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1.
Food Chem Toxicol ; 135: 110933, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31682930

RESUMO

Chelerythrine (CHE), a benzophenanthridine alkaloid, is usually used as a nutritional and functional additive in variety of health foods. However, it should be paid enough attention because of its potential toxicity to human health. In this work, the binding mechanism of CHE with bovine serum albumin (BSA) was systematically investigated with spectroscopic approaches. The results showed that the mixture of BSA with CHE could spontaneously cause the formation of BSA-CHE complex through electrostatic interaction under simulative physiological conditions (0.01 mol L-1 Tris-HCl, 0.015 mol L-1 NaCl, pH = 7.4). Site marker competitive displacement experiments exhibited that CHE was primarily bound to the hydrophobic pocket of the site II (subdomain IIIA) of BSA. It has been reported that the binding of small functional molecules to serum albumins remarkably impacts their absorption, distribution, metabolism, conformation, and excretion features. Therefore, this study might be helpful for human to have an in-depth understanding of the biological effect of CHE in vivo and guide human to take it safely and reasonably.


Assuntos
Benzofenantridinas/metabolismo , Soroalbumina Bovina/metabolismo , Animais , Sítios de Ligação , Bovinos , Dicroísmo Circular , Ligação Proteica , Conformação Proteica em alfa-Hélice/efeitos dos fármacos , Espectrometria de Fluorescência , Termodinâmica
2.
Biosci Biotechnol Biochem ; 84(1): 143-153, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31549575

RESUMO

Brevinin-GR23 (B-GR23) was a brevinin-2 like antimicrobial peptide, which had antimicrobial activity against Staphylococcus aureus with minimum inhibitory concentration (MIC) of 16 µM. B-GR23 increased the bacterial membrane permeation, leading to the damage of membrane integrity and the leakage of genomic DNA, then causing the cell death. The peptide nearly inhibited all plantonic bacteria to start the initial attachment of biofilm at the concentration of 1 × MIC. Whereas the disruption rates on immature and mature biofilm decreased from 60% to 20%. B-GR23 reduced the production of extracellular polysaccharides (EPS) in the planktonic growth of S. aureus, which is a crucial structure of biofilm formation. B-GR23 with the concentration of ½ × MIC inhibited 50% water-soluble EPS, and 48% water-insoluble EPS, which contributed to the antibiofilm activity. B-GR23 had no significant toxicity to human blood cells under-tested concentration (200 µM), making it a potential template for designing antimicrobial peptides.


Assuntos
Proteínas de Anfíbios/farmacologia , Antibacterianos/farmacologia , Peptídeos Catiônicos Antimicrobianos/farmacologia , Biofilmes/efeitos dos fármacos , Staphylococcus aureus/fisiologia , Animais , Antibacterianos/síntese química , Peptídeos Catiônicos Antimicrobianos/síntese química , Peptídeos Catiônicos Antimicrobianos/química , Permeabilidade da Membrana Celular/efeitos dos fármacos , DNA Bacteriano/efeitos dos fármacos , DNA Bacteriano/metabolismo , Eritrócitos/efeitos dos fármacos , Hemólise/efeitos dos fármacos , Temperatura Alta , Humanos , Concentração de Íons de Hidrogênio , Testes de Sensibilidade Microbiana/métodos , Polissacarídeos Bacterianos/antagonistas & inibidores , Conformação Proteica em alfa-Hélice , Estabilidade Proteica/efeitos da radiação , Ranidae , Infecções Estafilocócicas/tratamento farmacológico
3.
Phys Chem Chem Phys ; 22(3): 1359-1370, 2020 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-31854397

RESUMO

Depending on the amino acid sequence, as well as the local environment, some peptides have the capability to fold into multiple secondary structures. Conformational switching between such structures is a key element of protein folding and aggregation. Specifically, understanding the molecular mechanism underlying the transition from an α-helix to a ß-hairpin is critical because it is thought to be a harbinger of amyloid assembly. In this study, we explore the energy landscape for an 18-residue peptide (DP5), designed by Araki and Tamura to exhibit equal propensities for the α-helical and ß-hairpin forms. We find that the degeneracy is encoded in the multifunnel nature of the underlying free energy landscape. In agreement with experiment, we also observe that mutation of tyrosine at position 12 to serine shifts the equilibrium in favor of the α-helix conformation, by altering the landscape topography. The transition from the α-helix to the ß-hairpin is a complex stepwise process, and occurs via collapsed coil-like intermediates. Our findings suggest that even a single mutation can tune the emergent features of the landscape, providing an efficient route to protein design. Interestingly, the transition pathways for the conformational switch seem to be minimally perturbed upon mutation, suggesting that there could be universal microscopic features that are conserved among different switch-competent protein sequences.


