Aromatic Side Chains Research Articles

A novel F30S mutation in γS-crystallin causes autosomal dominant congenital nuclear cataract by increasing susceptibility to stresses

Despite of increasingly accumulated genetic variations of autosomal dominant congenital cataracts (ADCC), the causative genes of many ADCC patients remains unknown. In this research, we identified a novel F30S mutation in γS-crystallin from a three-generation Chinese family with ADCC. The patients possessing the F30S mutation exhibited nuclear cataract phenotype. The potential molecular mechanism underlying ADCC by the F30S mutation was investigated by comparing the structural features, stability and aggregatory potency of the mutated protein with the wild type protein. Spectroscopic experiments indicated that the F30S mutation did not affect γS-crystallin secondary structure compositions, but modified the microenvironments around aromatic side-chains. Thermal and chemical denaturation studies indicated that the mutation destabilized the protein and increased its aggregatory potency. The mutation altered the two-state unfolding of γS-crystallin to a three-state unfolding with the accumulation of an unfolding intermediate. The almost identical values in the changes of Gibbs free energies for transitions from the native state to intermediate and from the intermediate to unfolded state suggested that the mutation probably disrupted the cooperativity between the two domains during unfolding. Our results expand the genetic variation map of ADCC and provide novel insights into the molecular mechanism underlying ADCC caused by mutations in β/γ-crystallins.

Synthesis of New Cyclopeptide Analogues of the Miuraenamides.

Miuraenamides belong to natural marine compounds with interesting biological properties. Miuraenamides initiate polymerization of monomeric actin and therefore show high cytotoxicity by influencing the cytoskeleton. New derivatives of the miuraenamides have been synthesized containing an N-methylated amide bond instead of the more easily hydrolysable ester in the natural products. Incorporation of an aromatic side chain onto the C-terminal amino acid of the tripeptide fragment also led to highly active new miuraenamides. In this study, we showed that the ester bond of the natural product miuraenamide can be replaced by an N-methyl amide. The yields in the cyclization step were high and generally much better than with the corresponding esters. On the other hand, the biological activity of the new amide analogs was lower compared to the natural products, but the activity could significantly be increased by incorporation of a p-nitrophenyl group at the C-terminus of the peptide fragment.

Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides.

A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.

Flavin mimetics: Synthesis and photophysical properties

We report the synthesis of new isoalloxazines using a microwave-assisted approach to make N -substituted-2-nitroanilines followed by one-pot reduction and condensation via Hemmerich’s method. The influence of substituents on positions 7, 8, and 10 of flavin core on the optical properties is investigated. The aliphatic functionalities on N10 give rise to quantum yields of 0.7, while aromatic side-chains quench fluorescence. Relaxed geometries (DFT) of chiral and achiral derivatives have been used for TD-DFT calculations, which yielded good agreement with the experimental UV and CD data.

Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding.

Simple SummaryProteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. The abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. Proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to DNA or RNA binding. These functions include the regulation of transcription, RNA splicing, translation, stability and sequestration. Cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. Because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between DNA and RNA. Many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains.The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.

The effects of long and bulky aromatic pendent groups with flexible linkages on the thermal, mechanical and electrical properties of the polyimides and their nanocomposites with functionalized silica.

A novel diamine bis(4-aminophenyl)bis{3,4[(4-(8-quinolyloxymethyl carbonyl)]}methane, containing two long/bulky aromatic pendent chains was synthesized by incorporating aromatic and hetero aromatic groups with flexible linkages. Flexible, stretchable, thermally stable and processable polyimides were prepared by reacting this newly synthesized diamine with commercial tetracarboxylic acid dianhydrides like 3,3′,4,4′-benzophenone tetra carboxylic acid dianhydride (BTDA) and 4,4′-(4,4′-isopropylidenediphenoxy)diphthalic Anhydride (BPADA). Nanocomposites of polyimides were prepared using aromatic amine functionalized silica as a filler by solution casting method. The current work investigates the effects of incorporating long/bulky aromatic side chains and flexible linkages on the thermal, mechanical, electrical and optical properties of the polyimides and nanocomposites. The polyimides showed good thermal stability (T10% = 364 & 388), high flame resistance, low glass transition temperatures (Tg = 130 °C & 156 °C), very low dielectric constants (2.5 & 2.8 at 1 MHz) and good optical transparency. The neat polyimides displayed good elongation at break (133–155%) but possessed low tensile strength. The chemically imidized polyimides showed good solubility in low and high boiling solvents. Nanocomposites of polyimides based on aromatic amine functionalized silica exhibited enhanced properties with T10% values varying between 409–482 °C, Tg between 165–280 °C and higher dielectric constants (3–5.7 at 1 MHz).

