Rigid and flexible region in lysozyme and the invariant features in its hydration shell

Water-mediated transformations provide a useful handle for exploring the flexibility in protein molecules and the invariant features in their hydration shells. Low-humidity monoclinic hen egg white lysozyme, resulting from such a transformation, has perhaps the lowest solvent content observed in any protein crystal so far and has a well-ordered structure. A detailed comparison involving this structure, low-humidity tetragonal lysozyme, and the other available refined crystal structures of the enzyme permits the delineation of the relatively rigid, moderately flexible and highly flexible regions of the molecule. The relatively rigid region forms a contiguous structural unit close to the molecular centroid and encompasses parts of of the main beta-structure and three alpha-helices. The hydration shell of the protein contains 30 invariant water molecules. Many of them are involved in holding different parts of the molecule together or in stabilizing local structure. Five of the six invariant water molecules attached to the substrate-binding region form part of a water cluster contiguous with the side-chains of the catalytic residues Glu-35 and Asp-52.

Sign Of The Order Parameter In Oriented Systems And Its Utility In The Study Of The Dynamic Properties Of Molecules

Novel one and two dimensional NMR techniques are proposed and utilized for the determination of the signs of the order parameters used for the study of the mobility of the fatty acid chains. The experiments designed to extract this information involve the use of the intensities of the side bands in the spectra of oriented systems spinning at the magic angle. Advantages of the two dimensional technique over the one dimensional method are discussed. The utility of the method in the study of the dynamic properties of membranes and model systems is pointed out.

Structure of bovine prothrombin fragment 1 refined at 2.25 Å resolution

The structure of bovine prothrombin fragment 1 has been refined at 2.25 Å resolution using high resolution measurements made with the synchrotron beam at CHESS. The synchrotron data were collected photographically by oscillation methods (R-merge = 0.08). These were combined with lower order diffractometer data for refinement purposes. The structure was refined using restrained least-squares methods with the program PROLSQ to a crystallographic R-value of 0.175. The structure includes 105 water molecules with occupancies of >0·6. The first 35 residues (Ala1-Leu35) of the N-terminal ?-carboxy glutamic acid-domain (Ala1-Cys48) of fragment 1 are disordered as are two carbohydrate chains of Mr ? 5000; the latter two combine to render 40% of the structure disordered. The folding of the kringle of fragment 1 is related to the close intramolecular contact between the inner loop disulfide groups. Half of the conserved sequence of the kringle forms an inner core surrounding these disulfide groups. The remainder of the sequence conservation is associated with the many turns of the main chain. The Pro95 residue of the kringle has a cis conformation and Tyr74 is ordered in fragment 1, although nuclear magnetic resonance studies indicate that the comparable residue of plasminogen kringle 4 has two positions. Surface accessibility calculations indicate that none of the disulfide groups of fragment 1 is accessible to solvent.

The contribution of polarons, bipolarons and intersite tunneling to low temperature conductivity in doped polypyrrole

The conductivity of highly doped polypyrrole is less than that of intermediately doped samples, by two orders of magnitude, at 4.2 K. This may be due to more number of bipolarons in highly doped samples. Bipolarons require four times more activation energy than single polarons to hop by thermally induced virtual transitions to intermediate dissociated polaron states than by the nondissociated process. The conduction process in these polyconjugated systems involve ionization from deep trapped states, having a View the MathML source dependence, hopping from localised states, having View the MathML source dependence, and intersite tunnel percolation, having T−1 dependence. The interplay of these factors leads to a better fit by View the MathML source. The mechanism for this exponential behaviour need not be same as that of Motts variable range hopping. Conduction by percolation is possible, if an infinite cluster of chains can be connected by impurity centers created by dopant ions. The tendency for the saturation of conductivity at very low temperatures is due to the possibility of intersite tunnel percolation is disordered polaronic systems.

Analysis of side-chain conformation in proteins

The crystal structures of a number of globular proteins are currently available. An analysis of the distribution of side-chains among different allowed conformations in these proteins has been carried out. The observed conformations of individual residues are discussed on the basis of well-known stereochemical criteria. The population distribution of side-chains in different allowed regions in conformational space can be explained largely on the basis of simple steric considerations. In addition to examining the conformational behaviour of individual residues, some population distributions of conformational angles of general interest involving groups of residues have also been analyzed.

