Methyl Branches Research Articles

Isoprenoid-chained lipid β-XylOC 16+4—A novel molecule for in meso membrane protein crystallization

Here we report a successful use of a recently developed isoprenoid-chained lipid family for in meso crystallization of membrane proteins. The isoprenoid-chained lipid 1-O-(3,7,11,15-tetramethylhexadecyl)-β– d-xyloside (β-XylOC 16+4) used as a host lipid for in meso crystallization provided high quality bacteriorhodopsin (bR) crystals (P6 3 space group) diffracting to high resolution and characterized by low twinning ratio. β-XylOC 16+4 has an isoprenoid chain with methyl branches at each 4th position and a xylose group in the water-soluble part. These peculiarities make the lipid clearly distinguishable in the bR crystalline lattice and provides a unique opportunity to study the role of the host lipid in the in meso crystallization. We conclude that β-XylOC 16+4 may have a general application for in meso crystallization for a wide range of membrane proteins. The cubic phase of β-XylOC 16+4 is present over a wide range of temperatures and is stable at low temperature (down to about 8 °C). This opens up the possibility of using temperature as a tool for the optimization of in meso crystallization with additional advantages for the crystallization of membrane proteins at lower temperatures where the proteins of interest may be more stable.

Lipid chain branching at the iso- and anteiso-positions in complex chlamydia membranes: A molecular dynamics study

Membranes in the intracellular eubacterial parasite Chlamydia trachomatis consist of the elementary body (EB) and reticular body (RB), and contain methyl branches at the iso- and anteiso-positions for some phospholipid chains. Acyl chain branching is the focus of this study. Molecular dynamics simulations were used to study bilayers of 1-13-methylpentadecanoyl-2-palmitoyl-phosphatidylcholine (13-MpPPC), 1-14-methylpentadecanoyl-2-palmitoyl-phosphatidylcholine (14-MpPPC), and diphytanoylphosphatidylcholine (DPhPC). These three membranes were simulated at 323K and simulations of DPhPC at 298K were also performed for better comparison to existing experimental data. Two simulations of representative EB and RB membranes of C. trachomatis composed of nine different lipid components were performed at 310.15K, to accurately reflect compositions determined by experiment and physiological conditions. Based on nearly 0.5μs of simulation data, we report that branching increases average lipid surface area, area elastic moduli, and lipid axial relaxation times, while decreasing lipid chain order. Branching also has a distinct effect on electron density profiles. Due to their high cholesterol concentrations, the EB and RB membranes were found to have relatively high area elastic moduli, which may have important biological implications.

Structural and Kinetic Analysis of Free Methionine-R-sulfoxide Reductase from Staphylococcus aureus: CONFORMATIONAL CHANGES DURING CATALYSIS AND IMPLICATIONS FOR THE CATALYTIC AND INHIBITORY MECHANISMS

Free methionine-R-sulfoxide reductase (fRMsr) reduces free methionine R-sulfoxide back to methionine, but its catalytic mechanism is poorly understood. Here, we have determined the crystal structures of the reduced, substrate-bound, and oxidized forms of fRMsr from Staphylococcus aureus. Our structural and biochemical analyses suggest the catalytic mechanism of fRMsr in which Cys(102) functions as the catalytic residue and Cys(68) as the resolving Cys that forms a disulfide bond with Cys(102). Cys(78), previously thought to be a catalytic Cys, is a non-essential residue for catalytic function. Additionally, our structures provide insights into the enzyme-substrate interaction and the role of active site residues in substrate binding. Structural comparison reveals that conformational changes occur in the active site during catalysis, particularly in the loop of residues 97-106 containing the catalytic Cys(102). We have also crystallized a complex between fRMsr and isopropyl alcohol, which acts as a competitive inhibitor for the enzyme. This isopropyl alcohol-bound structure helps us to understand the inhibitory mechanism of fRMsr. Our structural and enzymatic analyses suggest that a branched methyl group in alcohol seems important for competitive inhibition of the fRMsr due to its ability to bind to the active site.