Enhancement of Lipolysis in 3T3-L1 Adipocytes by Nitroarene Capsaicinoid Analogs

Transient receptor potential vanilloid 1 (TRPV1) activation by capsaicin binding increased intracellular calcium influx and stimulated adipocyte-to-adipocyte communication, leading to lipolysis. Generally, enhancement of π-stacking capabilities improves certain binding interactions. Notably, nitroarenes exhibit strong binding interactions with aromatic amino acid side chains in proteins. New capsaicinoid analogs were designed by substitution of the OCH3 group with a nitrogen dioxide (NO2) group on the vanillyl ring to investigate how π-stacking interactions in capsaicinoid analogs contribute to lipolysis. Capsaicinoid analogs, nitro capsaicin (5), and nitro dihydrocapsaicin (6) were prepared in moderate yields via coupling of a nitroaromatic amine salt and fatty acids. Oil Red O staining and triglyceride assays with 10 µM loading of capsaicin (CAP), dihydrocapsaicin (DHC), 5, and 6 were performed to investigate their effect on lipolysis in 3T3-L1 adipocytes. Both assay results indicated that 5 and 6 decreased lipid accumulation by 13.6% and 14.7%, respectively, and significantly reduced triglyceride content by 26.9% and 28.4%, respectively, in comparison with the control experiment. Furthermore, the decrease in triglyceride content observed in response to nitroarene capsaicinoid analogs was approximately 2-folds higher than that of CAP and DHC. These results arose from the NO2 group augmented π-π stacking with Tyr511 and the attractive charge interaction with Glu570 affecting binding interactions with TRPV1 receptors.

Elucidating the anticancer activities of guanidinium-functionalized amphiphilic random copolymers by varying the structure and composition in the hydrophobic monomer.

Rationale: Use of traditional anticancer chemotherapeutics has been hindered by the multifactorial nature of multi-drug resistance (MDR) development and metastasis. Recently, cationic polycarbonates were reported as novel unconventional anticancer agents that mitigated MDR and inhibited metastasis. The aim of this study is to explore structure-anticancer activity relationship. Specifically, a series of cationic guanidinium-based random copolymers of varying hydrophobicity was synthesized with a narrow polydispersity (Ð = 1.12-1.27) via organocatalytic ring-opening polymerization (OROP) of functional cyclic carbonate monomers, and evaluated for anticancer activity, killing kinetics, degradability and functional mechanism.Methods: Linear, branched and aromatic hydrophobic side chain units, such as ethyl, benzyl, butyl, isobutyl and hexyl moieties were explored as comonomer units for modulating anticancer activity. As hydrophobicity/hydrophilicity balance of the polymers determines their anticancer efficacy, the feed ratio between the two monomers was varied to tune their hydrophobicity.Results: Notably, incorporating the hexyl moiety greatly enhanced anticancer efficiency and killing kinetics on cancer cells. Degradation studies showed that the polymers degraded completely within 4-6 days. Flow cytometry and lactate dehydrogenase (LDH) release analyses demonstrated that anticancer mechanism of the copolymers containing a hydrophobic co-monomer was concentration dependent, apoptosis at IC50, and both apoptosis and necrosis at 2 × IC50. In contrast, the homopolymer without a hydrophobic comonomer killed cancer cells predominantly via apoptotic mechanism.Conclusion: The hydrophobicity of the polymers played an important role in anticancer efficacy, killing kinetics and anticancer mechanism. This study provides valuable insights into designing novel anticancer agents utilizing polymers.

Organic amine mediated cleavage of Caromatic-Cα bonds in lignin and its platform molecules.

The activation and cleavage of C–C bonds remains a critical scientific issue in many organic reactions and is an unmet challenge due to their intrinsic inertness and ubiquity. Meanwhile, it is crucial for the valorization of lignin into high-value chemicals. Here, we proposed a novel strategy to enhance the Caromatic–Cα bond cleavage by pre-functionalization with amine sources, in which an active amine intermediate is first formed through Markovnikov hydroamination to reduce the dissociation energy of the Caromatic–Cα bond which is then cleaved to form target chemicals. More importantly, this strategy provides a method to achieve the maximum utilization of the aromatic nucleus and side chains in lignin or its platform molecules. Phenols and N,N-dimethylethylamine compounds with high yields were produced from herbaceous lignin or the p-coumaric acid monomer in the presence of industrially available dimethylamine (DMA).

