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1.
Molecules ; 26(16)2021 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-34443377

RESUMO

We here investigate the Electronic Circular Dichroism (ECD) Spectra of two representative Guanine-rich sequences folded in a Quadruple helix (GQ), by using a recently developed fragment diabatisation based excitonic model (FrDEx). FrDEx can include charge transfer (CT) excited states and consider the effect of the surrounding monomers on the local excitations (LEs). When applied to different structures generated by molecular dynamics simulations on a fragment of the human telomeric sequence (Tel21/22), FrDEx provides spectra fully consistent with the experimental one and in good agreement with that provided by quantum mechanical (QM) method used for its parametrization, i.e., TD-M05-2X. We show that the ECD spectrum is moderately sensitive to the conformation adopted by the bases of the loops and more significantly to the thermal fluctuations of the Guanine tetrads. In particular, we show how changes in the overlap of the tetrads modulate the intensity of the ECD signal. We illustrate how this correlates with changes in the character of the excitonic states at the bottom of the La and Lb bands, with larger LE and CT involvement of bases that are more closely stacked. As an additional test, we utilised FrDEx to compute the ECD spectrum of the monomeric and dimeric forms of a GQ forming sequence T30695 (5'TGGGTGGGTGGGTGGG3'), i.e., a system containing up to 24 Guanine bases, and demonstrated the satisfactory reproduction of the experimental and QM reference results. This study provides new insights on the effects modulating the ECD spectra of GQs and, more generally, further validates FrDEx as an effective tool to predict and assign the spectra of closely stacked multichromophore systems.


Assuntos
Dicroísmo Circular , DNA/química , Elétrons , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Dimerização , Espectroscopia de Ressonância Magnética , Temperatura
2.
Int J Mol Sci ; 22(15)2021 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-34360665

RESUMO

In this work we examined the properties of thrombin-binding aptamer (TBA) modified by the introduction of inversion of polarity sites (IPS) in order to assess the effect of modification on the activation of TBA to serve as DNAzyme with peroxidase-like activity. Two oligonucleotides were designed to possess one (IPS1) or three (IPS2) inversion sites. TBA typically forms antiparallel G-quadruplexes with two G-tetrads, which exhibits very low DNAzyme peroxidise activity. DNAzyme activity is generally attributed to parallel G-quadruplexes. Hence, inversion of polarity was introduced in the TBA molecule to force the change of G-quadruplex topology. All oligonucleotides were characterized using circular dichroism and UV-Vis melting profiles. Next, the activity of the DNAzymes formed by studied oligonucleotides and hemin was investigated. The enhancement of peroxidase activity was observed when inversion of polarity was introduced. DNAzyme based on IPS2 showed the highest peroxidase activity in the presence of K+ or NH4+ ions. This proves that inversion of polarity can be used to convert a low-activity DNAzyme into a DNAzyme with high activity. Since TBA is known for its anticoagulant properties, the relevant experiments with IPS1 and IPS2 oligonucleotides were performed. Both IPS1 and IPS2 retain some anticoagulant activity in comparison to TBA in the reaction with fibrinogen. Additionally, the introduction of inversion of polarity makes these oligonucleotides more resistant to nucleases.


Assuntos
Anticoagulantes/farmacologia , Aptâmeros de Nucleotídeos/farmacologia , DNA Catalítico/metabolismo , Fibrinogênio/metabolismo , Quadruplex G , Hemina/metabolismo , Aptâmeros de Nucleotídeos/química , Dicroísmo Circular , Humanos , Modelos Moleculares
3.
J Phys Chem Lett ; 12(33): 8096-8102, 2021 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-34406777

RESUMO

Nucleic acid sequences rich in guanines can organize into noncanonical DNA G-quadruplexes (G4s) of variable size. The design of small molecules stabilizing the structure of G4s is a rapidly growing area for the development of novel anticancer therapeutic strategies and bottom-up nanotechnologies. Among a multitude of binders, porphyrins are very attractive due to their light activation that can make them valuable conformational regulators of G4s. Here, a structure-based strategy, integrating complementary probes, is employed to study the interaction between TMPyP4 porphyrin and a 22-base human telomeric sequence (Tel22) before and after irradiation with blue light. Porphyrin binding is discovered to promote Tel22 dimerization, while light irradiation of the Tel22-TMPyP4 complex controls dimer fraction. Such a change in quaternary structure is found to be strictly correlated with modifications at the secondary structure level, thus providing an unprecedented link between the degree of dimerization and the underlying conformational changes in G4s.