Positions and Stereochemistry of Methyl Branches in the Novel Sex Pheromone Components Produced by a Lichen Moth, Lyclene dharma dharma

Female moths of Lyclene dharma dharma (Arctiidae, Lithosiinae) produce three sex pheromone components (I-III), for which we assigned the following novel chemical structures; 6-methyl-2-octadecanone (1) for I, 14-methyl-2-octadecanone (2) for II, and 6,14-dimethyl-2-octadecanone (3) for III. In the Iriomote Islands where the insects were collected, a lure including racemic 1 and 2 attracted the male moths without mixing 3. In this study for further confirmation of the plane structures, the positional isomers with a methyl branch at the 4-, 5-, 7-, 13-, or 15-position (4-8, respectively) were synthesized. The GC-MS analyses revealed that natural components I and II were best fitted with those of 1 and 2, respectively, among the methyl-2-octadecanones examined, indicating the usefulness of this analytical instrument and authentic standards for the determination of the positions of methyl branches. In field trapping tests, 4-8 could not substitute for 1 or 2, nor did these compounds inhibit the active binary lure of 1 and 2, indicating that the males strictly recognized the 2-ketones with a methyl branch at the 6- or 14-positions. Next, the absolute configurations of I and II were determined by HPLC with a normal-phased chiral column (Chiralpak AD-H), which could separate the enantiomers of both 1 and 2. The chiral HPLC analysis of a crude pheromone extract indicated that the females exclusively produced (S)-1 and (S)-2. Furthermore, a field evaluation of each enantiomer revealed that (S)-1 and (S)-2 were bioactive but (R)-1 and (R)-2 were not.

Molecular volumes of phospholipids and glycolipids in membranes

Data on the molecular volumes of phospholipids and glycolipids in membranes are collected together in order to determine the contributions from the component groups, for as wide a range of lipids as possible, including sphingolipids. Wherever possible, the volumes of the methylene groups in the lipid chains are established from the dependence on chain length at fixed temperature in a given phase. In this way, it is also possible to determine the constant contribution from cis double bonds in the chains of monoenoic unsaturated phosphatidylcholines, and the volume of the branched methyl groups in isoacyl phosphatidylcholines. Issues concerning separation of contributions from the polar head groups from those of the chain terminal methyl groups are discussed. Molecular volumes of lipids in crystals are also analysed to provide information on head-group packing that can be compared with the situation in membranes, and used to set limits on the relative contributions from polar groups and terminal methyl groups. Comparisons are made with volumetric analyses based on diffraction studies of bilayers of single lipids. The parameters derived can be used to estimate molecular volumes of lipids for which dilatometric or densitometric data are lacking. Lipid volumes are determining parameters for lipid dynamics, membrane partitioning and permeation of solutes, and are essential quantities for the structural analysis of lipid membranes.

Deciphering the Chemical Basis of Nestmate Recognition

Social insects maintain colony cohesion by recognizing and, if necessary, discriminating against conspecifics that are not part of the colony. This recognition ability is encoded by a complex mixture of cuticular hydrocarbons (CHCs), although it is largely unclear how social insects interpret such a multifaceted signal. CHC profiles often contain several series of homologous hydrocarbons, possessing the same methyl branch position but differing in chain length (e.g., 15-methyl-pentatriacontane, 15-methyl-heptatriacontane, 15-methyl-nonatriacontane). Recent studies have revealed that within species these homologs can occur in correlated concentrations. In such cases, single compounds may convey the same information as the homologs. In this study, we used behavioral bioassays to explore how social insects perceive and interpret different hydrocarbons. We tested the aggressive response of Argentine ants, Linepithema humile, toward nest-mate CHC profiles that were augmented with one of eight synthetic hydrocarbons that differed in branch position, chain length, or both. We found that Argentine ants showed similar levels of aggression toward nest-mate CHC profiles augmented with compounds that had the same branch position but differed in chain length. Conversely, Argentine ants displayed different levels of aggression toward nest-mate CHC profiles augmented with compounds that had different branch positions but the same chain length. While this was true in almost all cases, one CHC we tested elicited a greater aggressive response than its homologs. Interestingly, this was the only compound that did not occur naturally in correlated concentrations with its homologs in CHC profiles. Combined, these data suggest that CHCs of a homologous series elicit the same aggressive response because they convey the same information, rather than Argentine ants being unable to discriminate between different homologs. This study contributes to our understanding of the chemical basis of nestmate recognition by showing that, similar to spoken language, the chemical language of social insects contains “synonyms,” chemicals that differ in structure, but not meaning.