Glycans to improve efficacy and solubility of protein aggregation inhibitors.

Glycans to improve efficacy and solubility of protein aggregation inhibitors.

An interesting possibility of forming special hole stepping stones with high-stacking aromatic rings in proteins: three-π five-electron and four-π seven-electron resonance bindings.

Long-range hole transfer of proteins plays an important role in many biological processes of living organisms. Therefore, it is highly useful to examine the possible hole stepping stones, which can facilitate hole transfer in proteins. However, the structures of stepping stones are diverse because of the complexity of the protein structures. In the present work, we proposed a series of special stepping stones, which are instantaneously formed by three and four packing aromatic side chains of amino acids to capture a hole, corresponding to three-π five-electron (π:π∴π↔π∴π:π) and four-π seven-electron (π:π∴π:π↔π:π:π∴π) resonance bindings with appropriate binding energies. The aromatic amino acids include histidine (His), phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp). The formations of these special stepping stones can effectively reduce the local ionization potential of the high π-stacking region to efficiently capture the migration hole. The quick formations and separations of them promote the efficient hole transfer in proteins. More interestingly, we revealed that a hole cannot delocalize over infinite aromatic rings along the high π–π packing structure at the same time and the micro-surroundings of proteins can modulate the formations of π:π∴π↔π∴π:π and π:π∴π:π↔π:π:π∴π bindings. These results may contribute a new avenue to better understand the potential hole transfer pathway in proteins.

TNF-α detection using gold nanoparticles as a surface-enhanced Raman spectroscopy substrate.

Background: TNF-αis a cytokine involved in inflammation. Surface-enhanced Raman spectroscopy (SERS) could be useful in its detection. Aim: Identify the TNF-α in an aqueous solution, using gold nanoparticles (AuNPs) as a SERS substrate. Materials & methods: Raman and SERS spectra were obtained from TNF-α samples, combined with AuNPs, with decreasing concentrations of TNF-α. The samples were analyzed using optical transmission spectroscopy, dynamic light scattering, and transmission electron microscopy. Results: Transmission electron microscopy/dynamic light scattering determined a change in the average diameter of the TNF-α/AuNPs (∼9.6nm). Raman bands obtained were associated with aromatic amino acid side chains. We observe Raman signals for TNF-α concentrationsas low as 0.125pg/ml. Conclusion: TNF-α signal at physiological concentrations was determined with SERS.

Antimicrobial Peptide K11 Selectively Recognizes Bacterial Biomimetic Membranes and Acts by Twisting Their Bilayers.

K11 is a synthetic peptide originating from the introduction of a lysine residue in position 11 within the sequence of a rationally designed antibacterial scaffold. Despite its remarkable antibacterial properties towards many ESKAPE bacteria and its optimal therapeutic index (320), a detailed description of its mechanism of action is missing. As most antimicrobial peptides act by destabilizing the membranes of the target organisms, we investigated the interaction of K11 with biomimetic membranes of various phospholipid compositions by liquid and solid-state NMR. Our data show that K11 can selectively destabilize bacterial biomimetic membranes and torque the surface of their bilayers. The same is observed for membranes containing other negatively charged phospholipids which might suggest additional biological activities. Molecular dynamic simulations reveal that K11 can penetrate the membrane in four steps: after binding to phosphate groups by means of the lysine residue at the N-terminus (anchoring), three couples of lysine residues act subsequently to exert a torque in the membrane (twisting) which allows the insertion of aromatic side chains at both termini (insertion) eventually leading to the flip of the amphipathic helix inside the bilayer core (helix flip and internalization).

Bacterial Alkyl-4-quinolones: Discovery, Structural Diversity and Biological Properties.

