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

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.

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Predicting protein distance maps according to physicochemical properties

Journal of Integrative Bioinformatics ◽

10.1515/jib-2011-181 ◽

2011 ◽

Vol 8 (3) ◽

pp. 158-175

Author(s):

Gualberto Asencio Cortés ◽

Jesús A. Aguilar-Ruiz

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Physicochemical Properties ◽

Structure Prediction ◽

Tertiary Structure ◽

Protein Structures ◽

Contact Map ◽

Acid Properties ◽

Amino Acid Properties ◽

3D Surfaces

SummaryThe prediction of protein structures is a current issue of great significance in structural bioinformatics. More specifically, the prediction of the tertiary structure of a protein con- sists in determining its three-dimensional conformation based solely on its amino acid sequence. This study proposes a method in which protein fragments are assembled according to their physicochemical similarities, using information extracted from known protein structures. Many approaches cited in the literature use the physicochemical properties of amino acids, generally hydrophobicity, polarity and charge, to predict structure. In our method, implemented with parallel multithreading, we used a set of 30 physicochemical amino acid properties selected from the AAindex database. Several protein tertiary structure prediction methods produce a contact map. Our proposed method produces a distance map, which provides more information about the structure of a protein than a contact map. We performed several preliminary analysis of the protein physicochemical data distributions using 3D surfaces. Three main pattern types were found in 3D surfaces, thus it is possible to extract rules in order to predict distances between amino acids according to their physicochemical properties. We performed an experimental validation of our method using five non-homologous protein sets and we showed the generality of this method and its prediction quality using the amino acid properties considered. Finally, we included a study of the algorithm efficiency according to the number of most similar fragments considered and we notably improved the precision with the studied proteins sets.

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Evolutionary Models of Amino Acid Substitutions Based on the Tertiary Structure of their Neighborhoods

10.1101/468173 ◽

2018 ◽

Author(s):

Elias Primetis ◽

Spyridon Chavlis ◽

Pavlos Pavlidis

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Amino Acid Substitution ◽

Tertiary Structure ◽

Protein Structures ◽

Amino Acid Substitutions ◽

Tertiary Structures ◽

Substitution Matrices ◽

Amino Acid Substitution Model ◽

Amino Acid Substitution Matrices

AbstractIntra-protein residual vicinities depend on the involved amino acids. Energetically favorable vicinities (or interactions) have been preserved during evolution, while unfavorable vicinities have been eliminated. We describe, statistically, the interactions between amino acids using resolved protein structures. Based on the frequency of amino acid interactions, we have devised an amino acid substitution model that implements the following idea: amino acids that have similar neighbors in the protein tertiary structure can replace each other, while substitution is more difficult between amino acids that prefer different spatial neighbors. Using known tertiary structures for α-helical membrane (HM) proteins, we build evolutionary substitution matrices. We constructed maximum likelihood phylogenies using our amino acid substitution matrices and compared them to widely-used methods. Our results suggest that amino acid substitutions are associated with the spatial neighborhoods of amino acid residuals, providing, therefore, insights into the amino acid substitution process.

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In-silico prediction and modeling of the Entamoeba histolytica proteins: Serine-rich Entamoeba histolytica protein and peroxiredoxin

10.7287/peerj.preprints.2392 ◽

2016 ◽

Author(s):

Kumar Manochitra ◽

Subhash Chandra Parija

Keyword(s):

Amino Acid ◽

Entamoeba Histolytica ◽

In Silico ◽

Structure Prediction ◽

Tertiary Structure ◽

Protein Structures ◽

Amino Acid Sequences ◽

Treatment Modalities ◽

Bioinformatic Tools ◽

Quaternary Structures

Background: Amoebiasis is the third most common parasitic cause of morbidity and mortality particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence arises a necessity for a better diagnostic approach. Serine-rich Entamoeba histolytica protein (SREHP), peroxiredoxin and Gal/GalNAc lectin are pivotal in E. histolytica virulence and are extensively studied as diagnostic and vaccine targets. For elucidating the cellular function of these proteins, details regarding their respective quaternary structures are essential which are not available till date. Hence, this study was carried out to predict the structure of these target proteins and characterize them structurally as well as functionally using relevant in-silico methods. Methods:The amino acid sequences of the proteins were retrieved from National Centre for Biotechnology Information database and aligned using ClustalW. Bioinformatic tools were employed in the secondary structure and tertiary structure prediction. The predicted structure was validated, and final refinement was carried out. Results: The protein structures predicted by i-TASSER were found to be more accurate than Phyre2 based on the validation using SAVES server. The prediction suggests SREHP to be a extracellular protein, peroxiredoxin was a peripheral membrane protein, while Gal/GalAc was found to be a cell-wall protein. Signal peptides were found in the amino-acid sequences of SREHP and Gal/GalNAc, whereas they were not present in the peroxiredoxin sequence. Gal/GalNAc lectin showed better antigenicity than the other two proteins studied. All three proteins exhibited similarity in their structures and were mostly composed of loops. Discussion:The structures of SREHP and peroxiredoxin were predicted successfully, while the structure of Gal/GalNAc lectin could not be predicted as it was a complex protein composed of three sub-units. Also, this protein showed less similarity with the available structural homologs. The quaternary structures predicted from this study would provide better structural and functional insights into these proteins and may aid in development of newer diagnostic assays or enhancement of the available treatment modalities.

