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1.
Front Nutr ; 9: 914273, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35548576

RESUMO

[This corrects the article DOI: 10.3389/fnut.2022.851402.].

2.
Front Nutr ; 9: 851402, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35284441

RESUMO

Dietary bioactive lipids, one of the three primary nutrients, is not only essential for growth and provides nutrients and energy for life's activities but can also help to guard against disease, such as Alzheimer's and cardiovascular diseases, which further strengthen the immune system and maintain many body functions. Many microorganisms, such as yeast, algae, and marine fungi, have been widely developed for dietary bioactive lipids production. These biosynthetic processes were not limited by the climate and ground, which are also responsible for superiority of shorter periods and high conversion rate. However, the production process was also exposed to the challenges of low stability, concentration, and productivity, which was derived from the limited knowledge about the critical enzyme in the metabolic pathway. Fortunately, the development of enzymatic research methods provides powerful tools to understand the catalytic process, including site-specific mutagenesis, protein dynamic simulation, and metabolic engineering technology. Thus, we review the characteristics of critical desaturase and elongase involved in the fatty acids' synthesis metabolic pathway, which aims to not only provide extensive data for enzyme rational design and modification but also provides a more profound and comprehensive understanding of the dietary bioactive lipids' synthetic process.

3.
Mar Drugs ; 20(2)2022 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-35200655

RESUMO

As an important enzyme involved in the marine carbon cycle, alginate lyase has received extensive attention because of its excellent degradation ability on brown algae, which is widely utilized for alginate oligosaccharide preparation or bioethanol production. In comparison with endo-type alginate lyases (PL-5, PL-7, and PL-18 families), limited studies have focused on PL-17 family alginate lyases, especially for those with special characteristics. In this study, a novel PL-17 family alginate lyase, Aly23, was identified and cloned from the marine bacterium Pseudoalteromonas carrageenovora ASY5. Aly23 exhibited maximum activity at 35 °C and retained 48.93% of its highest activity at 4 °C, representing an excellent cold-adaptation property. Comparative molecular dynamics analysis was implemented to explore the structural basis for the cold-adaptation property of Aly23. Aly23 had a high substrate preference for poly ß-D-mannuronate and exhibited both endolytic and exolytic activities; its hydrolysis reaction mainly produced monosaccharides, disaccharides, and trisaccharides. Furthermore, the enzymatic hydrolyzed oligosaccharides displayed good antioxidant activities to reduce ferric and scavenge radicals, such as hydroxyl, ABTS+, and DPPH. Our work demonstrated that Aly23 is a promising cold-adapted biocatalyst for the preparation of natural antioxidants from brown algae.


Assuntos
Antioxidantes/farmacologia , Oligossacarídeos/farmacologia , Polissacarídeo-Liases/metabolismo , Pseudoalteromonas/metabolismo , Antioxidantes/metabolismo , Dissacarídeos/metabolismo , Sequestradores de Radicais Livres/metabolismo , Sequestradores de Radicais Livres/farmacologia , Hidrólise , Simulação de Dinâmica Molecular , Monossacarídeos/metabolismo , Oligossacarídeos/metabolismo , Polissacarídeo-Liases/isolamento & purificação , Temperatura , Trissacarídeos/metabolismo
4.
Nat Commun ; 13(1): 102, 2022 01 10.
Artigo em Inglês | MEDLINE | ID: mdl-35013238

RESUMO

The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided. Here, we extract 1.7 million helices from the PDB and compile them into a database (Therapeutic Peptide Design database; TP-DB) that allows queries of compounded patterns to facilitate the identification of sequence motifs of helical structures. We show how TP-DB helps us identify a known purification-tag-specific antibody that can be repurposed into a diagnostic kit for Helicobacter pylori. We also show how the database can be used to design a new antimicrobial peptide that shows better Candida albicans clearance and lower hemolysis than its template homologs. Finally, we demonstrate how TP-DB can suggest point mutations in helical peptide blockers to prevent a targeted tumorigenic protein-protein interaction. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/ .