Assuntos
Peptídeos/química , Mutação , Peptídeos/genética , Conformação Proteica em alfa-Hélice/genética , Conformação Proteica em Folha beta/genética
4.
Phys Chem Chem Phys ; 22(3): 1543-1556, 2020 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-31872820

RESUMO

Amyloid aggregation modulators offer a promising treatment strategy for Alzheimer's disease (AD). We have recently reported a novel di-triazole based compound 6n as a multi-target-directed ligand (MTDL) against AD. 6n effectively inhibits Aß42 aggregation, metal-induced Aß42 aggregation, reactive oxygen species (ROS) generation, and rescues SH-SY5Y cells from Aß42 induced neurotoxicity. However, the underlying inhibitory mechanism remains uncovered. In this regard, molecular dynamics (MD) simulations were performed to understand the effect of 6n on the structure and stability of monomeric Aß42 and a pentameric protofibril structure of Aß42. Compound 6n binds preferably to the central hydrophobic core (CHC) and C-terminal regions of the Aß42 monomer as well as the protofibril structure. The secondary structure analysis suggests that 6n prevents the aggregation of the Aß42 monomer and disaggregates Aß42 protofibrils by sustaining the helical content in the Aß42 monomer and converting the ß-sheet into random coil conformation in the Aß42 protofibril structure. A significant decrease in the average number of hydrogen bonds, binding affinity, and residue-residue contacts between chains D-E of the Aß42 protofibril in the presence of 6n indicates destabilization of the Aß42 protofibril structure. The MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) analysis highlighted favourable binding free energy (ΔGbinding) for the Aß42 monomer-6n and Aß42 protofibril-6n complex. Overall, MD results highlighted that 6n stabilizes the native α-helix conformation of the Aß42 monomer and induces a sizable destabilization in the Aß42 protofibril structure. This work provides theoretical insights into the inhibitory mechanism of 6n against amyloid aggregation and will be beneficial as a molecular guide for structure-based drug design against AD.


Assuntos
Peptídeos beta-Amiloides/metabolismo , Fragmentos de Peptídeos/metabolismo , Triazóis/química , Amiloide/química , Amiloide/metabolismo , Peptídeos beta-Amiloides/química , Simulação de Dinâmica Molecular , Fragmentos de Peptídeos/química , Ligação Proteica , Conformação Proteica em alfa-Hélice , Estabilidade Proteica
5.
Phys Rev Lett ; 123(23): 238102, 2019 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-31868483

RESUMO

Collagen consists of three peptides twisted together through a periodic array of hydrogen bonds. Here we use this as inspiration to find design rules for programmed specific interactions for self-assembling synthetic collagenlike triple helices, starting from disordered configurations. The assembly generically nucleates defects in the triple helix, the characteristics of which can be manipulated by spatially varying the enthalpy of helix formation. Defect formation slows assembly, evoking kinetic pathologies that have been observed to mutations in the primary collagen amino acid sequence. The controlled formation and interaction between defects gives a route for hierarchical self-assembly of bundles of twisted filaments.


Assuntos
Colágeno/química , Modelos Químicos , Sequência de Aminoácidos , Modelos Moleculares , Nanoestruturas/química , Peptídeos/química , Conformação Proteica em alfa-Hélice
6.
Phys Rev Lett ; 123(18): 188102, 2019 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-31763918

RESUMO

The cytoskeleton is a composite network of three types of protein filaments, among which intermediate filaments (IFs) are the most extensible ones. Two very important IFs are keratin and vimentin, which have similar molecular architectures but different mechanical behaviors. Here we compare the mechanical response of single keratin and vimentin filaments using optical tweezers. We show that the mechanics of vimentin strongly depends on the ionic strength of the buffer and that its force-strain curve suggests a high degree of cooperativity between subunits. Indeed, a computational model indicates that in contrast to keratin, vimentin is characterized by strong lateral subunit coupling of its charged monomers during unfolding of α helices. We conclude that cells can tune their mechanics by differential use of keratin versus vimentin.


