Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 18.305
Filtrar
1.
PLoS Comput Biol ; 16(9): e1008103, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32956350

RESUMO

Highly coordinated water molecules are frequently an integral part of protein-protein and protein-ligand interfaces. We introduce an updated energy model that efficiently captures the energetic effects of these ordered water molecules on the surfaces of proteins. A two-stage method is developed in which polar groups arranged in geometries suitable for water placement are first identified, then a modified Monte Carlo simulation allows highly coordinated waters to be placed on the surface of a protein while simultaneously sampling amino acid side chain orientations. This "semi-explicit" water model is implemented in Rosetta and is suitable for both structure prediction and protein design. We show that our new approach and energy model yield significant improvements in native structure recovery of protein-protein and protein-ligand docking discrimination tests.


Assuntos
Sítios de Ligação/fisiologia , Simulação de Acoplamento Molecular , Ligação Proteica/fisiologia , Proteínas , Água , Algoritmos , Aminoácidos/química , Aminoácidos/metabolismo , Ligação de Hidrogênio , Ligantes , Método de Monte Carlo , Proteínas/química , Proteínas/metabolismo , Água/química , Água/metabolismo
2.
J Chromatogr A ; 1626: 461383, 2020 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-32797856

RESUMO

The potential of Micellar Electrokinetic Chromatography to achieve enantiomeric separations is reviewed in this article. The separation principles and the most frequently employed separation strategies to achieve chiral separations by Micellar Electrokinetic Chromatography are described. The use of chiral micellar systems alone or combined with other micellar systems or chiral selectors, as well as of mixtures of achiral micellar systems with chiral selectors is discussed together with the effect of different additives present in the separation medium. Indirect methods based on the derivatization of analytes with chiral derivatizing reagents and the use of achiral micelles are also considered. Preconcentration techniques employed to improve sensitivity and the main approaches developed to facilitate the coupling with Mass Spectrometry are included. The most recent and relevant methodologies developed by chiral Micellar Electrokinetic Chromatography and their applications in different fields are presented.


Assuntos
Cromatografia Capilar Eletrocinética Micelar/métodos , Aminoácidos/química , Ciclodextrinas/química , Análise de Alimentos , Espectrometria de Massas , Oryza/química , Oryza/metabolismo , Estereoisomerismo , Vinho/análise
3.
Int J Syst Evol Microbiol ; 70(8): 4432-4450, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32735208

RESUMO

The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.


Assuntos
Chryseobacterium/classificação , Filogenia , Aminoácidos/química , Extinção Biológica
4.
Nat Commun ; 11(1): 3818, 2020 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-32732937

RESUMO

The formation of peptide bonds by energetic processing of amino acids is an important step towards the formation of biologically relevant molecules. As amino acids are present in space, scenarios have been developed to identify the roots of life on Earth, either by processes occurring in outer space or on Earth itself. We study the formation of peptide bonds in single collisions of low-energy He2+ ions (α-particles) with loosely bound clusters of ß-alanine molecules at impact energies typical for solar wind. Experimental fragmentation mass spectra produced by collisions are compared with results of molecular dynamics simulations and an exhaustive exploration of potential energy surfaces. We show that peptide bonds are efficiently formed by water molecule emission, leading to the formation of up to tetrapeptide. The present results show that a plausible route to polypeptides formation in space is the collision of energetic ions with small clusters of amino acids.


Assuntos
Aminoácidos/química , Simulação de Dinâmica Molecular , Peptídeos/química , Termodinâmica , beta-Alanina/química , Dipeptídeos/síntese química , Dipeptídeos/química , Íons/química , Oligopeptídeos/síntese química , Oligopeptídeos/química , Peptídeos/síntese química , Espectrometria de Massas por Ionização por Electrospray/métodos , Água/química
5.
J Chromatogr A ; 1626: 461335, 2020 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-32797820

RESUMO

On-spot fixed-charge derivatization has been suggested for the modification of α-amino acids for their analysis by thin layer chromatography/matrix-assisted laser desorption ionization (TLC/MALDI) mass spectrometry. The approach was based on post-chromatographic treatment of separated analytes by tris(2,6-dimethoxyphenyl)methenium salt and triethylamine. The reaction proceeded smoothly in mild conditions and gave rise to pink-red colored derivatives, containing permanent positive charge. Their MALDI mass spectra, recorded directly from TLC plates, revealed intense peaks corresponding to decarboxylated cationic parts. All derivatives are characterized by high ionization efficiency, which indicates the high sensitivity of the developed method for analyzing amino acids. Applicability of the method to analysis of amino acids was demonstrated on artificial mixtures and dietary supplement.


