| Literature DB >> 27843978 |
Seyyed Mohsen Sohrabi1, Ali Niazi1, Mahmood Chahardoli1, Ali Hortamani1, Payam Setoodeh2.
Abstract
Lactoferrin (Lf) is an iron-binding multi-functional glycoprotein which has numerous physiological functions such as iron transportation, anti-microbial activity and immune response. In this study, different in silico approaches were exploited to investigate Lf protein properties in a number of mammalian species. Results showed that the iron-binding site, DNA and RNA-binding sites, signal peptides and transferrin motifs in the Lf structure were highly conserved. Examined sequences showed three conserved motifs which were repeated twice in the Lf structure, demonstrating ancient duplication events in its gene. Also, results suggest that the functional domains in mammalian Lf proteins are Zinc finger, Tubulin/FtsZ, GTPase, α/β hydrolase and Zinc knuckle. The potential site for nucleic acid binding and the major DNA and RNA- binding sites in this protein were found in the lactoferricin (Lfc) fragment. Due to its high positive charge, Lf is able to bind a large number of compounds. Our analysis also revealed that the interactions between Lf and ITLN1, LYZ, CSN2, and CD14 proteins played an important role in the protective activities of Lf. Analysis for the prediction of secondary structures indicated that high amounts of α-helix, β-strand and β-sheet were present in Lf. The high degree of conservation among mammalian Lf proteins indicates that there is a close relationship between these proteins, reflecting their important role.Entities:
Keywords: Anti-microbial activity; Bioinformatics tools; In silico study; Lactoferricin; Lactoferrin; Mammalian species
Year: 2014 PMID: 27843978 PMCID: PMC5047140
Source DB: PubMed Journal: Mol Biol Res Commun ISSN: 2322-181X
Identity of Lf protein between mammalian species
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| 100 | 96 | 75 | 92 | 72 | 69 | 69 | 64 | 92 | 74 |
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| 100 | 76 | 92 | 73 | 70 | 69 | 64 | 92 | 74 | |
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| 100 | 73 | 71 | 70 | 64 | 98 | 74 | |||
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| 100 | 75 | 74 | 66 | 74 | 72 | ||||
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| 100 | 89 | 70 | 71 | 70 | |||||
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| 100 | 70 | 71 | 72 | ||||||
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Figure 1Phylogenetic tree of Lf proteins from different species plotted by MEGA5 software
Figure 2Conserved amino acids in the iron binding site (IBS).
Figure 3Nucleic acids binding sites and signal peptides in Lf structure. Upper: DNA binding site. Lower: RNA binding sites. Rectangles show the signal peptides
Figure 4Multiple alignment of Lf motif amino acid sequences in mammalian species using MEME database. A. conserved motif of Lf in mammalians. B (motif 1), C (motif 2) and D (motif 3). Consensus of conserved motifs
Figure 5Multiple sequence alignment of Lf in Lfc fragment.
Functional domains in Lf structure.
