Thesis final - after defense-7 - Jacobs University

Chapter 2
∧
r
i
=
Si
S
∑
jεA
j
(2)
In equation (2),
Si
is the sum of the accessible surface area (ASA) for all the amino acids of
type i. S j is the total surface area of the protein. The r ∧ i is the fraction of surface area occupied
by amino acid i and A is the collection of 20 possible amino acids (93). The concept of this
approach was based on the assumption that each amino acid on the protein surface contributes
regarding its abundance, with the properties associated to the protein surface (32, 67).
Average hydrophobicity (AH), average polarity, average bulkiness and average flexibility
(AF) were calculated from the primary structure by using the scales available at Expasy
ProtScale tool (94). The average hydrophobicity values were measured employing three
different scales i.e. Tanford (T), Cowan-Whittaker (CW) and Miyazawa-Jernigan (MJ),
respectively (25, 92, 95). The average bulkiness was calculated by the scale proposed by
Zimmerman (96). The polarity values were calculated by adopting the Grantham’s and
Zimmerman’s scales (96, 97). The flexibility indices introduced by Bhaskaran and
Ponnuswamy were used to calculate the flexibility values of proteins (98).
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