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In-silico prediction and modeling of the Entamoeba histolytica proteins: Serine-rich Entamoeba histolytica protein and peroxiredoxin

10.7287/peerj.preprints.2392v1 ◽

2016 ◽

Author(s):

Kumar Manochitra ◽

Subhash Chandra Parija

Keyword(s):

Amino Acid ◽

Entamoeba Histolytica ◽

In Silico ◽

Structure Prediction ◽

Tertiary Structure ◽

Protein Structures ◽

Amino Acid Sequences ◽

Treatment Modalities ◽

Bioinformatic Tools ◽

Quaternary Structures

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In-silicoprediction and modeling of theEntamoeba histolyticaproteins: Serine-richEntamoeba histolyticaprotein and 29 kDa Cysteine-rich protease

PeerJ ◽

10.7717/peerj.3160 ◽

2017 ◽

Vol 5 ◽

pp. e3160 ◽

Cited By ~ 5

Author(s):

Kumar Manochitra ◽

Subhash Chandra Parija

Keyword(s):

Amino Acid ◽

Structure Prediction ◽

Tertiary Structure ◽

Protein Structures ◽

Amino Acid Sequences ◽

Treatment Modalities ◽

Bioinformatic Tools ◽

Complex Protein ◽

A Cell ◽

Quaternary Structures

BackgroundAmoebiasis is the third most common parasitic cause of morbidity and mortality, particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence there arises a necessity for a better diagnostic approach. Serine-richEntamoeba histolyticaprotein (SREHP), peroxiredoxin and Gal/GalNAc lectin are pivotal inE. histolyticavirulence and are extensively studied as diagnostic and vaccine targets. For elucidating the cellular function of these proteins, details regarding their respective quaternary structures are essential. However, studies in this aspect are scant. Hence, this study was carried out to predict the structure of these target proteins and characterize them structurally as well as functionally using appropriatein-silicomethods.MethodsThe amino acid sequences of the proteins were retrieved from National Centre for Biotechnology Information database and aligned using ClustalW. Bioinformatic tools were employed in the secondary structure and tertiary structure prediction. The predicted structure was validated, and final refinement was carried out.ResultsThe protein structures predicted by i-TASSER were found to be more accurate than Phyre2 based on the validation using SAVES server. The prediction suggests SREHP to be an extracellular protein, peroxiredoxin a peripheral membrane protein while Gal/GalNAc lectin was found to be a cell-wall protein. Signal peptides were found in the amino-acid sequences of SREHP and Gal/GalNAc lectin, whereas they were not present in the peroxiredoxin sequence. Gal/GalNAc lectin showed better antigenicity than the other two proteins studied. All the three proteins exhibited similarity in their structures and were mostly composed of loops.DiscussionThe structures of SREHP and peroxiredoxin were predicted successfully, while the structure of Gal/GalNAc lectin could not be predicted as it was a complex protein composed of sub-units. Also, this protein showed less similarity with the available structural homologs. The quaternary structures of SREHP and peroxiredoxin predicted from this study would provide better structural and functional insights into these proteins and may aid in development of newer diagnostic assays or enhancement of the available treatment modalities.

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Different Synergy in Amyloids and Biologically Active Forms of Proteins

International Journal of Molecular Sciences ◽

10.3390/ijms20184436 ◽

2019 ◽

Vol 20 (18) ◽

pp. 4436 ◽

Cited By ~ 2

Author(s):

Piotr Fabian ◽

Katarzyna Stapor ◽

Mateusz Banach ◽

Magdalena Ptak-Kaczor ◽

Leszek Konieczny ◽

...

Keyword(s):

Amino Acids ◽

Comparative Analysis ◽

Protein Structure ◽

Tertiary Structure ◽

Protein Structures ◽

Water Environment ◽

Biologically Active ◽

Radius Of Curvature ◽

Hydrophobic Core ◽

Structural Form

Protein structure is the result of the high synergy of all amino acids present in the protein. This synergy is the result of an overall strategy for adapting a specific protein structure. It is a compromise between two trends: The optimization of non-binding interactions and the directing of the folding process by an external force field, whose source is the water environment. The geometric parameters of the structural form of the polypeptide chain in the form of a local radius of curvature that is dependent on the orientation of adjacent peptide bond planes (result of the respective Phi and Psi rotation) allow for a comparative analysis of protein structures. Certain levels of their geometry are the criteria for comparison. In particular, they can be used to assess the differences between the structural form of biologically active proteins and their amyloid forms. On the other hand, the application of the fuzzy oil drop model allows the assessment of the role of amino acids in the construction of tertiary structure through their participation in the construction of a hydrophobic core. The combination of these two models—the geometric structure of the backbone and the determining of the participation in the construction of the tertiary structure that is applied for the comparative analysis of biologically active and amyloid forms—is presented.

