Short Linear Motifs Characterizing Snake Venom and Mammalian Phospholipases A2
Abstract
:1. Introduction
2. Results
2.1. Sequence Alignment Comparison
2.2. Amino Acid Composition Analysis of the Central and C-Terminal Regions
2.3. SLiMs Conserved in Toxins and Not in Mammalian PLA2s or Vice Versa
Motif Description | ELM Class | Sequence Section Start–End | Fraction of Proteins Containing the Motif in the Specified Section | ||
---|---|---|---|---|---|
Neuro-Myotoxins | Neurotoxins | PLA2G1B | |||
N-terminal | DEG_Nend_UBRbox_3 | 1 | 7/7 | 14/14 | 0/10 |
NEK2 phosph. site | MOD_NEK2_1 | 31–36 | 0/7 | 0/14 | 9/10 |
I-BAR binding site | LIG_IBAR_NPY_1 | 67–69 | 0/7 | 0/14 | 10/10 |
SH2 binding site | LIG_SH2_STAP1 | 69–73 | 0/7 | 0/14 | 10/10 |
GSK3 phosph. sites * | MOD_GSK3_1 | 67–80 | 0/7 | 1/14 | 10/10 |
SH2 binding site | LIG_SH2_NCK_1 | 105–109 | 3/7 | 6/14 | 0/10 |
PTB binding sites | LIG_PTB_Apo_2LIG_PTB_Phospho_1 | 104–111 | 1/7 | 9/14 | 0/10 |
Motif Description | ELM Class | Sequence Section Start–End | Fraction of Proteins Containing the Motif in the Specified Section | |||||
---|---|---|---|---|---|---|---|---|
Myotoxins | Neuro-Myotoxins | Neurotoxins | PLA2G2A | |||||
NOT D49 | D49 | NOT D49 | D49 | D49 | ||||
Pin1 site, and PDK and CDK phosph. sites | DOC_WW_Pin1_4 MOD_ProDKin_1 MOD_CDK_SPK_2 | 35–37 | 0/25 | 0/14 | 1/5 | 1/9 | 4/12 | 10/10 |
SH2 binding site | LIG_SH2_CRK | 51–55 | 23/25 | 9/14 | 3/5 | 6/9 | 9/12 | 0/10 |
PKA phosph. site | MOD_PKA_1 | 52–56 | 23/25 | 3/14 | 3/5 | 1/9 | 0/12 | 0/10 |
FHA binding site | LIG_FHA_1 | 59–65 | 0/25 | 0/14 | 0/5 | 2/9 | 4/12 | 10/10 |
Pin1 site and CDK phosph. site | DOC_WW_Pin1_4 MOD_CDK_SPK_2 | 119–121 | 0/25 | 0/14 | 0/5 | 0/9 | 0/12 | 7/10 |
PDZ binding site | LIG_PDZ_Class_3 | 119–121 | 23/25 | 9/14 | 5/5 | 5/9 | 10/12 | 0/10 |
ELM Class Identifier | Regular Expression | Interaction Partner(s) | Examples of Proteins * Containing the SLiM |
---|---|---|---|
DEG_Nend_ UBRbox_3 | ^M{0,1}([NQ]) | Aminohydrolases for deamidation | - |
DOC_WW_Pin1_4 | ...([ST])P. | Peptidyl prolyl isomerase 1 | Many |
LIG_FHA_1 | ..(T)..[ILV]. | Proteins containing the forkhead-associated domain, e.g., TIFA, TIFAB, AGGF1 | Kinesin interactors, TIFA |
LIG_IBAR_NPY_1 | NPY | I-BAR domain-containing proteins, involved in membrane dynamic | The bacterial protein Tir, SHANK2 |
LIG_PDZ_Class_3 | ...[DE].[ACVILF]$ | PDZ containing proteins, PDZ domains also bind to phospholipid headgroups | Many PDZ ligands are membrane proteins |
LIG_PTB_Apo_2 LIG_PTB_Phospho_1 | (.[^P].NP.[FY].)|(.[ILVMFY].N..[FY].) (.[^P].NP.(Y))|(.[ILVMFY].N..(Y)) | Proteins containing phosphotyrosine binding (PTB) domains, e.g., insulin receptor substrate 1 (IRS-1) | Integrins, LRP1 |
LIG_SH2_CRK | (Y)[^EPILVFYW][^HDEW][PLIV][^DEW] | Proteins containing SH2 domain of the CRK family | Transmembrane receptors, Phospholipase C-gamma-1 |
LIG_SH2_NCK_1 | (Y)[DESTNA][^GWFY][VPAI][DENQSTAGYFP] | Proteins containing SH2 domain of the NCK family | Transmembrane proteins, adapter protein docking 1 |
LIG_SH2_STAP1 | (Y)[DESTA][^GP][^GP][ILVFMWYA] | Proteins containing SH2 domain of the STAP1 family | Transmembrane proteins, lipid phosphatase |
MOD_CDK_SPK_2 | ...([ST])P[RK] | Cyclin-dependent kinases, proline directed kinase | Proteins involved in different biochemical pathways |
MOD_GSK3_1 | ...([ST])...[ST] | Glycogen synthase kinase 3, needs priming, inhibitory | |
MOD_NEK2_1 | [FLM][^P][^P]([ST])[^DEP][^DE] | Never in mitosis A (NimA)-related kinases | |
MOD_PKA_1 | [RK][RK].([ST])[^P].. | cAMP-dependent protein kinase A, basophilic kinase | |
MOD_ProDKin_1 | ...([ST])P.. | MAP Kinase, proline directed kinase |
3. Discussion
4. Conclusions
5. Materials and Methods
5.1. Sequence Collection and Alignment
5.2. Amino-Acidic Composition Analysis of the β-Sheet Containing Region and C-Terminal Stretch
5.3. Short Linear Motifs Identification
5.4. Tri-Dimensional Structure Representations
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Peggion, C.; Tonello, F. Short Linear Motifs Characterizing Snake Venom and Mammalian Phospholipases A2. Toxins 2021, 13, 290. https://doi.org/10.3390/toxins13040290
Peggion C, Tonello F. Short Linear Motifs Characterizing Snake Venom and Mammalian Phospholipases A2. Toxins. 2021; 13(4):290. https://doi.org/10.3390/toxins13040290
Chicago/Turabian StylePeggion, Caterina, and Fiorella Tonello. 2021. "Short Linear Motifs Characterizing Snake Venom and Mammalian Phospholipases A2" Toxins 13, no. 4: 290. https://doi.org/10.3390/toxins13040290