Dependence of volume expansion on alkyl chain length and the existence of branched methyl group of CO 2-expanded ketone systems at 40 °C

We measured the density and liquid-phase CO 2 mole fraction of CO 2-expanded ketones (acetone, methyl ethyl ketone, methyl propyl ketone, methyl butyl ketone, methyl i-propyl ketone, and t-methyl butyl ketone) at 40 °C and evaluated the expansion coefficient on the basis of the experimental results. Volume expansion was slow in the region of a low carbon dioxide mole fraction (<0.7) but rapid in the region of a high carbon dioxide mole fraction (>0.7). The dependence of the expansion coefficient on the carbon dioxide mole fraction could be attributed to the number of molecules in a certain volume. These phenomena were inferred from the partial molar volume estimated using the Peng–Robinson equation of state (PR-EOS).

Caste-specific tyramides from Myrmicine ants.

Analysis of the extracts of male ants of Monomorium minimum and Monomorium ebeninum by GC-MS and GC-FTIR revealed the presence of tyramides 2 and 4c, for which the structures were established by comparison with synthetic samples. These compounds and their analogues 1 and 3 were also found in males of other Monomorium species, males of Myrmicaria opaciventris, and males of several Solenopsis (Diplorhoptrum) species. Vapor-phase FTIR spectra revealed critically important structural clues to two of the tyramides, which had methyl branching in the tyramide acyl moiety. Tyramide 4c exhibited a strong intramolecular amide NH hydrogen bond where an alpha-keto group was deduced to be present in the acyl moiety and also showed the overlap of this ketone group frequency with that of the amide nu(C horizontal lineO). The biological function of these compounds is uncertain; however, their role in ant-mating behavior may be suggested by a large body of evidence.

Selective dimerisation of α-olefins using tungsten-based initiators

The selective dimerisation of the alpha-olefins 1-pentene through to 1-nonene is reported using an in situ-generated catalyst derived from tungsten hexachloride, aniline, triethylamine and alkylaluminium halide. The influence of reagent identity and reaction stoichiometry, along with activator, solvent and alpha-olefin substrate choice are probed. The catalyst is found to be highly selective towards dimerisation, minimising the formation of undesired heavier oligomers. Notably, the selectivity within the dimer fraction is found to favour the formation of products with methyl branches. The selectivity towards individual olefin isomers has been determined and the system is found to also produce trace levels of dienes and alkanes. A kinetic study of the system reveals a second order dependence on substrate. Comparison of the products observed, with those expected for metallacyclic and Cossee-type mechanisms, suggests that the latter is in operation, something confirmed by the results of a C(2)H(4)/C(2)D(4) co-dimerisation experiment which showed full isotopic scrambling in the products. Thus a mechanistic proposal is made to account for the observed behaviour of the system, including the diene and alkane formation.

Study on primary metabolites and possible biodegradation pathways of nonylphenol

In this paper, the primary metabolites and possible biodegradation pathways of nonylphenol (NP) were analysed by two experimental methods and the interpretation of GC-MS results. One was that activated sludge degraded blank and spiking simulating wastewater for NP. Another was that a dominant bacteria group metabolised the medium contained NP as the only organic carbon source. The results show that the NP primary metabolites are a series of short-chain alkyl phenols with butyl, amyl or hexyls and benzene acetic acid. One of the biodegradation pathways for NP is that the long branches are first degraded into short methyl branches.

Candida albicans sphingolipid C9-methyltransferase is involved in hyphal elongation

