Volume 2 Issue 1

Review Article: Proteomic Methodologies in Protein Phosphorylation

Rajasekhar Tulasi Baru*

The main focus of discovery biology for the past few years has been in the areas of diabetes, cardiovascular, cancer, inflammation and anti-infective. One of the key out of box approach for combating diabetes has been the regulation of key protein AMP kinase. For cancer therapy, several of the signal transduction kinases like ERK kinase, MAP kinase, Aurora kinase etc have been used as key protein targets. Kinases are enzymes that regulate downstream pathways by post translational modification (phosphorylation) of target proteins. Thus the detection of phosphorylation state of a protein is very important in these studies. Classically kinase assays were and are performed using radiolabeled P32 or P33 antibodies that have serious disadvantages. The regulation of proteins at the gene and mRNA level can be very well studied by genomics technology but the post translational modification of proteins can be studied exclusively by proteomic strategies. In view of the tremendous importance of kinases to discovery research, a non-radioactive, non-antibody, high throughput and safe assay for detection of in vivo phosphorylation of proteins -the proteomic way is proposed.

Cite this Article: Rajasekhar TB. Proteomic Methodologies in Protein Phosphorylation. Int J Proteom Bioinform. 2017;2(1): 031-041.

Published: 23 October 2017

Short Communication : T-Cell Epitope Prediction by Integration of Pattern Recognition and Motif Searching: Case Study on HLA-A*02, HLA-A*11 and HLA-A*24

Yee Ying Lim, Cheh Tat Law and Yee Siew Choong*

T-cell epitopes have a huge potential in the development of vaccine, disease prevention and diagnostics as well as therapeutics. As a numbers of epitopes have been identified experimentally in the past 20 years, databases focusing on different kinds of epitopes are now available. However, for vaccine development particularly, biochemical and immunological experiments are costly, time consuming, with low immunogenicity and reversible. Narrowing down the epitopes of interest could reduce the number of wet laboratory experiments and made vaccine designs cheaper and faster. In this works, we utilized support vector machine for pattern recognition in T-cell epitopes and further ranked the results by the present of anchor residues. We used the 9-mers peptide sequences obtained from Immune Epitope Database (IEDB) for HLA-A*02, HLA-A*11 and HLA-A*24 at that are related to Asian population for this works. The results showed that this two steps approach for T-cell epitope prediction is able to provide reasonable output. Therefore, the integration of pattern recognition and ranking by the present of anchor residue could be useful for future development of more alleles with various peptide lengths.

Cite this Article: Lim YY, Law CT, Choong YS. T-Cell Epitope Prediction by Integration of Pattern Recognition and Motif Searching: Case Study on HLA-A*02, HLA-A*11 and HLA-A*24. Int J Proteom Bioinform. 2017;2(1): 027-030.

Published: 13 October 2017

Research Article: Analysis of Spontaneous Abortions Using Genomics, Proteomics and In silico Tools

A. Carvalho, J. Ferreira, R. Pinto Leite, M. Souto, P. Botelho, O. Moutinho3, L. Pinto, H. Santos, J. Capelo and G. Igrejas*

Studies show that about 20% of all recognized clinical pregnancies end in spontaneous abortion, mainly in the first trimester. Risk factors associated with the occurrence of a sporadic miscarriage have been established, with genetic factors being the most prevalent. As a problem that affects many couples, it is important to increase the quality of prognosis and diagnosis.
In this study, the genomic sequences of spontaneous abortion samples with normal karyotypes were analyzed, and Single Nucleotide Polymorphisms (SNPs) were found to be the most common alterations in a selected set of candidate genes. Using the Human Splice Finder bioinformatics tool, it was estimated that 75% and 23% of these differences were in intronic and exonic regions, respectively. A total of 54% of the amino acid substitutions encoded by SNPs in exonic regions would lead to an alteration in the function of some protein domains and/or be deleterious to some protein structures, according to Prot Fun 2.2 and PolyPhen-2 predictions.
In a proteomic analysis comparing the samples, it was possible to identify 23 altered proteins that were related to glycolysis, regulation of the cell cycle, transcription and angiogenic mechanisms, or stress responses. Heat shock proteins 7C and 90 were also identified. In conclusion, genomics, proteomics and bioinformatics techniques can be used to provide an integrated molecular analysis of genotypic and phenotypic factors potentially related to sudden miscarriage.

Cite this Article: Carvalho A, Ferreira J, Pinto Leite R, Souto M, Botelho P, et al. Analysis of Spontaneous Abortions Using Genomics, Proteomics and In silico Tools. Int J Proteom Bioinform. 2017;2(1): 012-026.

Published: 03 October 2017

Research Article: Structural Analysis of Major Translocator-Chaperone Interaction from Ysa-Ysp Type III Secretion System of Yersinia Enterocolitica

Abhishek Basu*, Debjani Mandal, Manali Biswas, Gunjan Dhar and Shamsuzzaman Ahmed

YspB is a major translocator protein of Yersinia secretion apparatus- Yersinia secretion protein (Ysa-Ysp) Type III Secretion System (T3SS) of Yersinia enterocolitica Biovar 1B. SycB is the cognate class II chaperone of YspB. YspB is a highly alpha helical protein. It shows significant homology to IpaB-SipB family of proteins. YspB possesses transmembrane helices, intramolecular coiled-coil regions and intrinsically disordered regions, all characteristics of translocator proteins. Homology model of YspB showed an all helical structure interspersed by coiled regions. YspB has a star shaped three dimensional structure with five distinct arms. The first two Tetratricopeptide Repeat (TPR) regions of SycB are responsible for its interaction with YspB. The helices and the loops of YspB interacting with SycB exhibit evolutionary conservation. Besides this, some structurally conserved amino acid residues were also observed in other helices and loops of YspB. The nature of residues involved in the YspB-SycB interaction indicate towards an ionic or polar interaction between the two proteins. This model of translocator-chaperone interaction might prove to be potentially beneficial in understanding the regulation of Ysa-Ysp T3SS.
Keywords: Ysa-Ysp T3SS; Translocator protein; Consurf analysis; Homology model; Molecular docking; Translocator-chaperone interaction

Cite this Article: Basu A, Mandal D, Biswas M, Dhar G, Ahmed S. Structural Analysis of Major Translocator-Chaperone Interaction from Ysa-Ysp Type III Secretion System of Yersinia Enterocolitica. Int J Proteom Bioinform. 2017;2(1): 003-011.

Published: 04 September 2017

Short Communication: Revised Estimate of Total Collagen in the Human Body

Gary B. Smejkal* and Cody Fitzgerald

Based on global mean adult body mass, it was calculated that the human body, on average, contains 3.6 X 1021 molecules of collagen type 1. This revised estimate is nearly four times higher than previously published estimates.

Cite this Article: Smejkal GB, Fitzgerald C. Revised Estimate of Total Collagen in the Human Body. Int J Proteom Bioinform. 2017;2(1): 001-002.

Published: 18 August 2017

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