Dilute solution properties of methyl methacrylate—acrylonitrile copolymer (MA2)

This article deals with studies of the dilute solution properties of methyl methacrylate-acrylonitrile (MMA-AN) copolymer of 0.415 mole fraction (mf) of acrylonitrile composition. Mark—Houwink parameters for this copolymer have been evaluated in acetonitrile (MeCN), 2-butanone (MEK), dimethyl formamide (DMF), and γ-butyrolactone (γ-BL). The Mark-Houwink exponent a in all four solvents at all temperatures is larger than the corresponding values of the parent homopolymers. The solvent power is in the order of DMF < γ–BL < MEK < MeCN; [η] decreases with an increase in temperature, which is behavior characteristic of polymers in good solvent. The unperturbed dimensions (K0) values, obtained by the Stockmayer–Fixman method, are lower than those for the parent homopolymers and depend on solvent as well as temperature. The solute—solvent interaction parameter X1 values are close to 0.5; X1 is independent of temperature. The excess interaction parameter XABvalues are negative. The results for this copolymer system in regard to low second virial coefficient A2, large X1, and high a values suggest that the large extension of these copolymer chains is due to the unusual short-range interactions.

Operationalizing Supply Chain vs. Supply Chain Competion

Competition is an immensely important area of study in economic theory, business and strategy. It is known to be vital in meeting consumers’ growing expectations, stimulating increase in the size of the market, pushing innovation, reducing cost and consequently generating better value for end users, among other things. Having said that, it is important to recognize that supply chains, as we know it, has changed the way companies deal with each other both in confrontational or conciliatory terms. As such, with the rise of global markets and outsourcing destinations, increased technological development in transportation, communication and telecommunications has meant that geographical barriers of distance with regards to competition are a thing of the past in an increasingly flat world. Even though the dominant articulation of competition within management and business literature rests mostly within economic competition theory, this thesis draws attention to the implicit shift in the recognition of other forms of competition in today’s business environment, especially those involving supply chain structures. Thus, there is popular agreement within a broad business arena that competition between companies is set to take place along their supply chains. Hence, management’s attention has been focused on how supply chains could become more aggressive making each firm in its supply chain more efficient. However, there is much disagreement on the mechanism through which such competition pitching supply chain against supply chain will take place. The purpose of this thesis therefore, is to develop and conceptualize the notion of supply chain vs. supply chain competition, within the discipline of supply chain management. The thesis proposes that competition between supply chains may be carried forward via the use of competition theories that emphasize interaction and dimensionality, hence, encountering friction from a number of sources in their search for critical resources and services. The thesis demonstrates how supply chain vs. supply chain competition may be carried out theoretically, using generated data for illustration, and practically using logistics centers as a way to provide a link between theory and corresponding practice of this evolving competition mode. The thesis concludes that supply chain vs. supply chain competition, no matter the conceptualization taken, is complex, novel and can be very easily distorted and abused. It therefore calls for the joint development of regulatory measures by practitioners and policymakers alike, to guide this developing mode of competition.

Protein Hydration and Water Structure: X-ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content

Low-humidity monoclinic lysozyme, resulting from a water-mediated transformation, has one of the lowest solvent contents (22% by volume) observed in a protein crystal. Its structure has been solved by the molecular replacement method and refined to an R value of 0.175 for 7684 observed reflections in the 10–1.75 Å resolution shell. 90% of the solvent in the well ordered crystals could be located. Favourable sites of hydration on the protein surface include side chains with multiple hydrogen-bonding centres, and regions between short hydrophilic side chains and the main-chain CO or NH groups of the same or nearby residues. Major secondary structural features are not disrupted by hydration. However, the free CO groups at the C terminii and, to a lesser extent, the NH groups at the N terminii of helices provide favourable sites for water interactions, as do reverse turns and regions which connect β-structure and helices. The hydration shell consists of discontinuous networks of water molecules, the maximum number of molecules in a network being ten. The substrate-binding cleft is heavily hydrated, as is the main loop region which is stabilized by water interactions. The protein molecules are close packed in the crystals with a molecular coordination number of 14. Arginyl residues are extensively involved in intermolecular hydrogen bonds and water bridges. The water molecules in the crystal are organized into discrete clusters. A distinctive feature of the clusters is the frequent occurrence of three-membered rings. The protein molecules undergo substantial rearrangement during the transformation from the native to the low-humidity form. The main-chain conformations in the two forms are nearly the same, but differences exist in the side-chain conformation. The differences are particularly pronounced in relation to Trp 62 and Trp 63. The shift in Trp 62 is especially interesting as it is also known to move during inhibitor binding.

