Table 2 Differentially expressed proteins identified from 2D-DIGE profiling of neuroma and control saphenous nerve samples.
Spot no. | Protein name | Accession no. | % Cov | MOWSE score | Est. mass | Est. pI | Pred. mass | Pred. pI | Av. ratio (2 and 3 week neuroma vs. control) | P-value (t-test) | Function |
|---|---|---|---|---|---|---|---|---|---|---|---|
Structural proteins | |||||||||||
1171 | Beta-actin | IPI00110850 | 8 | 107/35 | 46073 | 5.1 | 42051 | 5.29 | -1.84 | 3.00E-05 | Major cytoskeletal protein involved in cell motility |
1173 | Beta-actin | IPI00110850 | 33 | 190/35 | 40780 | 5.2 | 42051 | 5.29 | -1.9 | 0.00095 | Major cytoskeletal protein involved in cell motility |
1234 | Macrophage capping protein | IPI00136906 | 9 | 154/35 | 39216 | 6.7 | 39241 | 6.73 | 2.64 | 2.90E-09 | Calcium-sensitive protein which reversibly blocks barbed ends of actin filaments. |
553 | Plastin-2 | IPI00118892 | 11 | 103/35 | 69112 | 5.1 | 70019 | 4.96 | 1.75 | 1.10E-05 | Actin-bundling protein |
638 | Plastin-2 | IPI00118892 | 4 | 36/35 | 66167 | 5.2 | 70019 | 4.96 | 4.03 | 5.00E-07 | Actin-bundling protein |
857 | Tubulin alpha-1 | IPI00110753 | 10 | 66/35 | 57828 | 5.0 | 50788 | 4.94 | -2.59 | 3.60E-05 | Major microtubule protein |
902 | Tubulin, alpha 6 | IPI00403810 | 44 | 100/64* | 56122 | 5.0 | 49877 | 4.96 | -3.29 | 4.00E-06 | Major microtubule protein |
912 | Tubulin alpha 2 | IPI00117348 | 23 | 122/64* | 55894 | 5.0 | 50120 | 4.94 | -3.77 | 4.40E-07 | Major microtubule protein |
966 | Tubulin, beta 5 | IPI00117352 | 16 | 708/35 | 54467 | 5,.0 | 49671 | 4.52 | -2.41 | 3.00E-05 | Major microtubule protein |
973 | Tubulin beta-2C | IPI00169463 | 7 | 365/35 | 53804 | 4.6 | 49832 | 4.52 | 2.47 | 1.70E-06 | Major microtubule protein |
196 | Neurofilament triplet M | IPI00323800 | 24 | 100/64* | 96041 | 4.8 | 95941 | 4.76 | -4.69 | 8.20E-07 | Maintenance of neuronal caliber |
636 | Neurofilament triplet L | IPI00169702 | 49 | 630/35 | 66257 | 4.7 | 61378 | 4.3 | -5.93 | 3.80E-06 | Maintenance of neuronal caliber |
939 | Vimentin | IPI00227299 | 25 | 113/35 | 55515 | 5.2 | 53557 | 4.77 | 1.76 | 0.00039 | Class-III intermediate filament protein |
997 | Vimentin | IPI00227299 | 21 | 191/35 | 52933 | 4.8 | 53557 | 5.06 | 2.19 | 7.20E-07 | Class-III intermediate filament protein |
1008 | Vimentin | IPI00227299 | 28 | 195/35 | 52431 | 5.1 | 53557 | 5.06 | 3.05 | 1.30E-07 | Class-III intermediate filament protein |
1108 | Vimentin | IPI00227299 | 27 | 349/35 | 48584 | 4.7 | 53557 | 5.06 | -2.67 | 0.00018 | Class-III intermediate filament protein |
1112 | Vimentin | IPI00227299 | 20 | 180/35 | 48123 | 5.0 | 53557 | 5.06 | 5.11 | 8.90E-09 | Class-III intermediate filament protein |
839 | Peripherin (isoform 5g) | IPI00129527 | 9 | 100/35 | 58302 | 5.5 | 54268 | 5.22 | -9.58 | 2.20E-06 | Class-III neuronal intermediate filament protein |