Assuntos
DNA/química , Quadruplex G , Porfirinas/química , Raios X , Dicroísmo Circular , Dimerização , Estrutura Molecular , Espalhamento de Radiação , Telômero
4.
Langmuir ; 37(34): 10319-10329, 2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34407374

RESUMO

This study highlights the role of time-dependent hydrolysis of ionic liquid anion, [BF4]-, of ionic liquid (IL), 1-ethyl-3-methylimidazolium tetrafluoroborate, [C2mim][BF4], which results in ever-changing pH conditions. Such pH changes along with the ionic interactions bring conformational changes in bovine serum albumin (BSA), leading to the formation of amyloid fibers at 37 °C without external control of pH or addition of electrolyte. The fibrillation of BSA occurs spontaneously with the addition of IL; however, the highest growth rate has been observed in aqueous solution of 10% IL (v/v %) among investigated systems. Thioflavin T (ThT) fluorescence emission has been employed to monitor the growth and development of ß-sheet content in amyloid fibrils. The structural alterations in BSA have also been investigated using intrinsic fluorescence measurements. Circular dichroism (CD) measurements confirmed the formation of amyloid fibrils. Transmission electron microscopy (TEM) has been explored to establish the morphologies of BSA fibrils at different intervals of time, whereas atomic force microscopy (AFM) has established the helically twisted nature of grown amyloid fibrils. The docking studies have been utilized to understand the insertion of IL ions in different domains of BSA, which along with decreased pH cause the unfolding and growth of BSA into amyloid fibrils. It is expected that the results obtained from this study would help to understand the impact of IL containing [BF4]- anion on protein stability and aggregation along with providing a new platform to control the formation of amyloid fibrils and other biomaterials driven via ionic interactions and alterations in pH.


Assuntos
Líquidos Iônicos , Soroalbumina Bovina , Amiloide , Dicroísmo Circular , Hidrólise , Temperatura
5.
Chem Pharm Bull (Tokyo) ; 69(8): 802-805, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34334525

RESUMO

A new rearranged nitrogenous bisabolone-type sesquiterpene, halichonic acid B (1), was isolated from a marine sponge Axinyssa sp. together with halichonic acid (2) and (6R,7S)-7-amino-7,8-dihydro-α-bisabolene (3). The structure of 1 was determined by extensive NMR and MS analyses, revealing an unprecedented carbon framework, and its absolute configuration was elucidated by time-dependent density-functional theory (TDDFT)-based electronic circular dichroism (ECD) spectrum calculation. We propose that 1 and 2 may be biosynthesized in the same pathway, involving the reaction between farnesyl pyrophosphate and glycine, followed by cyclization.


Assuntos
Poríferos/química , Sesquiterpenos/química , Animais , Dicroísmo Circular , Teoria da Densidade Funcional , Conformação Molecular , Sesquiterpenos/isolamento & purificação , Fatores de Tempo
6.
Nano Lett ; 21(17): 7298-7308, 2021 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-34428053

RESUMO

Chiral plasmonic nanostructures exhibit anomalously strong chiroptical signals and offer the possibility to realize asymmetric photophysical and photochemical processes controlled by circularly polarized light. Here, we use a chiral DNA-assembled nanorod pair as a model system for chiral plasmonic photomelting. We show that both the enantiomeric excess and consequent circular dichroism can be controlled with chiral light. The nonlinear chiroptical response of our plasmonic system results from the chiral photothermal effect leading to selective melting of the DNA linker strands. Our study describes both the single-complex and collective heating regimes, which should be treated with different models. The chiral asymmetry factors of the calculated photothermal and photomelting effects exceed the values typical for the chiral molecular photochemistry at least 10-fold. Our proposed mechanism can be used to develop chiral photoresponsive systems controllable with circularly polarized light.


