AMPDB_256 | Dermcidin

1 General Description

AMPDB ID: AMPDB_256

Protein Names: Dermcidin (EC 3.4.-.-) (Preproteolysin) [Cleaved into: Survival-promoting peptide; DCD-1]

Protein Family: Nil

Gene Name: DCD AIDD DSEP

Source Organism: Homo sapiens (Human)

Protein Length: 110 AA

Protein Existence: Evidence at protein level

2 Protein Sequence & Composition

MRFMTLLFLTALAGALVCAYDPEAASAPGSGNPCHEASAAQKENAGEDPGLARQAPKPRKQRSSLLEKGLDGAKKAVGGLGKLGKDAVEDLESVGKGAVHDVKDVLDSVL

FASTA format

Counts of Amino Acids

'A': 17, 'R': 4, 'N': 2, 'D': 8, 'C': 2, 'Q': 3, 'E': 7, 'G': 13, 'H': 2, 'I': 0, 'L': 14, 'K': 10, 'M': 2, 'F': 2, 'P': 6, 'S': 7, 'T': 2, 'W': 0, 'Y': 1, 'V': 8

Frequencies of Amino Acids

'A': 15.45%, 'R': 3.64%, 'N': 1.82%, 'D': 7.27%, 'C': 1.82%, 'Q': 2.73%, 'E': 6.36%, 'G': 11.82%, 'H': 1.82%, 'I': 0%, 'L': 12.73%, 'K': 9.09%, 'M': 1.82%, 'F': 1.82%, 'P': 5.45%, 'S': 6.36%, 'T': 1.82%, 'W': 0%, 'Y': 0.91%, 'V': 7.27%

Missing Amino Acid(s)

I, W

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

Hydrophobic Amino Acid(s) Count

Hydrophilic Amino Acid(s) Count

Basic Amino Acid(s) Count

Acidic Amino Acid(s) Count

Modified Amino Acid(s) Count

Modified Amino Acid(s) Frequencies

Computed by biopython (version 1.79) & proteinAnalysis (version 1)

3 Physicochemical Properties

Sl. No.	Properties	Values	Reference
1.	Molecular Mass	11283.9 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	86.182	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	24.407	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.225	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.622	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	6.516	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	-0.932	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.227, 0.255, 0.364 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.027	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	1490, 1615	Computed by ProtParam module (biopython 1.79)

4.1 Target Organism(s)

C.albicans, E.coli (Gram-negative), E.faecalis (Gram-positive), S.aureus (Gram-positive)

4.2 Antimicrobial Activity

Antibiotic, Antimicrobial, Fungicide, Anti-candida, Anti-gram-negative, Anti-gram-Positive

4.3 Enzymatic Activity

4.4 Inhibitory Effect

4.5 Other Biological Activity

Proteolytic, Non-hemolytic, Non-ribosomal

Activity data manually curated from Literature and UniProt

5 Database Cross-references

5.1 Literature Database

Citation 1: Schittek B, Hipfel R, Sauer B, et al. Dermcidin: a novel human antibiotic peptide secreted by sweat glands. Nat Immunol. 2001;2(12):1133-7. Published 2001 Dec. doi:10.1038/ni732

PMID: 11694882

Citation 2: Lee Motoyama JP, Kim-Motoyama H, Kim P, et al. Identification of dermcidin in human gestational tissue and characterization of its proteolytic activity. Biochem Biophys Res Commun. 2007;357(4):828-33. Published 2007 Jun 15. doi:10.1016/j.bbrc.2007.03.112

PMID: 17448443

Citation 3: Gerhard DS, Wagner L, Feingold EA, et al. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004;14(10B):2121-7. Published 2004 Oct. doi:10.1101/gr.2596504

PMID: 15489334

Citation 4: Azkargorta M, Soria J, Ojeda C, et al. Human Basal Tear Peptidome Characterization by CID, HCD, and ETD Followed by in Silico and in Vitro Analyses for Antimicrobial Peptide Identification. J Proteome Res. 2015;14(6):2649-58. Published 2015 Jun 5. doi:10.1021/acs.jproteome.5b00179

PMID: 25946035

Citation 5: Cunningham TJ, Hodge L, Speicher D, et al. Identification of a survival-promoting peptide in medium conditioned by oxidatively stressed cell lines of nervous system origin. J Neurosci. 1998;18(18):7047-60. Published 1998 Sep 15. doi:10.1523/JNEUROSCI.18-18-07047.1998

PMID: 9736629

Citation 6: Zhang Z, Henzel WJ, Henzel WJ. Signal peptide prediction based on analysis of experimentally verified cleavage sites. Protein Sci. 2004;13(10):2819-24. Published 2004 Oct. doi:10.1110/ps.04682504

PMID: 15340161

Citation 7: Choudhary C, Kumar C, Gnad F, et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science. 2009;325(5942):834-40. Published 2009 Aug 14. doi:10.1126/science.1175371

PMID: 19608861

Citation 8: Burkard TR, Planyavsky M, Kaupe I, et al. Initial characterization of the human central proteome. BMC Syst Biol. 2011;5:17. Published 2011 Jan 26. doi:10.1186/1752-0509-5-17

PMID: 21269460

Citation 9: Bian Y, Song C, Cheng K, et al. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. J Proteomics. 2014;96:253-62. Published 2014 Jan 16. doi:10.1016/j.jprot.2013.11.014

PMID: 24275569

Citation 10: Vaca Jacome AS, Rabilloud T, Schaeffer-Reiss C, et al. N-terminome analysis of the human mitochondrial proteome. Proteomics. 2015;15(14):2519-24. Published 2015 Jul. doi:10.1002/pmic.201400617

PMID: 25944712

Citation 11: Jung HH, Yang ST, Sim JY, et al. Analysis of the solution structure of the human antibiotic peptide dermcidin and its interaction with phospholipid vesicles. BMB Rep. 2010;43(5):362-8. Published 2010 May. doi:10.5483/bmbrep.2010.43.5.362

PMID: 20510021

Citation 12: Song C, Weichbrodt C, Salnikov ES, et al. Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proc Natl Acad Sci U S A. 2013;110(12):4586-91. Published 2013 Mar 19. doi:10.1073/pnas.1214739110

PMID: 23426625

5.2 Protein Sequence Databases

5.3 3D Structure Databases

	Sl. no.	PDB ID	Method	Resolution	Access Links	3D View

AlphaFoldDB: P81605

5.4 Nucleotide Sequence Databases

Sl. no.	Accession(s)	Access Link(s)
1.	AF144011	GenBank \|\| EMBL
2.	AY044239	GenBank \|\| EMBL
3.	AF418981	GenBank \|\| EMBL
4.	AY590150	GenBank \|\| EMBL
5.	EF503687	GenBank \|\| EMBL
6.	EF503688	GenBank \|\| EMBL
7.	EF503689	GenBank \|\| EMBL
8.	AC079310	GenBank \|\| EMBL
9.	CH471054	GenBank \|\| EMBL
10.	BC062682	GenBank \|\| EMBL
11.	BC069108	GenBank \|\| EMBL