Computational investigation of cis-1,4-polyisoprene binding to the latex-clearing protein LcpK30.

Latex clearing proteins (Lcps) catalyze the oxidative cleavage of the C = C bonds in cis-1,4-polyisoprene (natural rubber), producing oligomeric compounds that can be repurposed to other materials. The active catalytic site of Lcps is buried inside the protein structure, thus raising the question of how the large hydrophobic rubber chains can access the catalytic center. To improve our understanding of hydrophobic polymeric substrate binding to Lcps and subsequent catalysis, we investigated the interaction of a substrate model containing ten carbon-carbon double bonds with the structurally characterized LcpK30, using multiple computational tools. Prediction of the putative tunnels and cavities in the LcpK30 structure, using CAVER-Pymol plugin 3.0.3, fpocket and Molecular Dynamic (MD) simulations provided valuable insights on how substrate enters from the surface to the buried active site. Two dominant tunnels were discovered that provided feasible routes for substrate binding, and the presence of two hydrophobic pockets was predicted near the heme cofactor. The larger of these pockets is likely to accommodate the substrate and to determine the size distribution of the oligomers. Protein-ligand docking was carried out using GOLD software to predict the conformations and interactions of the substrate within the protein active site. Deeper insight into the protein-substrate interactions, including close-contacts, binding energies and potential cleavage sites in the cis-1,4-polyisoprene, were obtained from MD simulations. Our findings provide further justification that the protein-substrate complexation in LcpK30 is mainly driven by the hydrophobic interactions accompanied by mutual conformational changes of both molecules. Two potential binding modes were identified, with the substrate in either extended or folded conformations. Whilst binding in the extended conformation was most favorable, the folded conformation suggested a preference for cleavage of a central double bond, leading to a preference for oligomers with 5 to 6 C = C bonds. The results provide insight into further enzyme engineering studies to improve catalytic activity and diversify the substrate and product scope of Lcps.

Peering down the sink: A review of isoprene metabolism by bacteria.

Isoprene (2-methyl-1,3-butadiene) is emitted to the atmosphere each year in sufficient quantities to rival methane (>500 Tg C yr-1 ), primarily due to emission by trees and other plants. Chemical reactions of isoprene with other atmospheric compounds, such as hydroxyl radicals and inorganic nitrogen species (NOx ), have implications for global warming and local air quality, respectively. For many years, it has been estimated that soil-dwelling bacteria consume a significant amount of isoprene (~20 Tg C yr-1 ), but the mechanisms underlying the biological sink for isoprene have been poorly understood. Studies have indicated or confirmed the ability of diverse bacterial genera to degrade isoprene, whether by the canonical iso-type isoprene degradation pathway or through other less well-characterized mechanisms. Here, we review current knowledge of isoprene metabolism and highlight key areas for further research. In particular, examples of isoprene-degraders that do not utilize the isoprene monooxygenase have been identified in recent years. This has fascinating implications both for the mechanism of isoprene uptake by bacteria, and also for the ecology of isoprene-degraders in the environments.

A guanidinium group is an effective mimic of the tertiary carbocation formed by isopentenyl diphosphate isomerase.

Type I isopentenyl diphosphate isomerase is a metal-dependent enzyme that generates a tertiary carbocation intermediate during catalysis. This study describes an inhibitor (2-guanidinoethyl(dihydroxyphosphorylmethyl)phosphinate) of the isomerase that bears a guanidinium as a carbocation mimic and a phosphinylphosphonate as a non-hydrolyzable metal binding functionality. Inhibition kinetics show that the compound acts in a competitive manner with a Ki value of 129 nM (KM,IPP/Ki = 27). An analogous inhibitor bearing a tertiary ammonium as the carbocation mimic was 50-fold less potent, suggesting that the planar guanidinium is a more effective carbocation mimic. Inhibitors bearing an acylated methanesulfonamide or a hydroxamate group in place of the pyrophosphate inhibited the enzyme at millimolar concentrations indicating that the isomerase is highly specific for binding to the diphosphate portion of the intermediate.

Unidirectional Perpendicularly Aligned Lamella-Structured Oligosaccharide (A) ABA Triblock Elastomer (B) Thin Films Utilizing Triazolium+/TFSI- Ionic Nanochannels.