C9-methylated glucosylceramide is a fungus-specific sphingolipid. This lipid is a major membrane component in the cell and is thought to play important roles in the growth and virulence of several fungal species. To investigate the importance of the methyl branch of the long-chain base in glucosylceramides in pathogenic fungi, we identified and characterized a sphingolipid C9-methyltransferase gene (MTS1, C9-MethylTransferase for Sphingolipid 1) in the pathogenic yeast Candida albicans. The mts1 disruptant lacked (E,E)-9-methylsphinga-4,8-dienine in its glucosylceramides and contained (E)-sphing-4-enine and (E,E)-sphinga-4,8-dienine. Reintroducing the MTS1 gene into the mts1 disruptant restored the synthesis of (E,E)-9-methylsphinga-4,8-dienine in the glucosylceramides. We also created a disruptant of the HSX11 gene, encoding glucosylceramide synthase, which catalyses the final step of glucosylceramide synthesis, in C. albicans and compared this mutant with the mts1 disruptant. The C. albicans mts1 and hsx11 disruptants both had a decreased hyphal growth rate compared to the wild-type strain. The hsx11 disruptant showed increased susceptibility to SDS and fluconazole, similar to a previously reported sld1 disruptant that contained only (E)-sphing-4-enine in its glucosylceramides, suggesting that these strains have defects in their cell membrane structures. In contrast, the mts1 disruptant grew similarly to wild-type in medium containing SDS or fluconazole. These results suggest that the C9-methyl group of a long-chain base in glucosylceramides plays an important role in the hyphal elongation of C. albicans independent of lipid membrane disruption.

Structural and thermodynamic determinants of chain-melting transition temperatures for phospholipid and glycolipids membranes

For optimum function, biological membranes need a fluid environment, which is afforded by the liquid-disordered phase of lipids with low chain-melting temperatures or the liquid-ordered phase that is formed by combining high chain-melting lipids with cholesterol. The dependence of chain-melting transition temperature on lipid chain structure is therefore of central importance. The currently available database, including sphingolipids and glycolipids, is summarised here by parameterising systematic dependences on molecular structure in terms of suitable thermodynamic models. Chain-length dependence, chain asymmetry of lipids forming partially interdigitated and mixed interdigitated gel phases, chain unsaturation, positional dependence of methyl branching, headgroup-attached and α-branched chains, and length of zwitterionic headgroups are all covered. This type of information is essential for biophysical approaches to functional lipidomics.

Aminosilylene-bridged ansa-zirconocenes for branched polyethylenes with bimodal molecular weight distributions

Reactions of the dilithium salt of aminosilylene-bridged ligands with (Me 2N) 2ZrCl 2(THF) 2 followed by the treatment of Me 3SiCl are found to be an efficient synthetic route to aminosilylene-bridged ansa-zirconocenes, R 2N(Me)Si(η 5–C 5H 4) 2ZrCl 2 (R = Me ( 1), Et ( 2)) and Me 2N(Me)Si(η 5–C 5H 4)(η 5–C 5Me 4)ZrCl 2 ( 3). Crystal structure of 3 determined by X-ray diffraction study reveals the presence of π-bonding interaction between N and Si atoms, which is further supported by DFT calculation results. These complexes are very active (>1 × 10 3 Kg/(mol Cat.·atm·h)) for homopolymerization of ethylene in the presence of methylalumoxane (MAO) cocatalyst, generating polyethylenes that contain branches as well as bimodal molecular weight distribution (MWD). Methyl, ethyl, butyl, and other longer branches ( n ≥ 6) are observed in the resulting polyethylenes. The polyethylenes from 1, 2 and 3/MAO show a broad MWD range (6.3–42.2, 3.5–4.0 and 2.6–3.4, respectively).

Analysis of Two Additional Signaling Molecules in Streptomyces coelicolor and the Development of a Butyrolactone-Specific Reporter System

gamma-Butyrolactone bacterial hormones regulate antibiotic production and morphological differentiation in Streptomyces species. One gamma-butyrolactone, SCB1, has been previously characterized in Streptomyces coelicolor. Here we report the characterization of two additional gamma-butyrolactones, named SCB2 (2-[1'-hydroxyoctyl]-3-hydroxymethylbutanolide) and SCB3 (2-[1'-hydroxy-6'-methyloctyl]-3-hydroxymethylbutanolide), possessing an antibiotic stimulatory activity. To elucidate the specificity determinants of these ligands for the receptor protein, ScbR, 30 chemically synthesized gamma-butyrolactone analogs were tested by utilizing the release of ScbR from DNA upon binding to a gamma-butyrolactone, which can be detected by kanamycin resistance. The butyrolactone detection method developed here revealed that ScbR shows preference toward a ligand possessing a 7-10 carbon C-2 side chain, a C-1'-beta-hydroxyl group, and a C-6'-methyl branch that coincides with SCB3. Moreover, this method was successfully used to screen for potential gamma-butyrolactone producers from commercial-antibiotic-producing Streptomyces.

