Development of a suite of bioinformatics tools for the analysis and prediction of membrane protein structure

This thesis describes the development of a novel approach for prediction of the three-dimensional structure of transmembrane regions of membrane proteins directly from amino acid sequence and basic transmembrane region topology. The development rationale employed involved a knowledge-based approach. Based on determined membrane protein structures, 20x20 association matrices were generated to summarise the distance associations between amino acid side chains on different alpha helical transmembrane regions of membrane proteins. Using these association matrices, combined with a knowledge-based scale for propensity for residue orientation in transmembrane segments (kPROT) (Pilpel et al., 1999), the software predicts the optimal orientations and associations of transmembrane regions and generates a 3D structural model of a gi ven membrane protein, based on the amino acid sequence composition of its transmembrane regions. During the development, several structural and biostatistical analyses of determined membrane protein structures were undertaken with the aim of ensuring a consistent and reliable association matrix upon which to base the predictions. Evaluation of the model structures obtained for the protein sequences of a dataset of 17 membrane proteins of detennined structure based on cross-validated leave-one-out testing revealed generally high accuracy of prediction, with over 80% of associations between transmembrane regions being correctly predicted. These results provide a promising basis for future development and refinement of the algorithm, and to this end, work is underway using evolutionary computing approaches. As it stands, the approach gives scope for significant immediate benefit to researchers as a valuable starting point in the prediction of structure for membrane proteins of hitherto unknown structure

Draft genome sequence of Bacillus thuringiensis strain S601, a toxic strain to Anthonomous grandis / Sequência do genoma de Bacillus thuringiensis strain S601, uma estirpe tóxica para os Anthonomous grandis

Bacillus thuringiensis is an important bacterium showing insecticide proteins effective to control several agricultural pests, including boll weevil, Anthonomus grandis Boh. (Coleoptera: Curculionidae). This work describes the draft genome sequence of B. thuringiensis S601, which contains genes encoding the parasporal crystal cry1B, including other genes, like Vpa, Vpb, Sip and new ones described by new nomenclature of Bt toxins. Genes coding for bacteriocin, plant growth promotion pathway and tyrosinase were also identified

Draft genome sequence of Bacillus thuringiensis strain S1307, an isolate toxic for lepidoptera / Projecto de sequência genómica de Bacillus thuringiensis strain S1307, um tóxico isolado para lepidoptera

The bacterium Bacillus thuringiensis (Bt) produces multiple toxins with activity against a diverse range of insect, including Diptera, Coleoptera and Lepidoptera. The Bt strain S1307 contains genes encoding Cry1Ab, Cry1Bc, Cry1Ia, Cry1J, Cry2Aa, Mpp5Aa, Spp1Aa, Vpb1B, Vpb2Bb and Vip3Aa. Genes coding for plant growth promotion metabolic pathway were identified. And the operon which encodes the bacteriocins thuricin 17 and nisin were identified

Draft genome sequence of bacillus thuringiensis S906, a toxic strain to coleoptera and lepidoptera orders / Projeto de sequência do genoma de bacillus thuringiensis S906, uma cepa tóxica para as ordens coleoptera e lepidoptera

Bacillus thuringiensis is an important bacterium which shows insecticide action against several pests. This work describes the draft genome sequence of B. thuringiensis S906, that showed toxicity against insects from Lepidoptera order (Anticarsia gemmatalis, Helicoverpa armigera, Plutella xylostella and Spodoptera frugiperda), and Coleoptera order (Anthonomus grandis) which contains the genes cry1Ba, Vpa, Vpb and Spp1A. Genes coding for bacteriocin, plant growth promotion pathway, tyrosinase and enhancin were also identified

Draft Genome Sequence of Bacillus thuringiensis Strain 907, an Isolate Toxic for Coleopteran / Projecto de Sequência Genómica de Bacillus thuringiensis Strain 907, um Tóxico Isolado para Coleopteran

Bacillus thuringiensis is an important bactéria which shows insecticide action effective to control several Lepidoptera like Anticarsia gemmatalis, Helicoverpa armigera, Plutella xylostella and S. frugiperda, and Coleoptera like A. grandis. This work describes the draft genome sequence of B. thuringiensis S907, which contains the genes cry1Ba1, Vpb1Bc1, Vpa2Bb4 and Sip1Aa1. Genes coding for bacteriocin, plant growth promotion pathway and tyrosinase were identified

