Using computational biology, we have depicted the insulin phylogenetics. We have also analyzed the sequence alignment and sequence logos formation for both the insulin chain A and B for three groups namely, the mammalian group, vertebrates group and fish group. We have also analyzed cladograms of insulin for the mammalian group. In accordance with that path lengths, matrix for distance analysis, matching representation of nodes of the cladogram and dissimilarity between two nodes have been performed for both of the A and B chains of the mammalian group. Our results show that 12 amino acid residues (GlyA1, IleA2, ValA3, TyrA19, CysA20, AsnA21, LeuB6, GlyB8, LeuB11, ValB12, GlyB23 and PheB24) are highly conserved for all groups and among them some (GlyA1, IleA2, ValA3);(TyrA19, CysA20, AsnA21) are continuous. This study shows a rapid method to calculate the amino acid sequences in terms of evolutionary conservation rates as well as molecular phylogenetics. © 2011 Elsevier Ireland Ltd.

Sanjiban Sekhar Roy

Department of Software Systems

School of Computer Science and Engineering

Vellore Campus

Chakraborty C

Hsu M.J

Agoramoorthy G.

Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

VIT is one of the top ranked private universities in India according to NIRF, THE and QS Rankings.&nbsp;Govt. of India has recognized&nbsp;VIT, Vellore as an&nbsp;Institution of Eminence. This has allowed VIT to take independent quality initiatives and move up in world ranking.

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VIT University

Computer Methods and Programs in Biomedicine

Phosphoinositide 3-kinase (PI3K) enzyme plays a vital role in the insulin signaling pathway as well as in other pathways that are involved in the growth, migration, and survival of cells. In the insulin signaling pathway, PI3K proteins that include p50α, p85α, p85β, p55γ, p110α, p110β, and p110γ are associated with the critical node-2. This study has used bioinformatic tools to understand phylogenetics, conservation patterns, conserved domains, orientation of residues, and interactions among PI3K proteins. The phylogenetic analysis showed p110α and p110γ with a common origin while p50α and p85α sharing an evolutionary history. The sequence alignment showed the highest score (97) between p85α and p50α. Several highly conserved amino acid residues were found high in p110 beta (n = 102). Subsequently, the number of highly conserved amino acid restudies was low in p50alpha and p55γ (n = 15). The PI3K proteins are evidentially linked to other proteins and pathways as well.

Applied Biochemistry and Biotechnology

Profiling of Phosphatidylinositol 3-Kinase (PI3K) Proteins in Insulin Signaling Pathway

Maturity onset diabetes of the young (MODY) is a metabolic and genetic disorder. It is different from type 1 and type 2 diabetes with low occurrence level (1–2 %) among all diabetes. This disorder is a consequence of β-cell dysfunction. Till date, 11 subtypes of MODY have been identified, and all of them can cause gene mutations. However, very little is known about the gene mapping, molecular phylogenetics, and co-expression among MODY genes and networking between cascades. This study has used latest servers and software such as VarioWatch, ClustalW, MUSCLE, G Blocks, Phylogeny.fr, iTOL, WebLogo, STRING, and KEGG PATHWAY to perform comprehensive analyses of gene mapping, multiple sequences alignment, molecular phylogenetics, protein–protein network design, co-expression analysis of MODY genes, and pathway development. The MODY genes are located in chromosomes-2, 7, 8, 9, 11, 12, 13, 17, and 20. Highly aligned block shows Pro, Gly, Leu, Arg, and Pro residues are highly aligned in the positions of 296, 386, 437, 455, 456 and 598, respectively. Alignment scores inform us that HNF1A and HNF1B proteins have shown high sequence similarity among MODY proteins. Protein–protein network design shows that HNF1A, HNF1B, HNF4A, NEUROD1, PDX1, PAX4, INS, and GCK are strongly connected, and the co-expression analyses between MODY genes also show distinct association between HNF1A and HNF4A genes. This study has used latest tools of bioinformatics to develop a rapid method to assess the evolutionary relationship, the network development, and the associations among eleven MODY genes and cascades. The prediction of sequence conservation, molecular phylogenetics, protein–protein network and the association between the MODY cascades enhances opportunities to get more insights into the less-known MODY disease. © 2014, Springer Science+Business Media New York.

Cell Biochemistry and Biophysics

Exploring the Genomic Roadmap and Molecular Phylogenetics Associated with MODY Cascades Using Computational Biology

Cluster of differentiation (CD) is a group of proteins with highly immunological and medical importance, and some are established therapeutics. These membrane proteins are used to investigate of cell surface molecules of blood cells especially WBC. We selected a population of fifteen members with most medical importance, which includes CD2, CD4, CD5, CD6, CD7, CD9, CD14, CD16, CD19, CD22, CD28, CD33, CD36, CD38, and CD44 and performed in silico analysis using algorithm analysis and mathematical models. The results suggest that LEU (L) is well aligned. CD16 is rooted with CD22 and likewise, CD4 is closely related to CD44. Notably, highest number of highly conserved amino acids is recorded in CD22. WebLogo were formed up to 350 amino acid position and Met (M) is found to be tallest logo. Our results would be useful for upcoming researchers to obtain fundamental idea about the particular regions CD proteins which is having the structural and functional significance related to the evolutionary biology. © 2013 Springer Science+Business Media New York.

The Protein Journal

Does Computational Biology Help us to Understand the Molecular Phylogenetics and Evolution of Cluster of Differentiation (CD) Proteins?

Fulltext

3 Biotech

Understanding the conservation patterns and molecular phylogenetics of human death receptors family through computational biology

In human, Wnt/β-catenin signaling pathway plays a significant role in cell growth, cell development, and disease pathogenesis. Four human (Rspo)s are known to activate canonical Wnt/β-catenin signaling pathway. Presently, (Rspo)s serve as therapeutic target for several human diseases. Henceforth, basic understanding about the molecular properties of (Rspo)s is essential. We approached this issue by interpreting the biochemical and biophysical properties along with molecular evolution of (Rspo)s thorough computational algorithm methods. Our analysis shows that signal peptide length is roughly similar in (Rspo)s family along with similarity in aa distribution pattern. In Rspo3, four N-glycosylation sites were noted. All members are hydrophilic in nature and showed alike GRAVY values, approximately. Conversely, Rspo3 contains the maximum positively charged residues while Rspo4 includes the lowest. Four highly aligned blocks were recorded through Gblocks. Phylogenetic analysis shows Rspo4 is being rooted with Rspo2 and similarly Rspo3 and Rspo1 have the common point of origin. Through phylogenomics study, we developed a phylogenetic tree of sixty proteins (n=60) with the orthologs and paralogs seed sequences. Protein-protein network was also illustrated. Results demonstrated in our study may help the future researchers to unfold significant physiological and therapeutic properties of (Rspo)s in various disease models.

BioMed Research International

Computational Biophysical, Biochemical, and Evolutionary Signature of Human R-Spondin Family Proteins, the Member of Canonical Wnt/β-Catenin Signaling Pathway

Journal	Data powered by TypesetComputer Methods and Programs in Biomedicine
Publisher	Data powered by TypesetElsevier BV
ISSN	0169-2607
Open Access	0