Double Bond Migration to Methylidene Positions During Electron Ionization Mass Spectrometry of Branched Monounsaturated Fatty Acid Derivatives

Electron ionization mass spectra of several monounsaturated methyl-branched fatty acid methyl and trimethylsilyl esters were examined. These spectra exhibited some intensive fragment ions, whose formation could be explained after double-bond migration to methylidene position. This preferential migration (substantiated by deuterium labeling) acts significantly in the case of monounsaturated fatty acid methyl and trimethylsilyl esters possessing a methyl branch localized between the penultimate and the C(4) positions (relative to the ester group), whatever the position of the double-bond. Allylic cleavage and gamma-hydrogen rearrangement of the ionized methylidene group thus formed afforded very interesting fragment ions, which could be particularly useful to determine branching positions of monounsaturated methyl-branched fatty acid methyl and trimethylsilyl esters without additional treatment.

New Structural Variants of Homoserine Lactones in Bacteria

N-Acylhomoserine lactones (AHLs) are used by a wide variety of bacteria for cell-cell communication in "quorum-sensing". These compounds are derived from L-homoserine lactone and a fatty acid, which varies in chain-length, degree of saturation, and the presence or absence of an oxygen atom at C-3. In this study we describe for the first time the occurrence of acyl chains carrying a methyl branch, and present a GC-MS-based method that can be used to distinguish these compounds from unbranched isomers. The bacterium Aeromonas culicicola produces several methyl branched AHLs. In Jannaschia helgolandensis--a marine bacterium of the Roseobacter clade--a doubly unsaturated AHL, (2E,9Z)-N-(2,9-hexadecadienoyl)-L-homoserine lactone, occurs. The location and configuration of the double bonds was proven by spectrometric investigation and synthesis. Finally, a method was developed to establish the absolute configuration of 3-hydroxyalkanoyl-HSLs by mild cleavage and chiral gas chromatography. The AHLs synthesized during this study were tested in sensor systems specific for certain AHL types. The results show that these compounds display varying responses to the respective sensors; this underlines the importance of determining the whole bouquet of AHLs and its function to fully understand their importance for regulatory functions in bacteria.

Doubly carbon-branched pentoses: synthesis of both enantiomers of 2,4-di- C-methyl arabinose and 2-deoxy-2,4-di- C-methyl arabinose using only acetonide protection

An acetonide is the only protecting group used in the synthesis of both the enantiomers of 2,4-di- C-methyl arabinose and 2-deoxy-2,4-di- C-methyl arabinose via the enantiomeric 3- C-methyl- l-erythronolactone [from 2- C-methyl- d-ribono-lactone or d-ribose] and 3- C-methyl- d-erythronolactone [from d-tagatose or l-ribose]. NMR studies on unprotected C-methyl arabinoses show that methyl branching significantly affects the ratios of pyranose and furanose forms present in aqueous solution.

A critical approach to viscosity index

The viscosity index ( VI) is a useful tool for lubricant users and refiners, since it is a measure of the effect of temperature changes on the viscosity of the oil. However, it was found that the viscosity index does not correlate with the flow activation energy E a , which is the theoretically defined dependence of the viscosity on temperature. In this way, two oils may have the same flow activation energy but a viscosity index varying by up to 120. We therefore believe that the VI does not always give a proper representation of the effect of temperature on the kinematic viscosity. 13C NMR spectroscopy was used to identify the molecules with a high VI. Twenty different oil samples produced from eight different vacuum gas oils with viscosity indices ranging from −104 to 146 were analyzed and key parameters identified for high VI molecules: long alkyl chains, methyl branching in the centre of the molecule, low content of aromatic compounds, no ethyl branching and no tertiary carbons. A correlation based on four selected peaks was developed, giving a very good prediction of the viscosity index.

