Molecular modelling of urease accessory interaction proteins of Helicobacter Pylori J 99 and predicting an interruption in interaction by Vigna radiata Defensins

Abstract

Helicobacter pylori is the major causative agent of Gastric carcinoma. Significance of the urease accessory interaction proteins are emphasized in colonization of human gastric mucosa and efficient infection of H. pylori. Here an attempt is made to explore the structure and properties of urease accessory interaction proteins from Helicobacter pylori J 99. The proteins chosen for the study are ureH, ureI, nikR, groL and flgS based on the interaction map available from STRING database. The above mentioned proteins do not have a comprehensive three dimensional structure. Hence the models were generated using PSI-BLAST (Position Specific Iterative-Blast) and MODELLER 9V8. Physicochemical characterization encompasses pI, EC, AI, II and GRAVY. Secondary structure was predicted using PSI-PRED. Functional characterization was done by SOSUI and DISULFIND Servers and refinement of structure was done using Ramachandran plot analysis. RMS-Z values were calculated using Q-MEAN Server and CHIMERA was used for molecular simulation studies. Plant defensins from Vigna radiata are successfully docked to the modeled structures and thus interaction could be possibly prevented. These results will pave way for further selective inhibition of H. pylori colonization and in vivo survival by employing plant defensins from Vigna radiata (VrD1 & VrD2). The work will prove that plant defensins provides anticancer relief too.

Identification of genes involved in radioresistance of nasopharyngeal carcinoma by integrating gene ontology and protein-protein interaction networks

“…Proteinprotein interaction networks were done by STRING online software (http://string.embl.de) through inputting ID number (20,21). The following two criteria were applied to detect important nodes: i) required confidence: high confidence (score: 0.07), ii) interactors: no more than 5.…”

Modelación por homología de la proteína Luxs de Porphyromonas gingivalis cepa W83

“…La utilización de esta herramienta permite, por lo tanto, aproximar de manera temprana y confiable cual será la estructura secundaria del péptido, ya que existen combinaciones de ángulos típicas para cada estructura, tales como las -hélice y las hojas (Figura 4). De acuerdo a los resultados obtenidos en el servidor Rampage (49) , la ubicación de los ángulos y de las torsiones de los enlaces de los aminoácidos que forman la estructura secundaria evaluada se encuentran dentro de niveles aceptados y permitidos, obteniéndose una validación suficiente para el modelo propuesto. Otra estrategia de evaluación usada fue la valoración por Verify3D (50) y Errat (51) los resultados se muestra en la Tabla 7, de acuerdo con los valores umbrales permitidos, los modelos presentan valores no concordantes, principalmente el modelo de la cadena B.…”