Structural and Functional Enrichment Analyses for Antimicrobial Peptides
Abstract
:1. Introduction
2. Results
2.1. Enriched AMP Functions
2.1.1. Enriched AMP Functions in Terms of CATH Structures
2.1.2. Enriched AMP Functions in Terms of SCOP Structures
2.1.3. Enriched AMP Functions in Terms of TM Structures
2.2. Enriched AMP Structures
2.2.1. Enriched CATH Structures in Terms of AMP Functions
2.2.2. Enriched SCOP Structures in Terms of AMP Functions
2.2.3. Enriched TM Structures in Terms of AMP Functions
2.3. AMP Structure–Function Enrichment Analysis
2.4. AMP Structure–Function Enrichments Associated with Sequences
2.4.1. Superfamily-Like Sequence Motifs
2.4.2. Associated Pfam Families or Domains
3. Discussion
4. Materials and Methods
4.1. Antimicrobial Peptides
4.2. Antimicrobial Peptide Structures
4.3. Representative Antimicrobial Peptides
4.4. Structure Classification Methods
4.4.1. CATH Structural Classification
4.4.2. SCOP Structural Classification
4.4.3. TM Structural Classification
4.5. Enrichment Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ADAM | A Database of Anti-Microbial Peptides |
AMP | Antimicrobial peptide |
CATH | Class, Architecture, Topology, Homology |
SCOP | Structural Classification of Proteins |
TM | Template Modeling |
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Type | Structure | Sequence Identity Threshold (%) | F(x) | |||||||
---|---|---|---|---|---|---|---|---|---|---|
1st Level | 2nd Level | 100 | 90 | 80 | 70 | 60 | 50 | 40 | ||
CATH | α β | * | ⟷ | F | ||||||
2-Layer Sandwich | ⟷ | ⟷ | ⟷ | → | F | |||||
Roll | ← | G | ||||||||
Roll | ← | G- | ||||||||
Mainly α | * | ← | ← | ← | ← | G | ||||
* | ← | G+ | ||||||||
Orthogonal Bundle | ← | G | ||||||||
Mainly β | * | → | P | |||||||
Beta Barrel | ← | G- | ||||||||
SCOP | α and β (α + β) | * | ← | G | ||||||
* | ← | G+ | ||||||||
IL8-like | ⟷ | ← | ← | ← | G- | |||||
Peptides | * | → | G | |||||||
* | → | G+ | ||||||||
Small proteins | * | ⟷ | ⟷ | ⟷ | ⟷ | ⟷ | ⟷ | ⟷ | F | |
Knottins | ⟷ | ⟷ | ⟷ | ⟷ | → | ⟷ | → | F | ||
Crambin-like | ⟷ | ⟷ | ⟷ | C | ||||||
Defensin-like | ← | G- | ||||||||
TM | TM1 | ⟷ | ⟷ | ⟷ | → | ⟷ | ⟷ | → | F | |
TM2 | ⟷ | ⟷ | ⟷ | ⟷ | → | ⟷ | ⟷ | G- | ||
TM3 | ⟷ | G | ||||||||
TM3 | ⟷ | ⟷ | ⟷ | ⟷ | ← | ⟷ | → | G+ | ||
TM3 | ⟷ | ⟷ | ⟷ | ⟷ | ⟷ | ⟷ | ⟷ | G- | ||
TM4 | ← | G | ||||||||
TM4 | ← | G+ | ||||||||
TM4 | ← | G- | ||||||||
TM4 | ⟷ | → | → | → | → | V | ||||
TM5 | ⟷ | ⟷ | → | → | V |
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Lo, S.C.; Xie, Z.-R.; Chang, K.Y. Structural and Functional Enrichment Analyses for Antimicrobial Peptides. Int. J. Mol. Sci. 2020, 21, 8783. https://doi.org/10.3390/ijms21228783
Lo SC, Xie Z-R, Chang KY. Structural and Functional Enrichment Analyses for Antimicrobial Peptides. International Journal of Molecular Sciences. 2020; 21(22):8783. https://doi.org/10.3390/ijms21228783
Chicago/Turabian StyleLo, Sheng C., Zhong-Ru Xie, and Kuan Y. Chang. 2020. "Structural and Functional Enrichment Analyses for Antimicrobial Peptides" International Journal of Molecular Sciences 21, no. 22: 8783. https://doi.org/10.3390/ijms21228783
APA StyleLo, S. C., Xie, Z. -R., & Chang, K. Y. (2020). Structural and Functional Enrichment Analyses for Antimicrobial Peptides. International Journal of Molecular Sciences, 21(22), 8783. https://doi.org/10.3390/ijms21228783