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| Bos taurus | 176 | 217 | Zinc finger. C3HC4 type (RING | PF00097 | zf-C3HC4 |
| Bubalus bubalis | 189 | 217 | domain | PF00097 | zf-C3HC4 |
| Camelus | 176 | 217 | finger) | PF00097 | zf-C3HC4 |
| dromedarius | 387 | 415 | finger) | PF00091 | Tubulin |
| Capra hircus | 176 | 217 | domain | PF00097 | zf-C3HC4 |
| Equus caballus | 189 | 198 | finger) | PF00097 | zf-C3HC4 |
| Equus caballus | 189 | 217 | finger) | PF00097 | zf-C3HC4 |
| Macaca cyclopis | 313 | 359 | finger) | PF00561 | Abhydrolase_1 |
| Mus musculus | 186 | 201 | Zinc knuckle | PF00098 | zf-CCHC |
| Ovis aries | 176 | 217 | Zinc finger. C3HC4 type (RING | PF00097 | zf-C3HC4 |
| Suss crofa | - | - | - | - | - |
Lfc sequence analysis
| Organism | Lactoferricin sequence | PI | Net charge |
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| APRKNVRWCTISQPEWFKCRRWQWRMKKLGAPSITCVRRAFALECIRAI AEKKA | 8.43 | +11 |
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| APRKNVRWCTISQPEWLKCHRWQWRMKKLGAPSITCVRRAFVLECIRAI TEKKA | 7.95 | +10 |
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| ASKKSVRWCTTSPAESSKCAQWQRRMKKVRGPSVTCVKKTSRFECIQAI STEKA | 8.34 | +10 |
| APRKNVRWCAISLPEWSKCYQWQRRMRKLGAPSITCVRRTSALECIRAI AGKNA | 8.07 | +10 | |
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| APRKSVRWCTISPAEAAKCAKFQRNMKKVRGPSVSCIRKTSSFECIQAIA ANKA | 8.03 | +10 |
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| GRRRRSVQWCAVSQPEATKCFQWQRNMRKVRGPPVSCIKRDSPIQCIQA | 8.17 | +9 |
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| ARRRSVRWCAVSKPEATKCSQWQRNLRRVRGPPVSCIKRASPTNCIQAIA ANRA | 8.23 | +12 |
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| APRKNVRWCAISPPEGSKCYQWQRRMRKLGAPSITCVRRTSALECIRAIA GKKA | 8.07 | +11 |
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| APKKGVRWCVISTAEYSKCRQWQSKIRRTNPMFCIRRASPTDCIRAIAAK RADA | 8.31 | +10 |
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| ATTVRWCAVSNSEEEKCLRWQNEMRKVGGPPLSCVKKSSTRQCIQAIVT NRADA | 8.66 | +4 |
Figure 6Protein–protein interaction network of all proteins which interact with Lf
Predicted functional partners for Lf protein
| Protein name | Function | Accession number | Length (aa) | Score |
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| ITLN1 | Intelectin1(galactofuranose | AF271386_1 | 313 | 0.990 |
| binding) | ||||
| LYZ | Lysozyme (renal amyloidosis) | NP_000230 | 148 | 0.989 |
| CP | Ceruloplasmin (ferroxidase) | NP_000087 | 1065 | 0.979 |
| LCN1 | Lipocalin 1 (tear prealbumin) | NP_002288 | 176 | 0.979 |
| ALB | Albumin | NP_000468 | 609 | 0.965 |
| CSN2 | Casein β | NP_001882 | 226 | 0.953 |
| CSN3 | Casein kappa | NP_005203 | 182 | 0.953 |
| CD14 | CD14 | NP_000582 | 375 | 0.937 |
| DMBT1 | Deleted in malignant brain | NP_015568 | 2413 | 0.928 |
| tumors 1 | ||||
| CD79A | CD79a molecule | NP_001774 | 226 | 0.924 |
Sequence analysis of Lf.
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| 708 | 78.167 | 17 | 77.88 | -0.3 |
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| 708 | 77.729 | 8 | 79 | -0.25 |
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| 708 | 77.211 | 15 | 79.94 | -0.25 |
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| 708 | 77.339 | 10 | 77.9 | -0.24 |
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| 708 | 75.99 | 9 | 75.28 | -0.31 |
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| 711 | 78.409 | 11 | 74.51 | -0.35 |
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| 710 | 77.87 | 12 | 77.25 | -0.3 |
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| 708 | 77.282 | 10 | 76.94 | -0.24 |
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| 703 | 77.512 | 14 | 76.06 | -0.29 |
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| 707 | 77.837 | 21 | 72.76 | -0.42 |
Figure 7Predicted secondary structure of Lf.
Predicted secondary structure of Lf
| Organism | Helix (%) | β-Sheet (%) | Random coil (%) |
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| 22 | 19 | 59 |
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| 19 | 19 | 62 |
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| 21 | 19 | 61 |
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| 20 | 20 | 60 |
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| 24 | 17 | 59 |
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| 20 | 21 | 59 |
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| 20 | 19 | 61 |
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| 22 | 19 | 59 |
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| 21 | 20 | 59 |
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| 20 | 17 | 63 |
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| 21 | 20 | 59 |
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| 19 | 19 | 62 |