New User-Friendly Approach to Obtain an Eisenberg Plot and Its Use as a Practical Tool in Protein Sequence Analysis
Abstract
:1. Introduction
2. Results and Discussion
2.1. The Eisenberg Plot Approach Using the Original Databases
2.2. The Validity Check of the “New” Eisenberg Plot
2.3. The Meaning of the Eisenberg Plot for Novel Classes of Proteins and Peptides
2.4. Examples Illustrating the Power of the Total Approach
3. Method Section
3.1. Primary and Secondary Structures Identification
3.2. Determination Lipid-Binding Potential
3.3. Eisenberg Plot Approach
4. Conclusions
Supplementary Information
ijms-12-05577-s001.pdfReferences
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Name | Sequence | z | <H> | <μH> | D | Conf. |
---|---|---|---|---|---|---|
RW16 | RRWRRWWRRWWRRWRR | 10 | 0.213 | 0.975 | YES | S [17] |
RL16 | RRLRRLLRRLLRRLRR | 10 | 0.006 | 0.824 | YES | S [17] |
Pbuy | FRKLFRVYSNFLRGKLKL | 6 | 0.280 | 0.650 | YES | S [18] |
Pill | KQLIRFLKRLDRNLWGLA | 4 | 0.447 | 0.633 | YES | S [18] |
Pc9k | NRLARHFRDIAGRVNQRL | 4 | 0.096 | 0.591 | YES | S [18] |
Pqc7 | LKDVEEAQQKIINIIRRL | 1 | 0.280 | 0.650 | YES | S [18] |
Pc3c | WYSEMKRNVQRLERAIEE | 0 | 0.113 | 0.615 | NO | S [18] |
Pihf | RDAKELVELFFEEIRRAL | −1 | 0.276 | 0.566 | NO | S [18] |
KL | KLLKLLLKLLKLLLKLLL | 5 | 0.953 | 0.659 | YES | S [19] |
CRAMP18 | GEKLKKIGQKIKNFFQKL | 5 | 0.164 | 0.674 | YES | S [19] |
SPLN14–27 | SLSRYAKLANRLA | 3 | 0.254 | 0.530 | YES | S [20] |
SPLN28–41 | PKLLETFLSKWIG | 1 | 0.712 | 0.596 | YES | S [20] |
Histatin 5 | SHAKRHHGYKRKFHEKHH | 5 | −0.157 | 0.263 | YES | G [21] |
PGLaa | SKAGAIAGKIAKVALKAL | 3 | 0.398 | 0.501 | YES | S [21] |
SP-B(7–24) | YCWLCRALIKRIQAMIPK | 4 | 0.747 | 0.434 | YES | S [22] |
PC-TP196- | VPNFLKDMARACQNYLKK | 3 | 0.295 | 0.677 | YES | S [23] |
Equinatoxin II | ASLSFDILKTVLEALGNV | −1 | 0.591 | 0.458 | NO | S [24] |
KL4 | KLLLLKLLLLKLLLLKLL | 4 | 1.102 | 0.157 | YES | M [25] |
KALP23 | KKLALALALALALALALA | 2 | 0.783 | 0.154 | YES | M [26] |
WALP23 | WWLALALALALALALALA | 0 | 1.143 | 0.107 | NO | M [26] |
Glycophorin A (92–114) | ITLIIFGVMAGVIGTILLI | 0 | 1.133 | 0.213 | NO | M [27] |
TMX31 | WISFAISCFLLCVVLLGF | 0 | 1.321 | 0.216 | NO | M [28] |
MHCClassII | VLVALLLAGQATTAYFLY | 0 | 0.899 | 0.115 | NO | M [29] |
Name | Sequence | z | <H> | <μH> | D | Conf. |
---|---|---|---|---|---|---|
SP & LBP: | ||||||
1. prePhoE | KKSTLALVVMGIVASASV | 2 | 0.558 | 0.045 | Y | [31] |
2. preLamB | RKLPLAVAVAAGVMSAQA | 2 | 0.478 | 0.157 | Y | [32] |
3. proOmpA | KKTAIAIAVALAGFATVA | 2 | 0.569 | 0.204 | Y | [33] |
4. prePhoA | TIALALLPLLPTPVTKAR | 2 | 0.744 | 0.197 | Y | [34] |
5. Ovalbumin | IFYCPIAIMSALAMVTLG | 0 | 1.036 | 0.165 | N | [35] |
6. Aurein 1.2 | GLFDIKKVASVIGGL | 1 | 0.583 | 0.326 | N | [36,37] |
7. Citropin | GLFDVIKKVASVIGGL | 1 | 0.623 | 0.614 | Y | [36,37] |
8. Maculatin 1.1 | GLFGVLAKVAAHVVPAIA | 1 | 0.738 | 0.408 | Y | [36,37] |
9. VP1 | GTAMRILGGVI | 1 | 0.665 | 0.468 | Y | [38] |
10. HA2 FP | FGAIAGFIENGWEGMIDG | −3 | 0.579 | 0.533 | N | [38] |
11. AP1 | GEQGALAQFGEWL | −2 | 0.488 | 0.399 | N | [39] |
12. SIV peptide | GVFVLGFLGFLA | 0 | 1.102 | 0.259 | N | [40] |
13. Gaegurin 5 | LGALFKVASKVLPSVCAI | 2 | 0.749 | 0.463 | Y | [41] |
14. PBP5 | GNFFGKIIDYIKLMFHHW | 1 | 0.768 | 0.616 | Y | [42] |
