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1.
Phys Chem Chem Phys ; 21(32): 17821-17835, 2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-31373340

RESUMO

The rise of New Delhi metallo-beta-lactamase-1 (NDM-1) producers is a major public health concern due to carbapenem resistance. Infections caused by carbapenem-resistant enterobacteria (CRE) are classified as a serious problem. To understand the structure and function of NDM-1, an amino acid replacement approach is considered as one of the methods to get structural insight. Therefore, we have generated novel mutations (N193A, S217A, G219A and T262A) near active sites and an omega-like loop to study the role of conserved residues of NDM-1. The minimum inhibitory concentrations (MICs) of ampicillin, imipenem, meropenem, cefotaxime, cefoxitin and ceftazidime for all mutants were found to be reduced 2 to 6 fold, compared to a wild type NDM-1 producing strain. The Km values increased while Kcat and Kcat/Km values were decreased compared to wild type. The affinity as well as the catalysis properties of these mutants were reduced considerably for imipenem, meropenem, cefotaxime, cefoxitin, and ceftazidimem compared to wild type, hence the catalytic efficiencies (Kcat/Km) of all mutant enzymes were reduced owing to the poor affinity of the enzyme. The IC50 values of these mutants with respect to each drug were reduced compared to wild type NDM-1. MD simulations and docking results from the mutant protein models, along with the wild type example, showed stable and consistent RMSD, RMSF and Rg behavior. The α-helix content values of all mutant proteins were reduced by 13%, 6%, 14% and 9% compared to NDM-1. Hence, this study revealed the impact role of active sites near residues on the enzyme catalytic activity of NDM-1.


Assuntos
Antibacterianos/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , beta-Lactamases/química , Antibacterianos/farmacologia , Biocatálise , Domínio Catalítico , Farmacorresistência Bacteriana , Cinética , Testes de Sensibilidade Microbiana , Mutagênese Sítio-Dirigida , Mutação , Ligação Proteica , Estrutura Secundária de Proteína , Termodinâmica , beta-Lactamases/genética , beta-Lactamases/metabolismo
2.
Life Sci ; 234: 116777, 2019 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-31465734

RESUMO

This work aimed to characterize normal, benign and malignant excised breast tissues through the analysis of the FTIR spectra of their plasma membrane proteins. Tissue characterization parameters such as peak position, peak intensity, area under the peak, relative peak intensity and relative area under peak were evaluated mainly for protein spectral peaks; 1150 cm-1, Amide I, Amide II, Amide III, and Amide A. The sensitivity, specificity and diagnostic accuracy for each parameter were obtained and Receiver Operating Characteristic (ROC) Curves were plotted. Results showed significant spectral differences between normal and benign tissues compared to malignant tissues at 1536 and 1645 cm-1. The three tissues could be distinguished at 2900 cm-1, where the malignant peak uniquely split into two separate peaks. ROC curves showed that the Amide A peak position yielded a higher accuracy compared to all other investigated characterization parameters. The deconvolution of Amide I revealed the conformational changes in plasma proteins characterizing the transformation to malignancy (a decrease in the percentage of alpha helix accompanied by an increase in the percentage of beta sheets). The use of the present structure-based analysis in conjunction with histopathological examination of excised breast tissues would offer an enhanced characterization that might reduce possible personal diagnostic mistakes.


Assuntos
Neoplasias da Mama/diagnóstico , Mama/patologia , Proteínas de Membrana/análise , Espectroscopia de Infravermelho com Transformada de Fourier/métodos , Mama/química , Neoplasias da Mama/química , Neoplasias da Mama/patologia , Feminino , Humanos , Estrutura Secundária de Proteína
3.
Nat Commun ; 10(1): 3005, 2019 07 08.
Artigo em Inglês | MEDLINE | ID: mdl-31285450

RESUMO

How the stressosome, the epicenter of the stress response in bacteria, transmits stress signals from the environment has remained elusive. The stressosome consists of multiple copies of three proteins RsbR, RsbS and RsbT, a kinase that is important for its activation. Using cryo-electron microscopy, we determined the atomic organization of the Listeria monocytogenes stressosome at 3.38 Å resolution. RsbR and RsbS are organized in a 60-protomers truncated icosahedron. A key phosphorylation site on RsbR (T209) is partially hidden by an RsbR flexible loop, whose "open" or "closed" position could modulate stressosome activity. Interaction between three glutamic acids in the N-terminal domain of RsbR and the membrane-bound mini-protein Prli42 is essential for Listeria survival to stress. Together, our data provide the atomic model of the stressosome core and highlight a loop important for stressosome activation, paving the way towards elucidating the mechanism of signal transduction by the stressosome in bacteria.


