Modular design of synthetic protein mimics. Crystal structure of two seven-residue helical peptide segments linked by .epsilon.-aminocaproic acid

Two seven-residue helical segments, Val-Ala-Leu-Aib-Val-Ala-Leu, were linked synthetically with an epsilon-aminocaproic acid (Acp) linker with the intention of making a stable antiparallel helix-helix motif. The crystal structure of the linked peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Acp-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe (1) shows the two helices displaced laterally from each other by the linker, but the linker has not folded the molecule into a close-packed antiparallel conformation. Two strong intermolecular NH...O = C hydrogen bonds are formed between the top of the lower helix of one molecule and the bottom of the upper helix in a laterally adjacent molecule to give the appearance of an extended single helix. The composite peptide with Boc and OMe end groups, C76H137N15O18.H2O, crystallize in space group P2(1) with a = 8.802 (1) angstrom, b = 20.409 (4) angstrom, c = 26.315 (3) angstrom, and beta = 90.72 (1)degrees; overall agreement R = 7.86% for 5030 observed reflections (\F(o)\ > 3-sigma(F)); resolution = 0.93 angstrom. Limited evidence for a more compact conformation in solution consistent with an antiparallel helix arrangement is obtained by comparison of the HPLC retention times and CD spectra of peptide 1 with well-characterized continuous helices of similar length and sequence.

Valittujen makrolidien ominaisuudet ja niiden vaikutukset fermentoinnin jälkeiseen jatkokäsittelyyn

Työn kirjallisessa osuudessa tarkasteltiin makrolideja yleisellä tasolla keskittyen kahden makrolidin ominaisuuksiin molekyylitasolla. Näiden tautomerisoitumista käsitellään tuoden esiin sekä yhdisteiden rakenteelliset yhteneväisyydet ja eroavaisuudet että niiden vaikutukset yhdisteiden vaikutusmekanismiin ja metaboliaan. Kirjallisessa osuudessa perehdyttiin myös makrolidien biosynteesiin ja tuotantoprosessiin keskittyen downstream-prosessointiin ja erityisesti biosynteesistä peräisin oleviin epäpuhtauksiin. Lisäksi kirjallisessa osuudessa käsiteltiin argentaatiokromatografian perusteita. Kokeellisessa osuudessa yhdelle makrolidille kehitettiin argentaatiokromatografiaan perustuva puhdistusmenetelmä. Perinteisillä kromatografisilla menetelmillä yhdistettä ei voida puhdistaa kaikista sen epäpuhtauksista. Makrolidin puhtaus argentaatiokromatografian jälkeen oli 98,6 %. Lisäksi kehitettiin uusi kiteytysmenetlmä, jossa yhdiste kiteytettiin anhydridina tavanomaisen monohydraattimuodon sijasta. Makrolidin analysointiin kehitettiin HPLC-menetelmä, joka validoitiin ICH:n ohjeiden mukaisesti. Yhditeen tautomeerimuodot ja siinä esiintyvät epäpuhtaudet tutkittiin käyttäen LC/MS-analyysia. Yhden epäpuhtauden rakenne varmistettiin eristämisen jälkeen NMR:n avulla. Saatavilla olevien tietojen mukaan yhdisteen tulkittuja NMRspektrejä ei ole julkaistu. Lisäksi aiemmin tuntematon epäpuhtaus identifioitiin perustuen retentioaikaan ja MS-analyysiin.

Prognostic importance of the tumour microenvironment in follicular lymphoma patients treated with immunochemotherapy