Assuntos
Citoesqueleto/química , Queratinas/química , Modelos Biológicos , Vimentina/química , Fenômenos Biomecânicos , Tampões (Química) , Citoesqueleto/metabolismo , Queratinas/metabolismo , Microscopia de Força Atômica , Pinças Ópticas , Concentração Osmolar , Conformação Proteica em alfa-Hélice , Vimentina/metabolismo
7.
Phys Chem Chem Phys ; 21(44): 24601-24619, 2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31670335

RESUMO

Natural bond orbital (NBO) analysis of electron delocalization in a series of capped isolated peptides is used to diagnose amide-amide H-bonding and backbone-induced hyperconjugative interactions, and to rationalize their spectral effects. The sum of the stabilization energies corresponding to the interactions between NBOs that are involved in the H-bonding is demonstrated as an insightful indicator for the H-bond strength. It is then used to decouple the effect of the H-bond distance from that, intrinsic, of the donor/acceptor relative orientation, i.e., the geometrical approach. The diversity of the approaches given by the series of peptides studied enables us to illustrate the crucial importance of the approach when the acceptor is a carbonyl group, and emphasizes that efficient approaches can be achieved despite not matching the usual picture of a proton donor directly facing a lone pair of the proton acceptor, i.e., that encountered in intermolecular H-bonds. The study also illustrates the role of backbone flexibility, partly controlled by backbone-amide hyperconjugative interactions, in influencing the equilibrium structures, in particular by frustrating or enhancing the HB for a given geometrical approach. Finally, the presently used NBO-based HB strength indicator enables a fair prediction of the frequency of the proton donor amide NH stretching mode, but this simple picture is blurred by ubiquitous hyperconjugative effects between the backbone and amide groups, whose magnitude can be comparable to that of the weakest H-bonds.


Assuntos
Amidas/química , Peptídeos/química , Dimerização , Ligações de Hidrogênio , Modelos Moleculares , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Teoria Quântica
8.
Chem Asian J ; 14(23): 4408-4414, 2019 Dec 02.
Artigo em Inglês | MEDLINE | ID: mdl-31670907

RESUMO

Molecular chirality is ubiquitous in nature. The natural biopolymers, proteins and DNA, preferred a right-handed helical bias due to the inherent stereochemistry of the monomer building blocks. Here, we are reporting a rare co-existence of left- and right-handed helical conformations and helix-terminating property at the C-terminus within a single molecule of α,γ-hybrid peptide foldamers composed of achiral Aib (α-aminoisobutyric acid) and 3,3-dimethyl-substituted γ-amino acid (Adb; 4-amino-3,3-dimethylbutanoic acid). At the molecular level, the left- and right-handed helical screw sense of α,γ-hybrid peptides are representing a macroscopic tendril perversion. The pronounced helix-terminating behaviour of C-terminal Adb residues was further explored to design helix-Schellman loop mimetics and to study their conformations in solution and single crystals. The stereochemical constraints of dialkyl substitutions on γ-amino acids showed a marked impact on the folding behaviour of α,γ-hybrid peptides.


Assuntos
Peptídeos/química , Ácidos Aminoisobutíricos/química , Cristalografia por Raios X , Ligações de Hidrogênio , Simulação de Dinâmica Molecular , Conformação Proteica em alfa-Hélice , Estereoisomerismo
9.
J Phys Chem Lett ; 10(23): 7406-7413, 2019 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-31721587

RESUMO

Using enhanced-sampling replica exchange fully atomistic molecular dynamics simulations, we show that, individually, urea and guanidinium chloride (GdmCl) denature the Trpcage protein, but remarkably, the helical segment 1NLYIQWL7 of the protein is stabilized in mixed denaturant solutions. GdmCl induces protein denaturation via a combination of direct and indirect effects involving dehydration of the protein and destabilization of stabilizing salt bridges. In contrast, urea denatures the protein through favorable protein-urea preferential interactions, with peptide-specific indirect effects of urea on the water structure around the protein. In the case of the helical segment of Trpcage, urea "oversolvates" the peptide backbone by reorganizing water molecules from the peptide side chains to the peptide backbone. An intricate nonadditive thermodynamic balance between GdmCl-induced dehydration of the peptide and the urea-induced changes in solvation structure triggers partial counteraction to urea denaturation and stabilization of the helix.


