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1.
Nat Commun ; 15(1): 3797, 2024 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-38714656

RESUMO

Nucleoporins rich in phenylalanine/glycine (FG) residues form the permeability barrier within the nuclear pore complex and are implicated in several pathological cellular processes, including oncogenic fusion condensates. The self-association of FG-repeat proteins and interactions between FG-repeats play a critical role in these activities by forming hydrogel-like structures. Here we show that mutation of specific FG repeats of Nup98 can strongly decrease the protein's self-association capabilities. We further present a cryo-electron microscopy structure of a Nup98 peptide fibril with higher stability per residue compared with previous Nup98 fibril structures. The high-resolution structure reveals zipper-like hydrophobic patches which contain a GLFG motif and are less compatible for binding to nuclear transport receptors. The identified distinct molecular properties of different regions of the nucleoporin may contribute to spatial variations in the self-association of FG-repeats, potentially influencing transport processes through the nuclear pore.


Assuntos
Microscopia Crioeletrônica , Complexo de Proteínas Formadoras de Poros Nucleares , Complexo de Proteínas Formadoras de Poros Nucleares/metabolismo , Complexo de Proteínas Formadoras de Poros Nucleares/química , Complexo de Proteínas Formadoras de Poros Nucleares/genética , Complexo de Proteínas Formadoras de Poros Nucleares/ultraestrutura , Humanos , Mutação , Poro Nuclear/metabolismo , Poro Nuclear/ultraestrutura , Poro Nuclear/química , Glicina/química , Glicina/metabolismo , Fenilalanina/química , Fenilalanina/metabolismo , Sequências Repetitivas de Aminoácidos , Ligação Proteica , Modelos Moleculares , Interações Hidrofóbicas e Hidrofílicas
2.
Colloids Surf B Biointerfaces ; 238: 113878, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38565007

RESUMO

Nitrogen-doped carbon dots (NCD) were synthesized using a simple and fast hydrothermal route, employing citric acid and urea as precursors. The resulting NCDs were non-covalently functionalized (conjugated) with aromatic amino acids, namely phenylalanine (Phe) and tryptophan (Trp). Atomic force microscopy revealed that the NCDs exhibit a disk-like morphology with an average diameter of approximately 60 nm and an average height of about 0.5 nm. Following conjugation, the particle height increased to around 3 nm. UV-vis spectroscopy analysis indicated successful conjugation of the amino acids to the NCD nanostructures. Additionally, DFT numerical calculations based on three differently N-doped clusters were performed to elucidate the nature of the non-covalent interactions between NCDs and the corresponding amino acids. Photoluminescent spectra demonstrated a stable and strong fluorescence signal for both hybrids in the UV region. The most significant changes were observed in the case of Trp-conjugation. In contrast to phenylalanine, the non-covalent bonding of tryptophan to NCDs strongly influenced the visible emission (around 500 nm) originating from surface states of the dots.


Assuntos
Aminoácidos Aromáticos , Carbono , Nanoestruturas , Nitrogênio , Carbono/química , Nitrogênio/química , Aminoácidos Aromáticos/química , Nanoestruturas/química , Pontos Quânticos/química , Propriedades de Superfície , Fenilalanina/química , Tamanho da Partícula , Triptofano/química , Microscopia de Força Atômica , Fenômenos Ópticos , Teoria da Densidade Funcional
3.
J Phys Chem Lett ; 15(16): 4468-4476, 2024 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-38631022

RESUMO

The underlying mechanism and intermediate formation in the self-assembly of aromatic amino acids, peptides, and proteins remain elusive despite numerous reports. We, for the first time, report that one can stabilize the intermediates by tuning the metal ion-amino acid interaction. Microscopic and spectroscopic investigations of the self-assembly of carboxybenzyl (Z)-protected phenylalanine (ZF) reveal that the bivalent metal ions eventually lead to the formation of fibrillar networks similar to blank ZF whereas the trivalent ions develop vesicle-like intermediates that do not undergo fibrillation for a prolonged time. The time-lapse measurement of surface charge reveals that the surface charge of blank ZF and in the presence of bivalent metal ions changes from a negative value to zero, implying unstable intermediates leading to the fibril network. Strikingly, a prominent charge inversion from an initial negative value to a positive value in the presence of trivalent metal ions imparts unusual stability to the metastable intermediates.