Follicular lymphoma (FL) is the second most common non-Hodgkin lymphoma. It is an indolent and clinically heterogeneous disease, which is generally considered incurable. Currently, immunochemotherapy has significantly improved the outcome of FL patients. This is based on the combination of rituximab, a monoclonal anti-CD20 antibody, with chemotherapy, and is used at present as a standard first-line therapy in FL. Thus far, however, patients have been selected for treatment based on clinical risk factors and indices that were developed before the rituximab era. Therefore, there is a growing need to understand the molecular mechanisms underlying the disease, which would not only provide information to predict survival in the rituximab era, but also enable the design of more targeted therapeutic strategies. In this study, our aim was to identify genes predicting the outcome in FL patients treated with immunochemotherapy. Thus, we performed a cDNA microarray with 24 FL patients. When gene expression differences from diagnostic tumour samples were related to the clinical outcome, we identified novel genes with a prognostic impact on survival. The expression of selected genes was further characterized with quantitative PCR and immunohistochemistry (IHC). Interestingly, the prognostic influence of these genes was often associated with their expression in non-malignant cells instead of tumour cells. Based on the observed gene expression patterns, we analyzed the abundance and prognostic value of non-malignant immune cells in 95-98 FL patients treated with immunochemotherapy. We observed that a high content of tumour-associated macrophages was a marker of a favourable prognosis. In contrast, the accumulation of mast cells correlated with a poor outcome and was further associated with tumour vascularity. Increased microvessel density also correlated with an inferior outcome. In addition, we used the same microarray data with a systems biology approach to identify signalling pathways or groups of genes capable of separating patients with favourable or adverse outcomes. Among the transcripts, there were many genes associated with signal transducers and activators of the transcription (STAT5a) pathway. When IHC was used as validation, STAT5a expression was mostly observed in T-cells and follicular dendritic cells, and expression was found to predict a favourable outcome. In cell cultures, rituximab was observed to induce the expression of STAT5a-associated interleukins in human lymphoma cell lines, which might provide a possible link for the cross-talk between rituximab-induced FL cells and their microenvironment. In conclusion, we have demonstrated that the microenvironment has a prognostic role in FL patients treated with immunochemotherapy. The results also address the importance of re-evaluating the prognostic markers in the rituximab era of lymphoma therapies.

Chromatographic separation, fractionation and oxidation of selected beta-lactoglobulin peptides

The literature review elucidates the mechanism of oxidation in proteins and amino acids and gives an overview of the detection and analysis of protein oxidation products as well as information about ?-lactoglobulin and studies carried out on modifications of this protein under certain conditions. The experimental research included the fractionation of the tryptic peptides of ?-lactoglobulin using preparative-HPLC-MS and monitoring the oxidation process of these peptides via reverse phase-HPLC-UV. Peptides chosen to be oxidized were selected with respect to their amino acid content which were susceptible to oxidation and fractionated according to their m/z values. These peptides were: IPAVFK (m/z 674), ALPMHIR (m/z 838), LIVTQTMK (m/z 934) and VLVLDTDYK (m/z 1066). Even though it was not possible to solely isolate the target peptides due to co-elution of various fractions, the percentages of target peptides in the samples were satisfactory to carry out the oxidation procedure. IPAVFK and VLVLDTDYK fractions were found to yield the oxidation products reviewed in literature, however, unoxidized peptides were still present in high amounts after 21 days of oxidation. The UV data at 260 and 280 nm enabled to monitor both the main peptides and the oxidation products due to the absorbance of aromatic side-chains these peptides possess. ALPMHIR and LIVTQTMK fractions were oxidatively consumed rapidly and oxidation products of these peptides were observed even on day 0. High rates of depletion of these peptides were acredited to the presence of His (H) and sulfur-containing side-chains of Met (M). In conclusion, selected peptides hold the potential to be utilized as marker peptides in ?-lactoglobulin oxidation.

Crystal And Molecular-Structure Of 8-Acetoxy-6-(2,4-Dimethoxy-5-Bromophenyl)-3-Methyl-Tricyclo[5,2,1,03,8 ]Decan-2-One

The crystal and molecular structure has been determined by the heavy-atom method and refined by the least-squares procedure to R= 8"3 % for 2033 photographically observed reflexions. The compound crystallizes in the space group P]" with two molecules in a unit cell of dimensions a = 11"68 + 0-02, b = 12"91 +0"02, c= 10"43+0"02/~, e= 114"7+ 1, fl=90-2+ 1 and 7,= 118.3+ 1 °. The unit cell also contains one molecule of the solvent, benzene. The 'cage' part of the molecule exhibits a large number of elongated bonds and strained internal valency angles. The bridgehead angle in the bicyclic heptane ring system is 89 °. The acetate group at C(16) and the methyl group at C(15) are cis to each other.

