The structural insight of class III of polyhydroxyalkanoate synthase from Bacillus sp. PSA10 as revealed by in silico analysis

PhaC synthase is an enzyme responsible for PHA polymerization. In this work, the catalytic mechanism class III of PhaC synthase from Bacillus sp. PSA10 (BacPhaCSynt) was reported through in silico modelling approach based on the primary sequence of the PhaC synthase. The open reading frame BacPhaCSynt has been successfully isolated, cloned and overexpressed the recombinant protein in Escherichia coli BL21(DE3). To know the global architecture and catalytic mechanism, the structural prediction of BacPhaCSynt has been carried out by using MODELLER. The recombinant BacPhaCSynt exhibited monomeric molecular weight (MW) of 43.6 kDa, when it was analyzed on 12% SDS‐PAGE gel. Based on the structural prediction, BacPhaCSynt exhibited global architecture of α/β hydrolase fold, with the root mean square deviation (r.m.s.d) value of 0.94Å. The catalytic residues composition of BacPhaCSynt consists of C151, D307, and H336, but the H336 and D307 residues of the model have been distorted 62.8o and 175.2o from the corresponding residues of the template. Since the D307 is quite a distance from the H336, it might act as a general base for the activation of ‐OH group of the substrate. The results strongly suggested that the mode of action of BacPhaCSynt obeyed the covalent catalysis mechanism.

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Cloning, Sequencing, and In Silico Analysis of β-Propeller Phytase Bacillus licheniformis Strain PB-13

Biotechnology Research International ◽

10.1155/2014/841353 ◽

2014 ◽

Vol 2014 ◽

pp. 1-11 ◽

Cited By ~ 8

Author(s):

Vinod Kumar ◽

Gopal Singh ◽

Punesh Sangwan ◽

A. K. Verma ◽

Sanjeev Agrawal

Keyword(s):

Phylogenetic Tree ◽

Bacillus Licheniformis ◽

In Silico ◽

Catalytic Mechanism ◽

Specific Activity ◽

In Silico Analysis ◽

Homology Search ◽

Multiple Sequence ◽

Bioinformatic Tools ◽

C Terminus

β-Propeller phytases (BPPhy) are widely distributed in nature and play a major role in phytate-phosphorus cycling. In the present study, a BPPhy gene from Bacillus licheniformis strain was expressed in E. coli with a phytase activity of 1.15 U/mL and specific activity of 0.92 U/mg proteins. The expressed enzyme represented a full length ORF “PhyPB13” of 381 amino acid residues and differs by 3 residues from the closest similar existing BPPhy sequences. The PhyPB13 sequence was characterized in silico using various bioinformatic tools to better understand structural, functional, and evolutionary aspects of BPPhy class by multiple sequence alignment and homology search, phylogenetic tree construction, variation in biochemical features, and distribution of motifs and superfamilies. In all sequences, conserved sites were observed toward their N-terminus and C-terminus. Cysteine was not present in the sequence. Overall, three major clusters were observed in phylogenetic tree with variation in biophysical characteristics. A total of 10 motifs were reported with motif “1” observed in all 44 protein sequences and might be used for diversity and expression analysis of BPPhy enzymes. This study revealed important sequence features of BPPhy and pave a way for determining catalytic mechanism and selection of phytase with desirable characteristics.

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Ribonucleotide Reductases from Bifidobacteria Contain Multiple Conserved Indels Distinguishing Them from All Other Organisms: In Silico Analysis of the Possible Role of a 43 aa Bifidobacteria-Specific Insert in the Class III RNR Homolog

Frontiers in Microbiology ◽

10.3389/fmicb.2017.01409 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 4

Author(s):

Seema Alnajar ◽

Bijendra Khadka ◽

Radhey S. Gupta

Keyword(s):

In Silico ◽

In Silico Analysis ◽

Class Iii ◽

Ribonucleotide Reductases ◽

Conserved Indels ◽

Silico Analysis

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Global analysis of non-animal peroxidases provides insights into the evolution of this gene family in the green lineage

Journal of Experimental Botany ◽

10.1093/jxb/eraa141 ◽

2020 ◽

Vol 71 (11) ◽

pp. 3350-3360 ◽

Cited By ~ 2

Author(s):

Duchesse Lacour Mbadinga Mbadinga ◽

Qiang Li ◽

Philippe Ranocha ◽

Yves Martinez ◽

Christophe Dunand

Keyword(s):

