Structural Analysis

Question 1

Biophysical Properties on Proteins

Answer 1

• example alpha-helix
• often in transmembrane domains
• membranes consists of lipids and proteins
• transmembrane region is hydrophob
• idea: measure the average hydrophobicity for our aminoacid sequence over a window

Question 2

Secondary Structures

Answer 2

structure is the three dimensional form of local segments of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well.

Question 3

Hydrophobicity Scales

Answer 3

Janin and Rose et al. scales was to examine proteins with known 3-D structures and define the hydrophobic character as the tendency for a residue to be found inside of a protein rather than on its surface. For review see
Cornette et al. [1987].

Kyte and Doolittle; Rose et al, Wolfenden and Janin: all different scales of hydrophobicity

Question 4

Protscale Parameters

Answer 4

Window size: The window size is the length of the interval to
use for the profile computation. When computing the score for a given residue i, the amino acids in an interval of the chosen
length, centered round residue i, are considered. In other words, for a window size n, we use the i - (n-1)/2 neighboring residues on each side of residue i to compute the score for residue i. The score for residue i is the sum of the scale values for these amino acids, optionally weighted according to their position in the window.

Relative weight of the window edges: The central amino acid of the window always has a weight of 100%. By default, the amino acids at the remaining window positions have the same weight, but you can make the residue at the center of the window have a larger weight than the others by setting the weight value for the residues at the beginning and end of the interval to a value
between 0 and 100

Scale normalization: Normalize to range of 0 to 1 to allow comparison of different measures on the same scale

Question 5

Summary Biophysical Predictions of Secondary Structures

Answer 5

• various scales, scores
• window size
• score based predictions are just predictions, use with
care!
• other methods: xray is better but much mooooore laborious
• tools: ProtScale from expasy
• exercise: EMBOSS pepinfo