Assuntos
Fenilalanina , Fenilalanina/química , Propriedades de Superfície , Íons/química , Metais/química
4.
Org Biomol Chem ; 22(19): 3854-3859, 2024 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-38639197

RESUMO

The molecular recognition of saccharides by synthetic hosts has become an appealing but elusive task in the last decades. Herein, we combine Dynamic Combinatorial Chemistry (DCC) for the rapid self-assembly and screening of virtual libraries of receptors, with the use of ITC and NMR to validate the hits and molecular modelling to understand the binding mechanisms. We discovered a minimalistic receptor, 1F (N-benzyl-L-phenylalanine), with considerable affinity for fructose (Ka = 1762 M-1) and remarkable selectivity (>50-fold) over other common monosaccharides. The approach accelerates the discovery process of receptors for saccharides.


Assuntos
Técnicas de Química Combinatória , Monossacarídeos , Monossacarídeos/química , Modelos Moleculares , Fenilalanina/química , Fenilalanina/análogos & derivados , Fenilalanina/síntese química
5.
Nitric Oxide ; 147: 42-50, 2024 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-38631610

RESUMO

Nitric oxide (NO) donating drugs such as organic nitrates have been used to treat cardiovascular diseases for more than a century. These donors primarily produce NO systemically. It is however sometimes desirable to control the amount, location, and time of NO delivery. We present the design of a novel pH-sensitive NO release system that is achieved by the synthesis of dipeptide diphenylalanine (FF) and graphene oxide (GO) co-assembled hybrid nanosheets (termed as FF@GO) through weak molecular interactions. These hybrid nanosheets were characterised by using X-ray diffraction, Raman spectroscopy, Fourier transform infrared spectroscopy, zeta potential measurements, X-ray photoelectron spectroscopy, scanning and transmission electron microscopies. The weak molecular interactions, which include electrostatic, hydrogen bonding and π-π stacking, are pH sensitive due to the presence of carboxylic acid and amine functionalities on GO and the dipeptide building blocks. Herein, we demonstrate that this formulation can be loaded with NO gas with the dipeptide acting as an arresting agent to inhibit NO burst release at neutral pH; however, at acidic pH it is capable of releasing NO at the rate of up to 0.6 µM per minute, comparable to the amount of NO produced by healthy endothelium. In conclusion, the innovative conjugation of dipeptide with graphene can store and release NO gas under physiologically relevant concentrations in a pH-responsive manner. pH responsive NO-releasing organic-inorganic nanohybrids may prove useful for the treatment of cardiovascular diseases and other pathologies.


Assuntos
Grafite , Nanoestruturas , Óxido Nítrico , Grafite/química , Concentração de Íons de Hidrogênio , Óxido Nítrico/química , Óxido Nítrico/metabolismo , Nanoestruturas/química , Humanos , Dipeptídeos/química , Fenilalanina/química , Fenilalanina/análogos & derivados
6.
Methods Enzymol ; 696: 341-354, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38658087

RESUMO

The site-specific encoding of noncanonical amino acids allows for the introduction of rationalized chemistry into a target protein. Of the methods that enable this technology, evolved tRNA and synthetase pairs offer the potential for expanded protein production and purification. Such an approach combines the versatility of solid-phase peptide synthesis with the scalable features of recombinant protein production. We describe the large scale production and purification of eukaryotic proteins bearing fluorinated phenylalanine in mammalian suspension cell preparations. Downstream applications of this approach include scalable recombinant protein preparation for ligand binding assays with small molecules and ligands, protein structure determination, and protein stability assays.


