1. (1) David Liu would like to know the possible functional sites of his new protein (from hw 6).
Please help him to identify any biologically significant sites or patterns.
(2) Please help him to analyze the enzymatic digestion by trypsin and endoproteinase Glu-C.
(3) Calculate the molecular weight of this protein.
2. Pick up one bioinformatic site and prepare to introduce to your classmates on 1/8.
Solution:
1. The polypeptide sequence:
MLECNELIPLFYETCPAGENICYEMFMVATPKVPCERGCIDVCPESSLIV
KYVCCNTDRCQ*
(1)Biologically Significant Sites or Patterns:
(2)Enzymatic Digestion:
(i)Trypsin
(ii)Endoproteinase Glu-C
(3)Molecular Weight:
ProSite Search Result
PS00005 (PDOC00005) Protein kinase C phosphorylation site.
Pattern: [ST]-x-[RK].
Matching residues 30-32: MFMVA TPK VPCER
Matching residues 57-59: YVCCN TDR CQ
PS00272 (PDOC00245) Snake toxins signature.
Pattern: G-C-x(1,3)-C-P-x(8,10)-C-C-x(2)-[PDEN].
Matching residues 38-58: VPCER GCIDVCPESSLIVKYVCCNTD RCQ
Enzymatic cleavage of
1 * 10 * 20 * 30 * 40 * 50
1 MLECNELIPLFYETCPAGENICYEMFMVATPKVPCERGCIDVCPESSLIV
51 KYVCCNTDRCQ
Cleavage at residues:
K/ (Hydrolysis on the C-terminal side of K)
R/ (Hydrolysis on the C-terminal side of R)
Average mass
Fragment Residues Mass B&B
1 1 - 32 -/M...K/V 3701.41 -265
1 - 2 1 - 37 -/M...R/G 4286.11 -212
1 - 3 1 - 51 -/M...K/Y 5730.85 -198
1 - 4 1 - 59 -/M...R/C 6685.93 -154
1 - 5 1 - 61 -/M...Q/- 6917.21 -127
2 33 - 37 K/V...R/G 602.71 128
2 - 3 33 - 51 K/V...K/Y 2047.45 -85
2 - 4 33 - 59 K/V...R/C 3002.53 -22
2 - 5 33 - 61 K/V...Q/- 3233.81 24
3 38 - 51 R/G...K/Y 1462.75 -162
3 - 4 38 - 59 R/G...R/C 2417.84 -56
3 - 5 38 - 61 R/G...Q/- 2649.11 3
4 52 - 59 K/Y...R/C 973.10 127
4 - 5 52 - 61 K/Y...Q/- 1204.37 235
5 60 - 61 R/CQ/- 249.29 665
Sorted according to mass
Fragment Residues Mass B&B
5 60 - 61 R/CQ/- 249.29 665
2 33 - 37 K/V...R/G 602.71 128
4 52 - 59 K/Y...R/C 973.10 127
4 - 5 52 - 61 K/Y...Q/- 1204.37 235
3 38 - 51 R/G...K/Y 1462.75 -162
2 - 3 33 - 51 K/V...K/Y 2047.45 -85
3 - 4 38 - 59 R/G...R/C 2417.84 -56
3 - 5 38 - 61 R/G...Q/- 2649.11 3
2 - 4 33 - 59 K/V...R/C 3002.53 -22
2 - 5 33 - 61 K/V...Q/- 3233.81 24
1 1 - 32 -/M...K/V 3701.41 -265
1 - 2 1 - 37 -/M...R/G 4286.11 -212
1 - 3 1 - 51 -/M...K/Y 5730.85 -198
1 - 4 1 - 59 -/M...R/C 6685.93 -154
1 - 5 1 - 61 -/M...Q/- 6917.21 -127
Enzymatic cleavage of
1 * 10 * 20 * 30 * 40 * 50
1 MLECNELIPLFYETCPAGENICYEMFMVATPKVPCERGCIDVCPESSLIV
51 KYVCCNTDRCQ
Cleavage at residues:
E/ (Hydrolysis on the C-terminal side of E)
Average mass
Fragment Residues Mass B&B
1 1 - 3 -/M...E/C 391.49 -600
1 - 2 1 - 6 -/M...E/L 737.85 -6