Assuntos
Aminoácidos/análise , Cromatografia em Camada Delgada/métodos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Aminoácidos/química , Etilaminas/química
6.
Acta Crystallogr C Struct Chem ; 76(Pt 7): 663-672, 2020 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-32624513

RESUMO

The reactivity of the cobalt(III) complexes dichlorido[tris(2-aminoethyl)amine]cobalt(III) chloride, [CoCl2(tren)]Cl, and dichlorido(triethylenetetramine)cobalt(III) chloride, [CoCl2(trien)]Cl, towards different amino acids (L-proline, L-asparagine, L-histidine and L-aspartic acid) was explored in detail. This study presents the crystal structures of three amino acidate cobalt(III) complexes, namely, (L-prolinato-κ2N,O)[tris(2-aminoethyl)amine-κ4N,N',N'',N''']cobalt(III) diiodide monohydrate, [Co(C5H8NO2)(C6H18N4)]I2·H2O, I, (L-asparaginato-κ2N,O)[tris(2-aminoethyl)amine-κ4N,N',N'',N''']cobalt(III) chloride perchlorate, [Co(C4H7N2O3)(C6H18N4)](Cl)(ClO4), II, and (L-prolinato-κ2N,O)(triethylenetetramine-κ4N,N',N'',N''')cobalt(III) chloride perchlorate, [Co(C4H7N2O3)(C6H18N4)](Cl)(ClO4), V. The syntheses of the complexes were followed by characterization using UV-Vis spectroscopy of the reaction mixtures and the initial rates of reaction were obtained by calculating the slopes of absorbance versus time plots. The initial rates suggest a stronger reactivity and hence greater affinity of the cobalt(III) complexes towards basic amino acids. The biocompatibility of the complexes was also assessed by evaluating the cytotoxicity of the complexes on cultured normal human fibroblast cells (WS1) in vitro. The compounds were found to be nontoxic after 24 h of incubation at concentrations up to 25 mM.


Assuntos
Cobalto/química , Complexos de Coordenação/química , Histidina/química , Aminoácidos/química , Cristalografia por Raios X , Ligantes , Percloratos/química
7.
J Chromatogr A ; 1625: 461255, 2020 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-32709316

RESUMO

A three-dimensional (3D) HPLC system in combination with fluorescence derivatization has been developed for the highly sensitive and selective analysis of chiral amino acids in extraterrestrial samples. As the targets, alanine (Ala), 2-aminobutyric acid (2AB), valine (Val), norvaline (nVal) and isovaline (iVal), frequently found chiral amino acids in the carbonaceous chondrites, were selected. These amino acids were pre-column derivatized with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F), and the target analytes were separated from other amino acids and organic compounds by a reversed-phase column in the first dimension. The targets were further separated from interferences by an anion-exchange column in the second dimension, and their enantiomers were separated and determined in the third dimension by a Pirkle-type enantioselective column. The present 3D-HPLC system was validated and applied to the Murchison meteorite and the Antarctic meteorites, and all of the target amino acid enantiomers were clearly observed (0.78-22.33 nmol/g in the Murchison meteorite and 1.79-78.84 nmol/g in the Antarctic meteorites) without severe interferences. The %L values of the non-proteinogenic amino acids were almost 50% in both meteorites, and even the proteinogenic amino acids were almost racemic in the Antarctic meteorites.