Assuntos
Aminoácidos/química , Antineoplásicos/química , Software , Sequência de Aminoácidos , Aminoácidos/metabolismo , Animais , /farmacologia , Antineoplásicos/metabolismo , Antineoplásicos/farmacologia , Bases de Dados de Proteínas , Desenho de Fármacos/métodos , Humanos , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Ligação Proteica , Conformação Proteica em alfa-Hélice , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/farmacologia , Relação Estrutura-Atividade
5.
Biotechnol Bioeng ; 117(11): 3345-3355, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32678455

RESUMO

With the aggravation of environmental pollution and energy crisis, the sustainable microbial fermentation process of converting glycerol to 1,3-propanediol (1,3-PDO) has become an attractive alternative. However, the difficulty in the online measurement of glycerol and 1,3-PDO creates a barrier to the fermentation process and then leads to the residual glycerol and therefore, its wastage. Thus, in the present study, the four-input artificial neural network (ANN) model was developed successfully to predict the concentration of glycerol, 1,3-PDO, and biomass with high accuracy. Moreover, an ANN model combined with a kinetic model was also successfully developed to simulate the fed-batch fermentation process accurately. Hence, a soft sensor from the ANN model based on NaOH-related parameters has been successfully developed which cannot only be applied in software to solve the difficulty of glycerol and 1,3-PDO online measurement during the industrialization process, but also offer insight and reference for similar fermentation processes.


Assuntos
Técnicas de Cultura de Células/métodos , Clostridium butyricum/metabolismo , Fermentação/fisiologia , Redes Neurais de Computação , Propilenoglicóis , Reatores Biológicos/microbiologia , Meios de Cultura/análise , Meios de Cultura/química , Meios de Cultura/metabolismo , Glicerol/análise , Glicerol/metabolismo , Cinética , Propilenoglicóis/análise , Propilenoglicóis/metabolismo
6.
Appl Biochem Biotechnol ; 191(2): 893-903, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31912425

RESUMO

Quorum quenching (QQ) enzymes, which degrade signaling molecules so as to disrupt the quorum sensing signaling process, have drawn much attention as alternative antimicrobial agents. However, the screening methods for evolution of such enzymes through constructing genetic circuits remain a challenge for its relatively high false positive rates caused by the higher basal expression level of the naturally acquired promoter. Thus, we presented an improved genetic circuit by introducing an artificial hybrid promoter PluxI-lacO combining PlacO originated from lactose promoter with QS regulatory promoter PluxI to control the expression of reporter gene rfp. Herein, we investigated the effect of various expression strengths of suppressive protein LacI and signaling molecule AHL on the expression of rfp. We found that the effect AHL exerted on the expression of rfp outweighed that from IPTG. The results also demonstrated that our genetic circuit could achieve the lower basal expression level of reporter gene and could respond to the expression of AiiA. The resulting circuits show the potential for screening the evolved AiiA more efficiently by virtue of inherent low basal expression level.


Assuntos
Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Percepção de Quorum/genética , Genes Bacterianos/genética , Metaloendopeptidases/genética , Regiões Promotoras Genéticas , Proteínas Repressoras , Transativadores
7.
Appl Biochem Biotechnol ; 190(1): 18-29, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31301008

RESUMO

NAD(P)H-dependent enzymes are ideal biocatalysts for the industrial production of chiral compounds, such as chiral alcohols, chiral amino acids, and chiral amines; however, efficient strategies for the regeneration of coenzyme are expected as costly of the coenzymes. Herein, a solvent-tolerant isopropanol dehydrogenase (IDH) showing lower similarity (37%) with other proteins was obtained and characterized. The enzyme exhibits high catalysis ability of its substrates methanol, ethanol, ethylene glycol, glycerol, isopropanol, n-butanol, isobutanol, and acetone. And it has good adaptability in organic solvents (isopropanol, acetonitrile, acetone, and acetophenone). Interaction force and the corresponding amino acid residues between IDH and NAD+ or NADP+ were parsed by docking. The wide substrate spectrum, excellent organic solvent tolerance, and good biocatalytic activity make the excavated enzyme a promising biocatalyst for the production of chiral compounds industrially and the construction of coenzyme regeneration systems in aqueous organic phase or organic phase.