Crystal And Molecular Structure Of A Dimethyl Sulphoxide Complex With Lanthanum Nitrate, La(No3)34.(Ch3)2so

The crystal structure of the complex La(NO3)3.4(CH3)2SO has been solved by the heavy-atom method. The complex crystallizes in the monoclinic space group C2/e with four formula units in a unit cell of dimensions a= 14.94, b= 11.04, c= 15.54 A and fl= 109 ° 10'. The parameters have been refined by threedimensional least-squares procedures with anisotropic thermal parameters for all atoms except hydrogen. The final R index for 1257 observed reflexions is 0.094. The La 3 + ion is coordinated by ten oxygen atoms with La-O distances varying from 2.47 to 2.71 A. The geometry of the coordination polyhedron is described.

Molecular Caches: A caching structure for dynamic creation of application-specific Heterogeneous cache regions

CMPs enable simultaneous execution of multiple applications on the same platforms that share cache resources. Diversity in the cache access patterns of these simultaneously executing applications can potentially trigger inter-application interference, leading to cache pollution. Whereas a large cache can ameliorate this problem, the issues of larger power consumption with increasing cache size, amplified at sub-100nm technologies, makes this solution prohibitive. In this paper in order to address the issues relating to power-aware performance of caches, we propose a caching structure that addresses the following: 1. Definition of application-specific cache partitions as an aggregation of caching units (molecules). The parameters of each molecule namely size, associativity and line size are chosen so that the power consumed by it and access time are optimal for the given technology. 2. Application-Specific resizing of cache partitions with variable and adaptive associativity per cache line, way size and variable line size. 3. A replacement policy that is transparent to the partition in terms of size, heterogeneity in associativity and line size. Through simulation studies we establish the superiority of molecular cache (caches built as aggregations of molecules) that offers a 29% power advantage over that of an equivalently performing traditional cache.

Glowworm-inspired robot swarm for simultaneous taxis towards multiple radiation sources

This paper presents a glowworm metaphor based distributed algorithm that enables a collection of minimalist mobile robots to split into subgroups, exhibit simultaneous taxis-behavior towards, and rendezvous at multiple radiation sources such as nuclear/hazardous chemical spills and fire-origins in a fire calamity. The algorithm is based on a glowworm swarm optimization (GSO) technique that finds multiple optima of multimodal functions. The algorithm is in the same spirit as the ant-colony optimization (ACO) algorithms, but with several significant differences. The agents in the glowworm algorithm carry a luminescence quantity called luciferin along with them. Agents are thought of as glowworms that emit a light whose intensity is proportional to the associated luciferin. The key feature that is responsible for the working of the algorithm is the use of an adaptive local-decision domain, which we use effectively to detect the multiple source locations of interest. The glowworms have a finite sensor range which defines a hard limit on the local-decision domain used to compute their movements. Extensive simulations validate the feasibility of applying the glowworm algorithm to the problem of multiple source localization. We build four wheeled robots called glowworms to conduct our experiments. We use a preliminary experiment to demonstrate the basic behavioral primitives that enable each glowworm to exhibit taxis behavior towards source locations and later demonstrate a sound localization task using a set of four glowworms.

Bicyclic Phosphazenes Derived from (Amino) Cyclotetraphosphazenes

Amination reactions of 2,6-bis(primary amino)cyclotetraphosphazenes yield not only the expected (amino)cyclotetraphosphazenes but also novel trans-annular bridged bicyclic phosphazenes by an intramolecular substitution pathway. In addition, resins are formed in some reactions by an intermolecular condensation. The effect of substituents attached to the phosphazene ring, the attacking nucleophile and solvent on the formation of the trans-annular P-N-P bridge is considered in detail in relation to plausible reaction mechanisms. Analytical separation of bicyclic phosphazenes by high performance liquid chromatography (HPLC) on a reverse phase silica column is demonstrated. Structural features of bicyclic phosphazenes and salient aspects of their NVR spectroscopic data are discussed.