Assuntos
Nanopartículas , Nanoestruturas , Nanotubos , Dicroísmo Circular , DNA
7.
J Phys Chem Lett ; 12(32): 7733-7737, 2021 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-34355918

RESUMO

The supramolecular chirality of the hindwing of Anomala albopilosa (male) was investigated using a microscopic vibrational circular dichroism (VCD) system, denoted as MultiD-VCD. The source of intense infrared (IR) light for the system was a quantum cascade laser. Two-dimensional maps of IR and VCD spectra were taken by scanning the surface area (ca. 2 mm × 2 mm) of the insect hindwing tissue. The spectra ranged from 1500 to 1700 cm-1, and the maps have a spatial resolution of 100 µm. The distribution of proteins, including their supramolecular structures, was analyzed from the location-dependent spectral shape of the VCD bands assigned to amides I and II. The results revealed that the hindwing consists of segregated domains of proteins with different secondary structures: an α-helix (in one part of the membrane), a hybrid of α-helix and ß-sheet (in another part of the membrane), and a coil (in a vein).


Assuntos
Proteínas de Insetos/química , Asas de Animais/química , Animais , Dicroísmo Circular/métodos , Besouros , Masculino , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Estereoisomerismo , Vibração
8.
Phytochemistry ; 190: 112892, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34343886

RESUMO

Large-scale culture is a complementary and practical method for genome mining and OSMAC approaches to discover novel natural products through accumulation and reprocessing effects. By employing a large-scale culture approach, twelve 3,5-dimethylorsellinic acid (DMOA)-based meroterpenoids, including five undescribed compounds, namely asperanstinoids A-E, were obtained from fungus Aspergillus calidoustus, which was isolated from the wetland soil collected at Dianchi Lake, Yunnan Province. The structures and absolute configurations of asperanstinoids A-E were determined by various spectroscopic analyses, including NMR spectroscopy, high-resolution electrospray ionization mass spectrometry (HRESIMS), single-crystal X-ray diffraction, and electronic circular dichroism (ECD) calculations, and the absolute configurations of three known compounds, dehydroaustinol, austinol, and austin, were confirmed via single-crystal X-ray diffraction for the first time. Notably, asperanstinoid A represents the second example of a DMOA-based meroterpenoid featuring a unique 6/5/6/6/6/5-fused hexacyclic skeleton with a rare "1,13-epoxy" moiety. The cytotoxicity assay of all these isolates revealed that asperanstinoid D, dehydroaustinol, and austin displayed considerable cytotoxicity against the HL-60 and SU-DHL-4 tumor cell lines with IC50 values ranging from 15.7 to 27.8 µM.


Assuntos
Aspergillus , China , Dicroísmo Circular , Resorcinóis
9.
Molecules ; 26(13)2021 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-34279403

RESUMO

A hydrogen-bonded (H-bonded) amide macrocycle was found to serve as an effective component in the host-guest assembly for a supramolecular chirality transfer process. Circular dichroism (CD) spectroscopy studies showed that the near-planar macrocycle could produce a CD response when combined with three of the twelve L-α-amino acid esters (all cryptochiral molecules) tested as possible guests. The host-guest complexation between the macrocycle and cationic guests was explored using NMR, revealing the presence of a strong affinity involving the multi-point recognition of guests. This was further corroborated by density functional theory (DFT) calculations. The present work proposes a new strategy for amplifying the CD signals of cryptochiral molecules by means of H-bonded macrocycle-based host-guest association, and is expected to be useful in designing supramolecular chiroptical sensing materials.


Assuntos
Dicroísmo Circular/métodos , Compostos Macrocíclicos/química , Aminoácidos/química , Ésteres/química
10.
Int J Mol Sci ; 22(11)2021 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-34199659

RESUMO

Herein we describe a combined experimental and in silico study of the interaction of a series of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives (PBTs) with parallel G-quadruplex (GQ) DNA aimed at correlating their previously reported anticancer activities and the stabilizing effects observed by us on c-myc oncogene promoter GQ structure. Circular dichroism (CD) melting experiments were performed to characterize the effect of the studied PBTs on the GQ thermal stability. CD measurements indicate that two out of the eight compounds under investigation induced a slight stabilizing effect (2-4 °C) on GQ depending on the nature and position of the substituents. Molecular docking results allowed us to verify the modes of interaction of the ligands with the GQ and estimate the binding affinities. The highest binding affinity was observed for ligands with the experimental melting temperatures (Tms). However, both stabilizing and destabilizing ligands showed similar scores, whilst Molecular Dynamics (MD) simulations, performed across a wide range of temperatures on the GQ in water solution, either unliganded or complexed with two model PBT ligands with the opposite effect on the Tms, consistently confirmed their stabilizing or destabilizing ability ascertained by CD. Clues about a relation between the reported anticancer activity of some PBTs and their ability to stabilize the GQ structure of c-myc emerged from our study. Furthermore, Molecular Dynamics simulations at high temperatures are herein proposed for the first time as a means to verify the stabilizing or destabilizing effect of ligands on the GQ, also disclosing predictive potential in GQ-targeting drug discovery.