Assuntos
Aminoácidos/análise , Cromatografia Líquida de Alta Pressão/métodos , Meteoroides , Alanina/análise , Aminoácidos/química , Aminobutiratos/análise , Cromatografia por Troca Iônica , Limite de Detecção , Estereoisomerismo , Valina/análogos & derivados , Valina/análise
8.
PLoS One ; 15(7): e0235863, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32706779

RESUMO

A comprehensive analysis of crystallographic data of 565 high-resolution protein homodimers comprised of over 250,000 residues suggests that amino acids form two groups that differ in their tendency to distort or symmetrize the structure of protein homodimers. Residues of the first group tend to distort the protein homodimer and generally have long or polar side chains. These include: Lys, Gln, Glu, Arg, Asn, Met, Ser, Thr and Asp. Residues of the second group contribute to protein symmetry and are generally characterized by short or aromatic side chains. These include: Ile, Pro, His, Val, Cys, Leu, Trp, Tyr, Phe, Ala and Gly. The distributions of the continuous symmetry measures of the proteins and the continuous chirality measures of their building blocks highlight the role of side chain geometry and the interplay between entropy and symmetry in dictating the conformational flexibility of proteins.


Assuntos
Aminoácidos/química , Conformação Proteica , Multimerização Proteica , Cristalografia por Raios X , Isomerismo
9.
Food Chem ; 331: 127369, 2020 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-32590262

RESUMO

To make better use of chicken liver, a byproduct of meat processing with rich proteins, the influence of ultrasound pretreatment on the extent of Maillard reaction (MR) and the properties of MR products (MRPs) of chicken liver protein (CLP) and its hydrolysate (CLPH) were investigated. The extent of MR of sonicated CLPH (SCLPHMs) was significantly higher than that of the other two MRPs. The decreased fluorescence intensity (FI) of the SCLPHMs indicated adequate reaction of d-xylose with sonicated CLPH (SCLPH). The particle size of the three MRPs was significantly larger than that of CLP, CLPH, and SCLPH, respectively. Ultrasound treatment increased the utilization of amino acids and enriched the variety of volatile compounds in all groups. Furfural was the main heterocyclic compound in the MRPs. Therefore, ultrasound pretreatment and enzymolysis of chicken liver may be a foundation for high-value development in flavors for the food industry.


Assuntos
Galinhas , Indústria de Processamento de Alimentos/métodos , Fígado/química , Reação de Maillard , Proteínas de Aves Domésticas/química , Compostos Orgânicos Voláteis/química , Aminoácidos/análise , Aminoácidos/química , Animais , Aromatizantes/química , Produtos Finais de Glicação Avançada/química , Produtos Avícolas , Hidrolisados de Proteína/química , Paladar , Ultrassom , Compostos Orgânicos Voláteis/análise , Xilose/química
10.
Proc Natl Acad Sci U S A ; 117(27): 15731-15739, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32561643

RESUMO

De novo emergence demands a transition from disordered polypeptides into structured proteins with well-defined functions. However, can polypeptides confer functions of evolutionary relevance, and how might such polypeptides evolve into modern proteins? The earliest proteins present an even greater challenge, as they were likely based on abiotic, spontaneously synthesized amino acids. Here we asked whether a primordial function, such as nucleic acid binding, could emerge with ornithine, a basic amino acid that forms abiotically yet is absent in modern-day proteins. We combined ancestral sequence reconstruction and empiric deconstruction to unravel a gradual evolutionary trajectory leading from a polypeptide to a ubiquitous nucleic acid-binding protein. Intermediates along this trajectory comprise sequence-duplicated functional proteins built from 10 amino acid types, with ornithine as the only basic amino acid. Ornithine side chains were further modified into arginine by an abiotic chemical reaction, improving both structure and function. Along this trajectory, function evolved from phase separation with RNA (coacervates) to avid and specific double-stranded DNA binding. Our results suggest that phase-separating polypeptides may have been an evolutionary resource for the emergence of early proteins, and that ornithine, together with its postsynthesis modification to arginine, could have been the earliest basic amino acids.