We designed and synthesized high χ-low N-maltoheptaose-(triazolium+/N(SO2CF3)2-)-polyisoprene-(triazolium+/N(SO2CF3)2-)-maltoheptaose ABA triblock elastomers featuring triazolium+/N(SO2CF3)2- (TFSI-) counteranion ionic interfaces separating their constituting polymeric sub-blocks. Spin-coated and solvent-vapor-annealed (SVA) MH1.2k-(T+/TFSI-)-PI4.3k-(T+/TFSI-)-MH1.2k thin films demonstrate interface-induced charge cohesion through ca. 1 nm "thick" ionic nanochannels which facilitate the self-assembly of a perpendicularly aligned lamellar structure. Atomic force microscopy (AFM) and (grazing-incidence) small-angle X-ray scattering ((GI)SAXS) characterizations of MH1.2k-(T+/TFSI-)-PI4.3k-(T+/TFSI-)-MH1.2k and pristine triBCP analogous thin films revealed sub-10 nm block copolymer (BCP) self-assembly and unidirectionally aligned nanostructures developed over several µm2 areas. Solvated TFSI- counterions enhance the oligosaccharide sub-block packing during SVA. The overall BCP phase behavior was mapped through SAXS characterizations comparing di- vs triblock polymeric architectures, a middle PI sub-block with two different molecular masses, and TFSI- or I- counteranion effects. This work highlights the benefits of inducing single-point electrostatic interactions within chemical structures of block copolymers to master the long-range self-assembly of prescribed morphologies.

Co-Production of Isoprene and Lactate by Engineered Escherichia coli in Microaerobic Conditions.

Lactate and isoprene are two common monomers for the industrial production of polyesters and synthetic rubbers. The present study tested the co-production of D-lactate and isoprene by engineered Escherichia coli in microaerobic conditions. The deletion of alcohol dehydrogenase (adhE) and acetate kinase (ackA) genes, along with the supplementation with betaine, improved the co-production of lactate and isoprene from the substrates of glucose and mevalonate. In fed-batch studies, microaerobic fermentation significantly improved the isoprene concentration in fermentation outlet gas (average 0.021 g/L), compared with fermentation under aerobic conditions (average 0.0009 g/L). The final production of D-lactate and isoprene can reach 44.0 g/L and 3.2 g/L, respectively, through fed-batch microaerobic fermentation. Our study demonstrated a dual-phase production strategy in the co-production of isoprene (gas phase) and lactate (liquid phase). The increased concentration of gas-phase isoprene could benefit the downstream process and decrease the production cost to collect and purify the bio-isoprene from the fermentation outlet gas. The proposed microaerobic process can potentially be applied in the production of other volatile bioproducts to benefit the downstream purification process.

Generation of Stable Isopentenyl Monophosphate Aryloxy Triester Phosphoramidates as Activators of Vγ9Vδ2 T Cells.

Aryloxy triester phosphoramidate prodrugs of the monophosphate derivatives of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) were synthesized as lipophilic derivatives that can improve cell uptake. Despite the structural similarity of IPP and DMAPP, it was noted that their phosphoramidate prodrugs exhibited distinct stability profiles in aqueous environments, which we show is due to the position of the allyl bond in the backbones of the IPP and DMAPP monophosphates. As the IPP monophosphate aryloxy triester phosphoramidates showed favorable stability, they were subsequently investigated for their ability to activate Vγ9/Vδ2 T cells and they showed promising activation of this subset of T cells. Together, these findings represent the first report of IPP and DMAPP monophosphate prodrugs and the ability of IPP aryloxy triester phosphoramidate prodrugs to activate Vγ9/Vδ2 T cells highlighting their potential as possible immunotherapeutics.

Cerebellar involvement in olfaction: An fMRI Study.