Assuntos
DNA/efeitos dos fármacos , Quadruplex G/efeitos dos fármacos , Proteínas Proto-Oncogênicas c-myc/química , Telômero/química , Sítios de Ligação/efeitos dos fármacos , Dicroísmo Circular , Simulação por Computador , DNA/química , DNA/ultraestrutura , Humanos , Ligantes , Simulação de Dinâmica Molecular , Regiões Promotoras Genéticas/genética , Proteínas Proto-Oncogênicas c-myc/ultraestrutura , Telômero/efeitos dos fármacos , Telômero/genética
11.
Int J Mol Sci ; 22(12)2021 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-34204483

RESUMO

Oxidative stress, photo-oxidation, and photosensitizers are activated by UV irradiation and are affecting the photo-stability of proteins. Understanding the mechanisms that govern protein photo-stability is essential for its control enabling enhancement or reduction. Currently, two major mechanisms for protein denaturation induced by UV irradiation are available: one generated by the local heating of water molecules bound to the proteins and the other by the formation of reactive free radicals. To discriminate which is the likely or dominant mechanism we have studied the effects of thermal and UV denaturation of aqueous protein solutions with and without DHR-123 as fluorogenic probe using circular dichroism (CD), synchrotron radiation circular dichroism (SRCD), and fluorescence spectroscopies. The results indicated that the mechanism of protein denaturation induced by VUV and far-UV irradiation were mediated by the formation of reactive free radicals (FR) and reactive oxygen species (ROS). The development at Diamond B23 beamline for SRCD of a novel protein UV photo-stability assay based on consecutive repeated CD measurements in the far-UV (180-250 nm) region has been successfully used to assess and characterize the photo-stability of protein formulations and ligand binding interactions, in particular for ligand molecules devoid of significant UV absorption.


Assuntos
Radicais Livres/química , Desnaturação Proteica , Proteínas/química , Espécies Reativas de Oxigênio/química , Raios Ultravioleta , Dicroísmo Circular , Calefação , Desnaturação Proteica/efeitos dos fármacos , Desnaturação Proteica/efeitos da radiação , Espécies Reativas de Oxigênio/metabolismo , Análise Espectral , Água/química
12.
Spectrochim Acta A Mol Biomol Spectrosc ; 262: 120105, 2021 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-34245970

RESUMO

Azaphenothiazines (AZA), modified phenothiazine derivatives, have been reported to exhibit a wide spectrum of biological activities, including anticancer activities, but the mechanisms of their interactions with biomolecules are not fully recognized. In this work, the mode of interaction of selected AZA with calf thymus DNA was investigated using UV-Vis absorption, fluorescence spectroscopy (competition experiment with ethidium bromide, quenching of fluorescence) and molecular docking. The investigated AZA represent dipyrido[3,4-b;3'4'-e][1,4]thiazine, quino[3,2-b]benzo[1,4]thiazine and diquino[3,2-b;2',3'-e][1,4]thiazine possessing tricyclic, tetracyclic and pentacyclic ring system with the additional N,N-dimethylaminopropyl group at the nitrogen atom in the 1,4 thiazine ring. The results obtained from spectroscopic studies showed that AZA bind to DNA by insertion of a fragment of the fused rings system between the base pair stack in the double helix of DNA. In addition, the number of rings in the AZA structures seemed to be related to the strength of the interaction, because pentacyclic AZA (binding constant Kb = 6.31 × 106 L/mol) demonstrated 10-fold higher affinity towards DNA than the tetracyclic AZA and about 100-fold higher affinity than that of tricyclic AZA. The molecular docking results showed that the binding mode of AZA to DNA helix was an intercalation mode with the partial insertion of one planar part of the AZA structure (the pyridine or quinoline ring) into the neighboring bases of one of the DNA chains with additional hydrogen bonding with the minor groove through the positively charged N,N-dimethylaminopropyl group. Chemical potential (µ), chemical hardness (ƞ), electronegativity (χ) and the value of electrons transferred from one system to another (ΔN) calculated from the HOMO and LUMO energies by the density functional theory method indicated that AZA acted as the electron acceptors to the DNA bases.


