01-03-2011, 04:21 PM
PRESENTED BY:
Dr. Arun G. Ingale
In silico structural analysis and molecular modeling studies on ERF.ppt (Size: 3.15 MB / Downloads: 100)
Ethylene response factors
Member of a multigene family of transcription factors
Plant transcriptional regulators
Regulation of downstream ethylene responsive genes
Ethylene signaling pathway
Plants ability to respond to environmental stimuli
Regulating traits of agronomic importance
Fruit ripening and floral senescence
Floral senescence, abscission, and root elongation
Physiological responses to environmental stresses such as water deficit, mechanical wounding, and pathogen attack
Ethylene response factors (ERF) belong to a plant-specific transcription factor family and play pivotal roles in plant’s adaptation to various types of stresses.
tomato ethylene responsive factor 1 (ERF1), that integrates ethylene and osmotic stress pathways.
ERF1 might function as a linker between the ethylene and osmotic stress pathways
What is bioinformatics?
In silico
Application of information technology to the storage, management and analysis of biological information
Facilitated by the use of computers
Promises of genomics and bioinformatics
Medicine
Knowledge of protein structure facilitates drug design
Understanding of genomic variation allows the tailoring of medical treatment to the individual’s genetic make-up
Genome analysis allows the targeting of genetic diseases
The effect of a disease or of a therapeutic on RNA and protein levels can be elucidated
The same techniques can be applied to biotechnology, crop and livestock improvement, etc...
What Can be done using bioinformatics?
Sequence analysis
Geneticists/ molecular biologists analyse genome sequence information to understand disease processes
Molecular modeling
Crystallographers/ biochemists design drugs using computer-aided tools
Phylogeny/evolution
Geneticists obtain information about the evolution of organisms by looking for similarities in gene sequences
Ecology and population studies
Bioinformatics is used to handle large amounts of data obtained in population studies
Medical informatics
Personalised medicine
Objectives
Analysis of Protein sequences of ERF
Multiple sequence alignment of ERF
Protein structure prediction
Prediction of Transmembrane Segments
Predict Secondary Structure
Prediction Conserved Domain
Determination of coil region
Prediction of MHC Class-II binding sites
Molecular modelling studies
Materials and Methods
Sequence retrieval
from Entrez database
Protein sequence – ERF
BLASTp MSA
Program- CLUSTAL W.1.8
Prediction of Coils (version 2.1).
Server- ISREC-Server
Antigenic peptides
Method- Antigen prediction.
Protein sequence – ERF
Format– FASTA.
software's/Servers
TMHMM2.0
MHC peptide binding software
CDD database used for the Conserved domain prediction
Biology workbench
Molecular modeling software
Swiss PDB, DS gene,
Swissmodel, modelar
CPH model
geneTheader,
procheck
Accelrys DS visualiser
Deepview,
Rasmol, Cn3D,