Engineering, 2013, 5, 78-84
http://dx.doi.org/10.4236/eng.2013.510B016 Published Online October 2013 (http://www.scirp.org/journal/eng)
Copyright © 2013 SciRes. ENG
2-Dimensional HP Foldings of Dermaseptin-J2
Shaomin Yan, Guang Wu
State Key Laboratory of Non-Food Biomass Enzyme Technology, National Engineering Research Center for
Non-Food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, Nanning, China
Email: hongguanglishibahao@yahoo.com
Received November 2012
ABSTRACT
Although the hydrophobic-polar (HP) model is a simple model to study protein folding, it is an approximation to the
real-life case. Dermaseptin is a subfamily of frog skin active peptide family, which has various antimicrobial activities,
and dermaseptin-J2 is a newly found peptide composed of 26 amino acids. In this study, the 2-dimensional HP model
was used to analyze the foldings of dermaseptin-J2 and its nine mutants, which were converted to different HP se-
quences according to the normalized amino acid hydrophobicity index with respect to pH levels and the conversion of
glycine as hydrophobic or polar, and each has 847,288,609,443 possible foldings. The results show that the foldings
with minimal energy have different native states, which are chiral and can be numerically distinguished and ranked ac-
cording to the normalized amino acid hydrophobicity index. The nine mutants of dermaseptin-J2 do not affect the mi-
nimal energy but affect their native states at pH 7. The results demonstrate that two pH levels and conversion of glycine
as hydrophobic or polar affect the native state and minimal energy, suggesting these are two ways to modify dermasep-
tin-J2.
Keywords: Dermaseptin; Folding Configuration; HP Model; Hydrophobicity Ind ex; Minimal Energy; Native State
1. Introduction
Protein folding is important to understand its structure-
function relationship and folding process. The hydro-
phobic-polar (HP) model is a very simple model, which
was based on the observation that hydrophobic interac-
tion was the driving force for protein folding and the
hydrophobicity of amino acids was the main force for
developing a native conformation of small globular pro-
teins [1].
The HP model suffers from critiques because its as-
sumption was simple for protein folding, its description
was far away from real-life case, its results were difficult
to cooperate with the folding obtained from experiments,
etc. Therefore, the HP model is not a model without li-
mitations, however, any model is an approximation to the
real-life case, and the difference between models relies
on the degree of their approximations. If one takes a
viewpoint from a single model, then all of the rest mod-
els will be problematic.
Actually, any model helps us to understand the world
from a different angle. There are several reasons to study
the HP model in great details: i) so far very few studies
using HP model were applied to real-life case because
the HP model needs extremely intensive computations,
therefore the studies using HP model is a way to test our
computing ability; ii) the extremely intensive computa-
tions in HP model was classified as NP problem [2], be-
ing the first problem listed millennium prize, so the study
on HP model is approaching to one of numerous un-
solved examples of NP problem; iii) the study on HP
model would help us develop optimal algorithms [3],
which sheds light on solving intensively computational
problems in biological branches such as phylogenetics,
RNA pseudoknot [4]; iv) the HP model provides differ-
ent insights into f olding pr oc ess; etc .
The HP model is workable for 2-dimensional (2D) and
3-dimensional (3D) folding. For both cases, each amino
acid, either hydrophobic (H) or polar (P), walks along a
line in 2D lattice or in 3D cube by taking a self-avoided
step, then an H-H connection, which does not come from
sequential step, has minus unity energy [5], and the fold-
ing with minimal energy would be a protein’s native
folding.
Current computing power can afford the studies on
folding in a 2-demensional HP model for very short pro-
tein. Dermaseptin is a subfamily of frog skin active pep-
tide family, which has various antimicrobial activities.
Dermaseptin-J2 was a relatively newly found peptide of
26 amino acids [6].
The number of foldings increases dramatically with
the increase in the length of protein sequence. For exam-
ple, each amino acid would have three directions to go in
self-avoided step in 2D lattice, so the number of three
S. M. YAN, G. WU
Copyright © 2013 SciRes. ENG
79
direction steps for n amino acids would be 3(n-1). In the
case of 26-residue dermaseptin-J2, the possible foldings
are 847,288,609,443 in 2D HP model. Practically, it is
useful to know all the possible foldings of protein. The
aim of this study is to use the 2D HP model to analyze all
possible foldings of dermaseptin-J2 with hope to get in-
sight int o de rmasept in-J2 antibiotic activity.
2. Materials and Methods
2.1. Data
The amino acid sequence of dermaseptin-J2 was obtained
from UniProt [7], and its accession number w as P86636.