Assuntos
Halogenação , Proteínas Recombinantes , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/química , Animais , Humanos , Fenilalanina/química , Fenilalanina/isolamento & purificação , Fenilalanina/metabolismo , Técnicas de Cultura de Células/métodos , Células HEK293
7.
Wei Sheng Yan Jiu ; 53(2): 282-287, 2024 Mar.
Artigo em Chinês | MEDLINE | ID: mdl-38604965

RESUMO

OBJECTIVE: To evaluate the changes in protein requirements of the elderly during the past five years. METHODS: Based on the previous study of protein requirements of 14 elderly in 2017, 4 of these elderly(70-80 y) were included as study participants and protein requirements were re-evaluated using the indicator amino acid oxidation method. There were seven protein levels: 0.1, 0.3, 0.6, 0.9, 1.2, 1.5 and 1.8 g/(kg·d). Maintenance diets were given for the first two days of each protein level. A stable isotope study was conducted on the day 3, using L-~(13)C-phenylalanine as an indicator on the basis of an amino acid rationed diet, which was orally ingested into the body along with the amino acid rationed diet, and breath and urine samples were collected when the metabolism of L-~(13)C-phenylalanine reached steady state in the body. By measuring the kinetic parameters of labeled amino acids in the samples, a nonlinear mixed-effects model was constructed for the protein intake to be tested and the oxidation rate of labeled amino acids. The mean protein requirement of the study population was determined by the protein intake corresponding to the inflection point of the curve. RESULTS: Based on the production rate of ~(13)CO_2 in exhaled breath of four elderly people at different protein levels, the mean protein requirement was 1.05(95%CI 0.51-1.60) g/(kg·d). The protein recommended nutrient intake was 1.31(95%CI 0.64-2.00) g/(kg·d) was estimated by applying the coefficient of variation of the mean protein requirement to derive the recommended nutrient intake. CONCLUSION: Protein requirements in the elderly have increased over a five-year period and sarcopenia may be the main cause of increased protein requirements.


Assuntos
Aminoácidos , Proteínas Alimentares , Humanos , Idoso , Isótopos de Carbono , Oxirredução , Fenilalanina/química , Fenilalanina/metabolismo , Necessidades Nutricionais
8.
Chirality ; 36(4): e23665, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38570326

RESUMO

In this paper, the amino acid chiral ionic liquid (AACIL) was prepared with L-phenylalanine and imidazole. It was characterized by CD, FT-IR, 1H NMR, and 13C NMR spectrum. The chiral recognition sensor was constructed with AACIL and Cu(II), which exhibited different chiral visual responses (solubility or color difference) to the enantiomers of glutamine (Gln) and phenylalanine (Phe). The effects of solvent, pH, time, temperature, metal ions, and other amino acids on visual chiral recognition were optimized. The minimum concentrations of Gln and Phe for visual chiral recognition were 0.20 mg/ml and 0.28 mg/ml, respectively. The mechanism of chiral recognition was investigated by FT-IR, TEM, SEM, TG, XPS, and CD. The location of the host-guest inclusion or molecular placement has been conformationally searched based on Gaussian 09 software.


Assuntos
Aminoácidos , Líquidos Iônicos , Aminoácidos/química , Fenilalanina/química , Glutamina , Líquidos Iônicos/química , Espectroscopia de Infravermelho com Transformada de Fourier , Estereoisomerismo
9.
Colloids Surf B Biointerfaces ; 238: 113918, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38669750