Assuntos
Guanidina/química , Peptídeos/química , Ureia/química , Sequência de Aminoácidos , Ligações de Hidrogênio , Conformação Proteica em alfa-Hélice , Desnaturação Proteica
10.
Nucleic Acids Res ; 47(16): 8874-8887, 2019 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-31616952

RESUMO

Localized arrays of proteins cooperatively assemble onto chromosomes to control DNA activity in many contexts. Binding cooperativity is often mediated by specific protein-protein interactions, but cooperativity through DNA structure is becoming increasingly recognized as an additional mechanism. During the site-specific DNA recombination reaction that excises phage λ from the chromosome, the bacterial DNA architectural protein Fis recruits multiple λ-encoded Xis proteins to the attR recombination site. Here, we report X-ray crystal structures of DNA complexes containing Fis + Xis, which show little, if any, contacts between the two proteins. Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery. Fis binding both molds the minor groove to potentiate insertion of the Xis ß-hairpin wing motif and bends the DNA to facilitate Xis-DNA contacts within the major groove. The Fis-structured minor groove shape that is optimized for Xis binding requires a precisely positioned pyrimidine-purine base-pair step, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA targets.


Assuntos
Bacteriófago lambda/genética , Cromossomos Bacterianos/química , DNA Nucleotidiltransferases/química , DNA Bacteriano/química , Proteínas de Escherichia coli/química , Escherichia coli/genética , Fator Proteico para Inversão de Estimulação/química , Proteínas Virais/química , Sítio Alostérico , Bacteriófago lambda/metabolismo , Sequência de Bases , Sítios de Ligação , Cromossomos Bacterianos/metabolismo , Clonagem Molecular , Cristalografia por Raios X , DNA Nucleotidiltransferases/genética , DNA Nucleotidiltransferases/metabolismo , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Fator Proteico para Inversão de Estimulação/genética , Fator Proteico para Inversão de Estimulação/metabolismo , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Cinética , Modelos Moleculares , Conformação de Ácido Nucleico , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Reparo de DNA por Recombinação , Alinhamento de Sequência , Termodinâmica , Proteínas Virais/genética , Proteínas Virais/metabolismo
11.
Phys Chem Chem Phys ; 21(44): 24393-24405, 2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31663524

RESUMO

Engineered repeat proteins have proven to be a fertile ground for studying the competition between folding, misfolding and transient aggregation of tethered protein domains. We examine the interplay between folding and inter-domain interactions of engineered FiP35 WW domain repeat proteins with n = 1 through 5 repeats. We characterize protein expression, thermal and guanidium melts, as well as laser T-jump kinetics. All experimental data is fitted by a global fitting model with two states per domain (U, N), plus a third state M to account for non-native states due to domain interactions present in all but the monomer. A detailed structural model is provided by coarse-grained simulated annealing using the AWSEM Hamiltonian. Tethered FiP35 WW domains with n = 2 and 3 domains are just slightly less stable than the monomer. The n = 4 oligomer is yet less stable, its expression yield is much lower than the monomer's, and depends on the purification tag used. The n = 5 plasmid did not express at all, indicating the sudden onset of aggregation past n = 4. Thus, tethered FiP35 has a critical nucleus size for inter-domain aggregation of n ≈ 4. According to our simulations, misfolded structures become increasingly prevalent as one proceeds from monomer to pentamer, with extended inter-domain beta sheets appearing first, then multi-sheet 'intramolecular amyloid' structures, and finally novel motifs containing alpha helices. We discuss the implications of our results for oligomeric aggregate formation and structure, transient aggregation of proteins whilst folding, as well as for protein evolution that starts with repeat proteins.


Assuntos
Proteínas/química , Cinética , Modelos Moleculares , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Engenharia de Proteínas , Dobramento de Proteína , Multimerização Proteica , Estabilidade Proteica , Proteínas/genética , Proteínas/metabolismo , Termodinâmica , Domínios WW
12.
Chem Commun (Camb) ; 55(86): 12920-12923, 2019 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-31608905

RESUMO

We report the direct observation of equilibrium folding-unfolding dynamics of a mechanically labile, three helix bundle protein GA using a commercial atomic force microscope (AFM). Our study extends the capability of commercial AFMs towards studying protein unfolding/refolding at equilibrium as well as increasingly complex biomolecular systems in the context of biological function.


