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Table 6.2. The six sequences considered and their estimated characteristic tem-
peratures T
and T
f
. (X)
y
means that X is repeated y times.
name
sequence
T
T
f
S
2
g
PH
9
(NP)
2
NHPH
3
PH
0:65
0:05
0:55
0:1
S
2
b
PHNPH
3
NHNH
4
(PH
2
)
2
PH
0:55
0:15
none
S
22
i
P
4
H
5
NHN
2
H
6
P
3
0:75
0:1
0:7
0:2
S
2
h
H
22
0:65
0:05
none
S
4
g
P(HP)
5
N
3
H
9
N
3
(HP)
4
N
3
H
9
0:65
0:03
0:65
0:05
S
4
h
H
46
0:70
0:03
none
the angle between the vectors n
i
= r
i+1;i
r
i+1;i+2
and n
i+1
= r
i+2;i+1
r
i+2;i+3
,
k
r
= 100, a = 1, k
#
= 20, #
0
= 105
, A
i
= 0 and B
i
= 0:2 if at least two among
the residues i;i + 1;i + 2;i + 3 are N, A
i
= B
i
= 1:2 otherwise. As to V
ij
, we have
V
ij
=
8
3
a
r
a
r
12
6
+
(6.22)
if i;j = P; P or i;j = P; H,
12
6
a
r
a
r
V
ij
= 4
(6.23)
if i;j = H; H and
6
a
r
V
ij
= 4
(6.24)
if either i or j are N [29]. Such a model is clearly very similar to the two-dimensional
one described in Sec. 6.2.
We considered six dierent sequences of \amino acids" H, P and N: four of
22 monomers, S
2
g
, S
22
i
, S
2
h
, and two sequences of 46 monomers, S
4
h
, S
4
g
.
The six sequences are listed in Table 6.2 together with their estimated collapse
and folding temperatures; the latter has been dened using a dierent protocol
with respect to the case of Sec. 6.2.2 (see [25]). Sequences S
22
, S
22
b
g
and S
46
g
are good
folders [25, 29, 30]: below a given temperature S
22
g
(resp. S
4
g
) always reach the
same -sheet-like structure (resp. -barrel-like structure). Homopolymers S
2
h
and
S
4
h
, on the other hand, show a hydrophobic collapse but no tendency to reach a
particular conguration in the collapsed phase, as expected. Sequence S
2
b
(which
has the same overall composition of S
2
g
rearranged in a dierent sequence) behaved
as a bad folder and did not reach a unique native state, while S
2
i
was constructed
by us to show a somehow intermediate behavior between good and bad folders: it
always forms the same structure involving the middle of the sequence, while the
beginning and the end of the chain uctuate also at low temperature.