The normalized amino acid hydrophobicity index was
obtaine d from SigmaAldri c h we bs i te [8].
2.2. HP Model
The HP model classifies amino acids as either hydro-
phobic or polar, but there is n o indication regarding neu-
tral amino acids. So we use the normalized amino acid
hydrophobicity index [8] to assign amino acids in der-
maseptin-J2 either as hydrophobic or as polar, however,
this assignment is still not sufficient because this norma-
lized amino acid hydrophobicity index is based on the
fact that glycine as zero, thus we have to choose glycine
either as hydrophobic or as polar. This leads to an ami-
no-acid sequence of dermaseptin-J2 to have two HP se-
quences in terms of assigning glycine as hydrophobic or
as polar. Again, the amino acid hydrophobicity is pH
dependent [8], which leads us to consider the assignment
of amino acids of dermaseptin-J2 at two pH levels. Tak-
en two considerations together, one amino-acid s equence
of dermaseptin-J2 has four HP sequences to be operated
in HP model.
There are nine uncertainties in amino-acid sequence of
dermaseptin-J2 [9], i.e. L2I, K4Q, L7I, I10L, K12Q,
L13I, L19I, K23Q, and L25I. So, we have totally 40 HP
sequences for HP model (Table 1), and each one theo-
retically has 847,288,609,443 foldings.
3. Results and Discussion
Currently we have no ability to compute every folding in
proteins longer than 30 amino acids. In this study, the
Lenovo ThinkPat laptop with due CPU of 2 GHz com-
puted 200,000 to 250,000 foldings per second, for a 26-
amino-acid dermaseptin-J2, the computing time was be-
tween 39 a nd 4 9 da y s .
With the normalized amino acid hydrophobicity index
[8], we can find how neutral amino acids affect the HP
sequences (Tab le 1), wh ere nine mutants have no effects
on HP sequences, so their HP foldings are identical im-
plying harmless mutations.
Of 847,288,609,443 possible foldings for each HP se-
Table 1. Amino acids of dermaseptin-J2 in HP sequence s.
Dermaseptin-J2 Classification Sequence
Original Amino acid glwknmlsgigklageaalgavktlv
G=H at pH2 hhhpphhphhhphhhhhhhhhhphhh
G=P at pH2 phhpphhpphpphhphhhhphhphhh
G=H at pH 7 hhhpphhphhhphhhphhhhhhphhh
G = P at pH 7 phhpphhpphpphhpphhhphhphhh
L2I mutant Amino acid giwknmlsgigklageaalgavktlv
G=H at pH2 hhhpphhphhhphhhhhhhhhhphhh
G=P at pH2 phhpphhpphpphhphhhhphhphhh
G=H at pH 7 hhhpphhphhhphhhphhhhhhphhh
G=P at pH 7 phhpphhpphpphhpphhhphhphhh
K4Q mutant Amino acid glwqnmlsgigklageaalgavktlv
G=H at pH2 hhhpphhphhhphhhhhhhhhhphhh
G=P at pH2 phhpphhpphpphhphhhhphhphhh
G=H at pH 7 hhhpphhphhhphhhphhhhhhphhh
G=P at pH 7 phhpphhpphpphhpphhhphhphhh
L7I mutant Amino acid glwknmisgigklageaalgavktlv
G=H at pH2 hhhpphhphhhphhhhhhhhhhphhh
G = P at pH2 phhpphhpphpphhphhhhphhphhh
G=H at pH 7 hhhpphhphhhphhhphhhhhhphhh
G = P at pH 7 phhpphhpphpphhpphhhphhphhh
I10L mutant Amino acid glwknmlsglgklageaalgavktlv
G=H at pH 2 hhhpphhphhhphhhhhhhhhhphhh
G=P at pH 2 phhpphhpphpphhphhhhphhphhh
G=H at pH 7 hhhpphhphhhphhhphhhhhhphhh
G=P at pH 7 phhpphhpphpphhpphhhphhphhh
K12Q mutant Amino acid glwknmlsgigqlageaalgavktlv
G=H at pH 2 hhhpphhphhhphhhhhhhhhhphhh
G=P at pH 2 phhpphhpphpphhphhhhphhphhh
G=H at pH 7 hhhpphhphhhphhhphhhhhhphhh
G=P at pH 7 phhpphhpphpphhpphhhphhphhh
L13I mutant Amino acid glwknmlsgigkiageaalgavktlv
G=H at pH 2 hhhpphhphhhphhhhhhhhhhphhh
