Bioinformatics Analysis and Functional Prediction of Transmembrane Proteins in Entamoeba histolytica.

Entamoeba histolytica is an invasive, pathogenic parasite causing amoebiasis. Given that proteins involved in transmembrane (TM) transport are crucial for the adherence, invasion, and nutrition of the parasite, we conducted a genome-wide bioinformatics analysis of encoding proteins to functionally classify and characterize all the TM proteins in E. histolytica. In the present study, 692 TM proteins have been identified, of which 546 are TM transporters. For the first time, we report a set of 141 uncharacterized proteins predicted as TM transporters. The percentage of TM proteins was found to be lower in comparison to the free-living eukaryotes, due to the extracellular nature and functional diversification of the TM proteins. The number of multi-pass proteins is larger than the single-pass proteins; though both have their own significance in parasitism, multi-pass proteins are more extensively required as these are involved in acquiring nutrition and for ion transport, while single-pass proteins are only required at the time of inciting infection. Overall, this intestinal parasite implements multiple mechanisms for establishing infection, obtaining nutrition, and adapting itself to the new host environment. A classification of the repertoire of TM transporters in the present study augments several hints on potential methods of targeting the parasite for therapeutic benefits.

Non-enzymatic glycation enhances human serum albumin binding capacity to sodium fluorescein at room temperature: A spectroscopic analysis.

BACKGROUND: Sodium fluorescein (SF) is a fluorescent tracer dye used extensively in diagnostic tools in the field of Ophthalmology, particularly in intravenous fluorescein angiography (IVFA). The binding of SF to human serum albumin (HSA) has been predicted by molecular docking and investigated by circular dichroism (CD) and fluorescence spectroscopy with or without glycation at temperatures 296, 301, and 310K. METHODS: The binding parameters were calculated by quenching of emission spectrum of a constant concentration of SF (2µmol/l) at 513nm against increasing concentrations of glycated or unmodified HSA as quencher starting from stoichiometry ratio of 1:1. RESULTS: The HSA-SF interaction found to be a static binding. The Stern-Volmer constants (Ksv) were in the range of ~104M-1 and other thermodynamic parameters like enthalpy (ΔH°), free energy (ΔG°) and entropy (ΔS°) are similar to albumin ligand bindings reported by previous workers. CONCLUSIONS: The interactions were found to be spontaneous, irrespective of temperature or glycation. Glycated HSA is clinically used to monitor unstable glycemic controls in diabetic patients. A 39% increase in binding affinity (log K) and free energy (ΔG°) is reported on glycation at 310K (room temperature), which may be important in the SF based angiographies. On glycation HSA-SF binding appears to change from an enthalpy-driven to an entropy-driven reaction. SF shows best binding to FA binding site III of HSA, which also overlaps with drug binding site II of subdomain IIIA. Leu430 seems to play a pivotal role in the interaction.

Deep Insight into the Phosphatomes of Parasitic Protozoa and a Web Resource ProtozPhosDB.

Phosphorylation dynamically regulates the function of proteins by maintaining a balance between protein kinase and phosphatase activity. A comprehensive understanding of the role phosphatases in cellular signaling is lacking in case of protozoans of medical and veterinary importance worldwide. The drugs used to treat protozoal diseases have many undesired effects and the development of resistance, highlights the need for new effective and safer antiprotozoal agents. In the present study we have analyzed phosphatomes of 15 protozoans of medical significance. We identified ~2000 phosphatases, out of which 21% are uncharacterized proteins. A significant positive correlation between phosphatome and proteome size was observed except for E. histolytica, having highest density of phosphatases irrespective of its proteome size. A difference in the number of phosphatases among different genera shows the variation in the signaling pathways they are involved in. The phosphatome of parasites is dominated by ser/thr phosphatases contrary to the vertebrate host dominated by tyrosine phosphatases. Phosphatases were widely distributed throughout the cell suggesting physiological adaptation of the parasite to regulate its host. 20% to 45% phosphatome of different protozoa consists of ectophosphatases, i.e. crucial for the survival of parasites. A database and a webserver "ProtozPhosDB" can be used to explore the phosphatomes of protozoans of medical significance.

Analysis of the Protein phosphotome of Entamoeba histolytica reveals an intricate phosphorylation network.