858 | Peripherin (isoform 5g) | IPI00129527 | 15 | 363/35 | 58064 | 5.4 | 54268 | 5.22 | -3.44 | 5.50E-07 | Class-III neuronal intermediate filament protein |
Metabolic enzymes | |||||||||||
734 | Aspartyl-tRNA synthetase | IPI00122743 | 21 | 70/64* | 62153 | 5.0 | 57117 | 6.06 | 1.84 | 0.00046 | Protein biosynthesis |
907 | Aspartyl-tRNA synthetase | IPI00122743 | 28 | 66/64* | 56122 | 6.5 | 57117 | 6.06 | 2.87 | 2.30E-06 | Protein biosynthesis |
817 | D-3-phosphoglycerate dehydrogenase | IPI00225961 | 8 | 111/35 | 59666 | 6.2 | 56455 | 6.5 | 2.5 | 3.90E-06 | Glycolytic enzyme |
1031 | Alpha-enolase | IPI00462072 | 33 | 526/35 | 51162 | 6.8 | 47010 | 6.37 | 1.78 | 0.00056 | Glycolytic enzyme and other functions |
1038 | Alpha-enolase | IPI00462072 | 10 | 40/35 | 50954 | 6.9 | 47010 | 6.37 | 2.06 | 1.20E-05 | Glycolytic enzyme and other functions |
1039 | Alpha-enolase | IPI00462072 | 56 | 369/35 | 51093 | 7.0 | 47010 | 6.37 | 1.9 | 3.10E-07 | Glycolytic enzyme and other functions |
1049 | Gamma-enolase | IPI00331704 | 15 | 90/35 | 50677 | 5.8 | 47166 | 4.73 | 2.08 | 3.80E-06 | Has neurotrophic and neuroprotective properties |
807 | Pyruvate kinase M2 | IPI00407130 | 4 | 55/35 | 59910 | 7.4 | 58004 | 7.52 | -1.85 | 5.20E-06 | Glycolytic enzyme |
965 | Cytosolic nonspecific dipeptidase | IPI00315879 | 6 | 72/35 | 54467 | 4.9 | 52768 | 5.38 | -2.62 | 3.70E-05 | Non-specific dipeptidase activity |
1359 | Lactate dehydrogenase B chain | IPI00229510 | 22 | 128/35 | 37311 | 5.8 | 36442 | 5.7 | -2.79 | 3.60E-06 | Glycolytic enzyme |
1567 | Carbonic anhydrase 3 | IPI00221890 | 62 | 307/35 | 26265 | 7.5 | 29235 | 6.89 | -2.15 | 8.40E-06 | Reversible hydration of carbon dioxide |
1570 | Carbonic anhydrase 3 | IPI00221890 | 31 | 413/35 | 26229 | 7.6 | 29235 | 6.89 | -2.54 | 2.70E-05 | Reversible hydration of carbon dioxide |
770 | Pyruvate kinase M2 | IPI00407130 | 10 | 148/35 | 60897 | 7.5 | 58536 | 7.18 | 2.19 | 9.40E-05 | Glycolytic enzyme |
801 | Pyruvate kinase M2 | IPI00407130 | 18 | 218/35 | 59910 | 7.3 | 58004 | 7.52 | -2.21 | 3.30E-06 | Glycolytic enzyme |
958 | ATP synthase subunit beta, mitochondrial precursor | IPI00468481 | 35 | 266/35 | 54616 | 4.9 | 56300 | 5.19 | -4.82 | 7.80E-07 | Produces ATP from ADP |
1011 | ATP synthase subunit beta, mitochondrial precursor | IPI00468481 | 6 | 787/35 | 52005 | 5.0 | 56300 | 5.19 | 2.08 | 3.30E-06 | Produces ATP from ADP |
1143 | Creatine kinase B-type | IPI00136703 | 30 | 337/35 | 47023 | 5.5 | 42714 | 5.42 | -1.89 | 0.00036 | Transfer of phosphate between ATP and phosphogens |
1189 | Creatine kinase B-type | IPI00136703 | 32 | 244/35 | 45388 | 4.8 | 42714 | 5.42 | 4.71 | 5.00E-08 | Transfer of phosphate between ATP and phosphogens |
Redox regulation | |||||||||||
1666 | Protein DJ-1 | IPI00117264 | 25 | 68/35 | 20021 | 6.3 | 20021 | 6.32 | 9.91 | 1.60E-09 | Positive regulator of androgen receptor-dependent transcription, protects neurons against oxidative stress and cell death |