16. Penetratin | RQIKIWFQNRRMKWKK | 7 | 0.193 | 0.327 | Y | [43] |
17. Polyarginine-R9 | RRRRRRRRR | 9 | −1.010 | 0.146 | Y | [44] |
18. Substance-P | RPKPQQFFGLM | 2 | 0.501 | 0.298 | Y | [45] |
19. Dermaseptin B2 | IKEVGKEAAKAAAKAAGK | 3 | −0.058 | 0.395 | Y | [46] |
Amphitropics: | ||||||
20. SecA(1–21) | MLIKLLTKVFGSRNDRTL | 3 | 0.442 | 0.303 | Y | [14] |
21. SecA(108–125) | KTLTATLPAYLNALTGKG | 2 | 0.437 | 0.352 | Y | [47] |
22. SecA(593–614) | ALMRIFASDRVSGMMRKL | 3 | 0.425 | 0.131 | Y | [48] |
23. SecA(865–882) | AAAAALAAQTGERKVGRN | 2 | 0.049 | 0.088 | Y | [14] |
24. FtsY(1–18) | MAKEKKRGFFSWLGFGQK | 4 | 0.277 | 0.332 | Y | [49] |
25. FtsY(188–208) | KPTKEGFFARLKRSLLKT | 5 | 0.198 | 0.254 | Y | [50] |
26. Apocyt c2–21 | VEKGKKIFVQKCAQCHTV | 3 | 0.333 | 0.341 | Y | [51] |
27. Apocyt c80–101 | AGIKKKTEREDLIAYLKK | 3 | 0.046 | 0.129 | Y | [51] |
28. EcMinD251–269 | RPFRFIEEEKKGFLKRLF | 3 | 0.287 | 0.498 | Y | [52] |
29. α-synuclein1–15 | MDVFMKGLSKAKEGV | 1 | 0.285 | 0.517 | Y | [53] |
30. ARF1 | MGNIFANLFKGLFGKKEM | 2 | 0.474 | 0.400 | Y | [54] |
31. K-segment dehydrins | EKKGIMDKIKEKLPG | 2 | 0.017 | 0.363 | Y | [55] |
Miscellaneous: | ||||||
32. Kes 1p (7–29) | SSSWTSFLKSIASFNGDL | 0 | 0.500 | 0.523 | N | [56] |
33. PBP4 | RRIPLVRFESRLYKDIYQNN | 3 | 0.331 | 0.285 | Y | [42] |
34. KCNQ1354–372 | KVQQKQRQKHFNRQIPAA | 5 | −0.023 | 0.154 | Y | [57] |
35. ABP280(49–71) | FTRWCNEHLKCVSKRIAN | 3 | 0.370 | 0.560 | Y | [58] |
36. L15K7 | KLLKLLLKLLKLLLKLLLKLLK | 5 | 0.953 | 0.659 | Y | [59] |
Name | Sequence | z | <H> | <μH> | D | Confirmed |
---|---|---|---|---|---|---|
M13 coat protein: | ||||||
2KKSLVLKASVAVATLVPM19 | 3 | 0.559 | 0.072 | YES | [65] | |
47YAWAMVVVIVGATIGIKL64 | 1 | 0.923 | 0.062 | NO | [65] | |
54VIVGATIGIKLFKKFTSK71 | 4 | 0.553 | 0.288 | YES | - | |
Ffh: | ||||||
(P0AGD7) | 1MFDNLTDRLSRTLRNISG18 | 1 | 0.255 | 0.663 | YES | - |
44ALPVVREFINRVKEKAVG61 | 2 | 0.313 | 0.365 | YES | - | |
166QKPVDIVNAALKEAKLKF183 | 2 | 0.272 | 0.331 | YES | - | |
309SKVDRAQAEKLASKLKKG326 | 4 | −0.118 | 0.297 | YES | - | |
336EQLRQMKNMGGMASLMGK353 | 2 | 0.218 | 0.261 | YES | - | |
395KGSRKRRIAAGCGMQVQD412 | 4 | 0.008 | 0.140 | YES | - | |
415RLLKQFDDMQRMMKKMKK432 | 5 | 0.064 | 0.606 | YES | - | |
428KKMKKGGMAKMMRSMKGM445 | 7 | 0.039 | 0.327 | YES | - | |
Fis1: | ||||||
(P40515) | 35PTATIQSRFNYAWGLIKS52 | 2 | 0.514 | 0.349 | YES | [67] |
60LGVKILTDIYKEAESRRR77 | 2 | 0.147 | 0.326 | YES | - | |
108RNNKQVGALKSMVEDKIQ125 | 2 | 0.023 | 0.305 | YES | - | |
133VVAGGVLAGAVAVASFFL150 | 0 | 0.811 | 0.145 | YES | [67] |
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Keller, R.C.A. New User-Friendly Approach to Obtain an Eisenberg Plot and Its Use as a Practical Tool in Protein Sequence Analysis. Int. J. Mol. Sci. 2011, 12, 5577-5591. https://doi.org/10.3390/ijms12095577
Keller RCA. New User-Friendly Approach to Obtain an Eisenberg Plot and Its Use as a Practical Tool in Protein Sequence Analysis. International Journal of Molecular Sciences. 2011; 12(9):5577-5591. https://doi.org/10.3390/ijms12095577
Chicago/Turabian StyleKeller, Rob C.A. 2011. "New User-Friendly Approach to Obtain an Eisenberg Plot and Its Use as a Practical Tool in Protein Sequence Analysis" International Journal of Molecular Sciences 12, no. 9: 5577-5591. https://doi.org/10.3390/ijms12095577