Structure of columbin, a diterpenoid furanolactone from Tinospora cordifolia Miers

(1S,4R,5R,8S, IOR,12S)-4-Hydroxy-15,16-epoxycleroda-2,13 (16), 14-trieno- 17,12:18,1-biscarbolactone,C20H2206, Mr = 358.2, m.p. = 453-454 K,orthorhombic, P212121, a = 7.3869 (6), b = 11.986 (1),c=19.896(2) A, V=1761.65A 3, Z=4, D x=1.351, Din(by flotation)= 1.349gem -3, 2(CuKa)=1.5418 A, /l = 8.36 cm -1, F(000) = 760, T= 295 K,R = 0.0432 for 1662 observed reflections. Two terpenerings, two ~-lactones, two methyl groups, a tertiary hydroxyl group and a fl-substituted furan ring are present in the structure. The H atoms at C(12) and C(8) are a- and fl-oriented. The terpene ring A is locked into a boat conformation by the C(1)-C(4) lactone bridge. The furan ring is attached equatoriaUy at atom C(12). The hydroxyl group is involved in intramolecular hydrogen bonding.

Improved synthesis of carbon nanotubes with junctions and of single-walled carbon nanotubes

Pyrolysis of thiophene over nickel nanoparticles dispersed on silica is shown to yield Y-junction carbon nanotubes with smaller diameters than those obtained by the pyrolysis of organometallic-thiophene mixtures. In the presence of water vapour, the pyrolysis of organometallic-hydrocarbon mixtures yields single-walled nanotubes, as well as relatively narrow-diameter carbon nanotubes with Y-junctions. Pyrolysis-of organometallic-hydrocarbon mixtures, in the absence of water vapour, only gives nanotubes with T- and Y-junctions.

Novel Approaches to the Sampling of Atmospheric Aerosols and Determination of Chemical Composition

The Earth s climate is a highly dynamic and complex system in which atmospheric aerosols have been increasingly recognized to play a key role. Aerosol particles affect the climate through a multitude of processes, directly by absorbing and reflecting radiation and indirectly by changing the properties of clouds. Because of the complexity, quantification of the effects of aerosols continues to be a highly uncertain science. Better understanding of the effects of aerosols requires more information on aerosol chemistry. Before the determination of aerosol chemical composition by the various available analytical techniques, aerosol particles must be reliably sampled and prepared. Indeed, sampling is one of the most challenging steps in aerosol studies, since all available sampling techniques harbor drawbacks. In this study, novel methodologies were developed for sampling and determination of the chemical composition of atmospheric aerosols. In the particle-into-liquid sampler (PILS), aerosol particles grow in saturated water vapor with further impaction and dissolution in liquid water. Once in water, the aerosol sample can then be transported and analyzed by various off-line or on-line techniques. In this study, PILS was modified and the sampling procedure was optimized to obtain less altered aerosol samples with good time resolution. A combination of denuders with different coatings was tested to adsorb gas phase compounds before PILS. Mixtures of water with alcohols were introduced to increase the solubility of aerosols. Minimum sampling time required was determined by collecting samples off-line every hour and proceeding with liquid-liquid extraction (LLE) and analysis by gas chromatography-mass spectrometry (GC-MS). The laboriousness of LLE followed by GC-MS analysis next prompted an evaluation of solid-phase extraction (SPE) for the extraction of aldehydes and acids in aerosol samples. These two compound groups are thought to be key for aerosol growth. Octadecylsilica, hydrophilic-lipophilic balance (HLB), and mixed phase anion exchange (MAX) were tested as extraction materials. MAX proved to be efficient for acids, but no tested material offered sufficient adsorption for aldehydes. Thus, PILS samples were extracted only with MAX to guarantee good results for organic acids determined by liquid chromatography-mass spectrometry (HPLC-MS). On-line coupling of SPE with HPLC-MS is relatively easy, and here on-line coupling of PILS with HPLC-MS through the SPE trap produced some interesting data on relevant acids in atmospheric aerosol samples. A completely different approach to aerosol sampling, namely, differential mobility analyzer (DMA)-assisted filter sampling, was employed in this study to provide information about the size dependent chemical composition of aerosols and understanding of the processes driving aerosol growth from nano-size clusters to climatically relevant particles (>40 nm). The DMA was set to sample particles with diameters of 50, 40, and 30 nm and aerosols were collected on teflon or quartz fiber filters. To clarify the gas-phase contribution, zero gas-phase samples were collected by switching off the DMA every other 15 minutes. Gas-phase compounds were adsorbed equally well on both types of filter, and were found to contribute significantly to the total compound mass. Gas-phase adsorption is especially significant during the collection of nanometer-size aerosols and needs always to be taken into account. Other aims of this study were to determine the oxidation products of β-caryophyllene (the major sesquiterpene in boreal forest) in aerosol particles. Since reference compounds are needed for verification of the accuracy of analytical measurements, three oxidation products of β-caryophyllene were synthesized: β-caryophyllene aldehyde, β-nocaryophyllene aldehyde, and β-caryophyllinic acid. All three were identified for the first time in ambient aerosol samples, at relatively high concentrations, and their contribution to the aerosol mass (and probably growth) was concluded to be significant. Methodological and instrumental developments presented in this work enable fuller understanding of the processes behind biogenic aerosol formation and provide new tools for more precise determination of biosphere-atmosphere interactions.