Assuntos
Complexos Multienzimáticos/ultraestrutura , Fosfoproteínas/ultraestrutura , Proteínas Serina-Treonina Quinases/ultraestrutura , Estresse Fisiológico , Microscopia Crioeletrônica , Regulação Bacteriana da Expressão Gênica/fisiologia , Ácido Glutâmico/metabolismo , Listeria monocytogenes/fisiologia , Complexos Multienzimáticos/metabolismo , Fosfoproteínas/metabolismo , Fosforilação/fisiologia , Domínios Proteicos/fisiologia , Estrutura Secundária de Proteína , Proteínas Serina-Treonina Quinases/metabolismo , Fator sigma/metabolismo , Transdução de Sinais/fisiologia
4.
Nat Commun ; 10(1): 2511, 2019 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-31175284

RESUMO

Chemical shifts (CS) are determined from NMR experiments and represent the resonance frequency of the spin of atoms in a magnetic field. They contain a mixture of information, encompassing the in-solution conformations a protein adopts, as well as the movements it performs. Due to their intrinsically multi-faceted nature, CS are difficult to interpret and visualize. Classical approaches for the analysis of CS aim to extract specific protein-related properties, thus discarding a large amount of information that cannot be directly linked to structural features of the protein. Here we propose an autoencoder-based method, called ShiftCrypt, that provides a way to analyze, compare and interpret CS in their native, multidimensional space. We show that ShiftCrypt conserves information about the most common structural features. In addition, it can be used to identify hidden similarities between diverse proteins and peptides, and differences between the same protein in two different binding states.


Assuntos
Redes Neurais (Computação) , Ressonância Magnética Nuclear Biomolecular/métodos , Proteínas/ultraestrutura , Aminoácidos , Fenômenos Biofísicos , Imagem por Ressonância Magnética , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Estrutura Secundária de Proteína
5.
Biochemistry (Mosc) ; 84(5): 464-478, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31234762

RESUMO

Bacteriocins are bacterial antimicrobial peptides that, unlike classical peptide antibiotics, are products of ribosomal synthesis and usually have a narrow spectrum of antibacterial activity against species closely related to the producers. Pediocin-like bacteriocins (PLBs) belong to the class IIa of the bacteriocins of Gram-positive bacteria. PLBs possess high activity against pathogenic bacteria from Listeria and Enterococcus genera. Molecular target for PLBs is a membrane protein complex - bacterial mannose-phosphotransferase. PLBs can be synthesized by components of symbiotic microflora and participate in the maintenance of homeostasis in various compartments of the digestive tract and on the surface of epithelial tissues contacting the external environment. PLBs could give a rise to a new group of antibiotics of narrow spectrum of activity.


Assuntos
Peptídeos Catiônicos Antimicrobianos/metabolismo , Bactérias Gram-Positivas/metabolismo , Pediocinas/metabolismo , Sequência de Aminoácidos , Peptídeos Catiônicos Antimicrobianos/química , Peptídeos Catiônicos Antimicrobianos/farmacologia , Enterococcus/efeitos dos fármacos , Bactérias Gram-Positivas/imunologia , Listeria/efeitos dos fármacos , Pediocinas/química , Pediocinas/farmacologia , Sistema Fosfotransferase de Açúcar do Fosfoenolpiruvato/química , Sistema Fosfotransferase de Açúcar do Fosfoenolpiruvato/metabolismo , Estrutura Secundária de Proteína , Alinhamento de Sequência
6.
J Chem Theory Comput ; 15(8): 4708-4720, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31241933