BACKGROUND AND PURPOSE: The role of the cerebellum in olfactory function is not fully understood. In this study, we tried to combine resting state and task functional MRI (fMRI) to improve the understanding of the cerebellum during olfactory processing. METHODS: A resting state and a block paradigm of olfactory stimulation fMRI were scanned in 50 subjects. The olfactory stimuli, including phenylethyl alcohol and isovaleric acid, were alternately delivered to the subject using a custom-built olfactometer through air flow. The cerebellar activations elicited by isovaleric acid were subsequently used in the seed-based resting-state functional connectivity study. RESULTS: Phenylethyl alcohol did not induce any cerebellum activation, while isovaleric acid with a more unpleasant smell elicited significant cerebellum activations, primarily in the bilateral posterior lateral hemispheres (bilateral lobule crus I and right lobule VI). Seed-based functional connectivity analysis revealed significant within-cerebellum and corticocerebellar connections. CONCLUSIONS: The results imply that the cerebellum is probably involved in olfactory-related responses caused by unpleasant odor but does not directly participate in olfactory perception. Our results may further improve the understanding of the cerebellum in olfactory function.

Structure-function studies of ultrahigh molecular weight isoprenes provide key insights into their biosynthesis.

Some plant trans-1,4-prenyltransferases (TPTs) produce ultrahigh molecular weight trans-1,4-polyisoprene (TPI) with a molecular weight of over 1.0 million. Although plant-derived TPI has been utilized in various industries, its biosynthesis and physiological function(s) are unclear. Here, we identified three novel Eucommia ulmoides TPT isoforms-EuTPT1, 3, and 5, which synthesized TPI in vitro without other components. Crystal structure analysis of EuTPT3 revealed a dimeric architecture with a central hydrophobic tunnel. Mutation of Cys94 and Ala95 on the central hydrophobic tunnel no longer synthesizd TPI, indicating that Cys94 and Ala95 were essential for forming the dimeric architecture of ultralong-chain TPTs and TPI biosynthesis. A spatiotemporal analysis of the physiological function of TPI in E. ulmoides suggested that it is involved in seed development and maturation. Thus, our analysis provides functional and mechanistic insights into TPI biosynthesis and uncovers biological roles of TPI in plants.

Shape and Temperature Expansion of Free Volume Holes in Some Cured Polybutadiene-Polyisoprene Rubber Blends.

The free volume fraction of a macromolecular structure can be assessed theoretically by using a suitable model; however, it can also be evaluated from experimental data obtained from dilatometry and positron annihilation lifetime spectra. In this second case, a regular geometry of the sub-nanometric cavities forming the free volume has to be assumed, although in fact they are irregularly shaped. The most popular approach is to guess spherical holes, which implies an isotropic growth of these last with temperature. In this work, we compared the free volume fraction, as obtained from experiments in a set of polybutadiene and polyisoprene cured rubbers and their blends, with the analogous quantity expected by using the lattice-hole model. The results allowed us to obtain insights on the approximate shape of the holes. Indeed, a cylindrical flattened geometry of the cavities produced a better agreement with the theory than the spherical shape. Furthermore, the best fit was obtained for holes that expanded preferentially in the radial direction, with a consequent decrease of the aspect ratio with temperature.

Biogenic secondary organic aerosols: A review on formation mechanism, analytical challenges and environmental impacts.

The review initiates with current state of information on the atmospheric reaction mechanism of biogenic volatile organic compounds (BVOCs) and its fate in the atmosphere. The plants release BVOCs, i.e., isoprene, monoterpenes, and sesquiterpenes, which form secondary organic aerosols (SOA) upon oxidation. These oxidation reactions are primarily influenced by solar radiations along with other meteorological parameters viz.; temperature and relative humidity, therefore, the chemistry behind SOA formation is different during day than the night time. The review throws light upon the day and nighttime formation mechanism of SOA, recent advancements in the analytical techniques available for the measurements, and its impact on the environment. Studies have revealed that day time SOA formation is dominated by OH and O3, however, NOx initiated SOA production is dominated during night. The formation mechanism addresses that the gaseous products of VOCs are firstly formed and then partitioned over the pre-existing particles. New particle formation and biomass-derived aerosols are found to be responsible for enhanced SOA formation. 2-Dimensional gas chromatography-mass spectrometer (2D-GC/MS) is observed to be best for the analysis of organic aerosols. Radiative forcing (RF) SOA is observed to be a useful parameter to evaluate the environmental impacts of SOA and reviewed studies have shown mean RF in the ranges of -0.27 to +0.20 W m-2.