RESUMO

The supramolecular-based macrocyclic amphiphiles have fascinating attention and find extensive utilization in the pharmaceutical industry for efficient drug delivery. In this study, we designed and synthesized a new supramolecular amphiphilic macrocycle to serve as an efficient nanocarrier, achieved by treating 4-hydroxybenzaldehyde with 1-bromotetradecane. The derivatized product was subsequently treated with resorcinol to cyclize, resulting in the formation of a calix(4)-resorcinarene-based supramolecular amphiphilic macrocycle. The synthesized macrocycle and intermediate products were characterized using mass spectrometry, IR, and 1H NMR spectroscopic techniques. The amphotericin-B (Amph-B)-loaded and unloaded amphiphiles were screened for biocompatibility studies, vesicle formation, particle shape, size, surface charge, drug entrapment, in-vitro release profile, and stability through atomic force microscopy (AFM), Zetasizer, HPLC, and FT-IR. Amph-B -loaded macrocycle-based niosomal vesicles were investigated for in-vivo bioavailability in rabbits. The synthesized macrocycle exhibited no cytotoxicity against normal mouse fibroblast cells and was found to be hemocompatible and safe in mice following an acute toxicity study. The drug-loaded macrocycle-based vesicles appeared spherical, nano-sized, and homogeneous in size, with a notable negative surface charge. The vesicles remained stable after 30 days of storage. The results of Amph-B oral bioavailability and pharmacokinetics revealed that the newly tailored niosomal formulation enhanced drug solubility, protected drug degradation at gastric pH, facilitated sustained drug release at the specific target site, and delayed plasma drug clearance. Incorporating such advanced niosomal formulations in the field of drug delivery systems has the potential to revolutionize therapeutic outcomes and improve the quality of patient well-being.


Assuntos
Anfotericina B , Disponibilidade Biológica , Calixarenos , Portadores de Fármacos , Calixarenos/química , Animais , Camundongos , Portadores de Fármacos/química , Portadores de Fármacos/síntese química , Coelhos , Anfotericina B/farmacocinética , Anfotericina B/química , Anfotericina B/farmacologia , Anfotericina B/administração & dosagem , Administração Oral , Fenilalanina/química , Fenilalanina/análogos & derivados , Compostos Macrocíclicos/química , Compostos Macrocíclicos/farmacocinética , Compostos Macrocíclicos/farmacologia , Compostos Macrocíclicos/síntese química , Tamanho da Partícula , Liberação Controlada de Fármacos , Nanopartículas/química , Tensoativos/química , Tensoativos/síntese química , Masculino
10.
Chem Commun (Camb) ; 60(28): 3802-3805, 2024 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-38487891

RESUMO

An efficient functionalization of tyrosine residues in phenolic regions is achieved under metal-free conditions. The strategy involves the conversion of a tyrosine residue to 4-amino phenylalanine or 4-amino-3-methoxy phenylalanine in short peptides through a controlled oxidative dearomatization. This transformation is achieved in one pot with good yields and excellent regioselectivity. Consequently, the self-assembly of the peptide compounds has been studied at the nanoscopic level before and after functionalization. The results suggest that the peptide derivatives comprising amide groups promote intermolecular H-bonding interactions and the difference in -OH and -NH2 functional groups is found to be responsible for the morphological changes. Morphological transitions from 1D nanowires to 2D nanosheets were observed during functional group modification.


Assuntos
Peptídeos , Tirosina , Tirosina/química , Peptídeos/química , Fenilalanina/química
11.
Protein Expr Purif ; 219: 106461, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38460621

RESUMO

Nuclear magnetic resonance (NMR) spectroscopy NMR is a well-established technique for probing protein structure, dynamics and conformational changes. Taking advantage of the high signal sensitivity and broad chemical shift range of 19F nuclei, 19F NMR has been applied to investigate protein function at atomic resolution. In this report, we extend the unnatural amino acid site-specific incorporation into V. natriegens, an alternate protein expression system. The unnatural amino acid L-4-trifluoromethylphenylalanine (tfmF) was site-specifically introduced into the mitogen-activated protein kinase MEKK3 in V. natriegens using genetically encoded technology, which will be an extensive method for in-cell protein structure and dynamic investigation.