Draft genome sequence of Bacillus thuringiensis strain S2195, an isolate toxic for lepidoptera / Projeto de sequência do genoma de Bacillus thuringiensis strain S2195, um tóxico isolado para lepidoptera

Bacillus thuringiensis is a Gram-positive bacterium which produces insecticidal proteins effective to control several medical and agriculture insect pests. These proteins belong to the Cry, Cyt, Vip and Sip families. This work describes the draft genome sequence of B. thuringiensis S2193, which contains genes encoding the parasporal crystal cry1Ad, cry1Ca, cry1Da, cry1Fa, cry1Ia, cry2A, cry9Ea and vip3Ca. Genes coding for plant growth promotion pathway were identified. And the operon which encodes the bacteriocin Thuricin 17 were annoted. We found the gene which encodes the toxin enhancin

Draft genome sequence of Bacillus thuringiensis strain S1287, an isolate showing insecticidal activity against coleoptera / Projeto de sequência do genoma de Bacillus thuringiensis strain S1287, um isolado mostrando actividade insecticida contra coleoptera

Bacillus thuringiensis is an important bacterium showing insecticide proteins effective to control several important medical pests, including several Diptera species, like Diptera, Coleoptera and Lepidoptera. This work describes the draft genome sequence of B. thuringiensis S1287, which contains genes encoding the parasporal crystal cry, like Cry1Ab, Cry1Bb, Cry1C, Cry1D, Cry1Fb, Cry1Hb, Cry1Id, Cry1Ja, Cry1Ka and Cry1Nn. The genes belonging to the Vip Family were identified, Vpb1Aa, Vpa2Aa and Vip3Ag. Genes coding for plant growth promotion pathway were found

Draft genome sequence of Bacillus thuringiensis strain s908, an isolate toxic for coleopteran / Projeto de sequência genómica de Bacillus thuringiensis strain s908, um tóxico isolado para coleopteran

Bacillus thuringiensis (Bt) produces pore forming toxins that have been used for Diptera, Lepidoptera and Coleoptera pest control in agriculture for many years. This work describes the draft genome sequence of B. thuringiensis S908, which contains the genes cry1B, Vpa, Vpb and Sip. Genes coding for bacteriocin, enhancin, plant growth promotion pathway and tyrosinase were identifie

Draft genome sequence of Bacillus thuringiensis strain S1905, an isolate toxic for lepidoptera / Projeto de sequência genómica de Bacillus thuringiensis strain S1905, um tóxico isolado para lepidoptera

Bacillus thuringiensis Cry, Cyt, Vip and, Sip protein families show activity against insects of the orders Lepidoptera, Coleoptera and, Diptera. The Cry action toxins is to lyse midgut epithelial cells by forming pores in the target membrane. This work describes the draft genome sequence of B. thuringiensis S1905, which contains genes encoding Cry1A, Cry1I, Cry2A, Cry8K, and Vip3A. We found the spp1Aa gene and genes coding for plant growth promotion metabolic pathway and Thuricin 17. One gene encoding the toxin enhancin and a locus which encodes the CRISPR were identified

STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

BACKGROUND: The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user. RESULTS: We are reporting here about new Sting Millennium Suite (SMS) version which is fully accessible (including for local files at client end), web based software for molecular structure and sequence/structure/function analysis. The new SMS client version is now operational also on Linux boxes and it works with non-public pdb formatted files (structures not deposited at the RCSB/PDB), eliminating earlier requirement for the registration if SMS components were to be used with user's local files. At the same time the new SMS offers some important additions and improvements such as link to ProTherm as well as significant re-engineering of SMS component ConSSeq. Also, we have added 3 new SMS mirror sites to existing network of global SMS servers: Argentina, Japan and Spain. CONCLUSION: SMS is already established software package and many key data base and software servers worldwide, do offer either a link to, or host the SMS. SMS (Sting Millennium Suite) is web-based publicly available software developed to aid researches in their quest for translating information about the structures of macromolecules into knowledge. SMS allows to a user to interactively analyze molecular structures, cross-referencing visualized information with a correlated one, available across the internet. SMS is already used as a didactic tool by some universities. SMS analysis is now possible on Linux OS boxes and with no requirement for registration when using local files