RESUMO

Molecular dynamics simulations using physics-based atomistic force fields have been increasingly used to characterize the heterogeneous structural ensembles of intrinsically disordered proteins (IDPs). To evaluate the accuracy of the latest atomistic explicit-solvent force fields in modeling larger IDPs with nontrivial structural features, we focus on the 61-residue N-terminal transactivation domain (TAD) of tumor suppressor p53, an important protein in cancer biology that has been extensively studied, and abundant experimental data is available for evaluation of simulated ensembles. We performed extensive replica exchange with solute tempering simulations, in excess of 1.0 µs/replica, to generate disordered structural ensembles of p53-TAD using six latest explicit solvent protein force fields. Multiple local and long-range structural properties, including chain dimension, residual secondary structures, and transient long-range contacts, were analyzed and compared against available experimental data. The results show that IDPs such as p53-TAD remain highly challenging for atomistic simulations due to conformational complexity and difficulty in achieving adequate convergence. Structural ensembles of p53-TAD generated using various force fields differ significantly from each other. The a99SB-disp force field demonstrates the best agreement with experimental data at all levels and proves to be suitable for simulating unbound p53-TAD and how its conformational properties may be modulated by phosphorylation and other cellular signals or cancer-associated mutations. Feasibility of such detailed structural characterization is a key step toward establishing the sequence-disordered ensemble-function-disease relationship of p53 and other biologically important IDPs.


Assuntos
Proteínas Intrinsicamente Desordenadas/química , Proteína Supressora de Tumor p53/química , Humanos , Simulação de Dinâmica Molecular , Neoplasias/química , Fosforilação , Conformação Proteica , Domínios Proteicos , Estrutura Secundária de Proteína
7.
Dokl Biochem Biophys ; 485(1): 123-125, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31201630

RESUMO

Previously, we synthesized a dimeric dipeptide mimetic of the brain-derived neurotrophic factor (BDNF) loop 4, GSB-106, which, similarly to BDNF, activated TrkB, PI3K/AKT, and MAPK/ERK. When administered systemically, it exhibited neuroprotective, antidepressant, and antidiabetic activities and stimulated neurogenesis and synaptogenesis. In this study, we established that GSB-106 also exhibits the analgesic activity, typical for BDNF, which was revealed in rats in hot plate and tail flick tests 0.5-48 h after intraperitoneal injection at doses of 0.1 and 1 mg/kg.


Assuntos
Analgésicos , Fator Neurotrófico Derivado do Encéfalo , Dipeptídeos , Peptidomiméticos , Analgésicos/química , Analgésicos/farmacologia , Animais , Fator Neurotrófico Derivado do Encéfalo/química , Fator Neurotrófico Derivado do Encéfalo/farmacologia , Dipeptídeos/química , Dipeptídeos/farmacologia , Humanos , Masculino , Peptidomiméticos/química , Peptidomiméticos/farmacologia , Estrutura Secundária de Proteína , Ratos
8.
BMC Bioinformatics ; 20(1): 346, 2019 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-31208321

RESUMO

BACKGROUND: Acetylation on lysine is a widespread post-translational modification which is reversible and plays a crucial role in some biological activities. To better understand the mechanism, it is necessary to identify acetylation sites in proteins accurately. Computational methods are popular because they are more convenient and faster than experimental methods. In this study, we proposed a new computational method to predict acetylation sites in human by combining sequence features and structural features including physicochemical property (PCP), position specific score matrix (PSSM), auto covariation (AC), residue composition (RC), secondary structure (SS) and accessible surface area (ASA), which can well characterize the information of acetylated lysine sites. Besides, a two-step feature selection was applied, which combined mRMR and IFS. It finally trained a cascade classifier based on SVM, which successfully solved the imbalance between positive samples and negative samples and covered all negative sample information. RESULTS: The performance of this method is measured with a specificity of 72.19% and a sensibility of 76.71% on independent dataset which shows that a cascade SVM classifier outperforms single SVM classifier. CONCLUSIONS: In addition to the analysis of experimental results, we also made a systematic and comprehensive analysis of the acetylation data.


