THGS: a web-based database of Transmembrane Helices in Genome Sequences

Fernando, S.; Selvarani, Ponnuthai; Das, Soma; Kumar, Ch. Kiran; Mondal, Sukanta; Ramakumar, Suryanarayanarao; Sekar, K.

doi:10.1093/nar/gkh130

Cited by 10 publications

(4 citation statements)

References 15 publications

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“…In this study, the high‐throughput expression pipeline of the Joint Center for Structural Genomics (Lesley et al 2002) was used to assay the expression of Thermotoga maritima α‐helical membrane proteins in E. coli . T. maritima has ∼446 putative α‐helical membrane proteins that vary from one to 16 transmembrane helices (Fernando et al 2004; http://www.144.16.71.10/thgs/). Forty‐five of the smallest α‐helical membrane proteins (MW < 16 kDa; shown in Supplemental Fig.…”

Section: Detergent Propertiesmentioning

confidence: 99%

Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination

et al. 2006

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Structural studies of integral membrane proteins typically rely upon detergent micelles as faithful mimics of the native lipid bilayer. Therefore, membrane protein structure determination would be greatly facilitated by biophysical techniques that are capable of evaluating and assessing the fold and oligomeric state of these proteins solubilized in detergent micelles. In this study, an approach to the characterization of detergent-solubilized integral membrane proteins is presented. Eight Thermotoga maritima membrane proteins were screened for solubility in 11 detergents, and the resulting soluble protein-detergent complexes were characterized with small angle X-ray scattering (SAXS), nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD) spectroscopy, and chemical crosslinking to evaluate the homogeneity, oligomeric state, radius of gyration, and overall fold. A new application of SAXS is presented, which does not require density matching, and NMR methods, typically used to evaluate soluble proteins, are successfully applied to detergent-solubilized membrane proteins. Although detergents with longer alkyl chains solubilized the most proteins, further characterization indicates that some of these protein-detergent complexes are not well suited for NMR structure determination due to conformational exchange and protein oligomerization. These results emphasize the need to screen several different detergents and to characterize the protein-detergent complex in order to pursue structural studies. Finally, the physical characterization of the protein-detergent complexes indicates optimal solution conditions for further structural studies for three of the eight overexpressed membrane proteins.Keywords: membrane proteins; NMR; SAXS; protein-detergent complexes; detergent micelles

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Section: Detergent Propertiesmentioning

confidence: 99%

Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination

et al. 2006

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“…The web interface is developed in HTML/CSS; PHP and Java scripts are used for retrieving the stored data. The Basic Local Alignment Search Tools (BLAST) explore web interface and its scripts are implemented in PHP, based on [56][57][58]. The overall structure of the biomaterial database is shown in Fig.…”

Section: Methodsmentioning

confidence: 99%

Biomat _dBase: A Database on Biomaterials

Subia¹

2012

TOTERMJ

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Abstract:Biomaterial science provides a platform for the development of bio-artificial implants. Growth or development of engineered tissues for the purpose of repairing, restoring and enhancing the function of a damaged tissue or organ needs designed biomaterials. The most studied tissue engineering strategy consists on using cells growth factors and temporary three-dimensional (3D) porous scaffolds. 3D scaffolds play a very important role in the success of tissue engineering and regenerative medicine. They provide structural support for cells to proliferate and maintain their differentiated phenotype and permit the convenient delivery of cells into the patients. Several features of scaffold can influence the cell growth and its functions. The artificial extracellular matrices can be produced from different biomaterials including ceramics, natural or synthetic polymers and composites. Recent discoveries and innovations in this emerging field adopt varieties of techniques ranging from biotechnology to material science and nanotechnology. The result is a huge amount of data. To maintain and keep updated, this would not be an easy task. New advances in computers and information technology help to create and organize the databases quite easy. Their contents can easily be accessed, managed and updated. A WWW interface benefits the users to search the different types of data based on the types of biomaterials, their abundance, structure and applications. This provides the scope and archive of information on this emerging field of biomaterials to the global scientific community. The database is freely accessible through http://dbbiomat.iitkgp.ernet.in.

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“…gov/nucleotide). Amino acids composition of selected genes was detected using Aminocomp software (Fernando et al 2004). By using this software, we obtained the percentage contribution of each amino acid in the whole sequence.…”

Section: Methodsmentioning

confidence: 99%

In silico comparative genome analysis of malaria parasite Plasmodium falciparum and Plasmodium vivax chromosome 4

et al. 2009

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Malarial parasite has long been a subject of research for a large community of scientists and has yet to be conquered. One of the main obstacles to effectively control this disease is rapidly evolving genetic structure of Plasmodium parasite itself. In this study, we focused on chromosome 4 of the Plasmodium falciparum and Plasmodium vivax species and carried out comparative studies of genes that are responsible for antigenic variation in respective species. Comparative analysis of genes responsible for antigenic variation (var and vir genes in P. falciparum and P. vivax, respectively) showed significant difference in their respective nucleotide sequence lengths as well as amino acid composition. The possible association of exon's length on pathogenecity of respective Plasmodium species was also investigated, and analysis of gene structure showed that on the whole, exon lengths in P. falciparum are larger compared to P. vivax. Analysis of tandem repeats across the genome has shown that the size of repetitive sequences has a direct effect on chromosomes length, which can also be a potential reason for P. falciparum's greater variability and hence pathogenecity than P. vivax.

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THGS: a web-based database of Transmembrane Helices in Genome Sequences

Cited by 10 publications

References 15 publications

Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination

Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination

Biomat _dBase: A Database on Biomaterials

In silico comparative genome analysis of malaria parasite Plasmodium falciparum and Plasmodium vivax chromosome 4

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