Assuntos
Ressonância Magnética Nuclear Biomolecular , Fenilalanina/química , Fenilalanina/metabolismo , Fenilalanina/genética , Flúor/química , Aminoácidos/química , Aminoácidos/genética , Aminoácidos/metabolismo
12.
ACS Appl Mater Interfaces ; 16(8): 10532-10544, 2024 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-38367060

RESUMO

Materials made of assembled biomolecules such as amino acids have drawn much attention during the past decades. Nevertheless, research on the relationship between the chemical structure of building block molecules, supramolecular interactions, and self-assembled structures is still necessary. Herein, the self-assembly and the coassembly of fluorenylmethoxycarbonyl (Fmoc)-protected aromatic amino acids (tyrosine, tryptophan, and phenylalanine) were studied. The individual self-assembly of Fmoc-Tyr-OH and Fmoc-Phe-OH in water formed nanofibers, while Fmoc-Trp-OH self-assembled into nanoparticles. Moreover, when Fmoc-Tyr-OH or Fmoc-Phe-OH was coassembled with Fmoc-Trp-OH, the nanofibers were transformed into nanoparticles. UV-vis spectroscopy, Fourier transform infrared spectroscopy, and fluorescence spectroscopy were used to investigate the supramolecular interactions leading to the self-assembled architectures. π-π stacking and hydrogen bonding were the main driving forces leading to the self-assembly of Fmoc-Tyr-OH and Fmoc-Phe-OH forming nanofibers. Further, a mechanism involving a two-step coassembly process is proposed based on nucleation and elongation/growth to explain the structural transformation. Fmoc-Trp-OH acted as a fiber inhibitor to alter the molecular interactions in the Fmoc-Tyr-OH or Fmoc-Phe-OH self-assembled structures during the coassembly process, locking the coassembly in the nucleation step and preventing the formation of nanofibers. This structural transformation is useful for extending the application of amino acid self- or coassembled materials in different fields. For example, the amino acids forming nanofibers could be applied for tissue engineering, while they could be exploited as drug nanocarriers when they form nanoparticles.


Assuntos
Aminoácidos Aromáticos , Nanopartículas , Aminoácidos/química , Fenilalanina/química , Hidrogéis/química
13.
Amino Acids ; 56(1): 9, 2024 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-38315214

RESUMO

Nanostructures formed by the self-assembly of modified/unmodified amino acids have the potential to be useful in several biological/nonbiological applications. In that regard, the greater conformational space provided by γ-amino acids, owing to their additional backbone torsional degrees of freedom and enhanced proteolytic stability, compared to their α-counterparts, should be explored. Though, modified single amino acid-based nanomaterials such as nanobelts or hydrogels are developed by utilizing the monosubstituted γ-amino acids derived from the backbone homologation of phenylalanine (Phe). Examples of a single γ-amino acid-based porous nanostructure capable of accommodating solvent molecules are not really known. The crystal structures of a modified γ4(R)Phe residue, Boc-γ4(R)Phe-OH, at different temperatures, showed that hydrogen-bonded water molecules are forming a wire inside hydrophilic nanochannels. The dynamics of intermolecular interactions between the water wire and the inner wall of the channel with relation to the temperature change was investigated by analyzing the natural bonding orbital (NBO) calculation results performed with the single crystal structures obtained at different temperature points. The NBO results showed that from 325 K onward, the strength of water-water interactions in the water wire are getting weaker, whereas, for the water-inner wall interactions, it getting stronger, suggesting a favorable change in the orientation of water molecules with temperatures, for the latter.


Assuntos
Aminoácidos , Água , Aminoácidos/química , Fenilalanina/química , Aminas/química , Conformação Molecular , Ligação de Hidrogênio
14.
J Mol Biol ; 436(5): 168451, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38246412

RESUMO

Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors distantly related to the phytochromes sensing red and far-red light reversibly. Only the cGMP phosphodiesterase/Adenylate cyclase/FhlA (GAF) domain is needed for chromophore incorporation and proper photoconversion. The CBCR GAF domains covalently ligate linear tetrapyrrole chromophores and show reversible photoconversion between two light-absorbing states. In most cases, the two light-absorbing states are stable under dark conditions, but in some cases, the photoproduct state undergoes thermal relaxation back to the dark-adapted state during thermal relaxation. In this study, we examined the engineered CBCR GAF domain, AnPixJg2_BV4. AnPixJg2_BV4 covalently binds biliverdin IX-alpha (BV) and shows reversible photoconversion between a far-red-absorbing Pfr dark-adapted state and an orange-absorbing Po photoproduct state. Because the BV is an intrinsic chromophore of mammalian cells and absorbs far-red light penetrating into deep tissues, BV-binding CBCR molecules are useful for the development of optogenetic and bioimaging tools used in mammals. To obtain a better developmental platform molecule, we performed site-saturation random mutagenesis on the Phe319 position. We succeeded in obtaining variant molecules with higher chromophore-binding efficiency and higher molar extinction coefficient. Furthermore, we observed a wide variation in thermal relaxation kinetics, with an 81-fold difference between the slowest and fastest rates. Both molecules with relatively slow and fast thermal relaxation would be advantageous for optogenetic control.