Assuntos
Oxirredutases do Álcool/metabolismo , Coenzimas/metabolismo , Solventes/metabolismo , Oxirredutases do Álcool/genética , Sítios de Ligação , Clonagem Molecular , Cinética , Simulação de Acoplamento Molecular , NAD/metabolismo , NADP/metabolismo , Compostos Orgânicos/metabolismo , Especificidade por Substrato
8.
Appl Biochem Biotechnol ; 186(3): 789-804, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-29740797

RESUMO

As phenylalanine dehydrogenase (PheDH) plays an important role in the synthesis of chiral drug intermediates and detection of phenylketonuria, it is significant to obtain a PheDH with specific and high activity. Here, a PheDH gene, pdh, encoding a novel BhPheDH with 61.0% similarity to the known PheDH from Microbacterium sp., was obtained. The BhPheDH showed optimal activity at 60 °C and pH 7.0, and it showed better stability in hot environment (40-70 °C) than the PheDH from Nocardia sp. And its activity and thermostability could be significantly increased by sodium salt. After incubation for 2 h in 3 M NaCl at 60 °C, the residual activity of the BhPheDH was found to be 1.8-fold higher than that of the control group (without NaCl). The BhPheDH could tolerate high concentration of ammonium chloride and its activity could be also enhanced by the high concentration of ammonium salts. These characteristics indicate that the BhPheDH possesses better thermostability, ammonium chloride tolerance, halophilic mechanism, and high salt activation. The mechanism of thermostability and high salt tolerance of the BhPheDH was analyzed by molecular dynamics simulation. These results provide useful information about the enzyme with high-temperature activity, thermostability, halophilic mechanism, tolerance to high concentration of ammonium chloride, higher salt activation and enantio-selectivity, and the application of molecular dynamics simulation in analyzing the mechanism of these distinctive characteristics.


Assuntos
Aminoácido Oxirredutases/química , Cloreto de Amônio/química , Bacillus/enzimologia , Proteínas de Bactérias/química , Estabilidade Enzimática
9.
Biotechnol Bioeng ; 115(3): 684-693, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29105732

RESUMO

1,3-propanediol production by Clostridium butyricum is a low productivity process due to the long time seed cultivation and thus hinders its industrial scale production. In the present study, repeated batch fermentation coupled with activated carbon adsorption strategy was first established which conduced not only to saving the time of seed cultivation and enhancing the productivity, but also to reducing the costs for the seed cultivation to achieve the purpose of 1,3-propanediol continuous production. The concentration of 1,3-propanediol from first to fourth cycle was 42.89, 45.78, 44.48, 42.39 (g/L), and the corresponding volumetric productivity was 2.14, 1.91, 1.85, 2.12 (g/L · h-1 ) respectively. More importantly, a relatively complete schematic diagram of the proposed metabolic pathways was firstly mapped out based on the intracellular metabolites analysis through GC-MS. At the same time, metabolic pathway and principal components analyses were carried out to give us deep insight into metabolic state. Many metabolites occurred to response to the stress in Cycle II. Even resting body formed and lipid accumulated owing to the worsening environment in the group without activated carbon in Cycle III. Thus, it demonstrated that activated carbon provided a favorable microenvironment for Clostridium butyricum in the repeated batch fermentation process to achieve the purpose of 1,3-propanediol continuous production.


Assuntos
Carbono/metabolismo , Clostridium butyricum/crescimento & desenvolvimento , Propilenoglicóis/metabolismo , Adsorção
10.
Crit Rev Biotechnol ; 37(8): 1024-1037, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28423958

RESUMO

Multi-enzyme complexes have the potential to achieve high catalytic efficiency for sequence reactions due to their advantages in eliminating product inhibition, facilitating intermediate transfer and in situ regenerating cofactors. Constructing functional multi-enzyme systems to mimic natural multi-enzyme complexes is of great interest for multi-enzymatic biosynthesis and cell-free synthetic biotransformation, but with many challenges. Currently, various assembly strategies have been developed based on the interaction of biomacromolecules such as DNA, peptide and scaffolding protein. On the other hand, chemical-induced assembly is based on the affinity of enzymes with small molecules including inhibitors, cofactors and metal ions has the advantage of simplicity, site-to-site oriented structure control and economy. This review summarizes advances and progresses employing these strategies. Furthermore, challenges and perspectives in designing multi-enzyme systems are highlighted.