Assuntos
DNA , Fenotiazinas , Dicroísmo Circular , Simulação de Acoplamento Molecular , Espectrometria de Fluorescência , Espectrofotometria Ultravioleta , Termodinâmica
13.
Int J Mol Sci ; 22(13)2021 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-34281151

RESUMO

The application of siRNA in gene therapy is mainly limited because of the problems with its transport into cells. Utilization of cationic dendrimers as siRNA carriers seems to be a promising solution in overcoming these issues, due to their positive charge and ability to penetrate cell membranes. The following two types of carbosilane dendrimers were examined: CBD-1 and CBD-2. Dendrimers were complexed with pro-apoptotic siRNA (Mcl-1 and Bcl-2) and the complexes were characterized by measuring their zeta potential, circular dichroism and fluorescence of ethidium bromide associated with dendrimers. CBD-2/siRNA complexes were also examined by agarose gel electrophoresis. Both dendrimers form complexes with siRNA. Moreover, the cellular uptake and influence on the cell viability of the dendrimers and dendriplexes were evaluated using microscopic methods and XTT assay on MCF-7 cells. Microscopy showed that both dendrimers can transport siRNA into cells; however, a cytotoxicity assay showed differences in the toxicity of these dendrimers.


Assuntos
RNA Interferente Pequeno/uso terapêutico , Silanos/farmacologia , Cátions , Sobrevivência Celular , Dicroísmo Circular , Dendrímeros/química , Dendrímeros/farmacologia , Terapia Genética/métodos , Humanos , Células MCF-7 , Proteína de Sequência 1 de Leucemia de Células Mieloides/genética , Proteína de Sequência 1 de Leucemia de Células Mieloides/metabolismo , Tamanho da Partícula , Proteínas Proto-Oncogênicas c-bcl-2/genética , Proteínas Proto-Oncogênicas c-bcl-2/metabolismo , RNA de Cadeia Dupla/genética , RNA Interferente Pequeno/genética , Silanos/química , Silanos/metabolismo
14.
Anal Chem ; 93(29): 9965-9969, 2021 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-34251808

RESUMO

A new strategy has been developed for the direct chirality fixation, which is induced by electrochemical polymerization, of macrocyclic hosts pillar[5]arene. Taking advantage of electrochemical polymerization, thiophene-modified pillar[5]arene monomers (Th-P[5]A) have been regularly arranged under the action of an electric field to form chiral nanofiber-like crystalline pillar[5]arene-based polymers (poly-Th-P[5]A), showing a significant circular dichroism (CD) signal. With the active photochemical properties, poly-Th-P[5]A is first used as a photoelectrochemical (PEC) chiral sensor for the identification and determination of l- and d-ascorbic acid (l-AA, d-AA) without adding any extra photoactive probes. Importantly, the chiral recognition between poly-Th-P[5]A and l-AA also triggers a polarity conversion for the photocurrent of the polymer, and it greatly results in a broad chiral detection range for l-AA, crossing 6 orders of magnitude. This work provides a promotional strategy for building a PEC chiral recognition platform based on pillararenes.


Assuntos
Ácido Ascórbico , Polímeros , Dicroísmo Circular , Polimerização
15.
Int J Mol Sci ; 22(14)2021 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-34299001

RESUMO

G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene RPB1, coding for the RNA polymerase II large subunit. We found that this G-quadruplex-forming locus is highly evolutionarily conserved amongst plants sensu lato (Archaeplastida) that share a common ancestor more than one billion years old. Finally, we discussed a new hypothesis regarding G-quadruplexes interacting with UV light in plants to potentially form an additional layer of the regulatory network.