Assuntos
Arginina/química , Nucleoproteínas/genética , Ornitina/química , Peptídeos/genética , Sequência de Aminoácidos/genética , Aminoácidos/química , Aminoácidos/genética , Arginina/genética , DNA/química , DNA/genética , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Nucleoproteínas/química , Ornitina/genética , Peptídeos/química , Proteínas/química , Proteínas/genética , RNA/química , RNA/genética
11.
Proc Natl Acad Sci U S A ; 117(25): 13967-13974, 2020 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-32503918

RESUMO

Molecular dynamics and free energy simulations have been carried out to elucidate the structural origin of differential protein-protein interactions between the common receptor protein angiotensin converting enzyme 2 (ACE2) and the receptor binding domains of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [A. E. Gorbalenya et al., Nat. Microbiol. 5, 536-544 (2020)] that causes coronavirus disease 2019 (COVID-19) [P. Zhou et al., Nature 579, 270-273 (2020)] and the SARS coronavirus in the 2002-2003 (SARS-CoV) [T. Kuiken et al., Lancet 362, 263-270 (2003)] outbreak. Analysis of the dynamic trajectories reveals that the binding interface consists of a primarily hydrophobic region and a delicate hydrogen-bonding network in the 2019 novel coronavirus. A key mutation from a hydrophobic residue in the SARS-CoV sequence to Lys417 in SARS-CoV-2 creates a salt bridge across the central hydrophobic contact region, which along with polar residue mutations results in greater electrostatic complementarity than that of the SARS-CoV complex. Furthermore, both electrostatic effects and enhanced hydrophobic packing due to removal of four out of five proline residues in a short 12-residue loop lead to conformation shift toward a more tilted binding groove in the complex in comparison with the SARS-CoV complex. On the other hand, hydrophobic contacts in the complex of the SARS-CoV-neutralizing antibody 80R are disrupted in the SARS-CoV-2 homology complex model, which is attributed to failure of recognition of SARS-CoV-2 by 80R.


Assuntos
Betacoronavirus/fisiologia , Peptidil Dipeptidase A/metabolismo , Ligação Proteica , Receptores Virais/metabolismo , Aminoácidos/química , Anticorpos Neutralizantes/metabolismo , Anticorpos Antivirais/metabolismo , Infecções por Coronavirus , Humanos , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Modelos Moleculares , Simulação de Dinâmica Molecular , Pandemias , Pneumonia Viral , Domínios Proteicos , Eletricidade Estática
12.
Nat Commun ; 11(1): 3128, 2020 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-32561732

RESUMO

Whole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein-protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, a small molecule which is known to rapidly penetrate into all cellular compartments and to preserve the protein structure. In light of these benefits, it is surprising that identification of formaldehyde cross-links by mass spectrometry has so far been unsuccessful. Here we report mass spectrometry data that reveal formaldehyde cross-links to be the dimerization product of two formaldehyde-induced amino acid modifications. By integrating the revised mechanism into a customized search algorithm, we identify hundreds of cross-links from in situ formaldehyde fixation of human cells. Interestingly, many of the cross-links could not be mapped onto known atomic structures, and thus provide new structural insights. These findings enhance the use of formaldehyde cross-linking and mass spectrometry for structural studies.


Assuntos
Reagentes para Ligações Cruzadas/química , Formaldeído/química , Mapeamento de Interação de Proteínas/métodos , Proteínas/química , Aminoácidos/química , Linhagem Celular Tumoral , Humanos , Espectrometria de Massas , Simulação de Acoplamento Molecular , Proteínas/metabolismo
13.
Nucleic Acids Res ; 48(W1): W36-W40, 2020 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-32459331

RESUMO

Nuclear magnetic resonance (NMR) spectroscopy data provides valuable information on the behaviour of proteins in solution. The primary data to determine when studying proteins are the per-atom NMR chemical shifts, which reflect the local environment of atoms and provide insights into amino acid residue dynamics and conformation. Within an amino acid residue, chemical shifts present multi-dimensional and complexly cross-correlated information, making them difficult to analyse. The ShiftCrypt method, based on neural network auto-encoder architecture, compresses the per-amino acid chemical shift information in a single, interpretable, amino acid-type independent value that reflects the biophysical state of a residue. We here present the ShiftCrypt web server, which makes the method readily available. The server accepts chemical shifts input files in the NMR Exchange Format (NEF) or NMR-STAR format, executes ShiftCrypt and visualises the results, which are also accessible via an API. It also enables the "biophysically-based" pairwise alignment of two proteins based on their ShiftCrypt values. This approach uses Dynamic Time Warping and can optionally include their amino acid code information, and has applications in, for example, the alignment of disordered regions. The server uses a token-based system to ensure the anonymity of the users and results. The web server is available at www.bio2byte.be/shiftcrypt.


