The networks of copper metabolism |
| Copper transport at the cell surface and the delivery of copper into intracellular compartments depend on a series of membrane proteins and small soluble peptides, the copper chaperones. Many integral membrane proteins such as Fre(Ferric ion reductase enzyme) and CTR(Copper transporter protein) form the channels to assist the permeation of the ions through the plasm membranes. The chaperones, for example, ATX1(Anti-oxidant 1), COX17(Cytochrome oxidase 17 copper chaperone) and LYS7(Lysine biosynthesis 7) specially bind and hand copper ions to their target proteins. All these proteins comprise a functionally integrated system for maintaining cellular copper homeostasis. |
 |
| Figure 1. Contents of hydrophilic (a, b) and hydrophobic (c, d) amino acids of proteins in DCCP_3D (a, c) and the same amount of general proteins selected from PDB (b, d) |
| Table 1. The statistical features of hydrophilic and hydrophobic amino acids contents of copper-chelating proteins and general proteins |
| Table 2. Secondary structure prediction accuracies of copper-chelating proteins in DCCP_3D based on five widely-used secondary-structure-predicting software |
| Table 3. SCOP classifications of copper-chelating proteins in DCCP_3D and general proteins selected from PDB |
| Table 4. Calculated binding-energies of the proteins involved in the transportation of copper ions from outside to inside of cell |
| Figure 1. Contents of hydrophilic (a, b) and hydrophobic (c, d) amino acids of proteins in DCCP_3D (a, c) and the same amount of general proteins selected from PDB (b, d) [Top] |
|
| Table 1. The statistical features of hydrophilic and hydrophobic amino acids contents of copper-chelating proteins and general proteins [Top] |
| Statistical
parameters
| Hydrophilic
amino acids content
| Hydrophobic
amino acids content
|
|
|
Copper-chelating proteins |
General proteins |
Copper-chelating proteins |
General proteins |
| Average |
0.4395 |
0.4769 |
0.4676 |
0.4595 |
| Standard deviation |
0.0627 |
0.0627 |
0.0592 |
0.0558 |
| Skew |
-0.9117 |
-0.1816 |
0.2639 |
0.0219 |
|
|
| Table 2. Secondary structure prediction accuracies of copper-chelating proteins in DCCP_3D based on five widely-used secondary-structure-predicting software [Top] |
| |
| Copper-chelating proteins |
|
Criterion
1*
|
Criterion
2*
|
Criterion
3*
|
|
|
Average
accuracy for General proteins |
| PHD |
| PROF |
| NNPREDICT |
| PSIPRED |
| JPRED |
|
| 74.82 |
74.83 |
75.82 |
| 76.92 |
76.94 |
77.73 |
| 60.60 |
60.60 |
61.69 |
| 79.13 |
79.13 |
79.90 |
| 74.54 |
74.56 |
75.80 |
|
| 71.9-73.5 |
| >78 |
| >65 |
| 78-80.6 |
| 72.9-74.8 |
|
|
* Conversion criteria from 8 types to 3 types
- H, G, I--H£» E, B--E£» other--C.
- H, G--H£» E, B--E£» other--C.
- H, G--H£» E--E£» other--C.
|
| Table 3. SCOP classifications of copper-chelating proteins in DCCP_3D and general proteins selected from PDB [Top] |
| SCOP classification£¨domain£© |
Copper-chelating proteins |
General proteins |
|
All alpha proteins
|
182
|
159
|
|
All beta protein
|
913
|
505
|
|
Alpha and beta
proteins (a/b)
|
103
|
346
|
|
Alpha and beta
proteins (a+b)
|
225
|
250
|
|
Multi-domain
proteins (alpha and beta)
|
8
|
24
|
|
Membrane and
cell surface proteins and peptides
|
112
|
14
|
|
Small proteins
|
45
|
28
|
|
Coiled coil
proteins
|
0
|
19
|
|
Low resolution
protein structures
|
45
|
1
|
|
Peptides
|
1
|
0
|
|
Designed proteins
|
0
|
0
|
|
| Table 4. Calculated binding-energies of the proteins involved in the transportation of copper ions from outside to inside of cell [Top] |
| Protein Name |
PDB ID
|
pH
|
Resolution
|
Binding Energy
|
Cellular Localization
|
| Peptidylglycine |
3PHM
|
5.5
|
2.10
|
401.16
|
Excreted
|
| Peptidylglycine |
1OPM
|
5.5
|
2.10
|
403.71
|
Excreted
|
| Azurin |
1A4A
|
6.5
|
1.89
|
608.40
|
Periplasm
|
| Auracyanin |
1QHQ
|
7.0
|
1.55
|
713.61
|
Peripheral
membrane
|
| Pseudoazurin |
3PAZ
|
7.0
|
1.73
|
713.73
|
Periplasm
|
| Dissimilatory nitrite reductase |
1HAW
|
8.5
|
1.90
|
717.57
|
Periplasm
|
| Pseudoazurin |
4PAZ
|
7.0
|
1.76
|
723.44
|
Periplasm
|
| Azurin ii |
1DZO
|
6.0
|
1.75
|
723.62
|
Periplasm
|
| Azurin |
1JZF
|
7.0
|
1.50
|
725.10
|
Periplasm
|
| Azurin ii |
1DYZ
|
6.0
|
1.75
|
726.90
|
Periplasm
|
| Plastocyanin |
1BYO
|
5.5
|
2.00
|
738.37
|
Chloroplast
|
| Plastocyanin |
1BYP
|
7.0
|
1.75
|
748.84
|
Chloroplast
|
| Superoxide dismutase |
1SPD
|
-
|
2.40
|
1170.61
|
Cytoplasm
|
| Cu, Zn superoxide dismutase |
1XSO
|
-
|
1.49
|
1322.56
|
Cytoplasm
|
|