Assuntos
Quadruplex G , Proteínas de Plantas/química , Plantas/química , RNA Polimerase II/química , Sequência de Aminoácidos , Arabidopsis/química , Arabidopsis/genética , Arabidopsis/efeitos da radiação , Dicroísmo Circular , Biologia Computacional , Evolução Molecular , Quadruplex G/efeitos da radiação , Regulação da Expressão Gênica de Plantas/genética , Glaucófitas/química , Glaucófitas/genética , Glaucófitas/efeitos da radiação , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/efeitos da radiação , Plantas/genética , Plantas/efeitos da radiação , RNA Polimerase II/genética , Rodófitas/química , Rodófitas/genética , Rodófitas/efeitos da radiação , Alinhamento de Sequência , Raios Ultravioleta
16.
Int J Mol Sci ; 22(13)2021 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-34201610

RESUMO

The accumulation of aggregated protein is a typical hallmark of many human neurodegenerative disorders, including polyglutamine-related diseases such as chorea Huntington. Misfolding of the amyloidogenic proteins gives rise to self-assembled complexes and fibres. The huntingtin protein is characterised by a segment of consecutive glutamines which, when exceeding ~ 37 residues, results in the occurrence of the disease. Furthermore, it has also been demonstrated that the 17-residue amino-terminal domain of the protein (htt17), located upstream of this polyglutamine tract, strongly correlates with aggregate formation and pathology. Here, we demonstrate that membrane interactions strongly accelerate the oligomerisation and ß-amyloid fibril formation of htt17-polyglutamine segments. By using a combination of biophysical approaches, the kinetics of fibre formation is investigated and found to be strongly dependent on the presence of lipids, the length of the polyQ expansion, and the polypeptide-to-lipid ratio. Finally, the implications for therapeutic approaches are discussed.


Assuntos
Membrana Celular/metabolismo , Proteína Huntingtina/metabolismo , Peptídeos/metabolismo , Benzotiazóis/química , Dicroísmo Circular , Difusão Dinâmica da Luz , Éxons , Fluorescência , Humanos , Proteína Huntingtina/química , Proteína Huntingtina/genética , Bicamadas Lipídicas , Fragmentos de Peptídeos/genética , Fragmentos de Peptídeos/metabolismo , Peptídeos/química
17.
J Phys Chem B ; 125(27): 7351-7358, 2021 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-34213353

RESUMO

Cationic or anionic residues are frequently located at the termini of proteins because their charged side chain can form electrostatic interactions with a terminal carboxylate or ammonium group to stabilize the structure under physiological conditions. Here, we used collagen-mimetic peptides (CMPs) to examine how the terminal charge-charge interactions affect the collagen triple helix stability. We designed a series of CMPs with either a Lys or Glu incorporated into the terminus and measured their pH-dependent stability. The results showed that the terminal electrostatic attractions stabilized the triple helix, while the terminal electrostatic repulsions destabilized the trimer. The data also revealed that the repulsions imposed a greater effect than did the attractions on the triple helix. An amino acid with a shorter side chain, such as aspartate and ornithine, was also installed to investigate the length effect on electrostatic interactions, which was found to be insignificant. Meanwhile, simultaneously incorporating cationic and anionic residues into the termini showed slight additive stabilization effects but pronounced additive destabilization consequences. We have demonstrated that the collagen triple helix stability can be modulated by introducing a cationic or anionic residue into the terminus of a peptide, giving useful information for the design of collagen-associated materials.


Assuntos
Colágeno , Peptídeos , Aminoácidos , Dicroísmo Circular , Eletricidade Estática
18.
J Phys Chem B ; 125(28): 7662-7670, 2021 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-34232040

RESUMO

We studied the stability and folding and unfolding kinetics of the tryptophan zipper, containing different double thioamide subsitutions. Conformation change was triggered by photoisomerization of an integrated AMPP photoswitch in the turn region of the hairpin, and transient spectra were recorded in the deep UV and the mid-IR, covering the time window of the (un)folding transition from picoseconds to tens of microseconds. Thio-substitution of inward-pointing backbone carbonyls was found to strongly destabilize the ß-hairpin structures, whereas molecules with two outward pointing thio-carbonyls showed similar or enhanced stability with respect to the unsubstituted sequence, which we attribute to stronger interstrand hydrogen bonding. Thiolation of the two Trp residues closest to the turn can even prevent the opening of the hairpin after cis-trans isomerization of the switch. The circular dichroism due to the two thioamide ππ* transitions is spectrally well-separated from the aromatic tryptophan signal. It changes upon photoswitching, reflecting a local change in coupling and geometry.


