Breese, 1974; p17 - Rosema, 1988; p18 - Welling et al., 1985; p19 - Parker et al., 1986; p20 -
Cowan and Whittaker, 1990; p21 - Manavalan and Ponnuswamy, 1978; p22 - Fauchere and
Pliska, 1983; p23 - Rao and Argos, 1986; p24 - Wilson et al., 1981), partition coefficients (p13 -
Abraham and Leo, 1987) and energies (p15 - Guy, 1985), inter-residue contact energies (p16 -
Miyazawa and Jernigen, 1985). The data are presented in Table 1.
Twenty Amino Acids: Investigated Properties
Table 1
|
Name_____ |
L |
pɪ |
p2_ |
p3__ |
p4 |
p5 |
p6 |
p7 |
p8 |
p9 |
p10 |
pn |
p12 |
p13 |
p14 |
p15 |
p16 |
p17 |
p18 |
p19 |
p20 |
p21___ |
p22 |
p23 |
p24 |
|
Alanine |
A |
0.62 |
1.8 |
-0.17 |
0.11 |
47 |
-0.50 |
0.20 |
0.62 |
0.74 |
0.30 |
1.60 |
-0.40 |
0.44 |
0.61 |
0.10 |
5.33 |
0.39 |
1.15 |
2.10 |
0.35 |
12.97 |
0.31 |
1.36 |
-0.30 |
|
Arginine |
R |
0.00 |
-4.5 |
-0.81 |
2.58 |
-26 |
3.00 |
1.40 |
-2.53 |
0.64 |
-1.40 |
-12.3 |
-0.59 |
-2.42 |
0.69 |
1.91 |
4.18 |
-3.95 |
0.58 |
4.20 |
-1.50 |
11.72 |
-1.01 |
0.15 |
-1.10 |
|
Asparagine |
N |
0.24 |
-3.5 |
-0.42 |
2.05 |
-41 |
0.20 |
-0.50 |
-0.78 |
0.63 |
-0.50 |
-4.80 |
-0.92 |
-1.32 |
0.89 |
0.48 |
3.71 |
-1.91 |
-0.77 |
7.00 |
-0.99 |
11.42 |
-0.60 |
0.33 |
-0.20 |
|
Aspartate |
D |
0.03 |
-3.5 |
-1.23 |
3.49 |
-18 |
3.00 |
-3.10 |
-0.90 |
0.62 |
-0.60 |
-9.20 |
-1.31 |
-0.31 |
0.61 |
0.78 |
3.59 |
-3.81 |
0.65 |
10.0 |
-2.15 |
10.85 |
-0.77 |
0.11 |
-1.40 |
|
Cysteine |
C |
0.68 |
2.5 |
0.24 |
-0.13 |
52 |
-1.00 |
4.10 |
0.29 |
0.91 |
0.90 |
2.00 |
0.17 |
0.58 |
0.36 |
-1.42 |
7.93 |
0.25 |
-1.20 |
1.40 |
0.76 |
14.63 |
1.54 |
1.27 |
6.30 |
|
Glutamine |
Q |
0.25 |
-3.5 |
-0.58 |
2.36 |
-18 |
0.20 |
-2.80 |
-0.85 |
0.62 |
-0.70 |
-4.10 |
-0.91 |
-0.71 |
0.97 |
0.95 |
3.87 |
-1.30 |
-0.11 |
6.00 |
-0.93 |
11.76 |
-0.22 |
0.33 |
-0.20 |
|
Glutamate |
E |
0.04 |
-3.5 |
-2.02 |
2.68 |
8 |
3.00 |
-1.80 |
-0.74 |
0.62 |
-0.70 |
-8.20 |
-1.22 |
-0.34 |
0.51 |
0.83 |
3.65 |
-2.91 |
-0.71 |
7.80 |
-1.95 |
11.89 |
-0.64 |
0.25 |
0.00 |
|
Glycine |
G |
0.50 |
-0.4 |
-0.01 |
0.74 |
0 |
0.00 |
0.00 |
0.48 |
0.72 |
0.30 |
1.00 |
-0.67 |
0.00 |
0.81 |
0.33 |
4.48 |
0.00 |
-1.84 |
5.70 |
0.00 |
12.43 |
0.00 |
1.09 |
1.20 |
|
Histidine |
H |
0.16 |
-3.2 |
-0.96 |
2.06 |
-42 |
-0.50 |
0.50 |
-0.40 |
0.78 |
-0.10 |
-3.00 |
-0.64 |
-0.01 |
0.69 |
-0.50 |
5.10 |
-0.64 |
3.12 |
2.10 |
-0.65 |
12.16 |
0.13 |
0.68 |
-1.30 |
|
Isoleucine |
I_ |
0.94 |
4.5 |
0.31 |
-0.6 |
100 |
-1.80 |
4.80 |
1.38 |
0.88 |
0.70 |
3.10 |
1.25 |
2.46 |
-1.45 |
-1.13 |
8.83 |
1.82 |
-2.92 |
-8.00 |
1.83 |
15.67 |
1.80 |
1.44 |
4.30 |
|
Leucine |
L |
0.94 |
3.8 |
0.56 |
-0.55 |
100 |
-1.80 |
5.70 |
1.06 |
0.85 |
0.50 |
2.80 |
1.22 |
2.46 |
-1.65 |
-1.18 |
8.47 |
1.82 |
0.75 |
-9.20 |
1.80 |
14.90 |
1.70 |
1.47 |
6.60 |
|
Lysine______ |
K |
0.28 |
-3.9 |
-0.99 |
2.71 |
-37 |
3.00 |
-3.10 |
-1.50 |
0.52 |
-1.80 |
-8.80 |
-0.67 |
-2.45 |
0.46 |
1.40 |
2.95 |
-2.77 |
2.06 |
5.70 |
-1.54 |
11.36 |
-0.99 |
0.09 |
-3.60 |
|
Methionine |
M |
0.74 |
1.9 |
0.23 |
-0.1 |
74 |
-1.30 |
4.20 |
0.64 |
0.85 |
0.40 |
3.40 |
1.02 |
1.10 |
-0.66 |
-1.59 |
8.95 |
0.96 |
-3.85 |
