An Introduction to Bioinformatics Protein Structure Prediction
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05.06.2018
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An
Introduction to Bioinformatics
Protein Structure Prediction
Introduction
Structure has several levels
1 primary
2 secondary
3 tertiary
4
quaternary
1 primary
Amino acid sequence
2 secondary
Localized organisation -helices and -sheets
3 tertiary
Three-dimensional organisation
4 quaternary
Multi
protein assembly
The problem…..
Signal peptides
Short N-terminal amino acid sequences
Direct to membrane
Cleaved after translocation
SignalP
Nobel Prize 1999
Günter Blobel
Intracellular targeting
TargetP
Predict subcellular location of eukaryotic protein
Presequences
Chloroplasts
Mitochondria
signal peptide
Transmembrane Domains
Lots of programs
TMHMM
-helices
hydrophobic
helix
topology
R or K +ve charge cytoplasmic side
Hidden Markov Modelling
-helices and -sheets
-helices and -sheets
Super-secondary
Structure
Secondary structure elements combined into specific geometric arrangements known as motifs
Super-secondary Structure
Several programs/websites for specific domains e.g.
PAIRCOIL and MULTICOIL - detect coiled-coiled regions
regions separating domains
TRESPASSER - detects Leucine Zippers
Leu-X6-Leu-X6-Leu-X6-Leu protein interaction domain
NPS@nalysis
Helix-Turn-Helix
Protein interaction/DNA binding
Integrated stucture prediction
One stop shop!
Predict Protein at EBI
secondary structure
solvent accessibility globular regions
transmembrane
helices coiled-coil regions
a multiple sequence alignment ProSite sequence motifs
low-complexity retions
ProDom domain assignments
Tertiary Structure Prediction
Homology
modelling
Fold recognition
Threading
Model building
Homology Modelling
Method of choice following BLAST search
SWISS
Model is a good WWW Interface
Homology Modelling
Homology Modelling
What if I have no homologue?
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