G=P at pH 2 phhpphhpphpphhphhhhphhphhh
G=H at pH 7 hhhpphhphhhphhhphhhhhhphhh
G=P at pH 7 phhpphhpphpphhpphhhphhphhh
L19I mutant Amino acid glwknmlsgigklageaaigavktlv
G=H at pH 2 hhhpphhphhhphhhhhhhhhhphhh
G=P at pH 2 phhpphhpphpphhphhhhphhphhh
G=H at pH 7 hhhpphhphhhphhhphhhhhhphhh
G=P at pH 7 phhpphhpphpphhpphhhphhphhh
K23Q mutant Amino acid glwknmlsgigklageaalgavqtlv
G=H at pH 2 hhhpphhphhhphhhhhhhhhhphhh
G=P at pH 2 phhpphhpphpphhphhhhphhphhh
G=H at pH 7 hhhpphhphhhphhhphhhhhhphhh
G=P at pH 7 phhpphhpphpphhpphhhphhphhh
L25I mutant Amino acid glwknmlsgigklageaalgavktiv
G=H at pH 2 hhhpphhphhhphhhhhhhhhhphhh
G=P at pH 2 phhpphhpphpphhphhhhphhphhh
G=H at pH 7 hhhpphhphhhphhhphhhhhhphhh
G=P at pH 7 Phhpphhpphpphhpphhhphhphhh
S. M. YAN, G. WU
Copyright © 2013 SciRes. ENG
80
quence listed in Table 1, it was important to know how
many native states the dermaseptin-J2 had (Table 2),
where dermaseptin-J2 has more than one native state, for
example, 12 native states are found at pH 2 with glycine
assigned as polar, and each native state has the same
amount of minimal energy, –13. The fact that there is
more than one native state suggests the flexibility of
folding mechanisms in dermaseptin-J2.
Figure 1 shows only 8 native states of dermaseptin -J2
at pH 7 with glycine assigned as polar, in order to have a
full picture on the folding process in 2D lattice. In any
folding, it begins from position 1 to position 26, which
can be viewed as a pathway to form a folding. An inter-
esting point is that the native state is chirally symmetric
between the left-hand side and the right-hand side,
namely, the pathways to construct the same folding are
chiral because they cannot be superimposed in mirror
image. The chiral symmetry in Figure 1 suggests that all
foldings of proteins hav e possibly chiral symmetry in 2D
HP lattice. Therefore a protein can find its native state
Table 2. Number of native states of foldings with minimal
energy of dermaseptin-J2 according to different HP con-
versions.
Conversion Native States Minimal Energy
G=H at pH 2 3016
G=P at pH 2 1213
G=H at pH 7 5415
G=P at pH 7 7212
Figure 1. 8 native states of folding under HP conversion of G=H at pH 7. Dotted lines are non-sequential H-H connection,
which is considered as a unit o f nega t iv e energy 1, and their sum is th e m inimal energy 15.
26H
25H
24H
23P 22H
21H
20H 19H
18H
17H 16P
15H
14H 13H
12P11H10H
9H
8P7H6H5P
4P 3H 2H
1H 26H
25H
24H
23P22H
21H
20H19H
18H
17H16P
15H
14H13H
12P 11H 10H
9H
8P 7H6H 5P
4P3H2H
1H
26H25H24H23P
22H 21H 20H
19H18H17H
16P 15H 14H
13H 12P
11H
10H 9H8P
7H
6H
5P4P
3H
2H1H
26H 25H 24H 23P
22H21H20H
19H 18H 17H
16P15H14H
13H12P
11H
10H9H8P
7H
6H
5P 4P
3H
2H 1H
26H
25H
24H
23P22H
21H
20H19H
18H
17H16P
15H
14H13H
12P 11H 10H
9H
8P 7H6H 5P
4P3H2H
1H 26H
25H
24H
23P 22H
21H
20H 19H
18H
17H 16P
15H
14H 13H
12P11H10H
9H
8P7H6H5P
4P 3H 2H
1H
Native state III
Native state INative state II
Native state IV
Native state VINative state V
26H25H24H23P
22H 21H 20H
19H18H17H
16P 15H 14H
13H 12P
11H
10H 9H8P
7H
6H
5P4P
3H
2H1H
26H 25H 24H 23P
22H21H20H
19H 18H17H
16P15H14 H
13H12P
11H
10H9H8P
7H
6H
5P 4P
3H
2H 1H
Native state VIIINative state VII
S. M. YAN, G. WU
Copyright © 2013 SciRes. ENG
81
through different pathways, which minimize the time
spending on searching for the native state.