Assuntos
Proteínas de Bactérias/química , Microscopia de Força Atômica , Conformação Proteica em alfa-Hélice , Domínios Proteicos , Dobramento de Proteína , Desdobramento de Proteína
13.
Phys Chem Chem Phys ; 21(40): 22396-22408, 2019 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-31577299

RESUMO

Our understanding of protein folds relies fundamentally on the set of secondary structures found in the proteomes. Yet, there also exist intriguing structures and motifs that are underrepresented in natural biopolymeric systems. One example is the polyproline II helix, which is usually considered to have a polar character and therefore does not form membrane spanning sections of membrane proteins. In our work, we have introduced specially designed polyproline II helices into the hydrophobic membrane milieu and used 19F NMR to monitor the helix alignment in oriented lipid bilayers. Our results show that these artificial hydrophobic peptides can adopt several different alignment states. If the helix is shorter than the thickness of the hydrophobic core of the membrane, it is submerged into the bilayer with its long axis parallel to the membrane plane. The polyproline helix adopts a transmembrane alignment when its length exceeds the bilayer thickness. If the peptide length roughly matches the lipid thickness, a coexistence of both states is observed. We thus show that the lipid thickness plays a determining role in the occurrence of a transmembrane polyproline II helix. We also found that the adaptation of polyproline II helices to hydrophobic mismatch is in some notable aspects different from α-helices. Finally, our results prove that the polyproline II helix is a competent structure for the construction of transmembrane peptide segments, despite the fact that no such motif has ever been reported in natural systems.


Assuntos
Bicamadas Lipídicas/metabolismo , Peptídeos/metabolismo , Flúor , Interações Hidrofóbicas e Hidrofílicas , Bicamadas Lipídicas/química , Espectroscopia de Ressonância Magnética , Peptídeos/síntese química , Peptídeos/química , Fosfatidilcolinas/química , Fosfatidilcolinas/metabolismo , Ligação Proteica , Conformação Proteica em alfa-Hélice
14.
Molecules ; 24(18)2019 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-31505731

RESUMO

To expand the utilization of oyster protein (OP), the effects of high pressure (100 to 500 MPa) on chemical forces, structure, microstructure, and digestibility properties were investigated. High pressure (HP) treatment enhanced the electrostatic repulsion (from -13.3Control to -27.8HP200 mV) between protein molecules and avoided or retarded the formation of protein aggregates. In addition, the HP treated samples showed uniform distribution and small particle size. The changes in electrostatic interaction and particle size contributed to the improvement of solubility (from 10.53%Control to 19.92%HP500 at pH 7). The stretching and unfolding of protein were modified by HP treatment, and some internal hydrophobic groups and -SH groups were exposed. HP treatment modified the secondary structure of OP. The treated samples contained less α-helix and ß-sheet structures, whereas the proportions of ß-sheet and random coil structures were increased. The treated samples have high digestibility in the stomach (from 26.3%Control to 39.5%HP500) and in the total digestive process (from 62.1%Control to 83.7%HP500). In addition, the total digestive production showed higher percentages of small peptides (<1 kDa) after HP treatment. The protein solubility and digestibility were increased after HP treatment, and high solubility and high digestibility might increase the chance that OP become a kind of protein supplement.


Assuntos
Ostreidae/química , Pressão/efeitos adversos , Agregados Proteicos , Proteínas/química , Animais , Interações Hidrofóbicas e Hidrofílicas , Tamanho da Partícula , Peptídeos/química , Peptídeos/metabolismo , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Estrutura Secundária de Proteína , Proteínas/metabolismo , Solubilidade , Estômago/química
15.
Biochimie ; 167: 93-105, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31560933

RESUMO

In this study, we tested the possibility of creating complexes of two proteins by fusing them with heterodimerizing helices. We used the fluorescent proteins GFP and mCHERRY expressed with a His-tag as our model system. We added heterodimer-forming sequences at the C- or N- termini of the proteins, opposite to the His-tag position. Heterodimerization was tested for both helices at the C-terminus or at the N- terminus and C-terminus. We observed complex formation with a nanomolar dissociation constant in both cases that was higher by one order of magnitude than the Kds measured for helices alone. The binding of two C-terminal helices was accompanied by an increased enthalpy change. The binding between helices could be stabilized by introducing an additional turn of the helix with cysteine, which was capable of forming disulphide bridges. Covalently linked proteins were obtained using this strategy and observed using fluorescence cross-correlation spectroscopy. Finally, we demonstrated the formation of complexes of protein dimers and quantum dots.