Assuntos
Proteínas de Bactérias , Biliverdina , Cianobactérias , Fotorreceptores Microbianos , Fitocromo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Biliverdina/química , Cianobactérias/metabolismo , Luz , Mutagênese , Fitocromo/química , Conformação Proteica , Fotorreceptores Microbianos/química , Fotorreceptores Microbianos/genética , Ligação Proteica , Fenilalanina/química , Fenilalanina/genética , Simulação de Dinâmica Molecular
15.
J Chem Theory Comput ; 20(1): 224-238, 2024 Jan 09.
Artigo em Inglês | MEDLINE | ID: mdl-38113378

RESUMO

The coarse-grained MARTINI force field, initially developed for membranes, has proven to be an exceptional tool for investigating supramolecular peptide assemblies. Over the years, the force field underwent refinements to enhance accuracy, enabling, for example, the reproduction of protein-ligand interactions and constant pH behavior. However, these protein-focused improvements seem to have compromised its ability to model short peptide self-assembly. In this study, we assess the performance of MARTINI 3 in reproducing peptide self-assembly using the well-established diphenylalanine (FF) as our test case. Unlike its success in version 2.1, FF does not even exhibit aggregation in version 3. By systematically exploring parameters for the aromatic side chains and charged backbone beads, we established a parameter set that effectively reproduces tube formation. Remarkably, these parameter adjustments also replicate the self-assembly of other di- and tripeptides and coassemblies. Furthermore, our analysis uncovers pivotal insights for enhancing the performance of MARTINI in modeling short peptide self-assembly. Specifically, we identify issues stemming from overestimated hydrophilicity arising from charged termini and disruptions in π-stacking interactions due to insufficient planarity in aromatic groups and a discrepancy in intermolecular distances between this and backbone-backbone interactions. This investigation demonstrates that strategic modifications can harness the advancements offered by MARTINI 3 for the realm of short peptide self-assembly.


Assuntos
Simulação de Dinâmica Molecular , Peptídeos , Peptídeos/química , Proteínas , Fenilalanina/química
16.
Bioorg Chem ; 142: 106940, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-37939508

RESUMO

A [10B]boron agent and a nuclear imaging probe for pharmacokinetic estimation form the fundamental pair in successful boron neutron capture therapy (BNCT). However, 4-[10B]borono-l-phenylalanine (BPA), used in clinical BNCT, has undesirable water solubility and tumor selectivity. Therefore, we synthesized fluorinated and α-methylated 3-borono-l-phenylalanine (3BPA) derivatives to realize improved water solubility, tumor targetability, and biodistribution. All 3BPA derivatives exhibited over 10 times higher water solubility than BPA. Treatment with α-methylated 3BPA derivatives resulted in decreased cell uptake via l-type amino acid transporter (LAT) 2 while maintaining LAT1 recognition, thereby significantly improving LAT1/LAT2 selectivity. Biodistribution studies showed that fluorinated α-methyl 3BPA derivatives exhibited reduced boron accumulation in nontarget tissues, including muscle, skin, and plasma. Consequently, these derivatives demonstrated significantly improved tumor-to-normal tissue ratios compared to 3BPA and BPA. Overall, fluorinated α-methyl 3BPA derivatives with the corresponding radiofluorinated compounds hold potential as promising agents for future BNCT/PET theranostics.