Assuntos
Biologia Computacional/métodos , Máquina de Vetores de Suporte , Acetilação , Sequência de Aminoácidos , Animais , Bases de Dados de Proteínas , Ontologia Genética , Humanos , Lisina/química , Camundongos , Anotação de Sequência Molecular , Matrizes de Pontuação de Posição Específica , Processamento de Proteína Pós-Traducional , Estrutura Secundária de Proteína , Proteínas/química , Proteínas/metabolismo , Ratos
9.
BMC Bioinformatics ; 20(1): 341, 2019 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-31208331

RESUMO

BACKGROUND: Protein secondary structure (PSS) is critical to further predict the tertiary structure, understand protein function and design drugs. However, experimental techniques of PSS are time consuming and expensive, and thus it's very urgent to develop efficient computational approaches for predicting PSS based on sequence information alone. Moreover, the feature matrix of a protein contains two dimensions: the amino-acid residue dimension and the feature vector dimension. Existing deep learning based methods have achieved remarkable performances of PSS prediction, but the methods often utilize the features from the amino-acid dimension. Thus, there is still room to improve computational methods of PSS prediction. RESULTS: We propose a novel deep neural network method, called DeepACLSTM, to predict 8-category PSS from protein sequence features and profile features. Our method efficiently applies asymmetric convolutional neural networks (ACNNs) combined with bidirectional long short-term memory (BLSTM) neural networks to predict PSS, leveraging the feature vector dimension of the protein feature matrix. In DeepACLSTM, the ACNNs extract the complex local contexts of amino-acids; the BLSTM neural networks capture the long-distance interdependencies between amino-acids. Furthermore, the prediction module predicts the category of each amino-acid residue based on both local contexts and long-distance interdependencies. To evaluate performances of DeepACLSTM, we conduct experiments on three publicly available datasets: CB513, CASP10 and CASP12. Results indicate that the performance of our method is superior to the state-of-the-art baselines on three publicly datasets. CONCLUSIONS: Experiments demonstrate that DeepACLSTM is an efficient predication method for predicting 8-category PSS and has the ability to extract more complex sequence-structure relationships between amino-acid residues. Moreover, experiments also indicate the feature vector dimension contains the useful information for improving PSS prediction.


Assuntos
Algoritmos , Aprendizado Profundo , Modelos Teóricos , Redes Neurais (Computação) , Proteínas/química , Domínios Proteicos , Estrutura Secundária de Proteína
10.
Microbiol Res ; 223-225: 22-32, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31178048

RESUMO

The Deinococcus radiodurans multipartite genome consists of 2 chromosomes and 2 plasmids Its genome encodes 4 ParA and 4 ParB proteins on different replicons. Multiple sequence alignments of ParBs encoded on these genome elements showed that ParB of primary chromosome (ParB1) is close to chromosomal type ParB and is found to be different from ParBs encoded on chromosome II (ParB2) and megaplasmid (ParB3) elements. We observed that ParB1, ParB2 and ParB3 exist as dimer in solution and these proteins interact to self but not to its homologs in D. radiodurans, suggesting the specificity in ParBs dimerization. The parB1 deletion mutant showed slow growth under normal condition and relatively reduced resistance to γ-radiation as compared to wild type. The parB2 and parB3 mutants maintained without selection pressure showed loss of radioresistance, which was not observed when maintained with selection pressure. Nearly half of the populations of these mutants showed resistance to antibiotics marked to respective genome elements. Interestingly, all the parB mutants showed increased copy numbers of cognate genome element in cells maintained with antibiotics possibly due to arrest in genome segregation. These results suggested that ParB proteins encoded on multipartite genome system in D. radiodurans form homodimer and not heterodimer with other ParB homologs, and they independently regulate the segregation of respective genome elements. The roles of ParB1 proteins in normal as well as radiation stressed growth of this bacterium have also been ascertained.


