Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data
Abstract
:1. Introduction
2. Results
2.1. Identification of Peptide-Interacting Residues in PDZ Domains
2.2. Domain Analysis and Motif Matcher (DAMM) Program
2.3. Binding Preferences of A9UPE9 PDZ
2.4. Endogenous Targets of A9UPE9 PDZ
3. Discussion
4. Materials and Methods
4.1. Protein Expression and Purification
4.2. Fluorescence Polarization
4.3. Design and Development of Domain Analysis and Motif Matcher (DAMM)
4.4. Protein Analyses
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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PDZ Domain | Sequence Identity | Sequence Similarity |
---|---|---|
INADL-10 | 42% (35/83) | 59% (49/83) |
SNTG2 | 41% (36/87) | 57% (50/87) |
GRIP1-2 | 41% (30/74) | 60% (45/74) |
GRIP2-2 | 41% (26/63) | 61% (39/63) |
GRIP1-4 | 35% (30/85) | 51% (44/85) |
PDZ Domain | Matching/Similar Residues | Sequence Identity |
---|---|---|
SYNJ2BP | 5/2 | 31% |
DLG1-2 | 4/2 | 29% |
DLG2-2 | 4/2 | 29% |
DLG4-2 | 4/2 | 29% |
MPDZ-12 | 4/2 | 32% |
DLG3-2 | 4/2 | 30% |
DLG1-1 | 4/2 | 30% |
DLG2-1 | 4/2 | 29% |
DLG4-1 | 4/2 | 29% |
DLG3-1 | 4/2 | 30% |
KI Values (μM) | |||
---|---|---|---|
Peptide | Sequence | A9UPE9 PDZ | DLG1-1 PDZ |
HPV18 E6 | RLQRRRETQV | 16 ± 1 | 2.8 ± 1.3 |
HPV16 E6 | SSRTRRETQL | 66 ± 24 | 23 ± 5 |
SRETTV | SRETTV | 83 ± 31 | 4.4 ± 1.9 |
SRETDV | SRETDV | 12 ± 3 | 7.9 ± 3.7 |
RRETTV | RRETTV | 33 ± 1 | 2.0 ± 1.6 |
RRETDV | RRETDV | 8.1 ± 3.1 | 9.5 ± 6.6 |
GIRK3 | ESESKV | >1000 | 350 ± 20 |
BPIX | WDETNL | 330 ± 160 | 460 ± 140 |
GAIP | QSSSEA | >1000 | 980 ± 180 |
TYRP1 | PNQSVV | 97 ± 24 | 46 ± 21 |
B1AR | ASESKV | 95 ± 30 | 44 ± 23 |
A9V7Z4 | EDETAL | 580 ± 160 | 460 ± 190 |
A9UP44 | QSESRL | 64 ± 35 | 39 ± 25 |
A9UXE1 | QDETAL | 460 ± 210 | 190 ± 20 |
KI (μM) | |||
---|---|---|---|
Peptide | Sequence | Reference Sequence | A9UPE9 PDZ |
A9V6G5_MONBE | HRESTV | HSETAL (TMIGD1) | 97 ± 30 |
A9UWH1_MONBE | STRSDV | HSETAL (TMIGD1) | >1000 |
A9UR52_MONBE | SRRTEV | RRETQV (HPV18 E6) | >1000 |
A9UWP5_MONVE | GSESSV | ASGSSV (SYNJ2BP) | 490 ± 110 |
A9UYY4_MONBE | RLASEV | VIATEV (DLL1/4) | >1000 |
A9VB85_MONBE | ARESEI | >1000 | |
DLL1/DLL4 | VIATEV | 240 ± 40 |
Number of Substitutions | UniProt ID | Matching Sequence | Reference Sequence |
---|---|---|---|
2 | tr|A9UQN5|A9UQN5_MONBE | GGCTLL | GGGTGL |
2 | tr|A9V457|A9V457_MONBE | YGGTSF | GGGTGL |
2 | tr|A9UZY0|A9UZY0_MONBE | RYGSGV | GGGTGL |
2 | tr|A9UWI6|A9UWI6_MONBE | GGCSLL | GGGTGL |
2 | tr|A9UR91|A9UR91_MONBE | GYGSTI | GGGTGL |
2 | tr|A9UU72|A9UU72_MONBE | GGPTDI | GGGTGL |
2 | tr|A9UX10|A9UX10_MONBE | GLGTTI | GGGTGL |
2 | tr|A9UNL7|A9UNL7_MONBE | GGSTQI | GGGTGL |
2 | tr|A9UPF5|A9UPF5_MONBE | GDGSSF | GGGTGL |
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Wofford, H.A.; Myers-Dean, J.; Vogel, B.A.; Alamo, K.A.E.; Longshore-Neate, F.A.; Jagodzinski, F.; Amacher, J.F. Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data. Molecules 2021, 26, 6034. https://doi.org/10.3390/molecules26196034
Wofford HA, Myers-Dean J, Vogel BA, Alamo KAE, Longshore-Neate FA, Jagodzinski F, Amacher JF. Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data. Molecules. 2021; 26(19):6034. https://doi.org/10.3390/molecules26196034
Chicago/Turabian StyleWofford, Haley A., Josh Myers-Dean, Brandon A. Vogel, Kevin Alexander Estrada Alamo, Frederick A. Longshore-Neate, Filip Jagodzinski, and Jeanine F. Amacher. 2021. "Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data" Molecules 26, no. 19: 6034. https://doi.org/10.3390/molecules26196034
APA StyleWofford, H. A., Myers-Dean, J., Vogel, B. A., Alamo, K. A. E., Longshore-Neate, F. A., Jagodzinski, F., & Amacher, J. F. (2021). Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data. Molecules, 26(19), 6034. https://doi.org/10.3390/molecules26196034