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Interrogation of the Perturbed Gut Microbiota in Gouty Arthritis Patients Through in silico Metabolic Modeling

10.1101/2020.09.02.20187013 ◽

2020 ◽

Author(s):

Michael A. Henson

Keyword(s):

Amino Acids ◽

Uric Acid ◽

Amino Acid ◽

Gut Microbiota ◽

In Silico ◽

Gouty Arthritis ◽

Metabolic Modeling ◽

Patient Specific ◽

Surprising Result ◽

Sulfur Containing

Recent studies have shown perturbed gut microbiota associated with gouty arthritis, a metabolic disease in which an imbalance between uric acid production and excretion leads to the deposition of uric acid crystals in joints. To mechanistically investigate altered microbiota metabolism in gout disease, 16S rRNA gene amplicon sequence data from stool samples of gout patients and healthy controls were computationally analyzed through bacterial community metabolic modeling. Patient-specific models were used to cluster samples according to their metabolic capabilities and to generate statistically significant partitioning of the samples into a Bacteroides-dominated, high gout cluster and a Faecalibacterium-elevated, low gout cluster. The high gout cluster samples were predicted to allow elevated synthesis of the amino acids D-alanine and L-alanine and byproducts of branched-chain amino acid catabolism, while the low gout cluster samples allowed higher production of butyrate, the sulfur-containing amino acids L-cysteine and L-methionine and the L-cysteine catabolic product H2S. The models predicted an important role for metabolite crossfeeding, including the exchange of acetate, D-lactate and succinate from Bacteroides to Faecalibacterium to allow higher butyrate production differences than would be expected based on taxa abundances in the two clusters. The surprising result that the high gout cluster could underproduce H2S despite having a higher abundance of H2S-synthesizing bacteria was rationalized by reduced L-cysteine production from Faecalibacterium in this cluster. Model predictions were not substantially altered by constraining uptake rates with different in silico diets, suggesting that sulfur-containing amino acid metabolism generally and H2S more specifically could be novel gout disease markers.

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In silico study to examine the role of amino acids in Jasmonate induced plant defense process

Brazilian Journal of Biological Sciences ◽

10.21472/bjbs.051009 ◽

2018 ◽

Vol 5 (10) ◽

pp. 289-301

Author(s):

Ruma Ganguly ◽

Sailesh K. Mehta

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Jasmonic Acid ◽

Plant Defense ◽

In Silico ◽

Induced Plant Defense ◽

In Silico Study

The role of amino acid is important to Jasmonate induce plant defense process. Jasmonic acid and amino acid Isoleucine conjugate (JA-Ile) has been found to be necessary to achieve such process effectively. We have examined the origin of such process computationally and showed that Isoleucine is more active compared to other Jasmonic acid conjugates. The epimerization process revealed that Isoleucine conjugated Jasmonic acid is energetically a favoured process compared to JA-Leu and JA-Val. Water has functioned as a catalyst in the whole epimerization process. This study would unravel the importance of Isoleucine in the Jasmonic acid induced plant defense process.

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

Indian Journal of Animal Research ◽

10.18805/ijar.b-3712 ◽

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.

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Computational Characterisation and Identification of Peptides for in silico Detection of Potentially Celiac-Toxic Proteins

Food Science and Technology International ◽

10.1177/1082013207077954 ◽

2007 ◽

Vol 13 (2) ◽

pp. 125-133 ◽

Cited By ~ 11

Author(s):

M. Darewicz ◽

J. Dziuba ◽

P. Minkiewicz

Keyword(s):

Celiac Disease ◽

Amino Acid ◽

In Silico ◽

In Silico Analysis ◽

Amino Acid Sequences ◽

Random Coil ◽

Sequence Motifs ◽

Peptide Epitopes ◽

High Degree ◽

Toxic Peptides

This work reports on in silico analysis of celiac-toxic peptide occurrence in proteins. The toxic properties of celiac disease are linked to the presence of specific amino acid sequences and the properties of their environment. The analysed celiac-toxic peptides were found to be predominated by unordered structures of random coil and β-turns. Proline and glutamine-rich amino acid sequences from hydrophilic β-turns were exposed on the surface of the precursor proteins. The sequence motifs represented by gluten peptide epitopes or tetrapeptides with surroundings seem to represent an immunodominant structure. The application of MS BLAST software enabled identification of a few fragments with high degrees of identity to the toxic peptides in one protein sequence. Rich sources of celiac-disease-potentiating peptides were wheat gliadins, barley hordeins and rye secalins as well as low-molecular weight fractions of glutenin. In addition, amino acid sequences with a high degree of identity to the toxic peptides examined were detected in maize zein, oat avenin, protein of rice, yeast and chicken muscles, as well as β-casein and galanin.

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