Physics 422 HW #4

Raymond Wong

1) The four main levels of classification are protein class (C), architecture (A), topology (T) and
homologous superfamily (H). Class is the simplest level, and it essentially describes the
secondary structure composition of each domain. In contrast, architecture summarizes the shape
revealed by the orientations of the secondary structure units, such as barrels and sandwiches. At
the topology level, sequential connectivity is considered, such that members of the same
architecture might have quite different topologies. When structures belonging to the same T-
level have suitably high similarities combined with similar functions, the proteins are assumed to
be evolutionarily related and put into the same homologous superfamily.
b) SCOP and CATH are the two databases generally accepted as the two main authorities in the
world of fold classification. According to SCOP there are 1393 different folds. The selected
architecture comprises two topologies, 1.50.10 and 1.50.30

3) protein domain protein domain is a polynomial is a portion of a protein subunit. (reference

https://m.youtube.com/watch?v=LDei1cd95tA)
b) SCOP and CATH are widely used as gold standards to benchmark novel protein structure
comparison methods as well as to train machine learning approaches for protein structure
classification and prediction. The two hierarchies result from different protocols which may
result in differing classifications of the same protein.
d) In many cases a protein family has a corresponding gene family, in which each h gene encodes
a corresponding protein with a 1:1 relationship proteins in a descend from a common ancestor
and typically have similar three dimensional structure, function and significance sequence
similarity.
3f) 139500 proteins
4)
6)
8) (a)∆G°=∆H°-T∆S°

Here,

T=25°C=298K

∆G°=40100-298×107.4

=8094.8 J/mol

∆G°=-RTlnK

8094.8=-8.314×298×lnk

lnk=-3.27

k=0.038

(b) spontaneously boils when ∆G is negative so equating it to 0.

∆H=T∆S

T=∆H/∆S

=40100/107.4

=373.37K

=100°C

(c)

1KJ=0.24kcal=6.24×10²¹ ev

∆G°=8.1 KJ/mol

=1.944kcal/mol

=5.05×10²² ev

∆H°=40.1KJ/mol

=9.624kcal/mol

=2.5×10²³ ev

∆S=0.1074KJ/mol

=0.0258kcal/mol
=6.7 ×10^20 ev

9 a and b)
9c) The dissociation constant can be calculated by the following formula:- Energy (Delta G) (Found in
the previous calculation) =RT In (Kd/c), where Kd is dissociation constant, R is universal gas
constant, T is temperature and c is standard reference concentration ie 1 mol/L.

10)