Assuntos
Dobramento de Proteína , Triptofano , Dicroísmo Circular , Cinética , Desnaturação Proteica , Estrutura Secundária de Proteína , Tioamidas
19.
J Phys Chem B ; 125(28): 7750-7762, 2021 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-34232651

RESUMO

Nitric oxide-containing drugs present a critical remedy for cardiovascular diseases. Nitroglycerin (NG, O-NO) and S-nitrosoglutathione (SNG, S-NO) are the most common nitric oxide drugs for cardiovascular diseases. Insights regarding the binding affinity of NO drugs with lysozyme and human serum albumin (HSA) proteins and their dissociation mechanism will provide inquisitive information regarding the potential of the proteins as drug carriers. For the first time, the binding interactions and affinities are investigated using molecular docking, conventional molecular dynamics, steered molecular dynamics, and umbrella sampling to explore the ability of both proteins to act as nitric oxide drug carriers. The molecular dynamics simulation results showed higher stability of lysozyme-drug complexes compared to HSA. For lysozyme, cardiovascular drugs were bound in the protein cavity mainly by the electrostatic and hydrogen bond interactions with residues ASP53, GLN58, ILE59, ARG62, TRP64, ASP102, and TRP109. For HSA, key binding residues were ARG410, TYR411, LYS414, ARG485, GLU450, ARG486, and SER489. The free energy profiles produced from umbrella sampling also suggest that lysozyme-drug complexes had better binding affinity than HSA-drug. Binding characteristics of nitric oxide-containing drugs NG and SNG to lysozyme and HSA proteins were studied using fluorescence and UV-vis absorption spectroscopy. The relative change in the fluorescence intensity as a function of drug concentrations was analyzed using Stern-Volmer calculations. This was also confirmed by the change in the UV-vis spectra. Fluorescence quenching results of both proteins with the drugs, based on the binding constant values, demonstrated significantly weak binding affinity to NG and strong binding affinity to SNG. Both computational and experimental studies provided important data for understanding protein-drug interactions and will aid in developing potential drug carrier systems in cardiovascular diseases.


Assuntos
Fármacos Cardiovasculares , Muramidase , Sítios de Ligação , Dicroísmo Circular , Portadores de Fármacos , Humanos , Simulação de Acoplamento Molecular , Óxido Nítrico , Ligação Proteica , Albumina Sérica/metabolismo , Albumina Sérica Humana/metabolismo , Espectrometria de Fluorescência , Termodinâmica
20.
J Phys Chem B ; 125(29): 8088-8098, 2021 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-34279936

RESUMO

G-quadruplexes play important roles in cellular regulatory functions, but despite significant experimental and theoretical efforts, their folding mechanisms remain poorly understood. In this context, we developed a T-jump experiment to access the thermal denaturation and renaturation dynamics of short intramolecular G-quadruplexes in vitro, on the time scale of a few hundred milliseconds. With this new setup, we compared the thermal denaturation and renaturation kinetics of three antiparallel topologies made of the human telomeric sequences d[(5'-GGG(TTAGGG)3-3']/Na+ and d[5'-AGGG(TTAGGG)3-3']/Na+ and the thrombin-binding aptamer sequence d[5'-GGTTGGTGTGGTTGG-3']/K+, with those of the parallel topology made of the human CEB25 minisatellite d[5'-AAGGGTGGGTGTAAGTGTGGGTGGGT-3']/Na+. In all cases, exponential kinetics of the order of several hundred milliseconds were observed. Measurements performed for different initial temperatures revealed distinct denaturation and renaturation dynamics, ruling out a simple two-state mechanism. The parallel topology, in which all guanines adopt an anti conformation, displays much slower dynamics than antiparallel topologies associated with very low activation barriers. This behavior can be explained by the constrained conformational space due to the presence of the single-base propeller loops that likely hinders the movement of the coiled DNA strand and reduces the contribution of the entropy during the renaturation process at high temperatures.


Assuntos
Quadruplex G , Dicroísmo Circular , Humanos , Conformação de Ácido Nucleico , Potássio , Telômero , Temperatura
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