Lecture 2 Flashcards
What is divergent evolution?
Starts from common ancestor and diverge
What is convergent evolution
No common ancestor become more similar
What causes functional similarity?
not sequence similarity or functional similarity it is the fact that they are ralated through divergent evolution
How can you detect homology?
sequence based, structure based or position based
When are two sequences homologous
Alignment used: alignment similarity of above 25%
Which alignment values are useful?
Raw result: Not useful for similarity just gives best alignment
E-value: useful for judging significance of homology
p-value: nearly identical to E-value
What is evolutionary correspondence?
Corresponding residues are derived from a common precursor of the ancestral gene
What is structural correspondence?
corresponding residues occupy analogous positions in the 3D structure
What is functional correspondence?
corresponding residues fullfill the same role in both proteins
Why are proteins better conserved than DNA?
Genetic code degeneracy
AA similarity / exchange frequency
How to predict a teritary structure?
Homolgy modelling (look at known structures and sequences and compare to new sequence), Fold recognition (comparison to many candidate templates and judged by structural aspects)
What is to be considered in machine learning datasets?
Training, Validation, Testing dataset. Training must be sufficiently diverese to avoid overfitting and out of scope cases.
How can you determine the structure of a protein experimentally?
X-Ray cristallography, Alphafold, NRM (Nuclear Magnetic resonance), Cryo EM
What is a downside of X-ray cristallography?
Frozen snapshot -> no flexible regions visible
What are coiled coil regions
long amphipathic helics with heptad repeat pattern
What is 3.6 aa
One helix turn (One heptad repeat is 7 aa) slightly less than 2 turns
What are domains and why are they important?
often carriers of unit functionality (functional domains)
protein function can be deduced from domain function
Often subject to independent evolution
What is neo-functionalization?
often consequence of gene duplication can be mild or drastic
How to define a new motif?
Data: experimental indentification of relevant proteins (ER-targeting) + AA frequencies
Step 1: AA groups with high information content
Step 2: Calculate enrichment factor + significance
How to calculate the enrichment factor
In a group of 100 lumenal ER proteins, 20 contain the motif K-D-E-L>
The proteome comprises 25000 proteins, of which 200 contain K-D-E-L>
Enrichment factor = (20 * 24720) / (80 * 180)
What is hydrophobicity in aqueous solution
hydrophobic core more hydrophobic than exposed residues
What is hydrophobicity in lipid solution
hydrophobic core less hydrophobic than exposed residues
How do you predict a transmembrane protein?
Classification of AA by hydrophobicity scale
Evaluation of all possible windows by averaged hydrophobicity
How do you predict an amphipathic helix
periodicity of 3.6aa -> angle of 100° between consecutive residues (helical wheel diagram)
What are the protein folding principles?
Non-polar inside and polar outside (can form hydrogen bonds)
What is the primary structure and how is it connected?
AA chain connected via peptide bonds
What is the secondary structure?
Free rotation and rotational angle defines the side chain. Stabilization of secondary structure mostly independent of side chains
What is a torsion angle?
The angle of the rotation due to the side chains
Why is Glycin special when it comes to torsion angles?
Has no side chain -> therefore less restricted
What stabilizes the tertiary structure?
electrostatic attraction, Hydrogen bridges and Van der Waals forces
What could exposed hydrophobic residues indicate in a protein?
Interaction surfaces
Why are protein sequences better suited for analysis?
Shows you: protein structure, function and localization -> establishes evolutionary relationship
What is the ER retention signal
KDEL
What can be complications with signal detection?
signal can be remote (outside of detection)
Mechanism can have mutliple signals
Multiple components not orthogonal
What is proteomics used for?
Detection proteomics: Which proteins are there, which part of the protein -> changes in protein abundance
Modification proteomics: PTMs, are there changes in modification levels
Interaction proteomics: Which proteins bind to each other…
Methods for protein detection
Gel Electrophoresis, MS, Antibodies (Wester blot)
What is two dimensional Gel electrophoresis
- Isoelectric focussing (seperates by charge)
- SDS-page (seperates by size)
