Homology modeling of membrane proteins: a critical assessment

Evaluation and validation of homology modeling protocols are indispensable for membrane proteins as experimental determination of their three-dimensional structure is an arduous task. The prediction ability of Modeller, MOE, InsightII-Homology and Swiss-PdbViewer (SPV) with different sequence alignments CLUSTALW, BLAST and 3D-JIGSAW have been assessed. The sequence identity of the target and template was chosen to be in the range of 25-35%. Validation protocols to assess the structure, fold and stereochemical quality, are employed by comparing with experimental structures. Two different ranking schemes are suggested to evaluate the performance of each methodology based on the validation scores. While unambiguous preference for any given procedure did not surface, statistically Modeller and the sequence alignment technique, 3D-JIGSAW, gave best results amongst the chosen protocols. The present study helps in selecting the right protocols when modeling membrane proteins, which form a major class of drug targets.     

Growth mechanism of long aligned multiwall carbon nanotube arrays by water-assisted chemical vapor deposition

Highly aligned arrays of multiwalled carbon nanotube (MWCNT) on layered Si substrates have been synthesized by chemical vapor deposition (CVD). The effect of the substrate design and the process parameters on the growth mechanism were studied. Adding water vapor to the reaction gas mixture of hydrogen and ethylene enhanced the growth which led to synthesis of longer CNT arrays with high density. Environmental scanning electron microscopy (ESEM), energy-dispersive spectroscopy (EDS), and atomic force microscopy (AFM) were used to analyze the CNT morphology and composition. Quadrupole mass spectroscopy (QMS) provided in-situ information on the gas spices within the reaction zone. On the basis of results, we verified the top growth mechanism and evaluated the reason of decline and stoppage of the CNT growth after extended period of deposition. Multilayered Si substrates with a top film of Al2O3, having appropriate roughness, provide favorable conditions to form catalyst islands with uniform distribution and size. Using water-assisted CVD process and optimized substrate design, our group succeeded to grow vertically aligned, patterned MWCNT up to 4-mm long. The arrays were of high purity and weak adhesion which allowed to be peeled off easily from the substrate.     

Characterisation of a series of acetals/ketals of bis(2-nitrophenyl) ethanediol and bis(4,5-dimethoxy-2-nitrophenyl) ethanediol under APCI mass spectrometric conditions

A series acetals/ketals of aldehydes and ketones formed by the reaction of two photolabile protecting groups, bis(2-nitrophenyl) ethanediol and bis(4,5-dimethoxy-2-nitrophenyl) ethanediol (I and II, respectively), were analysed under EI, LSIMS, ESI and APCI conditions to obtain molecular weights as well as structural information. The EI and LSIMS techniques failed to give molecular weight information. The positive ESI yielded [M + H](+) ions only for I; however, with added Na(+) both I and II formed [M + Na](+) adducts. But upon decomposition, the [M + Na](+) ions yielded Na(+) ion as the only product ion. Similarly, under negative ion ESI conditions both I and II gave molecular weight information by forming adduct ions with halide anions (F(-), Cl(-), Br(-) and I(-)); however, they did not give structural information as they resulted in only the halide anion as the abundant fragment ion upon dissociation. All the compounds formed abundant M(-*) ions under negative ion APCI conditions, and their MS/MS spectra showed characteristic fragment ions; hence the acetals/ketals of I and II could be successfully characterized under negative ion APCI conditions.     

SOM assembly of hydroxynaphthoquinone and its oxime: polymorphic X-ray structures and EPR studies

Investigation on solvent-induced polymorphism in X-ray structures of 2-hydroxy-1,4-naphthoquinone (Lawsone) 1, is carried out. In protic methanol, 1 crystallizes in monoclinic space group P2(1)/c (1a) comprising of 2D hydrogen bonded network via cyclic dimers. In aprotic solvent such as acetone on the other hand, 1 exhibits orthorhombic space group Pna 2(1) (1b) and emerges with 1D catemeric chain. Solvent-induced topological isomerism of cyclic dimers and helical catemeric chains arising from (i) bifurcated intra- and inter molecular hydrogen bondings viz. O-H...O=C interactions between C(2) hydroxyl and C(1), C(4) carbonyls, (ii) C-H...O interactions viz. C(3)-H...O(1)C(1) have been discussed. A signal for radical in 1 at g = 2.0058 is signatured by EPR spectrum and it's oxime derivative viz. 2-hydroxy-4-naphthoquinone-1-oxime 2, in solid state shows biradical and monoradical formation with aggregation of dimer and monomer due to non-covalent hydrogen bonds. Zero field split parameters for 2 are estimated to be D = 215 G, Ex = 13 G, Ey = 47 G at 298 K. A half field signal at 77 K indicates triplet ground state. Frozen glass EPR of 2 resolves as regioregular dimeric-monomeric species showing hyperfine interactions with 1-oximino nitrogen in dimer A (14N) = 15.5 G].     

Structure, magneto-structural transitions and magnetocaloric properties in Ni50−xMn37+xIn13 melt spun ribbons

Melt spun Ni_50−xMn_37+xIn₁₃ (2≤x≤5) ribbons were investigated for the structure, microstructure, magneto-structural transitions and inverse magnetocaloric effect (IMCE) associated with the first-order martensitic phase transition. The influence of excess Mn in Ni site (or Ni/Mn content) on the martensite transition and the associated magnetic and magnetocaloric properties are discussed. It was found that with the increase in Mn content, the martensitic transition shifted from 325 to 240 K as x is varied from 2 to 4, and the austenite phase was stabilized at room temperature. The x=5 ribbon did not show the martensitic transition. For the x=3 ribbon, the structural and magnetic transitions are close together unlike in the x=4 ribbon in which they are far (∼60 K) apart. The zero field cooled and field cooled curves support the presence of exchange bias blocking temperature due to antiferromagnetic interactions in the ribbons. A large change in the magnetization between the martensite and austenite phases was observed for a small variation in the Ni/Mn content, which resulted in large IMCE. A large positive magnetic entropy change (ΔS_M) of 32 J/kg K at room temperature (∼ 300 K) for a field change of 5 T with a net refrigeration capacity of 64 J/kg was obtained in the Ni₄₇Mn₄₀In₁₃ ribbon.     

Identification and structural characterization of in vivo metabolites of ketorolac using liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS)

In vivo metabolites of ketorolac (KTC) have been identified and characterized by using liquid chromatography positive ion electrospray ionization high resolution tandem mass spectrometry (LC/ESI-HR-MS/MS) in combination with online hydrogen/deuterium exchange (HDX) experiments. To identify in vivo metabolites, blood urine and feces samples were collected after oral administration of KTC to Sprague-Dawley rats. The samples were prepared using an optimized sample preparation approach involving protein precipitation and freeze liquid separation followed by solid-phase extraction and then subjected to LC/HR-MS/MS analysis. A total of 12 metabolites have been identified in urine samples including hydroxy and glucuronide metabolites, which are also observed in plasma samples. In feces, only O-sulfate metabolite and unchanged KTC are observed. The structures of metabolites were elucidated using LC-MS/MS and MS(n) experiments combined with accurate mass measurements. Online HDX experiments have been used to support the structural characterization of drug metabolites. The main phase I metabolites of KTC are hydroxylated and decarbonylated metabolites, which undergo subsequent phase II glucuronidation pathways.     

Quantum chromodynamics: Working group report

This is the report of the QCD working group at WHEPP-6. Discussions and work on heavy ion collisions, polarized scattering, and collider phenomenology are reported.