Assuntos
Enzimas/metabolismo , Biocatálise , Biotransformação
11.
Appl Biochem Biotechnol ; 181(4): 1454-1464, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-27866308

RESUMO

L-tert-Leucine (L-Tle) and its derivatives are extensively used as crucial building blocks for chiral auxiliaries, pharmaceutically active ingredients, and ligands. Combining with formate dehydrogenase (FDH) for regenerating the expensive coenzyme NADH, leucine dehydrogenase (LeuDH) is continually used for synthesizing L-Tle from α-keto acid. A multilevel factorial experimental design was executed for research of this system. In this work, an efficient optimization method for improving the productivity of L-Tle was developed. And the mathematical model between different fermentation conditions and L-Tle yield was also determined in the form of the equation by using uniform design and regression analysis. The multivariate regression equation was conveniently implemented in water, with a space time yield of 505.9 g L-1 day-1 and an enantiomeric excess value of >99 %. These results demonstrated that this method might become an ideal protocol for industrial production of chiral compounds and unnatural amino acids such as chiral drug intermediates.


Assuntos
Biotecnologia/métodos , Leucina/biossíntese , Modelos Teóricos , Valina/análogos & derivados , Aminação , Escherichia coli/genética , Escherichia coli/metabolismo , Formiato Desidrogenases/genética , Formiato Desidrogenases/metabolismo , Engenharia Genética , Leucina/química , Leucina Desidrogenase/genética , Leucina Desidrogenase/metabolismo , Ácido Pirúvico/química , Ácido Pirúvico/metabolismo , Análise de Regressão , Valina/biossíntese , Valina/química
12.
J Ind Microbiol Biotechnol ; 43(5): 577-84, 2016 May.
Artigo em Inglês | MEDLINE | ID: mdl-26819086

RESUMO

Phenylalanine dehydrogenase (PheDH) plays an important role in enzymatic synthesis of L-phenylalanine for aspartame (sweetener) and detection of phenylketonuria (PKU), suggesting that it is important to obtain a PheDH with excellent characteristics. Gene fusion of PheDH and formate dehydrogenase (FDH) was constructed to form bifunctional multi-enzymes for bioconversion of L-phenylalanine coupled with coenzyme regeneration. Comparing with the PheDH monomer from Microbacterium sp., the bifunctional PheDH-FDH showed noteworthy stability under weakly acidic and alkaline conditions (pH 6.5-9.0). The bifunctional enzyme can produce 153.9 mM L-phenylalanine with remarkable performance of enantiomers choice by enzymatic conversion with high molecular conversion rate (99.87 %) in catalyzing phenylpyruvic acid to L-phenylalanine being 1.50-fold higher than that of the separate expression system. The results indicated the potential application of the PheDH and PheDH-FDH with coenzyme regeneration for phenylpyruvic acid analysis and L-phenylalanine biosynthesis in medical diagnosis and pharmaceutical field.


Assuntos
Aminoácido Oxirredutases/metabolismo , Coenzimas/biossíntese , Formiato Desidrogenases/metabolismo , Proteínas Recombinantes de Fusão/metabolismo , Aminoácido Oxirredutases/química , Aminoácido Oxirredutases/genética , Bacillus/enzimologia , Candida/enzimologia , Coenzimas/metabolismo , Estabilidade Enzimática , Formiato Desidrogenases/química , Formiato Desidrogenases/genética , Formiatos/metabolismo , Concentração de Íons de Hidrogênio , Cinética , Fenilalanina/biossíntese , Fenilalanina/metabolismo , Ácidos Fenilpirúvicos/metabolismo , Proteínas Recombinantes de Fusão/genética , Estereoisomerismo , Temperatura
13.
Enzyme Microb Technol ; 54: 45-50, 2014 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-24267567

RESUMO

The conductive polymer, poly(3,4-ethylenedioxythiophene) (PEDOT), possesses attractive properties that show the potential applications in many fields. In this study, we have proposed a two-stage enzymatic synthesis of conductive PEDOT. Horseradish peroxidase (HRP) acts as the catalyst to promote the generation of EDOT free radicals followed by the polymerization under the room temperature in the presence of poly(sodium 4-styrenesulfonate) (PSS), then a mild heating process is employed for further chain extension. The final PEDOT:PSS is purified with n-butanol and subjected to various characterizations, which indicate that PEDOT with enzymatic approach exhibits a similar molecular structure to that with chemical method. However, the enzymatically synthesized PEDOT:PSS demonstrates advantages, such as stable integration of PEDOT with PSS and better electrochemical properties, suggesting its future prospective applications.