Una gramática descriptiva del chabacano de Ternate

This dissertation is a descriptive grammar of Ternate Chabacano, a Spanish-lexifier Creole spoken by 3.000 people in the town of Ternate, Philippines. The dissertation offers an analysis of the phonological, morphological, and syntactic system of the language. It includes an overview of the historical background, the current situation of the speech community and a collection of annotated texts. Ternate Chabacano shares many characteristics with its main adstrate language Tagalog as well as the dialectal varieties of Spanish. At present, English also exerts an influence, nevertheless mainly affecting its lexicon. The description offered is based on fieldwork conducted in Ternate. Spoken language collected through thematic interviews forms the main type of the material analysed. Information regarding the informants and text types is included in the examples. Ternate Chabacano has a five-vowel system and 17 consonant phonemes. The morphology of the language is largely isolating. Clitics are used extensively for expressing adverbial relations. The verbal system is based on the preverbal markers that express the category of tense, modality and aspect, among which aspect is the main dimension. Complex predicates and verbal chains are used in order to further distinguish aspect and modality, as well as changes of voice and valency. Intransitive verbs express motion, states, and reflexive actions, even though the majority of verbs can occur in both intransitive and transitive clauses. Ternate Chabacano is a nominative-accusative type language but the typological configuration of the Philippine languages influences the marking of its constituents. A case in point is constituted by the nominal determination system. The basic constituent order in a clause is VSO. Equative and attibutive clauses are formed by juxtaposition while the locative clauses feature a copula. Indefinite terms are expressed through existential constructions. The negation of existential clauses differs from standard negation but both are intensified in the same way. In spoken discourse, tag-questions are common. Pragmatic elements and social formulas reflect largely the corresponding Tagalog expressions. Coordination and subordination occur typically without overt markers but a variety of markers exists for expressing different relations, especially those made explicit by adverbial clauses. Verbal chains form a continuum from serial verbs to complementation and ultimately to coordination.

Harvesting undelimbed Scots pine (Pinus sylvestris L.) from first thinnings for integrated production of kraft pulp and energy

The present study evaluates the feasibility of undelimbed Scots pine (Pinus sylvestris L.) for integrated production of pulp and energy in a kraft pulp mill from the technical, economic and environmental points of view, focusing on the potential of bundle harvesting. The feasibility of tree sections for pulp production was tested by conducting an industrial wood-handling experiment, laboratory cooking and bleaching trials, using conventional small-diameter Scots pine pulpwood as a reference. These trials showed that undelimbed Scots pine sections can be processed in favourable conditions as a blend with conventional small-diameter pulpwood without reducing the pulp quality. However, fibre losses at various phases of the process may increase when using undelimbed material. In the economic evaluation, both pulp production and wood procurement costs were considered, using the relative wood paying capability of a kraft pulp mill as a determinant. The calculations were made for three Scots pine first-thinning stands with the breast-height diameter of the removal (6 12 cm) as the main distinctive factor. The supply chains included in the comparison were based on cut-to-length harvesting, whole-tree harvesting and bundle harvesting (whole-tree bundling). With the current ratio of pulp and energy prices, the wood paying capability declines with an increase in the proportion of the energy fraction of the raw material. The supply system based on the cut-to-length method was the most efficient option, resulting in the highest residual value at stump in most cases. A decline in the pulp price and an increase in the energy price improved the competitiveness of the whole-tree systems. With short truck transportation distances and low pulp prices, however, the harvesting of loose whole trees can result in higher residual value at stump in small-diameter stands. While savings in transportation costs did not compensate for the high cutting and compaction costs by the second prototype of the bundle harvester, an increase in transportation distances improved its competitiveness. Since harvesting undelimbed assortments increases nutrient export from the site, which can affect soil productivity, the whole-tree alternatives included in the present study cannot be recommended on infertile peatlands and mineral soils. The harvesting of loose whole trees or bundled whole trees implies a reduction in protective logging residues and an increase in site traffic or payloads. These factors increase the risk of soil damage, especially on peat soils with poor bearing capacity. Within the wood procurement parameters which were examined, the CO2 emissions of the supply systems varied from 13 27 kg m3. Compaction of whole trees into bundles reduced emissions from transportation by 30 39%, but these reductions were insufficient to compensate for the increased emissions from cutting and compaction.