On the other hand, we notice that the native states and
the minimal energy in Table 2 are different with respect
to pH levels and the conversion of glycine as hydro-
phobic or polar. Figure 2 shows the amino acid sequence
of dermaseptin-J2 and four foldings at pH 2 and ph 7
with glycine assigned as hydrophobic as well as polar.
But these four foldings have the same pathway. Here, we
need to see the non-sequential H-H connections due to
two pH levels and two assignments of glycine. At pH 2
with glycine assigned as hydrophobic (left-hand confi-
guration in middle panel in Figure 2), there are 13 non-
sequential H-H connections: 3H - 6H, 3H - 24H, 6H -
25H, 7H - 10H, 7H - 26H, 10H - 13H, 13H - 26 H, 14H -
17H, 16H - 19H, 17H - 26H, 18H - 21H, 18H - 25H, and
21H - 24H, whose minimal energy is 13 and larger than
that of the native states in Tab le 2. At pH 2 with glycine
assigned as polar (right-hand configuration in middle
panel in Figu re 2), th ere are 13 non-sequential H-H con-
nections, whose minimal energy is 13 and equal to that
of the native states in Table 2. At pH 7 with glycine as-
signed as hydrophobic (left-hand configuration in lower
panel in Figure 2), there are 12 non-sequen tial H-H
connections, whose minimal energy is 12 and larger
than that of the native states in Table 2. At pH 7 with
glycine assigned as polar (right-hand configuration in
lower panel in Figure 2), there are also 12 non-seq uen-
tial H-H connections, whose minimal energy is 12 and
equal to that of the native states in Table 2. Glycines in
dermaseptin-J2 marked by arrows are located at edge of
HP folding, so they generally do not construct H-H con-
nections with internal Hs, we would expect more dra-
matic difference if glycines are located in internal part of
protein.
Now let us look at Table 2 again, where a native state
has different numbers of folding, such as 40 folding con-
firmations at pH 2 with glycine assigned as hydrophobic.
An intriguing question raised here is whether we can
numerically distinguish and rank those folding confirma-
tions? This question comes from such a consideration
that a non-sequential H-H connection only gives a unit of
Figure 2. Dermaseptin-J2 sequence and four HP foldings at pH 2 and pH 7 with glycines assigned as hydrophobic as well as
polar.
26V
25L
24T
23K22V
21A20G
19L 18A
17A16E
15G 14A13L
12K 11G
10I 9G
8S7L
6M 5N
4K3W
2L 1G
26H
25H
24H
23P22H
21H20H
19H 18H
17H16H
15H 14H 13H
12P 11H
10H 9H
8P7H
6H 5P
4P3H
2H 1H
26H
25H
24H
23P22H
21H20P
19H 18H
17H16H
15P 14H 13H
12P 11P
10H 9P
8P7H
6H 5P
4P3H
2H 1P
26H
25H
24H
23P22H
21H20H
19H 18H
17H16P
15H 14H 13H
12P 11H
10H 9H
8P7H
6H 5P
4P3H
2H 1H
26H
25H
24H
23P22H
21H20P
19H 18H
17H16P
15P 14H 13H
12P 11P
10H 9P
8P7H
6H 5P
4P3H
2H 1P
G = H at pH 2
Amino acid s equence
G = P at pH 2
G = P at pH 7G = H at pH 7
S. M. YAN, G. WU
Copyright © 2013 SciRes. ENG
82
minimal energy, however, an H-H connection is com-
posed of amino acids with different hydrophobicity, and
therefore it would be important to further quantify
non-sequential H-H connections with normalized amino
acid hydrophobicity index [9]. Figure 3 shows the use of
the normalized amino acid hydrophobicity index to nu-
merically distinguish and rank 40 folding of native state
with the same minimal energy 16, we thus classify
those 40 foldings of native state with the same minimal
energy –16 into three groups wi th different foldi n gs.
Furthermore, Table 3 lists the native state of folding
with the minimal energy when the glycine is assigned as
hydrophobic or polar at pH 2 or pH 7, including derma-
septin-J2 and its nine mutations. Clearly, those mutants
do not have the effects on the folding with minimal
energy but have effects on their native states to different
degrees. An important observation is the fewer the Hs in
an HP sequence, the more the foldings with minimal
energy. For an antibiotic, if the number of foldings could
be related to the range of antibacterial spectrum, then the
state with minimal energy could be related to the speci-
ficity. On the other hand, the lower specificity would
imply less potency against targets.