Assuntos
Proteínas de Bactérias/genética , Deinococcus/genética , Genes Bacterianos/genética , Sequência de Aminoácidos , Cromossomos Bacterianos/genética , Clonagem Molecular , Deinococcus/efeitos da radiação , Escherichia coli/genética , Regulação Bacteriana da Expressão Gênica , Plasmídeos , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estrutura Secundária de Proteína , Alinhamento de Sequência , Deleção de Sequência
11.
Ann Hematol ; 98(8): 1827-1834, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31190133

RESUMO

In this study, we aimed to investigate the pattern and association of genetic mutations occurring within the alpha hemoglobin-stabilizing protein (AHSP) gene among HbE beta thalassemia patients with varying phenotypic expressions. Fifty-four diagnosed cases of HbE beta thalassemia (transfusion dependent and independent) were included in the study. Among them, 38 patients with similar genotypes (IVS 1-5, alpha gene deletion and triplication, Xmn polymorphism) were selected for further analysis. AHSP gene sequencing was done for these 38 samples to study associated mutations in AHSP gene. HbE beta thalassemia patients with similar genotypes but different phenotypic expressions were found to have mutations in the AHSP gene. There were five mutations found most prevalent among the samples analyzed for AHSP gene sequencing. Among these, two mutations were from intron 1 region of AHSP and three mutations were found in exon 3. The most prevalent mutation was found at the Oct binding site at intron 1 of AHSP. The mutations in exon 3 were more prevalent among the TDT groups. A mutation in exon 3 changing the amino acid (33rd) from serine to phenylalanine was found to be associated with only TDT group. This study documents that among the HbE beta thalassemia patients with varying severity, an exon mutation in AHSP is significantly prevalent only among the TDT group. Further understanding of the mechanism will shed light upon the impact of AHSP in modifying the disease severity in thalassemia.


Assuntos
Proteínas Sanguíneas/genética , Deleção de Genes , Duplicação Gênica , Hemoglobina E/genética , Chaperonas Moleculares/genética , Talassemia beta/genética , Adolescente , Adulto , Sequência de Bases , Proteínas Sanguíneas/metabolismo , Transfusão de Sangue/estatística & dados numéricos , Criança , Pré-Escolar , Análise Mutacional de DNA , Eritrócitos/metabolismo , Eritrócitos/patologia , Éxons , Feminino , Expressão Gênica , Genótipo , Hemoglobina E/metabolismo , Humanos , Íntrons , Masculino , Pessoa de Meia-Idade , Modelos Moleculares , Chaperonas Moleculares/metabolismo , Fenótipo , Estrutura Secundária de Proteína , Índice de Gravidade de Doença , Talassemia beta/metabolismo , Talassemia beta/patologia , Talassemia beta/terapia
12.
Food Chem ; 297: 124910, 2019 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-31253292

RESUMO

Polyphenols can inhibit the enzymatic browning in food, but their indistinct synergistic effect and conformational change have limited their applications. In this paper, the mixture of quercetin, cinnamic acid and ferulic acid (Group 11, KI = 0.239 mM) possessed a higher inhibition ability than quercetin (KI = 0.361 mM), which could promote the spontaneous binding process. The final Group 11-tyrosinase complex is more stable, and the hydrophobic effect is the major driving force during the binding process. Moreover, there is not a direct relationship between the destruction of secondary structures and catalytic activity of tyrosinase. The interaction between ferulic acid and tyrosinase could destroy the secondary structures of enzyme but it had little impact on the tyrosinase activity. Molecular docking suggested that three polyphenols from Group 11 have synergistic effect on tyrosinase. This study provides new perspectives about the development of tyrosinase inhibitors in food products.


Assuntos
Inibidores Enzimáticos/química , Monofenol Mono-Oxigenase/antagonistas & inibidores , Polifenóis/química , Sítios de Ligação , Cinamatos/química , Cinamatos/metabolismo , Ácidos Cumáricos/química , Ácidos Cumáricos/metabolismo , Inibidores Enzimáticos/metabolismo , Cinética , Simulação de Acoplamento Molecular , Monofenol Mono-Oxigenase/metabolismo , Estrutura Secundária de Proteína , Termodinâmica
13.
Food Chem ; 297: 124766, 2019 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-31253308