1618 | Peroxiredoxin 1 | IPI00121788 | 43 | 75/64* | 23048 | 7.3 | 22177 | 8.26 | 1.93 | 0.00022 | Involves in redox regulation of the cell |
1647 | Peroxiredoxin 1 | IPI00121788 | 46 | 211/35 | 22117 | 8.3 | 22177 | 8.26 | 3.52 | 1.40E-06 | Involves in redox regulation of the cell |
1678 | Peroxiredoxin 2 | IPI00117910 | 30 | 88/35 | 19551 | 5.1 | 21648 | 5.2 | 1.79 | 0.002 | Involves in redox regulation of the cell |
Cell signalling | |||||||||||
789 | Rab GDP dissociation inhibitor alpha | IPI00323179 | 24 | 290/35 | 60731 | 4.9 | 50522 | 4.7 | -2.01 | 1.00E-05 | Regulates the GDP/GTP exchange reaction of Rab |
1430 | Annexin A1 | IPI00230395 | 20 | 87/35 | 36121 | 4.9 | 35752 | 4.83 | 1.78 | 1.30E-05 | Promotes membrane fusion and is involved in exocytosis |
1454 | Annexin A4 | IPI00353727 | 44 | 136/35 | 32168 | 5.4 | 36121 | 5.43 | 2.4 | 1.60E-08 | Promotes membrane fusion and is involved in exocytosis |
Protein folding/chaperone function | |||||||||||
768 | Protein disulfide isomerase associated A3 | IPI00230108 | 8 | 103/35 | 60897 | 5.9 | 57099 | 5.88 | 2.03 | 2.60E-05 | Protein folding and electron transport |
820 | Protein disulfide isomerase associated A3 | IPI00230108 | 35 | 525/35 | 57099 | 5.9 | 57099 | 5.88 | 2.51 | 9.00E-08 | Protein folding and electron transport |
824 | Protein disulfide isomerase associated A3 | IPI00230108 | 5 | 67/35 | 59504 | 5.9 | 57099 | 5.88 | 1.91 | 0.00063 | Protein folding and electron transport |
825 | Prolyl 4-hydroxylase, beta polypeptide | IPI00122815 | 30 | 357/35 | 59343 | 4.8 | 57422 | 4.77 | 2.24 | 7.10E-07 | Catalyzes the rearrangement of -S-S- bonds in proteins |
778 | Calreticulin precursor | IPI00123639 | 12 | 159/35 | 60237 | 4.4 | 47995 | 4.09 | 2.67 | 8.10E-07 | Protein folding |
862 | T-complex protein 1 subunit beta | IPI00320217 | 6 | 62/35 | 57907 | 6.5 | 57347 | 6.37 | 2.22 | 0.00031 | Molecular chaperone, assist the folding of proteins upon ATP hydrolysis |
Others | |||||||||||
1572 | Calpain small subunit 1 | IPI00130992 | 9 | 85/35 | 25980 | 5.3 | 28464 | 5.34 | 4.83 | 4.30E-05 | Catalyzes limited proteolysis of substrates involved in cytoskeletal remodelling and signal transduction. |
1283 | Guanine nucleotide-binding protein G(o) subunit alpha 2 | IPI00115546 | 4 | 86/35 | 41603 | 5.8 | 39906 | 5.69 | -2.3 | 8.50E-05 | Modulator or transducer in various transmembrane signalling systems |
1415 | Mimecan precursor | IPI00120848 | 11 | 153/35 | 34668 | 5.9 | 34012 | 5.52 | -1.8 | 0.0032 | Induces bone formation in conjunction with TGF-beta-1 or TGF-beta-2 |
1821 | Gamma-synuclein | IPI00271440 | 65 | 247/35 | 13152 | 4.7 | 13160 | 4.68 | -1.87 | 0.00066 | Plays a role in neurofilament network integrity |
1598 | Ubiquitin C-terminal hydrolase isozyme L1 | IPI00313962 | 45 | 279/35 | 24437 | 5.2 | 24839 | 5.14 | -2 | 3.70E-05 | Ubiquitin-protein hydrolase |