cis-trans Enantiomerism in the Diels-Alder cycloadducts of 6-arylfulvenes with maleic anhydride: resolution of the exo adducts via the N-((1S)-1-(naphth-1-yl)ethyl)imide derivatives: assignment of the absolute configurations based on the crystal structure of an imide diastereomer

A new case of the uncommon cis-trans enantiomerism is presented. The titled anhydride adducts were prepared in good yields by the known reaction of three 6-arylfulvenes with maleic anhydride (aryl = phenyl, p-tolyl and p-anisyl). The exo adducts were converted to the corresponding imides by reaction with (1S)-1-(naphth-1-yl)ethylamine in similar to 80% yields, and the resulting diastereomeric imides separated by silica gel column chromatography. They were hydrolysed and recyclised to the chiral anhydrides, in `one-pot' with 10% NaOH-EtOH, followed by treatment with 2 M HCl, in similar to 40% yields. The titled anhydrides were thus obtained in homochiral form, in enantiomeric purities (generally) of similar to 90% as indicated by chiral HPLC. The chiral anhydrides were also converted to the corresponding imides (presumably stereospecifically), by treatment with ammonia solution in excellent yields. The crystal structure of one of the above diastereomeric imides (derived from 6-phenylfulvene) was determined, and based on the known (S)-configuration of the naphthylethylamine moiety, the `configurations' of the original anhydride adducts were assigned. (c) 2005 Elsevier Ltd. All rights reserved.

Structure of 1,2,4-oxadiazolidine-3,5-dione monohydrate

C2H2N203.H20, Mr= 120.07, monoclinic,P21/c, a= 5.011 (1), b= 11.796(2), c= 7.689 (2)A,fl= 95.22 (2) ° , V= 452.61 A 3, Z= 4, Dx= 1.76, D m = 1.75 gcm -3, /].(Cu Ks) = 1.5418 A, g = 14-0 cm -l,F(000) = 248, T = 293 K, crystal quality was poor and the final R =0.107, wR =0.090 for 881 observed reflections. The compound is derived from a novel form of the monopropellant oxalohydroxamic acid. The two exocyclic C-O bond lengths of 1.240 (3) and 1.228 (4)A indicate double bonds. The C-N bond lengths of 1.334 (4), 1.390 (4) and 1.359 (4) A are characteristic of the amide bond. The N atom covalently bonded to the two carbonyl C atoms acts as a proton donor in an intermolecular hydrogen bond to the ring O atom: N1...O3i = 2.854 ]k (i =x-- 1,y, z), H...O = 2.15 A, N-H...O = 159 °.

Structure of 6-acetoxycoumarin: topochemical photodimerization and analysis of acetoxy...acetoxy interactions in the solid state

C~HaO 4, Mr=204.2, monoclinic, P2Jn,a=3.900(1), =37.530(6), c=6.460(1)A, fl=103.7 (1) °, V= 918.5 (5) A 3, Z = 4, D m = 1.443, D x --- 1.476 Mg m -3, Cu Ks, 2 = 1.5418 ,/k, /t = 0.86 mm -~, F(000) = 424, T= 293 K, R = 0.075 for 1019 significant reflections. Molecules pack in fl-type stacking mode which is characterized by the close packing of parallel and nearly planar reactive double bonds with a separation of 3.900/~ along the a axis.The syn head-head dimer obtained is the direct consequence of this packing arrangement. Molecular packing is stabilized by intermolecular C-H...O hydrogen bonding. Analysis of acetoxy...acetoxy interactions in the acetoxy compounds retrieved from the Cambridge Structural Database reveal that the majority of them are anti-dipolar.