Assuntos
Compostos Bicíclicos Heterocíclicos com Pontes/metabolismo , Polímeros/metabolismo , Biotecnologia , Compostos Bicíclicos Heterocíclicos com Pontes/química , Catálise , Condutividade Elétrica , Técnicas Eletroquímicas , Peroxidase do Rábano Silvestre/metabolismo , Temperatura Alta , Estrutura Molecular , Polímeros/química , Poliestirenos/química , Poliestirenos/metabolismo , Espectrofotometria , Espectroscopia de Infravermelho com Transformada de Fourier , Análise Espectral Raman
14.
Protein Pept Lett ; 15(10): 1132-7, 2008.
Artigo em Inglês | MEDLINE | ID: mdl-19075826

RESUMO

By proposing a improved Chou's pseudo amino acid composition approach to extract the features of the sequences, a powerful predictor based on k-nearest neighbor was introduced to identify the types of lipases according to their sequences. To avoid redundancy and bias, demonstrations were performed on a dataset where none of the proteins has > or =25% sequence identity to any other. The overall success rate thus obtained by the 10-fold cross-validation test was over 90%, indicating that the improved Chou's pseudo amino acid composition might be a useful tool for extracting the features of protein sequences, or at lease can play a complementary role to many of the other existing approaches.


Assuntos
Aminoácidos/análise , Biologia Computacional , Lipase/química , Lipase/classificação , Sequência de Aminoácidos , Estudos de Viabilidade , Sensibilidade e Especificidade
15.
J Theor Biol ; 253(2): 310-5, 2008 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-18471832

RESUMO

Predicting the cofactors of oxidoreductases plays an important role in inferring their catalytic mechanism. Feature extraction is a critical part in the prediction systems, requiring raw sequence data to be transformed into appropriate numerical feature vectors while minimizing information loss. In this paper, we present an amino acid composition distribution method for extracting useful features from primary sequence, and the k-nearest neighbor was used as the classifier. The overall prediction accuracy evaluated by the 10-fold cross-validation reached 90.74%. Comparing our method with other eight feature extraction methods, the improvement of the overall prediction accuracy ranged from 3.49% to 15.74%. Our experimental results confirm that the method we proposed is very useful and may be used for other bioinformatical predictions. Interestingly, when features extracted by our method and Chou's amphiphilic pseudo-amino acid composition were combined, the overall accuracy could reach 92.53%.


Assuntos
Aminoácidos/análise , Coenzimas/química , Oxirredutases/química , Bases de Dados de Proteínas , Modelos Químicos
16.
Sheng Wu Gong Cheng Xue Bao ; 23(4): 715-8, 2007 Jul.
Artigo em Chinês | MEDLINE | ID: mdl-17822050

RESUMO

Bacillus pumilus xylanase was cloned and sequenced. Based on the tertiary structure that originated from homology modeling, the potential active pocket was searched and ligand-protein docking was performed using relative softwares. The information extracted from the molecular docking is analyzed; several amino acid residues might play a vital role in the xylanase catalytic reaction are obtained to instruct the further modification of xylanase directed-evolution.


Assuntos
Bacillus/enzimologia , Proteínas de Bactérias/metabolismo , Simulação por Computador , Endo-1,4-beta-Xilanases/metabolismo , Modelos Moleculares , Sequência de Aminoácidos , Bacillus/genética , Proteínas de Bactérias/genética , Sequência de Bases , Endo-1,4-beta-Xilanases/genética , Modelos Químicos , Dados de Sequência Molecular , Ligação Proteica , Especificidade por Substrato , Xilanos/genética , Xilanos/metabolismo
17.
Sheng Wu Gong Cheng Xue Bao ; 23(1): 133-7, 2007 Jan.
Artigo em Chinês | MEDLINE | ID: mdl-17366902

RESUMO

Degenerate PCR primers were designed by multiple alignment of the protein sequences of known structural genes encoding the catalytic subunits of NiFe-hydrogenases obtained from Swiss-Prot Protein Sequence Database through CLUSTAL-W software and compared for conserved sequence motifs. An amplified PCR product 1 kb in size was obtained from the genomic DNA of Klebsiella pneumoniae using a set of degenerate primers, and then inverse PCR technique was used to obtain the full hydrogenase coding region. A predicted secondary structure and 3D structural model were constructed by homology modeling and docking. On the basis of these results, it was inferred that NiFe-hydrogenase from Klebsiella pneumoniae belongs to the membrane-bound H2 evolving hydrogenase group (Ech hydrogenase group).


