In Silico Analysis of Amino Acid Sequences in Relation to Specificity and Physiochemical Properties of Some Microbial Nitrilases

2009 ◽  
Vol 02 (04) ◽  
pp. 185-192 ◽  
Author(s):  
Nikhil Sharma ◽  
Rekha Kushwaha ◽  
J.S. Sodhi ◽  
T. C. Bhalla
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Physiochemical Properties ◽  
Silico Analysis

scholarly journals Altered 3D Structure of Human Tryptophan Hydroxylase-2 Caused by Change in the amino acid 341: In Silico Analysis

2018 ◽  
Vol 35 (03) ◽  
pp. 198-202
Author(s):  
Juan Castaño Casas ◽  
Juan Barona ◽  
Flavio Betancourth ◽  
Doris Salazar
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Tryptophan Hydroxylase ◽  
In Silico Analysis ◽  
Structural Defects ◽  
Protein Chain ◽  
Functional Impairments ◽  
Tryptophan Hydroxylase 2 ◽  
Neuropsychiatric Diseases ◽  
Silico Analysis

Introduction Neuropsychiatric syndromes have an important connection with disorders in the regulation of serotonin, with human tryptophan hydroxylase-2 being one of the related biosynthetic enzymes of this neurotransmitter. Evidence-based genetic studies suggest a possible involvement of this enzyme in neuropsychiatric disorders caused by abnormalities in the synthesis and regulation of serotonin. Objective To analyze the structural effects of single nucleotide polymorphism (SNP) in the enzyme tryptophan hydroxylase-2 and the changes that lead to functional alterations. Materials and Methods In this study, we performed an in silico analysis of SNPs associated with abnormal folding of the tryptophan hydroxylase-2 protein. Different programs were used to identify amino acid changes evidencing pathogenic effects and possible functional impairments. Results A change in the amino acid 341 (lysine [L]for phenylalanine [F]) (L341F) of the protein chain affects the total enthalpy of the protein. The enthalpy turned positive due to the energy required for the amino acid to return to its original condition. The protein function is also affected negatively because of the altered structured. Conclusion The change in the L341F leads to serious structural defects in the tryptophan hydroxylase-2. Those defects can be further related with functional instability and associated to the etiology of neuropsychiatric diseases.

scholarly journals In Silico Analysis of B3GALTL Gene Reveling 13 Novel Mutations Associated with Peters’-plus syndrome

2020 ◽  
Author(s):  
Abdelrahman H. Abdelmoneim ◽  
Arwa A. Satti ◽  
Miysaa I. Abdelmageed ◽  
Naseem S. Murshed ◽  
Nafisa M. Elfadol ◽  
...  
Keyword(s):  
In Silico ◽  
Autosomal Recessive ◽  
In Silico Analysis ◽  
Autosomal Recessive Disorder ◽  
Coding Region ◽  
Novel Mutations ◽  
Physiochemical Properties ◽  
Peters Anomaly ◽  
Systemic Manifestations ◽  
Silico Analysis

AbstractBackgroundPeters’-plus syndrome is a rare autosomal recessive disorder, which is characterized by a specific malformation of the eye that includes corneal opaqueness and iridocorneal adhesions (Peters’ anomaly) along with other systemic manifestations. Furthermore, various researches report the association between B3GALTL gene and Peters’-plus syndrome. In the current work we aim to analyze the deleterious SNPs in B3GALTL gene that predispose to Peters’-plus syndrome.Methodthe associated SNPs of the coding region of the B3GALTL gene was acquired from National Center for Biotechnology Information and then analyzed by eight softwares (SIFT, Polyphen2, Proven, SNAP2, SNP@GO, PMut, Imutant and Mupro). The physiochemical properties of the resulted SNPs were then analyzed by Hope project website and visualized by chimera software.ResultThirteen novel mutations (Y172C, A222V, C260R, C260Y, D349G, I354K, R377C, G379C, G393R, G393E, G395E, G425E, R445W) are discovered in B3GALTL gene to cause deleterious effects leading to the development of Peters’-plus syndrome.ConclusionThirteen novel mutations in B3GALTL gene are predicted to cause Peters’-plus syndrome.

scholarly journals Working with Proteins in silico: A Review of Online Available Tools for Basic Identification of Proteins

2017 ◽  
Vol 5 (1) ◽  
pp. 65
Author(s):  
Caner Yavuz ◽  
Zahide Neslihan Öztürk
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
In Silico ◽  
In Silico Analysis ◽  
Tips And Tricks ◽  
Post Translational Modifications ◽  
Starting Point ◽  
Protein Research ◽  
Experimental Approaches ◽  
Silico Analysis

Increase in online available bioinformatics tools for protein research creates an important opportunity for scientists to reveal characteristics of the protein of interest by only starting from the predicted or known amino acid sequence without fully depending on experimental approaches. There are many sophisticated tools used for diverse purposes; however, there are not enough reviews covering the tips and tricks in selecting and using the correct tools as the literature mainly state the promotion of the new ones. In this review, with the aim of providing young scientists with no specific experience on protein work a reliable starting point for in silico analysis of the protein of interest, we summarized tools for annotation, identification of motifs and domains, determination isoelectric point, molecular weight, subcellular localization, and post-translational modifications by focusing on the important points to be considered while selecting from online available tools.

Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation

2020 ◽  
Vol 17 (2) ◽  
pp. 95-106
Author(s):  
Neerja Thakur ◽  
Nikhil Sharma ◽  
Vijay Kumar ◽  
Tek Chand Bhalla
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
In Silico Analysis ◽  
Amino Acid Residues ◽  
Aliphatic Amino Acid ◽  
Physiochemical Properties ◽  
Commodity Chemicals ◽  
Acid Tolerant ◽  
Ph Adaptation ◽  
Silico Analysis

Background: Amidases are ubiquitous enzymes and biological functions of these enzymes vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals synthesis, pharmaceuticals agrochemicals and wastewater treatments. Methods: They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides, arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic site and preferred substrate. Despite their economic importance, we lack knowledge as to how these amidases withstand elevated pH and temperature whereas others cannot. Results: The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic organisms revealed some striking trends as to how amino acid composition varies significantly. Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L) in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant and alkali tolerant amidases. Conclusion: The present investigation insights physiochemical properties and dominance of some crucial amino acid residues in the primary and secondary structure of some amidases from acid-tolerant, alkali tolerant and neutrophilic microorganisms.

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

2007 ◽  
Vol 13 (2) ◽  
pp. 125-133 ◽  
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.

scholarly journals Amino acid sequence based in silico analysis of β- galactosidases

2013 ◽  
Vol 3 (2) ◽  
pp. 37-44 ◽  
Author(s):  
Ratnaboli Bose ◽  
Shikha Arora ◽  
Vivek Dhar Dwivedi ◽  
Amit Pandey
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis
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