The alkyl-4-quinolones (AQs) are a class of metabolites produced primarily by members of the Pseudomonas and Burkholderia genera, consisting of a 4-quinolone core substituted by a range of pendant groups, most commonly at the C-2 position. The history of this class of compounds dates back to the 1940s, when a range of alkylquinolones with notable antibiotic properties were first isolated from Pseudomonas aeruginosa. More recently, it was discovered that an alkylquinolone derivative, the Pseudomonas Quinolone Signal (PQS) plays a key role in bacterial communication and quorum sensing in Pseudomonas aeruginosa. Many of the best-studied examples contain simple hydrocarbon side-chains, but more recent studies have revealed a wide range of structurally diverse examples from multiple bacterial genera, including those with aromatic, isoprenoid, or sulfur-containing side-chains. In addition to their well-known antimicrobial properties, alkylquinolones have been reported with antimalarial, antifungal, antialgal, and antioxidant properties. Here we review the structural diversity and biological activity of these intriguing metabolites.

Exploring polar hydrophobicity in organized media for extracting oligopeptides: application to the extraction of opiorphin in human saliva

Supramolecular solvents (dubbed SUPRAS) are gaining momentum as extractants of compounds of interest from complex matrixes such as foodstuff and biological and environmental samples. However, their powerful extraction mechanism, based on multiligand ability for solute binding, fails when applied to very polar compounds, hindering their applicability to the extraction of highly polar metabolites. In this work, we introduce the synthesis, characterization, and application of a new kind of SUPRAS formed by heptafluorobutyric acid (HFBA). The polar hydrophobicity of this perfluorinated acid results in a SUPRAS, which coacervates at acidic pHs, that shows a great capability to extract amino acids and oligopeptides (recoveries in the range 81-105%) with nonpolar alkyl, cyclic or aromatic side chain substituents (with log D > -3.62). To further demonstrate the potential of this novel SUPRAS, an analytical methodology for the determination of opiorphin in real saliva samples was developed and fully validated. The HFBA-based SUPRAS was synthetized in situ from 950 µL of stabilized saliva, by the addition of 150 µL of HFBA and 400 µL of HCl 37% (v/v). The resulting SUPRAS was directly injected into a LC-MS/MS system for further quantification. Quantitative recoveries in the range of 87-110% were obtained with relative standard deviations below 20%. The HFBA-based SUPRAS is, therefore, capable of efficiently extracting opiorphin from saliva samples and shows a high potential for the determination of several amino acids and oligopeptides from biological samples.

The Uniqueness of Tryptophan in Biology: Properties, Metabolism, Interactions and Localization in Proteins.

Tryptophan (Trp) holds a unique place in biology for a multitude of reasons. It is the largest of all twenty amino acids in the translational toolbox. Its side chain is indole, which is aromatic with a binuclear ring structure, whereas those of Phe, Tyr, and His are single-ring aromatics. In part due to these elaborate structural features, the biosynthetic pathway of Trp is the most complex and the most energy-consuming among all amino acids. Essential in the animal diet, Trp is also the least abundant amino acid in the cell, and one of the rarest in the proteome. In most eukaryotes, Trp is the only amino acid besides Met, which is coded for by a single codon, namely UGG. Due to the large and hydrophobic π-electron surface area, its aromatic side chain interacts with multiple other side chains in the protein, befitting its strategic locations in the protein structure. Finally, several Trp derivatives, namely tryptophylquinone, oxitriptan, serotonin, melatonin, and tryptophol, have specialized functions. Overall, Trp is a scarce and precious amino acid in the cell, such that nature uses it parsimoniously, for multiple but selective functions. Here, the various aspects of the uniqueness of Trp are presented in molecular terms.

Heterochirality and Halogenation Control Phe-Phe Hierarchical Assembly.

Diphenylalanine is an amyloidogenic building block that can form a versatile array of supramolecular materials. Its shortcomings, however, include the uncontrolled hierarchical assembly into microtubes of heterogeneous size distribution and well-known cytotoxicity. This study rationalized heterochirality as a successful strategy to address both of these pitfalls and it provided an unprotected heterochiral dipeptide that self-organized into a homogeneous and optically clear hydrogel with excellent ability to sustain fibroblast cell proliferation and viability. Substitution of one l-amino acid with its d-enantiomer preserved the ability of the dipeptide to self-organize into nanotubes, as shown by single-crystal XRD analysis, whereby the pattern of electrostatic and hydrogen bonding interactions of the backbone was unaltered. The effect of heterochirality was manifested in subtle changes in the positioning of the aromatic side chains, which resulted in weaker intermolecular interactions between nanotubes. As a result, d-Phe-l-Phe self-organized into homogeneous nanofibrils with a diameter of 4 nm, corresponding to two layers of peptides around a water channel, and yielded a transparent hydrogel. In contrast with homochiral Phe-Phe stereoisomer, it formed stable hydrogels thermoreversibly. d-Phe-l-Phe displayed no amyloid toxicity in cell cultures with fibroblast cells proliferating in high numbers and viability on this biomaterial, marking it as a preferred substrate over tissue-culture plastic. Halogenation also enabled the tailoring of d-Phe-l-Phe self-organization. Fluorination allowed analogous supramolecular packing as confirmed by XRD, thus nanotube formation, and gave intermediate levels of bundling. In contrast, iodination was the most effective strategy to augment the stability of the resulting hydrogel, although at the expense of optical transparency and biocompatibility. Interestingly, iodine presence hindered the supramolecular packing into nanotubes, resulting instead into amphipathic layers of stacked peptides without the occurrence of halogen bonding. By unravelling fine details to control these materials at the meso- and macro-scale, this study significantly advanced our understanding of these systems.