Assuntos
Ressonância Magnética Nuclear Biomolecular/métodos , Proteínas/química , Software , Aminoácidos/química , Redes Neurais de Computação , Desnaturação Proteica , Dobramento de Proteína , Desdobramento de Proteína
14.
J Food Sci ; 85(6): 1642-1650, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32430953

RESUMO

The effects of different mucor strains (Mucor racemosus, Actinomucor, and Mucor wutungkiao) on aroma and taste profiles based on proteolysis, lipolysis, and their catabolism in oil furu were studied. Gas chromatography-mass spectrometry and relative odor activity were used to monitor the changes of key volatile compounds and the differences in the characteristic aroma contents of oil furu. Using principal component analysis, the different fermentation strains had an effect on aroma profiles. The volatile compounds from metabolism of protein and fatty acid contributed to the aroma of oil furu with different contribution from the different strains, presumably due to their different enzymes. The electronic tongue and free amino acid profiles also showed strain differences of taste. Based on these results, optimization of the amount of each of the different mucor strains during cofermentation might achieve better flavor.


Assuntos
Aromatizantes/química , Mucor/metabolismo , Odorantes/análise , Alimentos de Soja/microbiologia , Soja/química , Soja/microbiologia , Aminoácidos/química , Aminoácidos/metabolismo , Nariz Eletrônico , Ácidos Graxos/química , Ácidos Graxos/metabolismo , Fermentação , Aromatizantes/metabolismo , Cromatografia Gasosa-Espectrometria de Massas , Humanos , Mucorales/metabolismo , Alimentos de Soja/análise , Soja/metabolismo , Paladar , Compostos Orgânicos Voláteis/química , Compostos Orgânicos Voláteis/metabolismo
15.
J Anim Sci ; 98(6)2020 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-32432323

RESUMO

Improving the ability of animals to convert feed resources into food for humans is needed for more sustainable livestock systems. Genetic selection for animals eating less while maintaining their performance (i.e., low residual feed intake [RFI]) appears a smart strategy but its effectiveness relies on high-throughput animal phenotyping. Here, we explored plasma nitrogen (N) isotope ratios in an attempt to identify easily superior young bulls in terms of RFI. For this, 48 Charolais young bulls fed two contrasting diets (corn vs. grass silage diets) were selected from a larger population as extreme RFI animals (24 low-RFI vs. 24 high-RFI) and their plasma analyzed for natural 15N abundance (δ15N) in the whole protein (bulk protein) and in the individual protein-bound amino acids (PbAA). For the first time, we showed that the δ 15N in plasma bulk protein differed (P = 0.007) between efficient (low-RFI) and inefficient (high-RFI) cattle regardless of diet. Furthermore, most analyzed PbAA followed the same trend as the bulk protein, with lower (P < 0.05) δ 15N values in more efficient (low-RFI) compared with less efficient (high-RFI) cattle, again regardless of diet. The only three exceptions were Phe, Met, and Lys (P > 0.05) for which the first metabolic reaction before being catabolized does not involve transamination, a pathway known naturally to enrich AAs in 15N. The contrasted isotopic signatures across RFI groups only in those PbAA undergoing transamination are interpreted as differences in transamination rates and N-use efficiency between low- and high-RFI phenotypes. Natural isotopic N signatures in bulk proteins and specific PbAA can be proposed as biomarkers of RFI in growing beef cattle fed different diets. However, the current study cannot delineate whether this effect only occurs post-absorption or to some extent also in the rumen. Our data support the conclusion that most efficient cattle in terms of RFI upregulate N conservation mechanisms compared with less efficient cattle and justify future research on this topic.