Phosphorylation is the most common mechanism for the propagation of intracellular signals. Protein phosphatases and protein kinases play a dynamic antagonistic role in protein phosphorylation. Protein phosphatases make up a significant fraction of eukaryotic proteome. In this article, we report the identification and analysis of protein phosphatases in the intracellular parasite Entamoeba histolytica. Based on an in silico analysis, we classified 250 non-redundant protein phosphatases in E. histolytica. The phosphotome of E. histolytica is 3.1% of its proteome and 1.3 times of the human phosphotome. In this extensive study, we identified 42 new putative phosphatases (39 hypothetical proteins and 3 pseudophosphatases). The presence of pseudophosphatases may have an important role in virulence of E. histolytica. A comprehensive phosphotome analysis of E. histolytica shows spectacular low similarity to human phosphatases, making them potent candidates for drug target.

Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus.

Influenza virus causes febrile respiratory illness. The infection results in significant mortality, morbidity and economic disruption. In this bioinformatics study, we used the NS1 (the conserved nonstructural) protein of influenza A virus to demonstrate its role in infectivity. Our in silico study revealed a new Casein kinase II (CKII) phosphorylation domain at position 151-154. This domain was formed due to the mutation at position 151 (T151I). Moreover, considerable difference in the secondary structure of this protein due to mutation was also reported. It is also confirmed by contact residue analysis that the changes in secondary structure are due to mutations.

In silico analysis of genes nucleoprotein, neuraminidase and hemagglutinin: a comparative study on different strains of influenza A (Bird flu) virus sub-type H5N1.

The avian influenza (bird flu) is an infectious disease of birds, ranging from a mild to a severe form of illness. Influenza viruses pose significant challenges to both human and animal health. The proteins, nucleoprotein (NP), neuraminidase (NA) and hemagglutinin (HA) of influenza A virus (Bird flu virus) sub-type A/Hatay/2004/(H5N1) from chicken were selected for this study. Our in silico analysis predicted that HA of influenza A virus is highly sensitive to mutations and hence it is significant for its pathogenic nature. None of the mutations was detected as an important change except in NA where K332R was at a PKC phosphorylation site. Analysis of the sequence comparison showed that the maximum number of mutations were observed in HA. These mutations are significant as they are involved in change in polarity or hydrophobicity as well as in propensity of each amino acid residue to stabilize the secondary structure. The program MAPMUTATION can be used to monitor the mutations, and predict the trend of mutations.

SSRscanner: a program for reporting distribution and exact location of simple sequence repeats.

UNLABELLED: Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. These repeated DNA sequences are found in both prokaryotes and eukaryotes. They are distributed almost at random throughout the genome, ranging from mononucleotide to trinucleotide repeats. They are also found at longer lengths (> 6 repeating units) of tracts. Most of the computer programs that find SSRs do not report its exact position. A computer program SSRscanner was written to find out distribution, frequency and exact location of each SSR in the genome. SSRscanner is user friendly. It can search repeats of any length and produce outputs with their exact position on chromosome and their frequency of occurrence in the sequence. AVAILABILITY: This program has been written in PERL and is freely available for non-commercial users by request from the authors. Please contact the authors by E-mail: huzzi99@hotmail.com.

MAP MUTATION: a program for analyzing mutations in protein sequences.

UNLABELLED: Avian influenza is an infectious disease of birds caused by type-A strains of the influenza virus. The unprecedented spread of the highly pathogenic avian influenza type A is a threat to veterinary and human health. Influenza viruses continuously undergo mutations and they lack proofreading mechanism. Hence, they evolve to new forms of the virus. We describe MAP MUTATION (developed using PERL script) to quickly compare two strains and display mutational information and report specific positions where mutation has occurred. AVAILABILITY: The PERL script is available from the authors for non-commercial purposes.

Matrix protein 1: A comparative in silico study on different strains of influenza A H5N1 Virus.

The importance of influenza viruses as worldwide infectious agents is well recognized. Specific mutations and evolution in influenza viruses is difficult to predict. We studied specific mutations in matrix protein 1 (M1) of H5N1 influenza A virus together with properties associated with it using prediction tools developed in Bioinformatics. Changes in hydrophobicity, polarity and secondary structure at the site of mutation were noticed and documented to gain insight towards its infection.