Assuntos
Cisteína/química , Proteínas de Fluorescência Verde/química , Proteínas Luminescentes/química , Multimerização Proteica , Pontos Quânticos/química , Sequência de Aminoácidos , Dimerização , Ligações de Hidrogênio , Modelos Moleculares , Conformação Proteica em alfa-Hélice
16.
Phys Chem Chem Phys ; 21(36): 20239-20251, 2019 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-31490518

RESUMO

The amyloid formation of human islet amyloid polypeptide (hIAPP)-an intrinsically disordered peptide, is associated with type II diabetes. Cellular membranes, especially those composed of negatively-charged lipids, accelerate the hIAPP amyloid fibrillation, and their integrity is disrupted during the aggregation process, leading to cell apoptosis. However, the underlying molecular mechanism is not well understood. Herein, we investigated the conformational dynamics during the interactions of hIAPP monomer with POPG membrane bilayer, by carrying out µs-long all-atom molecular dynamics simulations. Starting from the metastable coiled conformations in water, hIAPP monomers tend to adopt transient α-helical and ß-sheet structures when adsorbing to the membrane surface. The amphiphilic N-terminal region further inserts into the membrane interior and is located at the lipid head-tail interface, mainly in turn and α-helical structures. In contrast, the ß-hairpin structures reside on the membrane surface without insertion, and expand laterally with the hydrophobic residues exposed to the solvent. Moreover, the adsorption and insertion of hIAPP monomers induce two distinct local membrane deformations: (1) the hIAPP adsorption on the membrane surface mainly causes membrane bending; (2) the insertion of both turns and α-helices synchronizes with the formation of hydrophobic defects on the POPG membrane, leading to stronger membrane stretching and a longer coherence length of membrane thinning. Based on the structural and dynamical results, we propose that ß-hairpin structures may be a precursor for the fibrillation on the membrane surface due to the flat geometry and hydrophobic regions exposed to solvent, while N-terminal amphiphilic α-helices would facilitate hIAPP assembling into toxic oligomers inside the membrane.


Assuntos
Membrana Celular/química , Polipeptídeo Amiloide das Ilhotas Pancreáticas/química , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Humanos , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo
17.
Acta Biochim Pol ; 66(3): 329-336, 2019 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-31531422

RESUMO

The potential emergence of deadly pandemic influenza viruses is unpredictable and most have emerged with no forewarning. The distinct epidemiological and pathological patterns of the Spanish (H1N1), pandemic-2009 (H1N1), and avian influenza (H5N1), known as bird flu, viruses may allow us to develop a 'template' for possible emergence of devastating pandemic strains. Here, we provide a detailed molecular dissection of the structural and nonstructural proteins of this triad of viruses. GenBank data for three representative strains were analyzed to determine the polymorphic amino acids, genetic distances, and isoelectric points, hydrophobicity plot, and protein modeling of various proteins. We propose that the most devastating pandemic strains may have full-length PB1-F2 protein with unique residues, highly cleavable HA, and a basic NS1. Any newly emerging strain should be compared with these three strains, so that resources can be directed appropriately.


Assuntos
Simulação por Computador , Vírus da Influenza A Subtipo H1N1/genética , Virus da Influenza A Subtipo H5N1/genética , Influenza Aviária/virologia , Influenza Humana/virologia , Proteínas Virais/química , Animais , Aves , Transmissão de Doença Infecciosa , Genoma Viral , Humanos , Influenza Pandêmica, 1918-1919 , Vacinas contra Influenza , Influenza Aviária/epidemiologia , Influenza Aviária/prevenção & controle , Influenza Humana/epidemiologia , Influenza Humana/prevenção & controle , Pandemias , Conformação Proteica em alfa-Hélice , Proteínas Virais/genética
18.
Molecules ; 24(17)2019 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-31470504

