L7-9: Protein Structure, Function and Modelling Flashcards
What type of amino acids are found on the inside of proteins?
Aliphatic/non-polar/hydrophobic.
Example of structural protein
collagen
Example of storage protein
ovalbumin
Overall structure is a sufficient determinant for which typs of proteins?
Structural proteins
Which amino acids strongly absorb UV light and can aid in detection of proteins?
Tyrosine and tryptophan
Hydrophilic amino acids are often found in which part of the cell?
On the cell surface
Which amino acid can form disulphide bridges?
Cysteine
Degrees of freedom in the rotation of the peptide bonds depends upon:
The R group (side chain) and the environment around the amino acid
Four levels of protein structure
Primary, secondary, tertiary, quarternary
Primary structure of a protein
Order of the amino acids in the polypeptide chain
Secondary structure of a protein
Refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone
True or false:
Secondary structure of a protein does not involve R group interactions
True
Most common secondary structures
Alpha helices and beta-pleated sheets
Tertiary structure
Overall 3D structure of a polypeptide
Primarily due to interactions between the R groups of the amino acids.
A misfolded protein can be refolded properly using which chemical?
Urea
True or false:
Interior of a cell often contains charged amino acids
False. Interior of protein - uncharged amino acids or neutral charged regions
Which algorithm can be used to determine hydrophobicity?
Kyte-Doolittle
Which algorithm can be used to determine hydrophilicity/antigenicity?
Hopp-Woods
In motif language, [ ] mean
Either (one) amino acid within the brackets
In motif language, { } mean
Any amino acid except the ones in the curly brackets
In motif language, X means
Any amino acid
Which algorithm tool is used for detecting classically secreted proteins?
SignalP
Which algorithm tool is used for detecting non-classically secreted proteins?
SecretomeP
ICAM-1
90kD cell surface glycoprotein on antigen presenting cells
Central role in cell adhesion and in cell-cell contact-dependent immune mechanisms
Counter receptor to ICAM-1
LFA-1
Which amino acids are often found on the surface of cells?
Proline and glycine
Proteins in an aqueous environment generally adopt which shape?
Globular
An alpha helix is a _____-handed coil
right
Alpha helices are stabilised by hydrogen bonds between _________
amine and carboxyl groups of nearby amino acids
Peptide bond
O=C–NH
The angle of the peptide bond is typically ____ or ______
0 or 180
Amino acid with the most degrees of freedom around its phi and psi angles
Glycine
Amino acid with the least degrees of freedom around its phi and psi angles
Proline
Ramachandran (phi/psi) plots display _____
allowed and disallowed conformations of a polypeptide chain
True or false:
In an alpha helix, the side chains of amino acids project inwards.
False. Side chains project outwards in an alpha helix.
True or false:
Alpha helices are more thermally stable than beta pleated sheets.
True
Determining protein 3D structures using x-ray crystallography - step by step
- Grow high quality protein
- Collect x-ray diffraction
- Calculate electron density maps, build and refine crystal structure
- Display and interpret protein’s 3D structure
Characteristics of a protein domain
Spatially separated unit of protein structure
Folded independently from the rest of the structure
Often mediating a specific function
Protein folds
Secondary structures in the same arrangement - major structural similarity
Protein superfamilies
Similar 3D structures but often with low sequence identity between members (probably common evolutionary origin)
Protein families
Conserved 3D structures with moderate to high sequence identities (>30%) - clear evolutionary relationships
Why are new folds and superfamilies not being discovered?
- There are predicted to be a limited number of folds that are dynamically stable
- There will be a finite number of superfamilies
- We have identified the structure of all the “easy” ones
True or false:
Homology protein modelling is unique in that it doesn’t require the sequence of interest to share significant similarity with a protein of known structure.
False. Homology protein modelling requires the sequence of interest to share significant similarity (normally >30% but the higher the better) with a protein of known structure.
Homology protein modelling - step by step
- Identify a homologue of known structure (template)
- Produce a high quality alignment of your sequence (target) with that of the protein template of known structure.
- Generate model from template and run the modelling algorithm. Consequences of the changes to between overall structure of side chains is evaluated.
Models are optimised and scored against an energy and geometry based function that includes template-derived parameters (e.g. distance matrix). - Evaluate and improve the model:
- Look for unacceptable steric clashes or geometries (do a Ramachandran plot)
- Make sure any insertions are in appropriate positions (e.g. loops)
- Ensure that there are no obvious problems (e.g. buried polar residues)
- Adjust alignments and repeat model building if needed
Methods for predicting secondary structures
Chou-Fasman
Garnier-Osguthorpe-Robson
Which analysis method is used to identify transmembrane regions?
Kyte-Doolittle, Hopp-Woods
Which analysis method is used to identify antigenic regions?
Hopp-Wood, Jameson-Wolf
The peptide torsion or dihedral angles phi (F) and psi (Y) determine the conformation of the _________.
polypeptide backbone (main chain)
Name and angle of peptide bonds
Omega - typically 0 or 180 degrees.