RESUMO

The complexation of nanoparticles in extreme alkali treated (pH 10.0, 11.0 and 12.0) soy protein isolate (SPI) with 1-Octacosanol (1-Octa) was investigated. The nanoparticles were compared in complexing with the 1-Octa concerning their characteristics, along with the changes in secondary structure and stability of 1-Octa upon complexation. The nanoparticles did not display obvious changes in size and morphology upon complexation with 1-Octa, except the surface hydrophobicity. The encapsulation efficiency (EE) and loading amount (LA) of the SPI-Octa were first increased and then decreased with an enhanced pH value. The treatment conditions modified some secondary structures, causing greater protein unfolding to expose more hydrophobic clusters. Additionally, the nanocomplex had higher thermal and saline ion stability, the majority of the nanocomplexes were evenly dispersed in the aqueous phase.


Assuntos
Álcoois Graxos/química , Nanopartículas/química , Proteínas de Soja/química , Álcoois Graxos/metabolismo , Concentração de Íons de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Microscopia de Força Atômica , Tamanho da Partícula , Estrutura Secundária de Proteína , Desdobramento de Proteína , Proteínas de Soja/metabolismo , Propriedades de Superfície
14.
Phys Chem Chem Phys ; 21(22): 11924-11936, 2019 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-31134232

RESUMO

A comprehensive understanding of protein folding includes the knowledge of the formation of individual secondary structures, tertiary structure, and the effects of non-native contacts on these folding events. The measurement of these microscopic events has been posing challenges for experiment and molecular simulation. In this work, we performed enhanced sampling MD simulations for three proteins (NTL9, NuG2b, and CspA) and analyzed minimum free energy paths on multi-dimensional free energy landscapes to explore the underlying folding mechanisms. Consistencies can be seen between the present simulations and the existing experiments as well as other MD simulations. Quantitative analysis reveals the nucleation-condensation folding mechanism indicating the concurrent build-up of secondary and tertiary structures for the three proteins and gives the detailed formation sequence of individual native secondary structure elements. More importantly, nonnative contacts are generally observed among the proteins, creating a nonnative environment to affect the folding of individual secondary structure elements. A general tendency is that the secondary structure element(s) where the maximal nonnative contacts are observed have the largest formation free-energy barrier(s), corresponding to the rate-limiting step(s) of the folding for proteins that follow the nucleation-condensation mechanism. In summary, while native contacts determine the folding mechanism and pathway, non-native contacts play an important role in determining the protein folding thermodynamics by influencing the free energies of individual secondary structure element formation.


Assuntos
Proteínas e Peptídeos de Choque Frio/química , Proteínas de Escherichia coli/química , Proteínas de Ligação ao GTP/química , Dobramento de Proteína , Proteínas Ribossômicas/química , Sequência de Aminoácidos , Escherichia coli/química , Firmicutes/química , Proteínas de Ligação ao GTP/genética , Geobacillus stearothermophilus/química , Simulação de Dinâmica Molecular , Mutação , Estrutura Secundária de Proteína , Termodinâmica
15.
Phys Chem Chem Phys ; 21(20): 10423-10435, 2019 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-31066393

RESUMO

The dihedral energy function is the most influential parameter in molecular mechanics (MM) force field parameter optimization. A selective enhanced sampling of dihedral energy could effectively reflect the influence of dihedral energy settings on protein secondary structure representation, which in turn testifies the availability of the force field in folding simulation. Here, a Dihedral-based Selective Integrated-Tempering-Sampling Molecular Dynamics (D-SITSMD) simulation method is shown to provide a selective enhanced sampling of dihedral energy without introducing large energetic noise. Its capabilities of searching for protein natively folded structure and providing the underlying folding pathway are evaluated through the folding tests of three peptides (chignolin, TC5b, and HP35) with multiple AMBER force fields (FF14SBonlysc, FF99SBildn, or FF03) and the comparison to presented experimental data and REMD simulations. Both above-mentioned capabilities are improved, displaying the potential of D-SITSMD in the studies of in silico protein folding and structure refinement. Additionally, it is commonly observed among the test simulation systems that their folding processes are thermodynamically favorable for non-bonded vdW and electrostatic energies but unfavorable for dihedral energy, such that the folding barrier height correlated with the dihedral energy increase from the unfolded to folded state whereas the unfolding free energy barrier correlated with the combined increase of vdW and electrostatic energies in the unfolding process. It is speculated that the influence of a force field on the folding barrier of a protein is fulfilled mainly through regulating the contribution of dihedral energy to determine the secondary structure formation in the global folding process.


