Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Regional variation in social isolation amongst older Australians

Regional studies globally have a strong focus on understanding the causes of variation in the economic performance and wellbeing of regions and this emphasis acknowledges that the strength of the local or regional economy plays a determinant role in shaping quality of life. Regional research has been less active in considering spatial variation in other factors that are critical to individual and societal wellbeing. For example, the regional studies community has been absent from the debate on the social determinants of health and how these influences vary spatially. This paper considers the results of a cross sectional survey of Australians aged 65 and over that focussed on social connections and wellbeing. It examines regional variations in the incidence of social isolation within the older population. It finds that while the incidence of self-reported social isolation amongst older persons is broadly consistent with earlier studies, it demonstrates a spatial patterning that is unexpected. The paper considers community-building activities in addressing the impacts of social isolation, including the role of urban design, and suggests that there is a need to supplement the national overview presented there through more detailed studies focussed on individual localities.

A rare P2X7 variant Arg307Gln with absent pore formation function protects against neuroinflammation in multiple sclerosis

Multiple sclerosis (MS) is a chronic relapsing-remitting inflammatory disease of the central nervous system characterized by oligodendrocyte damage, demyelination and neuronal death. Genetic association studies have shown a 2-fold or greater prevalence of the HLA-DRB1*1501 allele in the MS population compared with normal Caucasians. In discovery cohorts of Australasian patients with MS (total 2941 patients and 3008 controls), we examined the associations of 12 functional polymorphisms of P2X7, a microglial/macrophage receptor with proinflammatory effects when activated by extracellular adenosine triphosphate (ATP). In discovery cohorts, rs28360457, coding for Arg307Gln was associated with MS and combined analysis showed a 2-fold lower minor allele frequency compared with controls (1.11% for MS and 2.15% for controls, P = 0.0000071). Replication analysis of four independent European MS case–control cohorts (total 2140 cases and 2634 controls) confirmed this association [odds ratio (OR) = 0.69, P = 0.026]. A meta-analysis of all Australasian and European cohorts indicated that Arg307Gln confers a 1.8-fold protective effect on MS risk (OR = 0.57, P = 0.0000024). Fresh human monocytes heterozygous for Arg307Gln have >85% loss of ‘pore’ function of the P2X7 receptor measured by ATP-induced ethidium uptake. Analysis shows Arg307Gln always occurred with 270His suggesting a single 307Gln–270His haplotype that confers dominant negative effects on P2X7 function and protection against MS. Modeling based on the homologous zP2X4 receptor showed Arg307 is located in a region rich in basic residues located only 12 Å from the ligand binding site. Our data show the protective effect against MS of a rare genetic variant of P2RX7 with heterozygotes showing near absent proinflammatory ‘pore’ function.

Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study

ingle tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G(7)) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the O6 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. There quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 Angstrom from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Nai counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. in the absence of any coordinated ion. due to strong mutual repulsion, O6 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.

A nanosecond molecular dynamics study of antiparallel d(G)(7) quadruplex structures: Effect of the coordinated cations

Nanosecond scale molecular dynamics simulations have been performed on antiparallel Greek key type d(G(7)) quadruplex structures with different coordinated ions, namely Na+ and K+ ion, water and Na+ counter ions, using the AMBER force field and Particle Mesh Ewald technique for electrostatic interactions. Antiparallel structures are stable during the simulation, with root mean square deviation values of similar to1.5 Angstrom from the initial structures. Hydrogen bonding patterns within the G-tetrads depend on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate different cations. However, alternating syn-anti arrangement of bases along a chain as well as in a quartet is maintained through out the MD simulation. Coordinated Na+ ions, within the quadruplex cavity are quite mobile within the central channel and can even enter or exit from the quadruplex core, whereas coordinated K+ ions are quite immobile. MD studies at 400 K indicate that K+ ion cannot come out from the quadruplex core without breaking the terminal G-tetrads. Smaller grooves in antiparallel structures are better binding sites for hydrated counter ions, while a string of hydrogen bonded water molecules are observed within both the small and large grooves. The hydration free energy for the K+ ion coordinated structure is more favourable than that for the Na+ ion coordinated antiparallel quadruplex structure.

Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures

Molecular modelling of saccharide-lipid interactions

Certain saccharides, including trehalose, sucrose and glucose, stabilize lipid bilayers against dehydration. It has been suggested that these saccharides replace waters of hydration as the system is dried, thereby maintaining the headgroups at their hydrated spacing. The lipid acyl chains consequently have sufficient free volume to remain in the liquid crystallines state, and the processes that disrupt membrane integrity are inhibited. Initial molecular graphic investigations of a model trehalose/DMPC system supported this idea (Chandrasekhar, I. and Gaber, B.P. (1988) J. Biomol. Stereodyn, 5, 1163–1171). We have extended these studies to glucose and sucrose. A set of AMBER potential parameters has been established that reproduce simple saccharide conformations, including the anomeric effect. Extensive energy minimizations have been conducted on all three systems. The saccharide-lipid interaction energies become less stable in the order trehalose

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis x Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. © 2012 Wiley Periodicals, Inc.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. (c) 2012 Wiley Periodicals, Inc.

Improved subject-independent acoustic-to-articulatory inversion

In subject-independent acoustic-to-articulatory inversion, the articulatory kinematics of a test subject are estimated assuming that the training corpus does not include data from the test subject. The training corpus in subject-independent inversion (SII) is formed with acoustic and articulatory kinematics data and the acoustic mismatch between training and test subjects is then estimated by an acoustic normalization using acoustic data drawn from a large pool of speakers called generic acoustic space (GAS). In this work, we focus on improving the SII performance through better acoustic normalization and adaptation. We propose unsupervised and several supervised ways of clustering GAS for acoustic normalization. We perform an adaptation of acoustic models of GAS using the acoustic data of the training and test subjects in SII. It is found that SII performance significantly improves (similar to 25% relative on average) over the subject-dependent inversion when the acoustic clusters in GAS correspond to phonetic units (or states of 3-state phonetic HMMs) and when the acoustic model built on GAS is adapted to training and test subjects while optimizing the inversion criterion. (C) 2014 Elsevier B.V. All rights reserved.

Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers

A new class of dendrimers, the poly(propyl ether imine) (PETIM) dendrimer, has been shown to be a novel hyperbranched polymer having potential applications as a drug delivery vehicle. Structure and dynamics of the amine terminated PETIM dendrimer and their changes with respect to the dendrimer generation are poorly understood. Since most drugs are hydrophobic in nature, the extent of hydrophobicity of the dendrimer core is related to its drug encapsulation and retention efficacy. In this study, we carry out fully atomistic molecular dynamics (MD) simulations to characterize the structure of PETIM (G2-G6) dendrimers in salt solution as a function of dendrimer generation at different protonation levels. Structural properties such as radius of gyration (R-g), radial density distribution, aspect ratio, and asphericity are calculated. In order to assess the hydrophilicity of the dendrimer, we compute the number of bound water molecules in the interior of dendrirner as well as the number of dendrimer-water hydrogen bonds. We conclude that PETIM dendrimers have relatively greater hydrophobicity and flexibility when compared with their extensively investigated PAMAM counterparts. Hence PETIM dendrimers are expected to have stronger interactions with lipid membranes as well as improved drug encapsulation and retention properties when compared with PAMAM dendrimers. We compute the root-mean-square fluctuation of dendrimers as well as their entropy to quantify the flexibility of the dendrimer. Finally we note that structural and solvation properties computed using force field parameters derived based on the CHARMM general purpose force field were in good quantitative agreement with those obtained using the generalized Amber force field (GAFF).

Herstellung und Zusammensetzung von asiatischen Fischsaucen

Abstract Fish sauce belongs to the most important condiments in Southeast Asian cuisine. It is a clear, amber to reddish liquid with an intensive smell. Fish sauce is used instead of salt for nearly each meal. Asian fish sauce is made from anchovies and other small fish. For the traditional process whole fresh fish are mixed with salt in the ratio 1:1 to 6:1 in wooden, clay or concrete tanks at tropical temperatures for 6 to 18 months. The liquefaction of the fish tissue is due to the action of endogenous enzymes in fish and exogenous enzymes from bacteria. During the fermentation amino acids, peptides and a lot of other substances are built, which are responsible for the characteristic aroma and flavour of these sauces. You can buy pure fish sauce, diluted fish sauce and fish sauce made from other types of animals like mussels, prawns and squids. In single Asian countries there are different national standards for the quality of fish sauces. In order to get a general idea of these products we have bought 16 fish and two oyster sauces from the retail trade in Hamburg and analyzed them with physical, chemical, sensory and microbiological methods. Kurzfassung Fischsauce gehört zu den wichtigsten Würzsaucen in der südostasiatischen Küche. Es ist eine klare, bernsteinfarbene bis rötlichbraune, sehr intensiv riechende Flüssigkeit. Sie wird anstelle von Salz verwendet und daher fast zu jedem Essen gereicht. Zur Herstellung von Fischsaucen werden hauptsächlich Anchovis und ähnliche kleine Fische verwendet. Bei der traditionellen Herstellung werden die ganzen Fische mit Meersalz in einem Holzfass, Tongefäß oder Betontank im Verhältnis 1:1 bis 6:1 gemischt. Während der anschließenden 6 – 18 Monate dauernden Lagerung bei tropischen Temperaturen bauen sich die Gewebeproteine durch fischeigene Enzyme und Mikroorganismen ab. Bei diesem mehrmonatigen Fermentationsprozess entstehen die für den Geschmack wichtigen Aminosäuren, Peptide und Aromastoffe. Es gibt neben reiner Fischsauce, auch verdünnte Fischsauce und Fischsaucen aus anderen Tieren wie Muscheln, Garnelen und Tintenfische. In den einzelnen asiatischen Ländern gibt es unterschiedliche nationale Qualitätsstandards. Um diese Produktgruppe näher kennen zu lernen, haben wir 16 Fisch- und 2 Austernsaucen aus dem Einzelhandel (Hamburg) mit physikalischen, chemischen, sensorischen und mikrobiologischen Verfahren untersucht.