1 - 3 1 - 13 -/M...E/T 1613.92 -569
1 - 4 1 - 19 -/M...E/N 2172.53 -262
1 - 5 1 - 24 -/M...E/M 2795.23 -254
1 - 6 1 - 36 -/M...E/R 4129.92 -237
1 - 7 1 - 45 -/M...E/S 5103.06 -168
1 - 8 1 - 61 -/M...Q/- 6917.21 -127
2 4 - 6 E/C...E/L 364.38 586
2 - 3 4 - 13 E/C...E/T 1240.44 -560
2 - 4 4 - 19 E/C...E/N 1799.06 -199
2 - 5 4 - 24 E/C...E/M 2421.76 -205
2 - 6 4 - 36 E/C...E/R 3756.45 -204
2 - 7 4 - 45 E/C...E/S 4729.59 -137
2 - 8 4 - 61 E/C...Q/- 6543.73 -103
3 7 - 13 E/L...E/T 894.08 -1051
3 - 4 7 - 19 E/L...E/N 1452.69 -380
3 - 5 7 - 24 E/L...E/M 2075.39 -337
3 - 6 7 - 36 E/L...E/R 3410.08 -284
3 - 7 7 - 45 E/L...E/S 4383.22 -193
3 - 8 7 - 61 E/L...Q/- 6197.37 -140
4 14 - 19 E/T...E/N 576.63 401
4 - 5 14 - 24 E/T...E/M 1199.33 117
4 - 6 14 - 36 E/T...E/R 2534.02 -50
4 - 7 14 - 45 E/T...E/S 3507.16 -5
4 - 8 14 - 61 E/T...Q/- 5321.30 -8
5 20 - 24 E/N...E/M 640.72 -224
5 - 6 20 - 36 E/N...E/R 1975.41 -210
5 - 7 20 - 45 E/N...E/S 2948.55 -100
5 - 8 20 - 61 E/N...Q/- 4762.69 -66
6 25 - 36 E/M...E/R 1352.71 -204
6 - 7 25 - 45 E/M...E/S 2325.85 -70
6 - 8 25 - 61 E/M...Q/- 4139.99 -45
7 37 - 45 E/R...E/S 991.16 107
7 - 8 37 - 61 E/R...Q/- 2805.30 30
8 46 - 61 E/S...Q/- 1832.16 -12
Sorted according to mass
Fragment Residues Mass B&B
2 4 - 6 E/C...E/L 364.38 586
1 1 - 3 -/M...E/C 391.49 -600
4 14 - 19 E/T...E/N 576.63 401
5 20 - 24 E/N...E/M 640.72 -224
1 - 2 1 - 6 -/M...E/L 737.85 -6
3 7 - 13 E/L...E/T 894.08 -1051
7 37 - 45 E/R...E/S 991.16 107
4 - 5 14 - 24 E/T...E/M 1199.33 117
2 - 3 4 - 13 E/C...E/T 1240.44 -560
6 25 - 36 E/M...E/R 1352.71 -204
3 - 4 7 - 19 E/L...E/N 1452.69 -380
1 - 3 1 - 13 -/M...E/T 1613.92 -569
2 - 4 4 - 19 E/C...E/N 1799.06 -199
8 46 - 61 E/S...Q/- 1832.16 -12
5 - 6 20 - 36 E/N...E/R 1975.41 -210
3 - 5 7 - 24 E/L...E/M 2075.39 -337
1 - 4 1 - 19 -/M...E/N 2172.53 -262
6 - 7 25 - 45 E/M...E/S 2325.85 -70
2 - 5 4 - 24 E/C...E/M 2421.76 -205
4 - 6 14 - 36 E/T...E/R 2534.02 -50
1 - 5 1 - 24 -/M...E/M 2795.23 -254
7 - 8 37 - 61 E/R...Q/- 2805.30 30
5 - 7 20 - 45 E/N...E/S 2948.55 -100
3 - 6 7 - 36 E/L...E/R 3410.08 -284
4 - 7 14 - 45 E/T...E/S 3507.16 -5
2 - 6 4 - 36 E/C...E/R 3756.45 -204
1 - 6 1 - 36 -/M...E/R 4129.92 -237
6 - 8 25 - 61 E/M...Q/- 4139.99 -45
3 - 7 7 - 45 E/L...E/S 4383.22 -193
2 - 7 4 - 45 E/C...E/S 4729.59 -137
5 - 8 20 - 61 E/N...Q/- 4762.69 -66
1 - 7 1 - 45 -/M...E/S 5103.06 -168
4 - 8 14 - 61 E/T...Q/- 5321.30 -8
3 - 8 7 - 61 E/L...Q/- 6197.37 -140
2 - 8 4 - 61 E/C...Q/- 6543.73 -103
1 - 8 1 - 61 -/M...Q/- 6917.21 -127
Average mass Molecular mass = 6917.21
Monoisotopic mass Molecular mass = 6912.08