13 2D-SLF technique to provide the geometry of the bent-core mesogens in a straightforward manner through the measurement of the C-13-H-1 dipolar couplings.

Serum proteomics of hepatitis C virus infection reveals retinol-binding protein 4 as a novel regulator

Persistent infection of hepatitis C virus (HCV) can lead to liver cirrhosis and hepatocellular carcinoma, which are currently diagnosed by invasive liver biopsy. Approximately 15-20% of cases of chronic liver diseases in India are caused by HCV infection. In North India, genotype 3 is predominant, whereas genotype 1 is predominant in southern parts of India. The aim of this study was to identify differentially regulated serum proteins in HCV-infected Indian patients (genotypes 1 and 3) using a two-dimensional electrophoresis approach. We identified eight differentially expressed proteins by MS. Expression levels of one of the highly upregulated proteins, retinol-binding protein 4 (RBP4), was validated by ELISA and Western blotting in two independent cohorts. We also confirmed our observation in the JFH1 infectious cell culture system. Interestingly, the HCV core protein enhanced RBP4 levels and partial knockdown of RBP4 had a positive impact on HCV replication, suggesting a possible role for this cellular protein in regulating HCV infection. Analysis of RBP4-interacting partners using a bioinformatic approach revealed novel insights into the possible involvement of RBP4 in HCV-induced pathogenesis. Taken together, this study provided information on the proteome profile of the HCV-infected Indian population, and revealed a link between HCV infection, RBP4 and insulin resistance.

C-11/C-9 Helices in Crystals of alpha beta Hybrid Peptides and Switching Structures between Helix Types by Variation in the alpha-Residue

Close-packed helices with mixed hydrogen bond directionality are unprecedented in the structural chemistry of alpha-polypeptides. While NMR studies in solution state provide strong evidence for the occurrence of mixed helices in (beta beta)(n) and (alpha beta)(n) sequences, limited information is currently available in crystals. The peptide structures presented show the occurrence of C-11/C-9 helices in (alpha beta)(n) peptides. Transitions between C-11 and C-11/C-9 helices are observed upon varying the alpha-amino acid residue.

Molecular topology of three ring nematogens from C-13-H-1 dipolar couplings

Molecules in their liquid crystalline phase undergo rotational motion about the long axis of the molecule and the shape adopted by the rotating molecule plays an important role in influencing the mesophase morphology. In this context, obtaining the topology and the relative orientation of the different sub-units are important steps. For studying the liquid crystalline phase, C-13 NMR spectroscopy is a convenient method and for certain specifically designed nematogens, 2-dimensional separated local field (2D-SLF) NMR spectroscopy provides a particularly simple and straightforward means of arriving at the molecular topology. We demonstrate this approach on two three ring based nematogens designed with a phenyl or a thiophene ring at one of the termini. From the C-13-H-1 dipolar couplings of the terminal carbon obtained using the 2D-SLF NMR technique, the order parameter of the local symmetry axis of the terminal phenyl ring as well as of the long molecular axis could be easily estimated. For the thiophene nematogen, the lack of symmetry of the thiophene moiety necessitates some additional computational steps. The results indicate that the thiophene unit has its local ordering axis oriented away from the long molecular axis by a small angle, consistent with a bent structure expected in view of the thiophene geometry. The experiment also demonstrates the ability of 2D-SLF NMR to provide high resolution spectra by separation of several overlapped resonances in terms of their C-13-H-1 dipolar couplings. The results are consistent with a rod-like topology of the core of the investigated mesogens. The investigation demonstrates the potential of 2D-SLF NMR C-13 spectroscopy for obtaining atomistic level information and its utility for topological studies of different mesogens.

New low band gap 2-(4-(trifluoromethyl)phenyl)-1H-benzod]imidazole and benzo1,2-c; 4,5-c `]bis1,2,5]thiadiazole based conjugated polymers for organic photovoltaics

Two new low band gap D-A structured conjugated polymers, PBDTTBI and PBDTBBT, based on 2-(4-(trifluoromethyl)phenyl)-1H-benzod]imidazole and benzo1,2-c; 4,5-c']bis1,2,5]thiadiazole acceptor units with benzo1,2-b; 3,4-b']dithiophene as a donor unit have been designed and synthesized via a Stille coupling reaction. The incorporation of the benzo1,2-c; 4,5-c']bis1,2,5]thiadiazole unit into PBDTBBT has significantly altered the optical and electrochemical properties of the polymer. The optical band gap estimated from the onset absorption edge is similar to 1.88 eV and similar to 1.1 eV, respectively for PBDTTBI and PBDTBBT. It is observed that PBDTBBT exhibited a deeper HOMO energy level (similar to 4.06 eV) with strong intramolecular charge transfer interactions. Bulk heterojunction solar cells fabricated with a configuration of ITO/PEDOT: PSS/PBDTBBT: PC71BM/Al exhibited a best power conversion efficiency of 0.67%, with a short circuit current density of 4.9 mA cm(-2), an open-circuit voltage of 0.54 V and a fill factor of 25%.

Regioselective Thiolation of Arenes and Heteroarenes: C-H Functionalization Strategy for C-S Bond Formation

A facile transition-metal-free oxidative cross-dehydrogenative coupling reaction involving selective formation of a C-S bond leading to the synthesis of arylthiobenzoxazoles, heteroarylthiobenzoxazoles, and arylthiobenzothiazoles has been described. This highly regioselective C-H functionalization reaction with electron-rich aromatic systems including heteroaromatics is achieved by reversing the reactivity of sulfur in the presence of a suitable oxidant and strong acid.

Uplift Resistance of Long Pipelines in the Presence of Seismic Forces

The vertical uplift resistance of long pipes buried in sands and subjected to pseudostatic seismic forces has been computed by using the lower-bound theorem of the limit analysis in conjunction with finite elements and nonlinear optimization. The soil mass is assumed to follow the Mohr-Coulomb failure criterion and an associated flow rule. The failure load is expressed in the form of a nondimensional uplift factor F-gamma. The variation of F-gamma is plotted as a function of the embedment ratio of the pipe, horizontal seismic acceleration coefficient (k(h)), and soil friction angle (phi). The magnitude of F-gamma is found to decrease continuously with an increase in the horizontal seismic acceleration coefficient. The reduction in the uplift resistance becomes quite significant, especially for greater values of embedment ratios and lower values of friction angle. The predicted uplift resistance was found to compare well with the existing results reported from the literature. (C) 2014 American Society of Civil Engineers.

The X-C center dot center dot center dot pi (X = F, Cl, Br, CN) Carbon Bond

High-level ab initio calculations have been used to study the interactions between the CH3 group of CH3X (X = F, Cl, Br, CN) molecules and pi-electrons. These interactions are important because of the abundance of both the CH3 groups and pi-electrons in biological systems. Complexes between C2H4/C2H2 and CH3X molecules have been used as model systems. Various theoretical methods such as atoms in molecules theory, reduced density gradient analysis, and natural bond orbital analysis have been used to discern these interactions. These analyses show that the interaction of the p-electrons with the CH3X molecules leads to the formation of X-C...p carbon bonds. Similar complexes with other tetrel molecules, SiH3X and GeH3X, have also been considered.