Assuntos
Terapia por Captura de Nêutron de Boro , Neoplasias , Humanos , Boro/metabolismo , Terapia por Captura de Nêutron de Boro/métodos , Distribuição Tecidual , Neoplasias/radioterapia , Neoplasias/tratamento farmacológico , Fenilalanina/química , Água , Compostos de Boro/química
17.
Phys Chem Chem Phys ; 25(48): 32824-32836, 2023 Dec 13.
Artigo em Inglês | MEDLINE | ID: mdl-38018404

RESUMO

The role of hydrophobicity of phenylalanine-glycine nucleoporins (FG-Nups) in determining the transport of receptor-bound cargo across the nuclear pore complex (NPC) is investigated using Langevin dynamics simulations. A coarse-grained, minimal model of the NPC, comprising a cylindrical pore and hydrophobic-hydrophilic random copolymers for FG-Nups was employed. Karyopherin-bound receptor-cargo complexes (Kaps) were modeled as rigid, coarse-grained spheres without (inert) and with (patchy) FG-binding hydrophobic domains. With a sequence-agnostic description of FG-Nups and the absence of any anisotropies associated with either NPC or cargo, the model described tracer transport only as a function of FG-Nup hydrophobicity, f. The simulations showed the emergence of two important features of cargo transport, namely, NPC selectivity and specificity. NPC selectivity to patchy tracers emerged due to hydrophobic Kap-FG interactions and despite the sequence-agnostic description of FG-Nups. Furthermore, NPC selectivity was observed only in a specific range of FG-hydrophobic fraction, 0.05 ≤ f ≤ 0.20, resulting in specificity of NPC transport with respect to f. Significantly, this range corresponded to the number fraction of FG-repeats observed in both S. cerevisiae and H. sapiens NPCs. This established the central role of the FG-hydrophobic fraction in determining NPC transport, and provided a biophysical basis for conservation of the FG-Nup hydrophobic fraction across evolutionarily distant NPCs. Specificity in NPC transport emerged from the formation of a hydrogel-like network inside the pore with a characteristic mesh size dependent on f. This network rejected cargo for f > 0.2 based on size exclusion, which resulted in enhanced translocation probability for 0.05 ≤ f ≤ 0.20. Extended brush configurations outside the pore resulted in entropic repulsion and exclusion of inert cargo in this range. Thus, our minimal NPC model exhibited a hybrid cargo translocation mechanism, with aspects of both virtual gate and selective-phase models, in this range of FG-hydrophobic fraction.


Assuntos
Poro Nuclear , Saccharomyces cerevisiae , Poro Nuclear/química , Complexo de Proteínas Formadoras de Poros Nucleares/análise , Complexo de Proteínas Formadoras de Poros Nucleares/química , Glicina/química , Fenilalanina/química
18.
Org Biomol Chem ; 21(48): 9562-9571, 2023 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-38009076

RESUMO

Two short pentapeptides rich in α-aminoisobutyric acid (Aib) residues have been shown to act as enantioselective organocatalysts for the conjugate addition of nucleophiles to nitroolefins. An L-alanine terminated peptide, (Aib)4(L-Ala)NHtBu, which has neither functionalised sidechains nor a highly designed reactive site, used an exposed N-terminal primary amine and the amide bonds of the backbone to mediate catalysis. Folding of this peptide into a 310 helical structure was observed by crystallography. Folding into a helix relays the conformational preference of the chiral alanine residue at the C-terminus to the primary amine at the N-terminus, 0.9 nm distant. The chiral environment and defined shape produced by the 310 helix brings the amine site into proximity to two exposed amide NHs. Reaction scope studies implied that the amine acts as a Brønsted base and the solvent-exposed NH groups of the helix, shown to weakly bind ß-nitrostyrene, are needed to obtain an enantiomeric excess. Replacement of L-alanine with D-phenylalanine gave (Aib)4(D-Phe)NHtBu, a peptide that now catalysed the benchmark reaction with the opposite enantioselectivity. These studies show how achiral residues can play a key role in enantioselective catalysis by peptides through the promotion of folding.