Assuntos
Aminoácidos/química , Aminoácidos/metabolismo , Ração Animal/análise , Bovinos/fisiologia , Dieta/veterinária , Comportamento Alimentar , Isótopos de Nitrogênio/química , Animais , Masculino , Rúmen/metabolismo , Silagem/análise
16.
J Chromatogr A ; 1622: 461135, 2020 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-32360058

RESUMO

Here we describe a new HPLC-MS/MS method using a mixed mode stationary phase and a binary gradient of elution for the rapid separation and quantification of AAs in human plasma without derivatization or ion pairing reagent addition. The sample preparation procedure consists in a single dilution step after protein precipitation with sulfosalicylic acid. The proposed method allows for the unambiguous identification and analysis of 52 AAs and related compounds including the separation of isomers and isobars in an 18 min chromatographic run including the conditioning and the equilibration times. AAs were detected by selective reaction monitoring. Internal calibration was used for the quantification of 37 AAs, including 25 using the corresponding isotopically labeled internal standards. External calibration (no internal standard) was used for five additional analytes. Qualitative detection was achieved for the remaining compounds. Validation studies evaluated accuracy, linearity, within- and between-run precision, lower limits of detection and quantification for 37 amino acids present in commonly used quality control samples. For within-run precision CVs averaged 3.8 % (n = 30) for all compounds. For between-run precision, CVs averaged 8.6 % for all compounds (n = 20). Correlation with the common standard ion-exchange chromatography with post-column derivatization method was also performed for 32 plasma samples. While the proposed method is at least 50 times more sensitive, the data showed good correlation with slopes equal or higher than 0.9 and correlation coefficients mostly higher than 0.90. The method was successfully applied for analysis of plasma samples for detection of inherited disorders of amino acid metabolism.


Assuntos
Aminoácidos/sangue , Cromatografia Líquida/métodos , Espectrometria de Massas em Tandem/métodos , Aminoácidos/química , Calibragem , Cromatografia Líquida de Alta Pressão/métodos , Feminino , Humanos , Recém-Nascido , Padrões de Referência , Reprodutibilidade dos Testes
17.
PLoS One ; 15(4): e0232613, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32353067

RESUMO

Inactivation of the tumor suppressor p53 resulting from the binding with a negative regulator HDM2 is among the predominant defects in human cancers. p53-mimicking peptides whose conformational and proteolytic stability is enhanced by an all-hydrocarbon staple are being recognized as promising anticancer agents for disrupting the p53-HDM2 binding and reactivating p53. Herein, we conduct a computational modeling and thermodynamic characterization of stapled p53/HDM2 complex via molecular docking, simulations, and binding free energy analysis. The binding thermodynamics analysis is done based on the end-point calculation of the effective binding energy-a sum of the direct peptide-protein interaction energy and the dehydration penalty-and on its decomposition into contributions from specific groups constituting the complex. This allows us to investigate how individual amino acids in the stapled p53 and HDM2 contribute to the binding affinity. We find that not only the epitope residues (F19, W23 and L26), but also the hydrocarbon linker of the stapled p53 impart significant contributions. Our computational approach will be useful in designing new stapled peptides in which the staple location is also optimized to improve the binding affinity.


Assuntos
Peptídeos/química , Proteínas Proto-Oncogênicas c-mdm2/química , Proteína Supressora de Tumor p53/química , Aminoácidos/química , Simulação de Acoplamento Molecular , Peptídeos/metabolismo , Ligação Proteica , Proteínas Proto-Oncogênicas c-mdm2/metabolismo , Termodinâmica , Proteína Supressora de Tumor p53/metabolismo
18.
PLoS One ; 15(5): e0232528, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32374785