A Single Amino Acid Switch Alters the Prenyl Donor Specificity of a Fungal Aromatic Prenyltransferase toward Biflavonoids.

Biflavonoids are pharmaceutically important compounds. Prenylation usually improves bioactivity; however, prenylated biflavonoids are rare in nature. Here, we report successful prenylation or geranylation of biflavonoids using fungal prenyltransferase CdpC3PT and its mutants. F253 was identified as a key residue related to donor selectivity, which enables the switching from utilizing DMAPP to GPP precisely at the same C-3''' site of biflavonoids. Furthermore, another residue W181 was discovered to generally increase prenylation activity toward biflavonoids.

Comparison of Chemical Composition between Kuromoji (Lindera umbellata) Essential Oil and Hydrosol and Determination of the Deodorizing Effect.

Kuromoji (Lindera umbellata) is a tree that grows throughout Japan. The components of kuromoji essential oil have antitumor and aromatherapy effects. However, the composition of the hydrosol, obtained as a by-product of the essential oil process, is unknown. Furthermore, it is unknown whether kuromoji essential oil has a deodorizing effect. Therefore, the purpose of the current study was to compare the chemical composition of kuromoji essential oil and hydrosol, as well as evaluate the deodorizing effect of the former. The chemical composition of samples was evaluated using gas chromatography-mass spectrometry (GC-MS). Additionally, the deodorizing effect of Kuromoji essential oil was investigated with the detector tube method using ammonia, hydrogen sulfide, methyl mercaptan, and isovaleric acid. Linalool was the most abundant component in both the essential oil and hydrosol; however, its proportion was higher in the hydrosol (57.5%) than in the essential oil (42.8%). The hydrosol contained fewer chemical components, but higher proportions of trans-geraniol and ethanol. Moreover, the essential oil eliminated 50% of ammonia and 97.6% or more of isovaleric acid. Interestingly, linalool was soluble in the hydrosol and did not irritate the skin. This suggests that the hydrosol may be an effective foot care product.

Satellite isoprene retrievals constrain emissions and atmospheric oxidation.

Isoprene is the dominant non-methane organic compound emitted to the atmosphere1-3. It drives ozone and aerosol production, modulates atmospheric oxidation and interacts with the global nitrogen cycle4-8. Isoprene emissions are highly uncertain1,9, as is the nonlinear chemistry coupling isoprene and the hydroxyl radical, OH-its primary sink10-13. Here we present global isoprene measurements taken from space using the Cross-track Infrared Sounder. Together with observations of formaldehyde, an isoprene oxidation product, these measurements provide constraints on isoprene emissions and atmospheric oxidation. We find that the isoprene-formaldehyde relationships measured from space are broadly consistent with the current understanding of isoprene-OH chemistry, with no indication of missing OH recycling at low nitrogen oxide concentrations. We analyse these datasets over four global isoprene hotspots in relation to model predictions, and present a quantification of isoprene emissions based directly on satellite measurements of isoprene itself. A major discrepancy emerges over Amazonia, where current underestimates of natural nitrogen oxide emissions bias modelled OH and hence isoprene. Over southern Africa, we find that a prominent isoprene hotspot is missing from bottom-up predictions. A multi-year analysis sheds light on interannual isoprene variability, and suggests the influence of the El Niño/Southern Oscillation.

The Beneficial Effects of Morusin, an Isoprene Flavonoid Isolated from the Root Bark of Morus.

The root bark of Morus has long been appreciated as an antiphlogistic, diuretic and expectorant drug in Chinese herbal medicine, albeit with barely known targets and mechanisms of action. In the 1970s, the development of analytic chemistry allowed for the discovery of morusin as one of 7 different isoprene flavonoid derivatives in the root bark of Morus. However, the remarkable antioxidant capacity of morusin with the unexpected potential for health benefits over the other flavonoid derivatives has recently sparked scientific interest in the biochemical identification of target proteins and signaling pathways and further clinical relevance. In this review, we discuss recent advances in the understanding of the functional roles of morusin in multiple biological processes such as inflammation, apoptosis, metabolism and autophagy. We also highlight recent in vivo and in vitro evidence on the clinical potential of morusin treatment for multiple human pathologies including inflammatory diseases, neurological disorders, diabetes, cancer and the underlying mechanisms.