-4.20 |
1.10 |
14.39 |
1.23 |
1.42 |
2.50 |
|
Phenylalanine |
F |
1.00 |
2.8 |
1.13 |
-0.32 |
92 |
-2.50 |
4.40 |
1.19 |
0.88 |
0.50 |
3.70 |
1.92 |
2.54 |
-1.52 |
-2.12 |
9.03 |
2.27 |
-1.41 |
-9.20 |
1.69 |
14.00 |
1.79 |
1.57 |
7.50 |
|
Proline_______ |
P |
0.71 |
-1.6 |
-0.45 |
2.23 |
-46 |
0.00 |
-2.20 |
0.12 |
0.64 |
-0.30 |
-0.20 |
0.49 |
1.29 |
-0.17 |
0.73 |
3.87 |
0.99 |
-0.53 |
2.10 |
0.84 |
11.37 |
0.72 |
0.54 |
2.20 |
|
Serine_______ |
S_ |
0.36 |
-0.8 |
-0.13 |
0.84 |
-7 |
0.30 |
-0.50 |
-0.18 |
0.66 |
-0.10 |
0.60 |
0.55 |
-0.84 |
0.42 |
0.52 |
4.09 |
-1.24 |
-0.26 |
6.50 |
-0.63 |
11.23 |
-0.04 |
0.97 |
-0.60 |
|
Threonine |
T |
0.45 |
-0.7 |
-0.14 |
0.52 |
13 |
-0.40 |
-1.90 |
-0.05 |
0.70 |
-0.20 |
1.20 |
-0.28 |
-0.41 |
0.29 |
0.07 |
4.49 |
-1.00 |
-0.45 |
5.20 |
-0.27 |
11.69 |
0.26 |
1.08 |
-2.20 |
|
Tryptophan |
W |
0.88 |
-0.9 |
1.85 |
0.3 |
84 |
-3.40 |
1.00 |
0.81 |
0.85 |
0.30 |
1.90 |
0.50 |
2.56 |
-1.20 |
-0.51 |
7.66 |
2.13 |
-1.14 |
-10.0 |
1.35 |
13.93 |
2.25 |
1.00 |
7.90 |
|
Tyrosine |
Y |
0.88 |
-1.3 |
0.94 |
0.68 |
49 |
-2.30 |
3.20 |
0.26 |
0.76 |
-0.40 |
-0.70 |
1.67 |
1.63 |
-1.43 |
-0.21 |
5.89 |
1.47 |
0.13 |
-1.90 |
0.39 |
13.42 |
0.96 |
0.83 |
7.10 |
|
Valine______ |
V |
0.83 |
4.2 |
-0.07 |
-0.31 |
79 |
-1.50 |
4.70 |
1.08 |
0.86 |
0.60 |
2.60 |
0.91 |
1.73 |
-0.75 |
-1.27 |
7.63 |
1.30 |
-0.13 |
-3.70 |
1.32 |
15.71 |
1.22 |
1.37 |
5.90 |
Collagen Type I
The alpha 1 (α1) and alpha 2 (α2) chains of collagen type I (CTI) of five species were
collected from the Nat. Center for Biotechnology Information [ http://www.ncbi.nlm.nih.gov/]
and have been investigated: Rattus norvegicus (Orjel at al., 2006); Bos taurus (Fietzek et al.,
1975; Shirai et al., 1998); Danio rerio (Dubois et al., 2002; Howden, 2007); Canis lupus
(Lowe et al., 2003); and Homo sapiens (Simon et al., 1997; Strausberg et al., 2002).
Method of Analysis
A multivariate analysis on collagen type I amino acids properties were performed by
using Principal Component Analysis (PCA) technique. A similarity analysis by using the
Oliver algorithm implemented in PHP (Hypertext Preprocessor) was applied on collagen type
I chains. The investigation of the minimal number of characters needed to replace, insert or
delete in order to transform one amino acid chain into another has also been performed in
order to analyze the similarity between and within specie.
RESULTS AND DISCUSSIONS
Principal Component on Amino Acids Properties
The following results were obtained using PCA of amino acids properties:
÷ With five exceptions the hydrophobic or hydrophilic character measured on different
scales were close to each other in terms of means and standard errors. The exceptions
were: p5 (Sereda et al., 1994), p11 (Engelman et al., 1986), p19 (Parker et al., 1986), p21
(Manavalan and Ponnuswamy, 1978), and p24 (Wilson et al., 1981).
÷ The correlation matrix on investigated properties identified a very good correlation (≥
0.95) between the following pairs of hydrophobicity: p1 (Black et al., 1991) - p17 (Rosema,
312
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