Accumulation of multiple mutations in linezolid-resistant Staphylococcus epidermidis causing bloodstream infections; in silico analysis of L3 amino acid substitutions that might confer high-level linezolid resistance

2016 ◽  
Vol 28 (6) ◽  
pp. 465-468 ◽  
Author(s):  
Alexandros Ikonomidis ◽  
Anastasia Grapsa ◽  
Charikleia Pavlioglou ◽  
Antonia Demiri ◽  
Alexandra Batarli ◽  
...  
Keyword(s):  
Amino Acid ◽  
Staphylococcus Epidermidis ◽  
In Silico ◽  
In Silico Analysis ◽  
Bloodstream Infections ◽  
Amino Acid Substitutions ◽  
Linezolid Resistance ◽  
High Level ◽  
Silico Analysis

scholarly journals In Silico Analysis of Missense Mutations as a First Step in Functional Studies: Examples from Two Sphingolipidoses

2018 ◽  
Vol 19 (11) ◽  
pp. 3409 ◽  
Author(s):  
Ana Duarte ◽  
Diogo Ribeiro ◽  
Luciana Moreira ◽  
Olga Amaral
Keyword(s):  
Amino Acid ◽  
Protein Level ◽  
In Silico ◽  
In Silico Analysis ◽  
Amino Acid Substitutions ◽  
Missense Mutations ◽  
Nucleotide Polymorphisms ◽  
Functional Studies ◽  
Analysis System ◽  
Silico Analysis

In order to delineate a better approach to functional studies, we have selected 23 missense mutations distributed in different domains of two lysosomal enzymes, to be studied by in silico analysis. In silico analysis of mutations relies on computational modeling to predict their effects. Various computational platforms are currently available to check the probable causality of mutations encountered in patients at the protein and at the RNA levels. In this work we used four different platforms freely available online (Protein Variation Effect Analyzer- PROVEAN, PolyPhen-2, Swiss-model Expert Protein Analysis System—ExPASy, and SNAP2) to check amino acid substitutions and their effect at the protein level. The existence of functional studies, regarding the amino acid substitutions, led to the selection of the distinct protein mutants. Functional data were used to compare the results obtained with different bioinformatics tools. With the advent of next-generation sequencing, it is not feasible to carry out functional tests in all the variants detected. In silico analysis seems to be useful for the delineation of which mutants are worth studying through functional studies. Therefore, prediction of the mutation impact at the protein level, applying computational analysis, confers the means to rapidly provide a prognosis value to genotyping results, making it potentially valuable for patient care as well as research purposes. The present work points to the need to carry out functional studies in mutations that might look neutral. Moreover, it should be noted that single nucleotide polymorphisms (SNPs), occurring in coding and non-coding regions, may lead to RNA alterations and should be systematically verified. Functional studies can gain from a preliminary multi-step approach, such as the one proposed here.

scholarly journals In silico analysis of GATA4 variants demonstrates main contribution to congenital heart disease

2021 ◽  
Author(s):  
Shiva Abbasi ◽  
Neda Mohsen-Pour ◽  
Niloofar Naderi ◽  
Shahin Rahimi ◽  
Majid Maleki ◽  
...  
Keyword(s):  
Congenital Heart Disease ◽  
Heart Disease ◽  
In Silico ◽  
Structure Prediction ◽  
Congenital Heart ◽  
In Silico Analysis ◽  
Different Types ◽  
Frequent Variant ◽  
High Level ◽  
Silico Analysis

Introduction: Congenital heart disease (CHD) is the most common congenital abnormality and the main cause of infant mortality worldwide. Some of the mutations that occur in the GATA4 gene region may result in different types of CHD. Here, we report our in silico analysis of gene variants to determine the effects of the GATA4 gene on the development of CHD. Methods: Online 1000 Genomes Project, ExAC, gnomAD, GO-ESP, TOPMed, Iranome, GME, ClinVar, and HGMD databases were drawn upon to collect information on all the reported GATA4 variations.The functional importance of the genetic variants was assessed by using SIFT, MutationTaster, CADD,PolyPhen-2, PROVEAN, and GERP prediction tools. Thereafter, network analysis of the GATA4protein via STRING, normal/mutant protein structure prediction via HOPE and I-TASSER, and phylogenetic assessment of the GATA4 sequence alignment via ClustalW were performed. Results: The most frequent variant was c.874T>C (45.58%), which was reported in Germany.Ventricular septal defect was the most frequent type of CHD. Out of all the reported variants of GATA4,38 variants were pathogenic. A high level of pathogenicity was shown for p.Gly221Arg (CADD score=31), which was further analyzed. Conclusion: The GATA4 gene plays a significant role in CHD; we, therefore, suggest that it be accorded priority in CHD genetic screening.

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 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.

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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