Experiments revealed that some dermaseptin has an
inherent propensity to an extended conformation in
aqueous solution and self-assembles into amyloid fibrils
in a reversible pH-controlled fashion [10]. Implication of
this study is one should increase the number of H in or-
der to decrease the minimal energy in a native state.
Practically, we can use a hydrophobic amino acid to re-
place a neutral or hydrophilic amino acid to get a native
state with lower minimal energy if this native state con-
cerns chemical reactions.
Finally, the results suggest the possible ways to modify
dermaseptin-J2 that we can either modify dermaseptin-J2
via replacing polar amino acids with hydrophobic amino
acids or modify dermaseptin-J2 via replacing amino acids
according to the normalized amino acid hydrophobicity
index. This is meaningful because the antibacterial activ-
ity of dermaseptin depends markedly on a threshold
number of hydrophobic residues to be present on both
extremities of t he he l ix [11].
Figure 3. Native states under G=H at pH 2 with normalized amino acid hydrophobici ty index. All has a minimal ene rgy –16,
which is the sum of dotted lines and different sum of hydrophobicity index of H-H connections. Left-hand site: HP sequence;
Right-hand site: Dermaseptin-J2 sequence.
26H25H24H23P
22H21H
20H 19H18H 17H
16H15H14H13H
12P 11H10H9H8P
7H
6H 5P
4P3H2H1 H
26H25H
24H23P
22H 21H20H
19H 18H
17H
16H15H14H13H
12P 11H10H9H8P
7H
6H 5P
4P3H
2H1H 26V25L
24T23K
22V21A 20G
19L 18A
17A
16E15G14A13L
12K 11G10I9G8S
7L
6M 5N
4K3W
2L1G
26H25H24H
23P 22H
21H 20H
19H 18H
17H
16H15H14H13H
12P 11H10H9H8P
7H
6H 5P
4P3H
2H1H
26V25L24T
23K 22V
21A 20G
19L 18A
17A
16E15G14A13L
12K 11G10I9G8S
7L
6M 5N
4K3W
2L1G
Native state = 1471
HP sequence
26V25L24T23K
22V21A
20G 19L 18A 17A
16E15G14A13L
12K 11G10I9G8S
7L
6M 5N
4K3W2L1G
Amino acid sequence
Native state = 1664
Native state = 1722
S. M. YAN, G. WU
Copyright © 2013 SciRes. ENG
83
Table 3. Native states classified according to norm alized amino acid hydrophobi city index.
Group State Nu mb e r Sum of hydrophobicity index of H-H connections (native states)
Original L2I K4Q L7I I10L K12Q L13I L19I K23Q L25I
G=H at pH 2 12 1471 1471 1471 1471 1471 1471 1471 1471 1471 1471
6 1664 1664 1664 1664 1664 1664 1664 1664 1664 1664
12 1722 1722 1722 1722 1722 1722 1722 1722 1722 1722
G=P at pH 2 12 1816 1816 1816 1816 1816 1816 1816 1816 1816 1816
G=H at pH 7 6 1393 1397 1393 1395 1391 1391 1393 1397 1393 1393
6 1548 1552 1548 1550 1544 1544 1550 1552 1548 1548
6 1553 1557 1553 1557 1551 1551 1553 1557 1553 1553
6 1566 1568 1566 1568 1564 1564 1566 1570 1566 1570
6 1576 1580 1576 1578 1572 1572 1576 1580 1576 1578
6 1708 1712 1708 1712 1704 1704 1710 1712 1708 1708
6 1721 1723 1721 1723 1717 1717 1723 1725 1721 1725
6 1726 1728 1726 1730 1724 1724 1726 1730 1726 1730
6 1881 1883 1881 1885 1877 1877 1883 1885 1881 1885
G=P at pH 7 12 1663 1663 1663 1667 1659 1659 1667 1663 1663 1667
6 1686 1688 1686 1690 1682 1682 1690 1686 1686 1690
12 1723 1725 1723 1727 1719 1719 1727 1725 1723 1727
12 1803 1805 1803 1807 1799 1799 1807 1807 1803 1805
12 1810 1810 1810 1814 1806 1806 1814 1814 1810 1814
6 1833 1835 1833 1837 1829 1829 1837 1837 1833 1837
12 1922 1924 1922 1926 1918 1918 1926 1926 1922 1926
The dermaseptin super-family encompasses a wide va-
riety of structural motifs, and combined approaches have
been used to elucidate their antimicrobial effects based
on biophysical and cellular biology methods [12]. This
study helps to understand dermaseptin folding in terms of
HP model.
4. Acknowledgements
This study was partly supported by Guangxi Science
Foundation (12237022 and 2013GXNSFDA019007).
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