Assuntos
Metabolismo Energético , Dobramento de Proteína , Proteínas/química , Simulação de Dinâmica Molecular , Estrutura Secundária de Proteína
16.
Nat Commun ; 10(1): 1967, 2019 04 29.
Artigo em Inglês | MEDLINE | ID: mdl-31036849

RESUMO

Autotransporters are the largest family of outer membrane and secreted proteins in Gram-negative bacteria. Most autotransporters are localised to the bacterial surface where they promote colonisation of host epithelial surfaces. Here we present the crystal structure of UpaB, an autotransporter that is known to contribute to uropathogenic E. coli (UPEC) colonisation of the urinary tract. We provide evidence that UpaB can interact with glycosaminoglycans and host fibronectin. Unique modifications to its core ß-helical structure create a groove on one side of the protein for interaction with glycosaminoglycans, while the opposite face can bind fibronectin. Our findings reveal far greater diversity in the autotransporter ß-helix than previously thought, and suggest that this domain can interact with host macromolecules. The relevance of these interactions during infection remains unclear.


Assuntos
Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Glicosaminoglicanos/metabolismo , Escherichia coli Uropatogênica/metabolismo , Adesinas Bacterianas/química , Adesinas Bacterianas/metabolismo , Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/metabolismo , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Fatores de Virulência/química , Fatores de Virulência/metabolismo
17.
Acta Crystallogr F Struct Biol Commun ; 75(Pt 5): 385-391, 2019 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-31045568

RESUMO

The inhibition of kallikrein 5 (KLK5) has been identified as a potential strategy for treatment of the genetic skin disorder Netherton syndrome, in which loss-of-function mutations in the SPINK5 gene lead to down-regulation of the endogenous inhibitor LEKTI-1 and profound skin-barrier defects with severe allergic manifestations. To aid in the development of a medicine for this target, an X-ray crystallographic system was developed to facilitate fragment-guided chemistry and knowledge-based drug-discovery approaches. Here, the development of a surrogate crystallographic system in place of KLK5, which proved to be challenging to crystallize, is described. The biochemical robustness of the crystallographic surrogate and the suitability of the system for the study of small nonpeptidic fragments and lead-like molecules are demonstrated.


Assuntos
Benzamidinas/química , Calicreínas/química , Inibidores de Proteases/química , Sequência de Aminoácidos , Animais , Baculoviridae/genética , Baculoviridae/metabolismo , Benzamidinas/farmacologia , Sítios de Ligação , Clonagem Molecular , Cristalografia por Raios X , Descoberta de Drogas , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Humanos , Calicreínas/antagonistas & inibidores , Calicreínas/genética , Calicreínas/metabolismo , Cinética , Modelos Moleculares , Mutação , Síndrome de Netherton/tratamento farmacológico , Síndrome de Netherton/enzimologia , Inibidores de Proteases/farmacologia , Ligação Proteica , Estrutura Secundária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Células Sf9 , Spodoptera , Eletricidade Estática , Especificidade por Substrato
18.
Int J Mol Sci ; 20(9)2019 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-31035335

RESUMO

The purpose of this paper was to outline the development of short peptide targeting of the human prostate specific antigen (hPSA), and to evaluate its effectiveness in staining PSA in human prostate cancer tissue. The targeting of the hPSA antigen by means of antisense peptide AVRDKVG was designed according to a three-step method involving: 1. The selection of the molecular target (hPSA epitope), 2. the modeling of an antisense peptide (paratope) based on the epitope sequence, and 3. the spectroscopic evaluation of sense-antisense peptide binding. We then modified standard hPSA immunohistochemical staining practice by using a biotinylated antisense peptide instead of the standard monoclonal antibody and compared the results of both procedures. Immunochemical testing on human tissue showed the applicability of the antisense peptide technology to human molecular targets. This methodology represents a new approach to deriving peptide ligands and potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines.