Assuntos
Proteínas de Bactérias/genética , Hidrogenase/genética , Klebsiella pneumoniae/genética , Proteínas de Bactérias/química , Clonagem Molecular , Códon/genética , DNA Bacteriano/química , DNA Bacteriano/genética , Bases de Dados de Proteínas , Ligação de Hidrogênio , Hidrogenase/química , Klebsiella pneumoniae/enzimologia , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Análise de Sequência de DNA
18.
Sheng Wu Gong Cheng Xue Bao ; 22(6): 950-5, 2006 Nov.
Artigo em Chinês | MEDLINE | ID: mdl-17168318

RESUMO

The gdrA, gdrB gene coding glycerol dehydratase reactivase factor were amplified by using the genomic DNA of Klebsiella pneumoniae as the template. The gdrA and gdrB were inserted in pMD-18T to yield the recombinant cloning vector pMD-gdrAB. After the DNA sequence was determined, the gdrAB gene was subcloned into expression vector pET-28a(+) to yield the recombinant expression vector pET-28gdrAB. Under screening pressure by ampicillin and kanamycin simultaneously, the activity of glycerol dehydratase reactivase was characterized by coexpression of pET-32gldABC, which carry the gldABC gene encoding glycerol dehydratase, and pET-28gdrAB in E. coli BL21(DE3).


Assuntos
Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Hidroliases/genética , Hidroliases/metabolismo , Proteínas de Bactérias/isolamento & purificação , Clonagem Molecular , Eletroforese em Gel de Poliacrilamida , Escherichia coli/genética , Expressão Gênica , Vetores Genéticos/genética , Hidroliases/isolamento & purificação , Plasmídeos/genética , Reação em Cadeia da Polimerase
19.
Sheng Wu Gong Cheng Xue Bao ; 22(6): 1026-31, 2006 Nov.
Artigo em Chinês | MEDLINE | ID: mdl-17168331

RESUMO

In this paper, the Boosting-based decision tree ensemble classifiers were applied to discriminate thermophilic and mesophilic proteins. Three methods, namely, self-consistency test, 5-fold cross-validation and independent testing with other dataset, were used to evaluate the performance and robust of the models. Logitboost, as a novel classifier in Boosting algorithm, performed better than Adaboost. The overall accuracy of the three methods was 100%, 88.4% and 89.5%, respectively. It was demonstrated that LogitBoost performed comparably or even better than that of neural network, a very powerful classifier widely used in biological literatures. The influence of protein size on discrimination was addressed. It is anticipated that the power in predicting many bio-macromolecular attributes will be further strengthened if the Boosting and some other existing algorithms can be effectively complemented with each other.


Assuntos
Algoritmos , Árvores de Decisões , Proteínas/classificação , Peso Molecular , Redes Neurais de Computação , Proteínas/química
20.
Sheng Wu Gong Cheng Xue Bao ; 22(2): 293-8, 2006 Mar.
Artigo em Chinês | MEDLINE | ID: mdl-16607959

RESUMO

In this work, the dipeptide composition of 3216 thermophilic and 4007 mesophilic protein sequences was systematically analyzed. We found that the thermophilic proteins contained more dipeptides such as EE, EK, KE, VE, EI, KI, EV, KK, VK and IE, whereas less dipeptides such as AA, LL, LA, AL, QA, QL, AQ, LT, TL and EQ. Based on this information, a statistical method for discriminating thermophilic and mesophilic proteins was developed. Our approach correctly picked up the thermophilic proteins with the accuracy of 94.0% and 89%, respectively, for the testing sets of 382 and 73 thermophilic proteins. And for the testing 325 and 73 mesophilic proteins, the accuracy was 85.2% and 89%, respectively. The influence of specific dipeptides on discrimination was also discussed.


Assuntos
Aminoácidos/química , Proteínas de Bactérias/química , Dipeptídeos/química , Análise de Sequência de Proteína , Bactérias/química , Análise Discriminante , Temperatura Alta , Termodinâmica
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