RESUMO

Brucellosis, also known as "undulant fever" is a zoonotic disease caused by Brucella, which is a facultative intracellular bacterium. Despite efforts to eradicate this disease, infection in uncontrolled domestic animals persists in several countries and therefore transmission to humans is common. Brucella evasion of the innate immune system depends on its ability to evade the mechanisms of intracellular death in phagocytic cells. The BvrR-BvrS two-component system allows the bacterium to detect adverse conditions in the environment. The BvrS protein has been associated with genes of virulence factors, metabolism, and membrane transport. In this study, we predicted the DNA sequence recognized by BvrR with Gibbs Recursive Sampling and identified the three-dimensional structure of BvrR using I-TASSER suite, and the interaction mechanism between BvrR and DNA with Protein-DNA docking and molecular dynamics (MD) simulation. Based on the Gibbs recursive Sampling analysis, we found the motif AAHTGC (H represents A, C, and T nucleotides) as a possible sequence recognized by BvrR. The docking and EMD simulation results showed that C-terminal effector domain of BvrR protein is likely to interact with AAHTGC sequence. In conclusion, we predicted the structure, recognition motif, and interaction of BvrR with DNA.


Assuntos
Proteínas de Bactérias/química , Brucella/química , DNA/química , Fatores de Virulência/química , Motivos de Aminoácidos , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Brucella/patogenicidade , DNA/metabolismo , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Motivos de Nucleotídeos , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Homologia Estrutural de Proteína , Termodinâmica , Fatores de Virulência/metabolismo
19.
DNA Cell Biol ; 38(10): 1056-1068, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31403329

RESUMO

The AP2/ERF (APETALA2/ETHYLENE RESPONSE FACTOR) transcription factor represents one of the largest plant-specific transcriptional regulators in plants. ERF plays important roles in the regulation of various developmental processes and acts as a mediator in plant external stress responses. However, the research of the ERF gene family is still limited in alfalfa (Medicago sativa L.), one of the most important forage legume species in the world. In the present study, a total of 159 ERF genes were identified, and the phylogenetic reconstruction, classification, conserved motifs, signal peptide prediction, and expression patterns under salt, drought, and low-temperature stresses of these ERF genes were comprehensively analyzed. The ERF genes family in alfalfa could be classified into 10 groups and predicted to be strongly homologous. Based on the structure and functions relationships, the III and IV subfamilies were more likely to play functions in abiotic stresses and 18 MsERF genes were selected for further quantitative real-time PCR validation in different stresses treatment. The results showed that all these MsERF genes were upregulated under three stresses except MsERF008. This study identified the possibility of abiotic tolerance candidate genes playing various roles in stress resistance at the whole-genome level, which would provide primary understanding for exploring ERF-mediated tolerance in alfalfa.


Assuntos
Proteínas de Ligação a DNA/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Medicago sativa/genética , Folhas de Planta/genética , Proteínas de Plantas/genética , Temperatura Baixa , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Secas , Perfilação da Expressão Gênica , Medicago sativa/classificação , Medicago sativa/metabolismo , Filogenia , Folhas de Planta/metabolismo , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Raízes de Plantas/genética , Raízes de Plantas/metabolismo , Caules de Planta/genética , Caules de Planta/metabolismo , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Mapeamento de Interação de Proteínas , Isoformas de Proteínas , Salinidade , Estresse Fisiológico
20.
Chem Commun (Camb) ; 55(70): 10484-10487, 2019 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-31414101

RESUMO

The de novo design of stapled peptide-based self-assemblies attracts vast interest, yet still remains challenging. The development of an oxidation trigger for peptide stapling and subsequent self-assembly is described here. A self-assembling sequence, Fmoc-R(RCEX)2-NH2, transformed from a random coil to an α-helical structure upon disulphide bonding of the flanking cysteine residues positioning at the i/i + 4 locations. The stapling form of this peptide enforces a conformational restraint that affords the driving force for self-assembly into nanorod/nanovesicle structures. Moreover, these assembled materials can transport siRNA into cancer cells and immediately release the cargo in a reductive environment.


Assuntos
Peptídeos/química , Microscopia de Força Atômica , Oxirredução , Conformação Proteica em alfa-Hélice
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