RESUMO

Protein secondary structure prediction remains a vital topic with broad applications. Due to lack of a widely accepted standard in secondary structure predictor evaluation, a fair comparison of predictors is challenging. A detailed examination of factors that contribute to higher accuracy is also lacking. In this paper, we present: (1) new test sets, Test2018, Test2019, and Test2018-2019, consisting of proteins from structures released in 2018 and 2019 with less than 25% identity to any protein published before 2018; (2) a 4-layer convolutional neural network, SecNet, with an input window of ±14 amino acids which was trained on proteins ≤25% identical to proteins in Test2018 and the commonly used CB513 test set; (3) an additional test set that shares no homologous domains with the training set proteins, according to the Evolutionary Classification of Proteins (ECOD) database; (4) a detailed ablation study where we reverse one algorithmic choice at a time in SecNet and evaluate the effect on the prediction accuracy; (5) new 4- and 5-label prediction alphabets that may be more practical for tertiary structure prediction methods. The 3-label accuracy (helix, sheet, coil) of the leading predictors on both Test2018 and CB513 is 81-82%, while SecNet's accuracy is 84% for both sets. Accuracy on the non-homologous ECOD set is only 0.6 points (83.9%) lower than the results on the Test2018-2019 set (84.5%). The ablation study of features, neural network architecture, and training hyper-parameters suggests the best accuracy results are achieved with good choices for each of them while the neural network architecture is not as critical as long as it is not too simple. Protocols for generating and using unbiased test, validation, and training sets are provided. Our data sets, including input features and assigned labels, and SecNet software including third-party dependencies and databases, are downloadable from dunbrack.fccc.edu/ss and github.com/sh-maxim/ss.


Assuntos
Redes Neurais de Computação , Estrutura Secundária de Proteína , Algoritmos , Sequência de Aminoácidos , Aminoácidos/química , Bases de Dados de Proteínas/estatística & dados numéricos , Aprendizado Profundo , Proteínas/química , Software
19.
Food Chem ; 327: 126998, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32438264

RESUMO

Cold-pressed rapeseed meal with high protein content (38.76% protein dry weight basis) was used to prepare rapeseed protein isolates (RPIs) by alkaline extraction (pH 8.0, 9.0, 10.0, 11.0, 12.0 and 13.0) and acid precipitation (pH 3.0, 3.5, 4.0, 4.5, 5.0 and 5.5). The protein with an intact structure and the highest yield (65.08%) was obtained at extraction pH 9.0 and precipitation pH 4.5, accompanied by the lowest D-amino acid content, the lightest colour and the lowest contents of glucosinolates (2.85 mmol/kg), phytic acid (1.05 mg/g) and sinapine (0.68 mg/g). Additionally, water/oil absorption, foaming and emulsifying capacities decreased with decreasing precipitation pH, while the solubility showed the reverse trend. During gastric simulation digestion, the α-polypeptide of cruciferin and napin in the RPIs showed digestive resistance. Overall, pH regulation might be an effective method to isolate high quality RPIs for use in the food processing industry.


Assuntos
Brassica napus/química , Proteínas de Plantas/isolamento & purificação , Proteínas de Plantas/farmacocinética , Albuminas 2S de Plantas/farmacocinética , Aminoácidos/análise , Aminoácidos/química , Antígenos de Plantas , Precipitação Química , Cor , Digestão , Emulsificantes/química , Indústria de Processamento de Alimentos/métodos , Glucosinolatos/análise , Concentração de Íons de Hidrogênio , Ácido Fítico/análise , Proteínas de Plantas/química , Óleo de Brassica napus/química , Proteínas de Armazenamento de Sementes/farmacocinética , Solubilidade
20.
Biochim Biophys Acta Proteins Proteom ; 1868(8): 140439, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32371148

RESUMO

The present article reviews the results of solid-state vibrational circular dichroism (SD-VCD) measurements on the crystals of amino acids. The investigated series were Ala, Ile, Leu, Phe, Ser, Val, and Thr. Spectra were recorded for the samples containing both D- and L-enantiomers. The molecular conformation in a crystalline state was compared among the series. Molecule optimization of their conformation under intermolecular interactions in crystalline states was revealed. One noteworthy aspect was that some VCD peaks were remarkably enhanced in comparison with the solution states. This fact was rationalized in terms of vibrationally coupled delocalization in a closely stacked pair. In addition, for a molecule with two asymmetric carbons, the signs of the VCD peaks were determined by the interplay between the two chiral centers. Lastly, the roles of the theoretical approach based on density functional theory calculations were described.


Assuntos
Aminoácidos/química , Dicroísmo Circular/métodos , Brometos/química , Cristalização , Conformação Molecular , Compostos de Potássio/química , Teoria Quântica , Estereoisomerismo , Vibração
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA