In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals

2019 ◽  
Author(s):  
P.R. Sahoo ◽  
S.R. Mishra ◽  
S. Mohapatra ◽  
Santoswini Sahu ◽  
G. Sahoo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
In Silico ◽  
Tertiary Structure ◽  
Alpha Helix ◽  
Domestic Animals ◽  
Random Coil ◽  
Local Alignment ◽  
Physiochemical Properties ◽  
Gapdh Gene ◽  
Time Of Divergence

This study has been able to determine the physiochemical properties, secondary and tertiary structure, and phylogenetic analysis of GAPDH among domestic animals under in silico platform. Eighteen nucleotide and protein sequence of GAPDH gene of different mammalian species were retrieved from National Centre for Biotechnology information (NCBI). The percentage of identity and similarity was done by Basic Local Alignment Search Tool (BLAST), physiochemical properties were analyzed by ExPASy”s ProtParam tool, the secondary and 3-D structure was predicted by GOR IV and Swiss modeling respectively. Phylogenetic analysis among the animals was done by Molecular Evolutionary Genetics Analysis. It was found that the percentage of identity and similarity among all animals were almost more than 90%. The physiochemical analysis showed this protein is very stable, hydrophilic and intracytoplasmic in nature. The secondary structure analysis showed that GAPDH has more number of random coil (49.85%) Extended strand (27.93%), alpha helix (22.22%) of the protein. The QMEAN Z score was found 0.33 under protein modeling which interfered that this protein is of comparable quality. The phylogenetic analysis of this gene showed that the highest time of divergence occurred between sheep and common chimpanzee but least time of divergence observed between killer whale and dolphin. So it can be concluded that the GAPDH gene is highly conserved along all animal species.

In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
In Silico ◽  
Alpha Helix ◽  
In Silico Analysis ◽  
Glycogen Storage ◽  
Docking Studies ◽  
Random Coil ◽  
Special Topic ◽  
Industrial Biotechnology ◽  
In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

scholarly journals BIOINFORMATIC STUDY OF AN ANTITUMOR PROTEIN, AZURIN

2018 ◽  
Vol 11 (6) ◽  
pp. 169 ◽  
Author(s):  
Abiraami Valli S ◽  
Mythili T
Keyword(s):  
Phylogenetic Analysis ◽  
Secondary Structure ◽  
Physicochemical Properties ◽  
Functional Property ◽  
Random Coil ◽  
Structure Identification ◽  
Local Alignment ◽  
Protein Sequence Analysis ◽  
Ramachandran Plot ◽  
Pseudomonas Nitroreducens

Objective: The main objective of this study is to analyze the structure and function of an antitumor protein, azurin, thereby giving validation to the protein structure and existing physicochemical properties in the anticancer protein which are responsible for the anticancer activity.Methods: Protein sequence analysis was done using Basic Local Alignment Search Tool (BLAST) with ten different randomly selected species of Pseudomonas obtained from GenBank. The physicochemical properties, prediction of secondary structure, identification of motifs and domains, three-dimensional (3-D) structure of the antitumor protein, validation through Ramachandran plot, multiple sequence alignment (MSA), and phylogenetic analysis were studied and functional property was confirmed through in silico docking.Results: The similarity search (BLAST-P analysis) for the primary sequence from GenBank carried out showed 86% similarity to the second sequence, azurin (Pseudomonas nitroreducens). The ProtParam, ExPASy tool server indicated the presence of essential physicochemical properties in azurin. Secondary structure prediction revealed random coil, extended strand, alpha helix, and beta turn. The study on domains indicated the presence of one domain in azurin responsible for the anticancer activity. The 3-D structural analysis revealed azurin as metalloprotein, of length-128, and polymer-1 with α-helices, β-sheets, and β-barrels. The validation carried out through Ramachandran plot showed the presence of two outliers (phi and psi). The biological relationship between the input sequences was studied through MSA and phylogenetic analysis. Further, azurin docked against the target protein (p53 tumor suppressor) showed the maximum binding affinity confirming its functional property of causing apoptosis.Conclusion: All the properties analyzed in the present study revealed that the azurin protein can act as a very good anticancer agent, and through the phylogenetic analysis, it was identified that Pseudomonas nitroreducens was closely related to the test organism Pseudomonas aeruginosa.

Comparative Insilco physiochemical and phylogenetic analysis of Insulin like growth factor 1 receptor (IGF-1R) in domestic animals

2018 ◽  
Author(s):  
P R. Sahoo ◽  
G. Sahoo ◽  
P. C. Behera
Keyword(s):  
Phylogenetic Analysis ◽  
Growth Factor ◽  
Evolutionary Genetics ◽  
Domestic Animals ◽  
Amino Acid Sequences ◽  
Insulin Like Growth Factor ◽  
Multiple Sequence ◽  
Lung Cancers ◽  
Physiochemical Parameters ◽  
Time Of Divergence

Insulin like growth factor 1receptors (IGF-1R) are the proteins which are expressed on the cell surface of almost all tissues in human as well as domestic animals with major involvement in growth, cancer, aging, production and in early embryonic development. Due to above importance, this protein needs to be characterized both in physiochemical and phylogenetically for further exploration in livestock research. In this study, the IGF1R amino acid sequences of selected domestic animals are retrieved from UniProt database and various physiochemical parameters were compared through ProtParam insilco tool. The multiple sequence alignment (MSA) and phylogenetic analysis was performed through Clustal omega and Molecular evolutionary genetics analysis (MEGA) application platform respectively. It was found that this protein is an unstable, hydrophilic in all domestic animals with amino acids varied from 1307 to 1412 in number. The phylogenetic analysis showed that highest time of divergence occurs in killer whale and rabbit, but least time of divergence occurs between goat and bovine. So this study will provide a better platform for the development of suitable anticancer therapeutics in domestic animals in nearest future as IGF-1R is implicated in several cancers, including breast, prostate, and lung cancers.

scholarly journals In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Hafiz Ishfaq Ahmad ◽  
Gulnaz Afzal ◽  
Adil Jamal ◽  
Shumaila Kiran ◽  
Musarrat Abbas Khan ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Alpha Helix ◽  
Beta Sheets ◽  
Random Coil ◽  
Functional Study ◽  
Motif Analysis ◽  
Alpha Helices ◽  
Random Coils ◽  
Metabolic Reactions ◽  
Exogenous Compounds

Cytochrome (CYP) enzymes catalyze the metabolic reactions of endogenous and exogenous compounds. The superfamily of enzymes is found across many organisms, regardless of type, except for plants. Information was gathered about CYP2D enzymes through protein sequences of humans and other organisms. The secondary structure was predicted using the SOPMA. The structural and functional study of human CYP2D was conducted using ProtParam, SOPMA, Predotar 1.03, SignalP, TMHMM 2.0, and ExPASy. Most animals shared five central motifs according to motif analysis results. The tertiary structure of human CYP2D, as well as other animal species, was predicted by Phyre2. Human CYP2D proteins are heavily conserved across organisms, according to the findings. This indicates that they are descended from a single ancestor. They calculate the ratio of alpha-helices to extended strands to beta sheets to random coils. Most of the enzymes are alpha-helix, but small amounts of the random coil were also found. The data were obtained to provide us with a better understanding of mammalian proteins’ functions and evolutionary relationships.

scholarly journals In-silico Structural Annotation of Methylthioadenosine Nucleosidase Protein Zm00014a_031618 in Maize (Zea mays L.)

2019 ◽  
pp. 1-8
Author(s):  
Gali Adamu Ishaku
Keyword(s):  
Zea Mays ◽  
In Silico ◽  
3D Structure ◽  
Alpha Helix ◽  
Random Coil ◽  
Chemical Parameters ◽  
Structural Annotation ◽  
In Silico Studies ◽  
Physical And Chemical Parameters ◽  
Physical And Chemical

Aims: The aim of this study was In-Silico structural annotation of an amino acid sequence of Methylthioadenosine Nucleosidase Protein Zm00014a_031618 in Maize (Zea mays) retrieved from NCBI with the accession number PWZ58979. Study Design: The use of In-Silico studies for the structural annotation of Methylthioadenosine Nucleosidase protein. Place and Duration of Study: The research was conducted at the Bioinformatics Laboratory, Chevron Biotechnology Centre, Modibbo Adama University of Yola, Nigeria. Between June 2018 to July 2018. Methodology: The Methylthioadenosine Nucleosidase protein was retrieved from NCBI, physical and chemical parameters were calculated using ExPASy - ProtParam tool, the server SOPMA was used for secondary structure analysis (helix, sheets, and coils) and I-TASSER was used to obtain the 3D structure. Results: ExPASy - Prot Param tool computated the various physical and chemical parameters such as molecular weight (MW) 30117.97, total number of positively (+R) 27, negatively charged residues (-R) 30, theoretical isoelectric point (pI) 5.96, aliphatic index (AI) 103.67 and grand average hydropathy (GRAVY) 0.293. The SOPMA server was used for calculating the secondary structural features of protein sequences as Alpha helix 39.16%, Extended strand 14.69%, Beta turn 6.64% and Random coil 39.51%. I-Tasser was used for predicting the 3D structure where 2qttA from PDB was used as the template. Conclusion: This study helped in understanding the structural analysis of the Methylthioadenosine Nucleosidase Protein Zm00014a_031618 in maize (Z. mays).

scholarly journals In silico characterization of the GH5-cellulase family from uncultured microorganisms: physicochemical and structural studies

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Rahmat Eko Sanjaya ◽  
Kartika Dwi Asni Putri ◽  
Anita Kurniati ◽  
Ali Rohman ◽  
Ni Nyoman Tri Puspaningsih
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
In Silico ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Glycoside Hydrolases ◽  
Random Coil ◽  
Wet Lab ◽  
Uncultured Microorganisms ◽  
Metagenomic Approach

Abstract Background Hydrolysis of cellulose-based biomass by cellulases produce fermented sugar for making biofuels, such as bioethanol. Cellulases hydrolyze the β-1,4-glycosidic linkage of cellulose and can be obtained from cultured and uncultured microorganisms. Uncultured microorganisms are a source for exploring novel cellulase genes through the metagenomic approach. Metagenomics concerns the extraction, cloning, and analysis of the entire genetic complement of a habitat without cultivating microbes. The glycoside hydrolase 5 family (GH5) is a cellulase family, as the largest group of glycoside hydrolases. Numerous variants of GH5-cellulase family have been identified through the metagenomic approach, including CelGH5 in this study. University-CoE-Research Center for Biomolecule Engineering, Universitas Airlangga successfully isolated CelGH5 from waste decomposition of oil palm empty fruit bunches (OPEFB) soil by metagenomics approach. The properties and structural characteristics of GH5-cellulases from uncultured microorganisms can be studied using computational tools and software. Results The GH5-cellulase family from uncultured microorganisms was characterized using standard computational-based tools. The amino acid sequences and 3D-protein structures were retrieved from the GenBank Database and Protein Data Bank. The physicochemical analysis revealed the sequence length was roughly 332–751 amino acids, with the molecular weight range around 37–83 kDa, dominantly negative charges with pI values below 7. Alanine was the most abundant amino acid making up the GH5-cellulase family and the percentage of hydrophobic amino acids was more than hydrophilic. Interestingly, ten endopeptidases with the highest average number of cleavage sites were found. Another uniqueness demonstrated that there was also a difference in stability between in silico and wet lab. The II values indicated CelGH5 and ACA61162.1 as unstable enzymes, while the wet lab showed they were stable at broad pH range. The program of SOPMA, PDBsum, ProSA, and SAVES provided the secondary and tertiary structure analysis. The predominant secondary structure was the random coil, and tertiary structure has fulfilled the structure quality of QMEAN4, ERRAT, Ramachandran plot, and Z score. Conclusion This study can afford the new insights about the physicochemical and structural properties of the GH5-cellulase family from uncultured microorganisms. Furthermore, in silico analysis could be valuable in selecting a highly efficient cellulases for enhanced enzyme production.

Genetic Diversity of Cryptosporidium Spp. in Njoro Sub County, Nakuru, Kenya

2021 ◽  
Author(s):  
Walter Miding'a Essendi ◽  
Charles Inyagwa Muleke ◽  
Miheso Manfred ◽  
Elick Onyango Otachi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Sequence Alignment ◽  
Evolutionary Genetics ◽  
Domestic Animals ◽  
Local Alignment ◽  
Cryptosporidium Spp ◽  
Potential Source ◽  
Search Tool ◽  
Great Genetic Diversity

Abstract Cryptosporidium spp. cause Cryptosporidiosis in humans through zoonotic and anthroponotic transmission. Previous studies have illustrated the significance of domestic animals as reservoirs of this parasite. However, there is no information on the Cryptosporidium spp. and genotypes circulating in Njoro Sub County. A total of 2174 samples from humans, cattle, chicken, sheep and goats were assessed for presence of Cryptosporidium spp. Thirty-three positive samples were successfully sequenced. The sequences obtained were compared to Cryptosporidium sequences in the GenBank using NCBI’s (National Center for Biotechnology Information) online BLAST (Basic Local Alignment Search Tool) algorithmic program. Sequence alignment was done using the Clustal W program and phylogenetic analysis was executed in MEGA 6 (Molecular Evolutionary Genetics Analysis version 6.0). The Cryptosporidium spp. present in the watershed showed great genetic diversity with nine (9) Cryptosporidium spp. namely: C. parvum, C. hominis, C. ubiquitum, C. meleagridis, C. andersoni, C. baileyi, C. muris, C. xiaoi and C. viatorum. Cattle were the biggest reservoirs of zoonotic Cryptosporidium spp. hence a potential source of zoonosis in humans while goats had the least species. This is the first study that reported presence of C. viatorum in Kenya.

scholarly journals In-silico characterization and structure-based functional annotation of a hypothetical protein from Campylobacter jejuni involved in propionate catabolism

2021 ◽  
Vol 19 (4) ◽  
pp. e43
Author(s):  
Lincon Mazumder ◽  
Mehedi Hasan ◽  
Ahmed Abu Rus'd ◽  
Mohammad Ariful Islam
Keyword(s):  
Campylobacter Jejuni ◽  
Protein Interactions ◽  
In Silico ◽  
Functional Annotation ◽  
3D Structure ◽  
Alpha Helix ◽  
Hypothetical Protein ◽  
Random Coil ◽  
Protein Protein Interactions ◽  
In Silico Characterization

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

Exploring PLAC1 Structure and Underlying Mechanisms to Design a Derivative Vaccine Against Breast Cancer Progression; In-Silico Study

2020 ◽  
Vol 17 (5) ◽  
pp. 379-391
Author(s):  
Farzaneh Afzali ◽  
Parisa Ghahremanifard ◽  
Mohammad Mehdi Ranjbar ◽  
Mahdieh Salimi
Keyword(s):  
Breast Cancer ◽  
Cancer Progression ◽  
In Silico ◽  
Tertiary Structure ◽  
Specific Antigen ◽  
Docking Simulation ◽  
Post Translational Modification ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Underlying Mechanisms

Background: The tolerogenic homeostasis in Breast Cancer (BC) can be surpassed by rationally designed immune-encouraging constructs against tumor-specific antigens through immunoinformatics approach. Objective: Availability of high throughput data providing the underlying concept of diseases and awarded computational simulations, lead to screening the potential medications and strategies in less time and cost. Despite the extensive effects of Placenta Specific 1 (PLAC1) in BC progression, immune tolerance, invasion, cell cycle regulation, and being a tumor-specific antigen the fundamental mechanisms and regulatory factors were not fully explored. It is also worth to design an immune response inducing construct to surpass the hurdles of traditional anti-cancer treatments. Methods and Result: The study was initiated by predicting and modelling the PLAC1 secondary and tertiary structures and then engineering the fusion pattern of PLAC1 derived immunodominant predicted CD8+ and B-cell epitopes to form a multi-epitope immunogenic construct. The construct was analyzed considering the physiochemical characterization, safety, antigenicity, post-translational modification, solubility, and intrinsically disordered regions. After modelling its tertiary structure, proteinprotein docking simulation was carried out to ensure the attachment of construct with Toll-Like Receptor 4 (TLR4) as an immune receptor. To guarantee the highest expression of the designed construct in E. coli k12 as an expressional host, the codon optimization and in-silico cloning were performed. The PLAC1 related miRNAs in BC were excavated and validated through TCGA BC miRNA-sequencing and databases; the common pathways then were introduced as other probable mechanisms of PLAC1 activity. Conclusion: Regarding the obtained in-silico results, the designed anti-PLAC1 multi-epitope construct can probably trigger humoral and cellular immune responses and inflammatory cascades, therefore may have the potential of halting BC progression and invasion engaging predicted pathways.

In Silico Study of Potential Cross-Kingdom Plant MicroRNA Based Regulation in Chronic Myeloid Leukemia

2020 ◽  
Vol 17 (2) ◽  
pp. 125-132
Author(s):  
Marjanu Hikmah Elias ◽  
Noraziah Nordin ◽  
Nazefah Abdul Hamid
Keyword(s):  
Targeted Therapy ◽  
In Silico ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Target Prediction ◽  
In Silico Analysis ◽  
Microrna Target ◽  
Good Target

Background: Chronic Myeloid Leukaemia (CML) is associated with the BCRABL1 gene, which plays a central role in the pathogenesis of CML. Thus, it is crucial to suppress the expression of BCR-ABL1 in the treatment of CML. MicroRNA is known to be a gene expression regulator and is thus a good candidate for molecularly targeted therapy for CML. Objective: This study aims to identify the microRNAs from edible plants targeting the 3’ Untranslated Region (3’UTR) of BCR-ABL1. Methods: In this in silico analysis, the sequence of 3’UTR of BCR-ABL1 was obtained from Ensembl Genome Browser. PsRNATarget Analysis Server and MicroRNA Target Prediction (miRTar) Server were used to identify miRNAs that have binding conformity with 3’UTR of BCR-ABL1. The MiRBase database was used to validate the species of plants expressing the miRNAs. The RNAfold web server and RNA COMPOSER were used for secondary and tertiary structure prediction, respectively. Results: In silico analyses revealed that cpa-miR8154, csi-miR3952, gma-miR4414-5p, mdm-miR482c, osa-miR1858a and osa-miR1858b show binding conformity with strong molecular interaction towards 3’UTR region of BCR-ABL1. However, only cpa-miR- 8154, osa-miR-1858a and osa-miR-1858b showed good target site accessibility. Conclusion: It is predicted that these microRNAs post-transcriptionally inhibit the BCRABL1 gene and thus could be a potential molecular targeted therapy for CML. However, further studies involving in vitro, in vivo and functional analyses need to be carried out to determine the ability of these miRNAs to form the basis for targeted therapy for CML.

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