Ferulic Acid Decarboxylase Controls Oxidative Maturation of the Prenylated Flavin Mononucleotide Cofactor.

Prenylated flavin mononucleotide (prFMN) is a recently discovered modified flavin cofactor containing an additional nonaromatic ring, connected to the N5 and C6 atoms. This cofactor underpins reversible decarboxylation catalyzed by members of the widespread UbiD enzyme family and is produced by the flavin prenyltransferase UbiX. Oxidative maturation of the UbiX product prFMNH2 to the corresponding oxidized prFMNiminium is required for ferulic acid decarboxylase (Fdc1; a UbiD-type enzyme) activity. However, it is unclear what role the Fdc1 enzyme plays in this process. Here, we demonstrate that, in the absence of Fdc1, prFMNH2 oxidation by O2 proceeds via a transient semiquinone prFMNradical species and culminates in a remarkably stable prFMN-hydroperoxide species. Neither forms of prFMN are able to support Fdc1 activity. Instead, enzyme activation using O2-mediated oxidation requires prFMNH2 binding prior to oxygen exposure, confirming that UbiD enzymes play a role in O2-mediated oxidative maturation. In marked contrast, alternative oxidants such as potassium ferricyanide support prFMNiminium formation both in solution and in Fdc1.

Mechanical Insights into the Enzymatic Cleavage of Double C-C Bond in Poly(cis-1,4-isoprene) by the Latex Clearing Protein.

The b-type cytochrome LcpK30 is a latex clearing protein (Lcp), which acts as an endotype dioxygenase to catalyze the extracellular cleavage of the chemically inert aliphatic polymer poly(cis-1,4-isoprene), producing oligo-isoprenoids with different terminal carbonyl groups (aldehyde and ketone, -CH2-CHO and -CH2-COCH3). On the basis of the fact that the muteins of E148A, E148Q, and E148H have substantially reduced reactivity, and the E148-initiated reaction mechanism has been previously proposed, in which a cyclic dioxetane intermediate or an epoxide intermediate may be involved, however, open questions still remain. In this paper, on the basis of the crystal structure of LcpK30, the enzyme-substrate reactant model was constructed, and the cleavage mechanism of the central double bond of poly(cis-1,4-isoprene) was elucidated by performing quantum mechanics/molecular mechanics calculations. Our calculation results revealed that the oxidative cleavage reaction is triggered by the addition of the heme-bound dioxygen to the double bond of the polymer, and E148 does not act as the catalytic base to extract the allylic proton to assist the reaction as previously suggested. Of the two considered pathways, the pathway that involves the dioxetane intermediate was calculated to be more favorable. During the catalysis, the distal oxygen first adds to the double bond of the substrate to form a radical intermediate, and then the Fe-O1 (proximal oxygen) bond cleaves to generate the dioxetane intermediate, which can easily collapse affording the final ketone and aldehyde products. In general, the cleavage mechanism of double C-C bond catalyzed by LcpK30 is similar to those of indoleamine 2,3-dioxygenase, tryptophan 2,3-dioxygenase, and the nonheme stilbene cleavage oxygenase NOV1 that all depend on the iron-bound dioxygen to initiate the cleavage reaction.

The characteristic smell emitted from two scale insects, Ceroplastes japonicus and Ceroplastes rubens.

The volatile components emitted from two scale insects, Ceroplastes japonicus and Ceroplastes rubens, were identified using GC-MS analysis. The major volatile components of the solvent extract from C. japonicus were α-humulene (35.8%) and δ-cadinene (17.0%), while those of C. rubens were ß-selinene (10.3%) and ß-elemene (5.1%). In GC/olfactometry, linalool, butyric acid, 3-methylbutyric acid, 2-methylbutyric acid, and vanillin were identified as the odor-active components of the extract from C. japonicus, in addition to trace amounts of trans-4,5-epoxy-(2E)-decenal, 4-methyl-(3E)-hexenoic acid, and phenylacetic acid. With regard to C. rubens, trans-4,5-epoxy-(2E)-decenal, 3-methylbutyric acid, and phenylacetic acid were identified as the odor-active components. Besides, decan-1,4-olide (γ-decalactone) with milky cherry-like note and 3-hydroxy-4,5-dimethylfuran-2(5H)-one (sotolone) with brown sugar-like note were also detected as the characteristic cherry-like sweet-and-sour note of these two scale insects. ABBREVIATIONS: GC: Gas chromatography; GC/O: gas chromatography/olfactometry.

Multiple Stable Isoprene-Ozone Complexes Reveal Complex Entrance Channel Dynamics in the Isoprene + Ozone Reaction.

Accurately characterizing isoprene ozonolysis continues to challenge atmospheric chemists. The reaction is believed to be a spontaneous, concerted cycloaddition. However, little information is available about the entrance channel and isoprene-ozone complexes thought to define the long-range portion of the reaction coordinate. Our coupled cluster and auxiliary field quantum Monte Carlo calculations predict multiple stable isoprene-ozone van der Waals complexes for trans-isoprene in the gas phase with moderate association energies. These results indicate that long-range dynamics in the isoprene-ozone entrance channel can impact the overall reaction in the troposphere and provide the spectroscopic information necessary to extend the microwave characterization of isoprene ozonolysis to prereactive complexes. At the air-water interface, Born-Oppenheimer molecular dynamics simulations indicate that the cycloaddition reaction between ozone and trans-isoprene follows a stepwise mechanism, which is quite distinct from our proposed gas-phase mechanism and occurs on a femtosecond time scale. The stepwise nature of isoprene ozonolysis on the aqueous surface is more consistent with the DeMore mechanism than with the Criegee mechanism suggested by the gas-phase calculations, suggesting that the reaction media may play an important role in the reaction. Overall, these predictions aim to provide a missing fundamental piece of molecular insight into isoprene ozonolysis, which has broad tropospheric implications due to its critical role as a nighttime source of hydroxyl radicals.

Biotransformation of poly(cis-1,4-isoprene) in a multiphase enzymatic reactor for continuous extraction of oligo-isoprenoid molecules.

Biotechnological processes for the partial degradation or transformation of poly(cis-1,4-isoprene) rubber have been investigated during recent decades with promising results. The use of the enzyme 'latex clearing protein' (Lcp) to transform the polymer into more hydrophilic oligo-isoprenoids results in modifications of the rubber structure and the synthesis of new material. In order to find an alternative process to recover the degradation products, a continuous extraction method using a biphasic system is described. The enzymatic activity of Lcp1VH2 was studied in the presence of ethyl acetate and pentane as extraction solvents. Oligo(cis-1,4-isoprene) molecular species were isolated from the organic phase and analyzed by Electrospray Ionization Mass Spectrometry. The enzymatic reaction process was evaluated in terms of the biotransformation yield of poly(cis-1,4-isoprene) rubber into the corresponding degradation products. Biotransformation yields of between 42-52 % were achieved depending on the enzymatic reactor design and the extraction solvent. The results also showed that the mass distribution of the oligo(cis-1,4-isoprene) depended on the organic solvent applied. A novel, simple and effective process is demonstrated for biotransformation of poly(cis-1,4-isoprene) rubber with high oligo-isoprenoid molecules recovery yields.

Molecular Mechanisms of Natural Rubber Biosynthesis.

Natural rubber (NR), principally comprising cis-1,4-polyisoprene, is an industrially important natural hydrocarbon polymer because of its unique physical properties, which render it suitable for manufacturing items such as tires. Presently, industrial NR production depends solely on latex obtained from the Pará rubber tree, Hevea brasiliensis. In latex, NR is enclosed in rubber particles, which are specialized organelles comprising a hydrophobic NR core surrounded by a lipid monolayer and membrane-bound proteins. The similarity of the basic carbon skeleton structure between NR and dolichols and polyprenols, which are found in most organisms, suggests that the NR biosynthetic pathway is related to the polyisoprenoid biosynthetic pathway and that rubber transferase, which is the key enzyme in NR biosynthesis, belongs to the cis-prenyltransferase family. Here, we review recent progress in the elucidation of molecular mechanisms underlying NR biosynthesis through the identification of the enzymes that are responsible for the formation of the NR backbone structure.