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

Definitions and nomenclature of nucleic acid structure parameters

At an EMBO Workshop on DNA Curvature and Bending, held at Churchill College, Cambridge, on 10-15 September 1988, two sessions were scheduled on definitions of parameters used to describe the geometry of nucleic acid chains and helices, and a common nomenclature for these parameters. The most widely used library of helix analysis programs, HELIB (Fratini et al., 1982; Dickerson, 1985) suffers from the fact that the translations and rotations as defined are not fully independent and depend to a certain extent upon the choice of overall helix axis. Several research groups have been engaged independently in developing alternative programs for the geometrical analysis of polynucleotide chains, but with different definitions of quantities calculated and with widely different nomenclature even when the same parameter was involved.

Electronic excitations and alternation of conjugated polymers

The electronic excitations and fluorescence of conjugated polymers are related to large or small alternation ? of the transfer integrals t(1 ± ?) along the backbone. The fluorescence of polysilanes (PSs) and poly (para-phenylenevinylene (PPV) is linked to large ?, which places the one-photon gap Eg below the lowest two-photon gap Ea and reduces distortions due to electron-phonon (e-p) coupling. In contrast to small ? not, vert, similar 0.1 in ?-conjugated polymers, such as polyacetylene (PA), para-conjugated phenyls lead to an extended ?-system with increased alternation, to states localized on each ring and to charge-transfer excitations between them. Surprisingly good agreement is found between semiempirical parametric method 3 (PM3) bond lengths and exact Pariser-Parr-Pople (PPP) ?-bond orders for trans-stilbene, where the PPV bipolarons are confined to two phenyls. Stilbene spectra are consistent with increased alternation and small e-p distortions.

Lipid-amphotericin B complex structure in solution: A possible first step in the aggregation process in cell membranes

The interactions between the polyene antibiotic amphotericin B with dipalmitoylphosphatidylcholine were investigated in vesicles (using circular dichroism) and in chloroform solution (using circular dichroism and IH, I3C, and 31P nuclear magnetic resonance). The results show that amphotericin B readily aggregates in vesicles and that the extent of aggregation depends on the 1ipid:drug concentration ratio. Introduction of sterol molecules into the membrane hastens the process of aggregation of amphotericin B. In chloroform solutions amphotericin B strongly interacts with phospholipid molecules to form a stoichiometric complex. The results suggest that there are interactions between the conjugated heptene stretch of amphotericin B and the methylene groups of lipid acyl chains, while the sugar moiety interacts with the phosphate head group by the formation of a hydrogen bond. A model is proposed for the lipid-amphotericin B complex, in which amphotericin B interacts equally well with the two lipid acyl chains, forming a 1:l complex.

Novel photocrosslinkable liquid-crystalline polymers: poly[bis(benzylidene)] esters

A new class of photo-cross-linkable main-chain liquid crystalline polymers (PMCLCPs) containing bis(benzylidene)cycloallranone groups have been synthesized and studied for their liquid crystalline and photochemical properties. The bis(benzylidene)cycloalkanone group in the chain functions both as a mesogen and as a photoreactive center. All of the polymers exhibit a nematic mesophase. Two kinds of photoreactions, namely, photoisomerization and photo-cross-linking, operate in these polymers. Above Tu at the initial stages of irradiation, photoisomerization predominates the cross-linking, which resulta in the disruption of the chromophore aggregates. Below T8, because of the restricted mobility of the chains, only cross-linking takes place. Studies on the model compound, bis(benzylidene)cyclopentanone, confii the above observations and demonstrate further that the cross-linking proceeds by the 2r + 2r cycloaddition reaction of the bis(benzylidene)cycloallranone moieties. The cross-linking rate decreases with increase in the size of the cycloalkanone ring. Heating the solution cast polymer fii results in the ordered aggregation of the chromophores just above TI and also at the crystal to crystal transition temperature, which facilitates the phobcross-linking reactions. In the isotropic phase, the random orientation of the chromophores drastically curtails the cross-linking rata