In Silico ◽

Global Analysis ◽

Wood Decay ◽

Large Family ◽

In Silico Analysis ◽

Evolutionary Analysis ◽

Class Iii ◽

Origin And Evolution ◽

Plant Degradation ◽

Eukaryotic Organisms

Abstract The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, a number of studies have provided an understanding of the origin and evolution of this protein family. Here, we report a comprehensive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical approaches. Thanks to the availability of numerous genomic sequences from more than 2500 species belonging to 14 kingdoms together with expert and comprehensive annotation of peroxidase sequences that have been centralized in a dedicated database, we have been able to use phylogenetic reconstructions to increase our understanding of the evolutionary processes underlying the diversification of non-animal peroxidases. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases correlates with the presence or absence of certain organelles or with specific biological processes. Examination of almost 2000 organisms determined that ascorbate peroxidases (APxs) and cytochrome c peroxidases (CcPs) are present in those containing chloroplasts and mitochondria, respectively. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class II peroxidases (CII Prxs) are only found in fungi with wood-decay and plant-degradation abilities. Class III peroxidases (CIII Prxs) are only found in streptophyte algae and land plants, and have been subjected to large family expansion. Biochemical activities of APx, CcP, and CIII Prx assessed using protein extracts from 30 different eukaryotic organisms support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of the non-animal peroxidase encoding sequences.

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In Silico Analysis of Class III Peroxidases: Hypothetical Structure, Ligand Binding Sites, Posttranslational Modifications, and Interaction with Substrates

Methods in Molecular Biology - Plant Proteomics ◽

10.1007/978-1-0716-0528-8_24 ◽

2020 ◽

pp. 325-339

Author(s):

Sabine Lüthje ◽

Kalaivani Ramanathan

Keyword(s):

Ligand Binding ◽

Posttranslational Modifications ◽

Binding Sites ◽

In Silico ◽

In Silico Analysis ◽

Class Iii ◽

Ligand Binding Sites ◽

Class Iii Peroxidases ◽

Silico Analysis ◽

Hypothetical Structure

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Prediction of Bioactive Peptides from Chlorella sorokiniana Proteins Using Proteomic Techniques in Combination with Bioinformatics Analyses

International Journal of Molecular Sciences ◽

10.3390/ijms20071786 ◽

2019 ◽

Vol 20 (7) ◽

pp. 1786 ◽

Cited By ~ 10

Author(s):

Lhumen A. Tejano ◽

Jose P. Peralta ◽

Encarnacion Emilia S. Yap ◽

Fenny Crista A. Panjaitan ◽

Yu-Wei Chang

Keyword(s):

In Silico ◽

Bioactive Peptides ◽

Biological Activities ◽

Polyacrylamide Gel Electrophoresis ◽

Sodium Dodecyl ◽

In Silico Analysis ◽

Chlorella Sorokiniana ◽

Molecular Characteristics ◽

Sds Page ◽

Silico Analysis

Chlorella is one of the most nutritionally important microalgae with high protein content and can be a good source of potential bioactive peptides. In the current study, isolated proteins from Chlorella sorokiniana were subjected to in silico analysis to predict potential peptides with biological activities. Molecular characteristics of proteins were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and proteomics techniques. A total of eight proteins were identified by proteomics techniques from 10 protein bands of the SDS-PAGE. The predictive result by BIOPEP’s profile of bioactive peptides tools suggested that proteins of C. sorokiniana have the highest number of dipeptidyl peptidase-IV (DPP IV) inhibitors, with high occurrence of other bioactive peptides such as angiotensin-I converting enzyme (ACE) inhibitor, glucose uptake stimulant, antioxidant, regulating, anti-amnestic and antithrombotic peptides. In silico analysis of enzymatic hydrolysis revealed that pepsin (pH > 2), bromelain and papain were proteases that can release relatively larger quantity of bioactive peptides. In addition, combinations of different enzymes in hydrolysis were observed to dispense higher numbers of bioactive peptides from proteins compared to using individual proteases. Results suggest the potential of protein isolated from C. sorokiniana could be a source of high value products with pharmaceutical and nutraceutical application potential.