Quantitative Determination of Isostearic Acid Isomers in Skin Creams by GC-MS-SIM

“Isostearic acid” is frequently listed as an ingredient of skin creams and other cosmetics. In the four skin creams analyzed, “isostearic acid” was esterified with isopropanol, as well as sorbitan or polyglycerols. “Isopropyl isostearate” was isolated by HCl treatment and saponification whereas emulsifiers (sorbitan or polyglycerol isostearates) were enriched by means of a C18-cartridge. Fatty acids in the resulting lipid fraction were transferred into methyl esters. 25:0 and 19:0 methyl esters were used as internal standards. GC-EI-MS was used to determine that “isostearic acid” was a mixture of many methyl-branched isomers of stearic acid (18:0) in all four skin creams. Thus, it may be better termed “isostearic acids”. The branched-chain nature of isostearates was verified by formation and analysis of picolinyl esters of skin cream fatty acids by GC-EI-MS. Twenty-five 18:0 isomers were detected and the main products had one methyl branch on carbons C10–C14. Two late eluting isostearic acid isomers were identified as 16-methyl heptadecanoic acid (i18:0) and 15-methyl heptadecanoic acid (a18:0). GC-EI-MS in the selected ion monitoring (SIM) mode with m/z 87 as quantification ion was used for the determination of i18:0 methyl ester. The quantities of i18:0 in the samples amounted to 10–20 mg g−1 skin cream. The contribution of i18:0 to the sum of all 18:0 isomers in the four skin cream samples was 8.5 ± 1.1%. Instead of determining all individual isostearates in a product, we suggest the quantitative determination of i18:0 followed by multiplication with factor 11.75 (~reciprocal value of 8.5%, see above) as a simple method for the quantification of isostearates in cosmetics.

Bimetallic Effects for Enhanced Polar Comonomer Enchainment Selectivity in Catalytic Ethylene Polymerization

The synthesis and characterization of the bimetallic 2,7-di-[(2,6-diisopropylphenyl)imino]-1,8-naphthalenediolato group 10 metal polymerization catalysts {[Ni(CH(3))](2)[1,8-(O)(2)C(10)H(4)-2,7-[CH=N(2,6-(i)Pr(2)C(6)H(3))](PMe(3))(2)} and {[Ni(1-naphthyl)](2)[1,8-(O)(2)C(10)H(4)-2,7-[CH=N(2,6-(i)Pr(2)C(6)H(3))](PPh(3))(2)} [FI(2)-Ni(2)(PR(3))(2)] are presented, along with the synthesis and characterization of the mononuclear analogues {Ni(CH(3))[3-(t)Bu-2-(O)C(6)H(3)CH=N(2,6-(i)Pr(2)C(6)H(3))](PMe)(3)} and {Ni(1-naphthyl)[3-(t)Bu-2-(O)C(6)H(3)CH=N(2,6-(i)Pr(2)C(6)H(3))](PPh)(3)} [FI-Ni (PR(3))]. Monometallic Ni catalysts were also prepared by functionalizing one ligation center of the bimetallic ligand with a trimethylsilyl group (TMS), yielding {Ni(CH(3))[1,8-(O)(TMSO)C(10)H(4)-2,7-[CH=N(2,6-(i)Pr(2)C(6)H(3))](PMe(3))} [TMS-FI(2)-Ni(PMe(3))]. The FI(2)-Ni(2) catalysts exhibit significant increases in ethylene homopolymerization activity versus the monometallic analogues, as well as increased branching and methyl branch selectivity, even in the absence of a Ni(cod)(2) cocatalyst. Increasing ethylene concentrations significantly suppress branching and alter branch morphology. FI(2)-Ni(2)-mediated copolymerizations with ethylene + polar-functionalized norbornenes exhibit a 4-fold increase in comonomer incorporation versus FI-Ni, yielding copolymers with up to 10% norbornene copolymer incorporation. FI(2)-Ni(2)-catalyzed copolymerizations with ethylene + methylacrylate or methyl methacrylate incorporate up to 11% acrylate comonomer, while the corresponding mononuclear FI-Ni catalysts incorporate negligible amounts. Furthermore, the FI(2)-Ni(2)-mediated polymerizations exhibit appreciable polar solvent tolerance, turning over in the presence of ethyl ether, acetone, and even water. The mechanism by which the present cooperative effects take place is investigated, as is the nature of the copolymer microstructures produced.