Evolution of insulin at the edge of foldability and its medical implications

Proteins have evolved to be foldable, and yet determinants of foldability may be inapparent once the native state is reached. Insight has emerged from studies of diseases of protein misfolding, exemplified by monogenic diabetes mellitus due to mutations in proinsulin leading to endoplasmic reticulum stress and β-cell death. Cellular foldability of human proinsulin requires an invariant Phe within a conserved crevice at the receptor-binding surface (position B24). Any substitution, even related aromatic residue TyrB24, impairs insulin biosynthesis and secretion. As a seeming paradox, a monomeric TyrB24 insulin analog exhibits a native-like structure in solution with only a modest decrement in stability. Packing of TyrB24 is similar to that of PheB24, adjoining core cystine B19-A20 to seal the core; the analog also exhibits native self-assembly. Although affinity for the insulin receptor is decreased ∼20-fold, biological activities in cells and rats were within the range of natural variation. Together, our findings suggest that the invariance of PheB24 among vertebrate insulins and insulin-like growth factors reflects an essential role in enabling efficient protein folding, trafficking, and secretion, a function that is inapparent in native structures. In particular, we envision that the para-hydroxyl group of TyrB24 hinders pairing of cystine B19-A20 in an obligatory on-pathway folding intermediate. The absence of genetic variation at B24 and other conserved sites near this disulfide bridge-excluded due to β-cell dysfunction-suggests that insulin has evolved to the edge of foldability. Nonrobustness of a protein's fitness landscape underlies both a rare monogenic syndrome and "diabesity" as a pandemic disease of civilization.

The Size-Accelerated Kinetic Resolution of Secondary Alcohols.

The factors responsible for the kinetic resolution of alcohols by chiral pyridine derivatives have been elucidated by measurements of relative rates for a set of substrates with systematically growing aromatic side chains using accurate competitive linear regression analysis. Increasing the side chain size from phenyl to pyrenyl results in a rate acceleration of more than 40 for the major enantiomer. Based on this observation a new catalyst with increased steric bulk has been designed that gives enantioselectivity values of up to s=250. Extensive conformational analysis of the relevant transition states indicates that alcohol attack to the more crowded side of the acyl‐catalyst intermediate is favoured due to stabilizing CH‐π‐stacking interactions. Experimental and theoretical results imply that enantioselectivity enhancements result from accelerating the transformation of the major enantiomer through attractive non‐covalent interactions (NCIs) rather than retarding the transformation of the minor isomer through repulsive steric forces.

Thermal denaturation of proteins in the muscle fibre and connective tissue from bovine muscles composed of type I (masseter) or type II (cutaneous trunci) fibres: DSC and FTIR microspectroscopy study

The changes in secondary structure of proteins with heating were characterised and compared for bovine masseter (fibre type I) and cutaneous trunci (fibre type II) muscles by Differential Scanning Calorimetry (DSC) and Fourier Transform InfraRed (FTIR) microspectroscopy. Heating led to a decrease in α- helices, and an increase in aggregated strands, random coils and aromatic side chains in the muscle fibres of both muscles. In the intramuscular connective tissue (IMCT) of both muscles, a decrease in α- helix, turn and unordered structures was complemented with an increase in aggregated strands. At temperatures < 60 °C, the greater thermal denaturation of proteins in cutaneous trunci than in masseter (FTIR), supported by a myosin associated peak at 55.8 °C for cutaneous trunci and no peak for masseter (DSC), indicates that myosin in type II fibres is more sensitive to thermal denaturation than myosin in type I fibres and this should be considered in thermal meat processing.