Assuntos
Amidas , Peptídeos , Estereoisomerismo , Modelos Moleculares , Peptídeos/química , Fenilalanina/química , Alanina/química , Catálise , Aminas , Conformação Proteica
19.
Chem Commun (Camb) ; 59(98): 14509-14523, 2023 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-37987167

RESUMO

Phenylketonuria (PKU) is an inborn metabolic disorder characterized by excess accumulation of phenylalanine (Phe) and its fibril formation, resulting in progressive intellectual disability. Several research groups have approached from various directions to understand the formation of toxic amyloid fibrils from the essential amino acid Phe. Different parameters like the nature of the solvent, pH, Phe concentration, temperature, etc. influence the fibril formation kinetics. In this article, we have summarized all major findings regarding the formation of Phe-based fibrils in aqueous and organic media and discussed how non-covalent interactions are involved in the self-assembly process using spectroscopic and microscopic techniques. The toxicity of Phe-based fibrils is compared with other neurodegenerative peptides. It is noted that the Phe-based fibrils can also induce various globular proteins into toxic fibrils. Later, we discuss the different approaches to inhibit fibril formation and reduce its toxicity. The presence of polyphenolic compounds, drugs, amino acids, nanoparticles, metal ions, crown ethers, and others showed a remarkable inhibitory effect on fibril formation. To the best of our knowledge, this is the first-ever etymological analysis of the Phe-fibrillar system and its inhibition to create a strong database against PKU.


Assuntos
Peptídeos , Fenilalanina , Fenilalanina/química , Peptídeos/química , Amiloide/química , Aminoácidos
20.
Peptides ; 170: 171113, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37923167

RESUMO

The current work demonstrates the synthesis and characterization of piperic acid conjugates with homochiral/heterochiral dipeptides containing phenylalanine as anti-skin cancer agents. The conjugates PA-DPhe-LPhe-OH, FC-1; PA-LPhe-DPhe-OH, FC-2; PA-DPhe-DPhe-OH, FC-3; and PA-DPhe-DPhe-OH, FC-4 were synthesized, characterized and assessed for cytotoxicity against melanoma cell lines of human and murine origin. Among all, PA-DPhe-DPhe-OH (FC-3) conjugate was identified as a potential cytotoxic lead against melanoma cells by delineating the anti-proliferative and anti-migratory potential together with its anti-inflammatory potential against pro-inflammatory interleukins (IL-1ß, IL-6, and IL-8). Evidences from western blotting, fractionation, and immunocytochemistry experiments suggest that Stat-3 is a critical signaling molecule involved in the FC-3 mechanism of action. The results denote that FC-3 profoundly ablates Stat-3 expression, phosphorylation, and nuclear translocation. Stat-3 mRNA analysis revealed that FC-3 did not alter the transcription of Stat-3. However, in cells where proteasome mediated degradation was inhibited, FC-3 failed to check the Stat-3 expression implying that FC-3 augments the proteasomal degradation of Stat-3. Of note, FC-3 failed to reverse the IL-6 mediated hyperactivation of Stat-3 in A375 cells. Critically, in Stat-3 deficient cancer cells, the anti-clonogenic and anti-migratory potential of FC-3 was significantly subdued. Further, the in vivo efficacy of FC-3 was validated in the two-step (DMBA/TPA) chemically induced mouse skin cancer model. The FC-3-treated cohorts of mice unveiled a significant decrease in the cumulative number of tumors besides attenuation of tumor growth with respect to the vehicle-treated mice. Lastly, in corroboration with our in vitro findings, serum collected from mice groups at various intervals during the treatment regimen demonstrated decrement in IL-1ß and IL-6 levels in FC-3 treated groups compared to the vehicle-treated group.


Assuntos
Antineoplásicos , Melanoma , Neoplasias Cutâneas , Camundongos , Humanos , Animais , Interleucina-6/genética , Fenilalanina/química , Dipeptídeos/farmacologia , Neoplasias Cutâneas/tratamento farmacológico , Antineoplásicos/farmacologia , Interleucina-1beta
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