An in vivo approach to tRNA identity

A leucine-inserting tRNA has been transformed into a serine-inserting tRNA by changing 12 nucleotides. Only 8 of the 12 changes are required to effect the conversion of the leucine tRNA to serine tRNA identity. The 8 essential changes reside in basepair 11-24 in the D stem, basepairs 3-70, 2-71 and nucleotides 72 and 73, all of the acceptor stem.

Functional amber suppressor tRNA genes were generated for 14 species of tRNA in E. coli, and their amino acid specificities determined. The suppressors can be classified into three groups, based upon their specificities. Class I suppressors, tRNA^(Ala2)_(CUA), tRNA^(GlyU)_(CUA), tRNA^(HisA)_(CUA), tRNA^(Lys)_(CUA), and tRNA^(ProH)_(CUA), inserted the predicted amino acid. The Class II suppressors, tRNA^(GluA)_(CUA) , tRNA^(GlyT)_(CUA), and tRNA^(Ile1)_(CUA) were either partially or predominantly mischarged by the glutamine aminoacyl tRNA synthetase (AAS). The Class III suppressors, tRNA^(Arg)_(CUA), tRNA^(AspM)_(CUA), tRNA^(Ile2)_(CUA), tRNA^(Thr2)_(CUA), tRNA^(Met(m))_(CUA) and tRNA^(Val)_(CUA) inserted predominantly lysine.

Eggs, Larvae and Young of The Striped Bass, Roccus saxatilis

Detailed descriptions of the early development of the striped bass, Roccus saxitilis (Walbaum), with emphasis on variation in size and morphology, sequence of fin formation, changes in body form, and attainment of the full complement of maristic numbers, are presented and illustrated for the first time. The egg is spherical, transparent, non-adhesive and relatively large. It is pelagic and buoyant, although it sinks in quiet fresh water. When unfertilized, it averages 1.3 mm, in diameter, but is 3.4 mm. when fertilized and water-hardened. The granular yolk sac, green when alive and whitish-yellow when preserved, averages 1.2 mm., and the single amber-colored oil globule is about 0.6 mm. in diameter. Newly hatched striped bass prolarvae, which range from 2.9-3.7 mm. in total length, are relatively undeveloped and nearly transparent, with no mouth opening, unpigmented eyes, and a greatly enlarged yolk sac with the large oil globule projecting beyond the head. When 5-6 mm. long the yolk sac and oil globule are assimilated and the postlarvae I show advanced development of the internal anatomy. Although the fish is still transparent, scattered melanophores are found on the head and body and chromatophores in the eyes and the ventro-posterior edge of the body. Postlarvae transform to young between 7 and 10 mm. in length when the finfolds are lost except in the dorsal, anal and caudal regions. The largest fish in this group possess a well-formed skeleton with a full complement of 25 vertebrae. Between 10 and 20 mm. in length all fish are fully transformed, muscular tissue renders most of the internal structure obscure, and the myotomes, which generally correspond in number with the vertebrae, are no longer visible. At fish lengths of 20-30 mm. scales are found on all specimens, and with the exception of the pectoral fin-rays, a full complement of meristic structures is present in all other fins. At this stage the body is pigmented uniformly with small spots. Linear regressions between several dependent variables and the , independent variable of standard length indicate that the rate of development of head, eye. and snout to anus lengths is proportional to the length of the larvae and young. Body depth and standard length are non-linear among newly-hatched larvae. Hatchery-reared striped bass demonstrated a slow rate of growth, and were regarded as "stunted," when compared to growth rates observed in another study and field collections. Observations were also made on abnormal eggs and teratological larvae and young. Blue-sac disease is tentatively identified and described for the first time in larvae and pugnosed larvae and young are also described for the first time in striped bass.