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Analisis In-Silico Protein Tiol-Disulfida Isomerase Bacillus sp. RP1

JURNAL ILMIAH SAINS ◽

10.35799/jis.12.1.2012.400 ◽

2012 ◽

Vol 12 (1) ◽

pp. 43 ◽

Cited By ~ 1

Author(s):

Vanda S Kamu ◽

Jemmy Abidjulu ◽

Maureen Kumaunang

Keyword(s):

Protein Folding ◽

Gene Product ◽

Active Site ◽

In Silico ◽

In Silico Analysis ◽

Bacillus Sp ◽

Disulfide Isomerase ◽

Disulfide Oxidoreductase ◽

Silico Analysis ◽

Bonding Site

ANALISIS IN-SILICO PROTEIN TIOL-DISULFIDA ISOMERASE Bacillus sp. RP1 ABSTRAK Pelipatan protein membutuhkan bantuan molekul chaperone serta katalis pelipatan. Penelitian ini bertujuan untuk mengkarakterisasi produk gen tiol-disulfida oksidoreduktase dari sumber organisme termofilik Bacillus sp. RP1. Metode yang dilaksanakan untuk mencapai tujuan tersebut, adalah mengkarakterisasi produk gen yang dihasilkan dengan menggunakan analisis in-silico. Dari hasil penelitian diperoleh bahwa karakterisasi terhadap produk gen yang dihasilkan menunjukkan adanya tiga protein, yaitu Bdbdred, Bdbdox, dan Etda, yang memiliki motif tioredoksin dan DsbA, serta sisi aktif dan sisi pengikatan dengan atom Zn. Prediksi struktur ketiga protein tersebut menunjukkan kemiripan satu sama lain. Kata kunci: Bdbd, chaperone, DsbA, tiol-disulfida oksidoreduktase, tioredoksin ANALYSIS OF IN-SILICO TIOL DISULFIDE ISOMERASE PROTEIN Bacillus sp. RP1 ABSTRACT Protein folding is facilitated by chaperone molecule as well as folding catalysts. The aim of this research was to characterize the gene product of thiol-disulfide oxidoreductase gene from thermophylic organism Bacillus sp. RP1, by using in-silico analysis. The characteristic of the gene product indicated three proteins, i.e. Bdbdred, Bdbdox, and Etda, which have thioredoxin motif, DsbA motif, active site and bonding site with Zn. The structure predicted of these three proteins showed similarity among them. Keywords: Bdbd, chaperone, DsbA, thiol-disulfide oxidoreductase, thioredoxin

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Potential Biological Activities of Peptides Generated during Casein Proteolysis by Curly Kale (Brassica oleracea L. var. sabellica L.) Leaf Extract: An In Silico Preliminary Study

Foods ◽

10.3390/foods10112877 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2877

Author(s):

Magdalena Polak-Berecka ◽

Magdalena Michalak-Tomczyk ◽

Katarzyna Skrzypczak ◽

Katarzyna Michalak ◽

Kamila Rachwał ◽

...

Keyword(s):

In Silico ◽

Leaf Extract ◽

Degradation Products ◽

Biological Activities ◽

Protein Profile ◽

In Silico Analysis ◽

Amino Acid Sequences ◽

Casein Hydrolysis ◽

Sds Page ◽

Silico Analysis

This study is a brief report on the proteolytic activity of curly kale leaf extract against casein. Casein degradation products and an in silico analysis of the biological activity of the peptides obtained was performed. The efficiency of casein hydrolysis by curly kale extract was determined using SDS–PAGE and by peptide concentration determination. The pattern of the enzymatic activity was determined by MALDI–TOF MS analysis. The results showed that α- and β-casein were more resistant to curly kale extract hydrolysis, whereas κ-casein was absent in the protein profile after 8 h of proteolysis, and all casein fractions were completely hydrolyzed after 24 h of incubation. Based on sequence analysis, seven peptides were identified, with molecular mass in the range of 1151–3024 Da. All the peptides were products of β-casein hydrolysis. The identified amino acid sequences were analyzed in BIOPEP, MBPDB, and FeptideDB databases in order to detect the potential activities of the peptides. In silico analysis suggests that the β-casein-derived peptides possess sequences of peptides with ACE inhibitory, antioxidant, dipeptidyl peptidase IV inhibitory, antithrombotic, immunomodulatory, and antiamnesic bioactivity. Our study was first to evaluate the possibility of applying curly kale leaf extract to generate biopeptides through β-casein hydrolysis.

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