Assuntos
Biomarcadores Tumorais/imunologia , Peptídeos/imunologia , Antígeno Prostático Específico/imunologia , Neoplasias da Próstata/imunologia , Humanos , Imuno-Histoquímica , Masculino , Nanomedicina/métodos , Estrutura Secundária de Proteína
19.
Microb Pathog ; 132: 243-253, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31075428

RESUMO

Ebola virus (EBOV), a non-segmented single-stranded RNA virus, is often-most transmitted through body fluids like sweat, tears, saliva, and nasal secretions. Till date, there is no licensed vaccine of EBOV is available in the market; however, the world is increasingly vulnerable to this emerging threat. Hence, it is the need of time to develop a vaccine for EBOV to hinder its dissemination. The current study has been designed for identification and characterization of the potential B and T-cell epitopes using the Immuno-informatics tools, and it helped in finding the potent vaccine candidates against EBOV. Prediction, antigenicity and allergenicity testing of predicted B and T cells' epitopes was done as well to identify their potential as a vaccine candidate and to measure their safety level respectively. Among B-cell epitopes "WIPAGIGVTGVIIA" showed a high antigenicity score and it would play an important role in evoking the immune response. In T-cell epitopes, peptides "AIGLAWIPY" and "IRGFPRCRY" presented high antigenicity score, which binds to MHC class-I and MHC class-II alleles respectively. All predicted epitopes were analyzed and compared with already reported peptides carefully. Comparatively, Peptides predicted in the present study showed more immunogenicity score than already reported peptides, used as positive control, and are more immunogenic as compared to them. Peptides reported in the present study do not target only Zaire EBOV (ZEBOV), as in previous studies, but also other species, i.e. Tai Forest EBOV (TAFV), Sudan EBOV (SUDV), Bundibugyo EBOV (BDBV), and Reston EBOV (RESTV) and would bring the promising results as potent vaccine candidates.


Assuntos
Vacinas contra Ebola/imunologia , Ebolavirus/imunologia , Epitopos de Linfócito B/imunologia , Epitopos de Linfócito T/imunologia , Glicoproteínas/imunologia , Alelos , Sequência de Aminoácidos , Vacinas contra Ebola/genética , Ebolavirus/genética , Genes MHC Classe I , Genes MHC da Classe II , Glicoproteínas/química , Glicoproteínas/genética , Antígeno HLA-B7 , Imunogenicidade da Vacina , Simulação de Acoplamento Molecular , Estrutura Secundária de Proteína
20.
Food Chem ; 294: 316-325, 2019 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-31126469

RESUMO

The present study studied the effects of fish gelatin (FG) incorporated with grape seed extract (GSE) through vacuum impregnation (VI) on refrigerated tilapia (Oreochromis niloticus) fillets over 12 days. The VI of FG-GSE significantly improved the quality of the fish by decreasing drip loss, texture changes, and microbial survival. It also delayed protein oxidation by inhibiting the formation of disulphide bonds and carbonyl groups, and maintaining a higher sulfhydryl content and Ca2+-ATPase activity. Regarding myofibril degradation, FG-GSE maintained their secondary structure by increasing the ratio of α-helices and ß-sheets (70.88-75.51%). Atomic force microscopy further revealed that the FG-GSE coating preserved the myofibril nanostructure by maintaining their length, width, and height. Overall, the synergistic effects of VI with 3% FG and 0.9% GSE suggested a promising approach for fillet preservation.


Assuntos
Proteínas de Peixes/química , Gelatina/química , Extrato de Sementes de Uva/química , Animais , ATPases Transportadoras de Cálcio/metabolismo , Proteínas de Peixes/metabolismo , Bactérias Gram-Negativas/efeitos dos fármacos , Extrato de Sementes de Uva/farmacologia , Dureza , Microscopia de Força Atômica , Miofibrilas/metabolismo , Oxirredução , Estrutura Secundária de Proteína , Alimentos Marinhos/análise , Compostos de Sulfidrila/metabolismo , Tilápia/metabolismo , Vácuo
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