| Resources | Objectives | |||
 |
 |
 |
 |
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| Kuby's Immunology |
Immunology Reference
Shelf |
Carney's Learning Techniques |
To Tortora's Microbiology |
Immunology Laboratory |
Protein Structure Laboratory
updated
18/01/01
| Resources | Objectives | |||
|
|
|
|
|
| Kuby's Immunology |
Immunology Reference
Shelf |
Carney's Learning Techniques |
To Tortora's Microbiology |
Immunology Laboratory |
1:To use the Protein
Data Bank
2: To use RasMol to construct three dimensional models of protein
3:Use SwissProt database to look at the secondary structure of
the lysozyme and myoglobin molecule
4: Use Prot Scale and ProtParam programs to predict epitopic
regions of lysozyme and myoglobin using the principles of
antigenicity prediction.
5: Apply those predictions to 3D molecule in RasMol.
OBJECTIVE 4: PREDICTION OF ANTIGENICITY
DEGREE OF PROTRUSION
Protrusions in the tertiary conformation of the protein allows to determine which residues are exposed on the surface and which hidden inside the molecule. Since B and T cells recognise different types of epitopes, protrusion index can be used in predicting antigenic sites of the proteins.
HYDROPHILICITY PLOTS
Distinguishing regions of the sequence that are buried from regions that are on the outside. The local maxima in hydrophilicity plots correspond to surface exposed regions of the molecules and were parts of epitopes. (Hopp and Woods, , Kyte and Doolittle, Rose et al. plots)
Prediction of the loops or turns positions also predict regions of highest hydrophilicity and may correspond to the epiotpes;
AMPHIPATHICITY
Amphipathicity is a contributory factor in the folding of the protein and arises from a periodicity of hydrophobic residues in the amino acid sequence. A presence of amphiphilic segments along a peptide can identify T cell antgenic site.
SEGMENTAL MOBILITY
Atomic temperature factors plotted against residue number provide image of the degree of mobility existing along the polypeptide chain. Regions of highest mobility usually coincide with highly accessible elements at the surface of the molecule. (Karakuls and Schulz)
CHAIN TERMINATION
In a majority of proteins , the N and C termini are located at the surface of the molecule and exhibit high values of relative flexibility. The termini of many proteins correspond to continuous epitopes.
STATIC SURFACE ACCESSIBILITY.
It was shown that most exposed portions of the surface correlates with known epitopes of these molecules. The accessible molecular surface is evaluated by algorithms of Lee and Richards and Connolly which calculate the surface accessible to contacts with spherical probes ranging from 1.4 to 10 A radius.
SEQUENCE VARIABILITY.
In homologous proteins regions that present high sequence variability tend to correspond to the location of epitopes. These regions represent sites which can tolerate local conformational changes arising from point mutations because they are not involved in long-range interactions that stabilise internal folding of the molecule
Protein Database : database for 3D protein structures
Rasmol Home Page : excellent viewer for those protein structures found in the Brookhaven Protein Database, contains different versions of Rasmol for Windows 3.1, Windows 95 Unix, Macs etc. instructions tips updates etc
Swiss Protein Sequence Database :database for protein sequencesGo to the resources section of the course website and download Protein Database files for B cell receptors and epitopes
Molecules: a collection of database files for molecules that are described in Kuby's immunology