Structural and Dynamic-Based Characterization of the Recognition Patterns of E7 and TRP-2 Epitopes by MHC Class I Receptors through Computational Approaches
Abstract
:1. Introduction
2. Results
2.1. Quality Assessment of AlphaFold Predictions
2.1.1. GP33Db System
2.1.2. TRP-2A68 System
2.2. Ab Initio Prediction of E7 Interaction with H2Db
2.2.1. AF Modeling: Evaluation of the Structural Models
2.2.2. A Dynamic View of the Interaction: MD Study
2.3. Ab Initio Prediction of TRP-2 Interaction with MHC Receptors
2.3.1. Selection of MHC-Peptide Systems
2.3.2. AF Modeling: Evaluation of the Structural Models
2.3.3. A Dynamic View of the Interaction: MD Study
3. Discussion
4. Materials and Methods
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Acknowledgments
Conflicts of Interest
References
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EPITOPE SEQUENCE | H2 CLASS I MHC | ||
---|---|---|---|
HLA-A68 UniProtKB ID P04439 | H2-Db UniProtKB ID P01899 | H2-Kb UniProtKB ID P01901 | |
GP33 KAVYNFATC | GP33Db * (1FG2) | ||
E7 RAHYNIVTF | E7Db | ||
TRP-2 SVYDFFVWL | TRP-2A68 *(4HX1) | TRP-2Db | TRP-2Kb |
GP33 | H2-Db | E7 | H2-Db | |||
---|---|---|---|---|---|---|
Residue | Atom | PDB ID 1FG2 * | AF Model | Residue | Atom | AF Model |
K1 | N | Y172OH | Y8OH | R1 | N | Y8OH Y172OH |
O | Y160OH | |||||
NZ | E164OE2 | NH | R63O | |||
A2 | N | E64OE1 | A2 | |||
V3 | O | Q71NE2 | H3 | O | Q71NE2 | |
NE2 | H156NE2 | |||||
Y4 | O | H156NE2 | H156NE2 | Y4 | ||
N5 | N | Q71OE1 | N5 | ND2 | Q98OE1 | |
OD1 | Q98OE1 Q98NE2 | Y157OH Q98OE1 Q98NE2 | ||||
ND2 | Q98OE1 Q98NE2 | Q71OE1 Q98OE1 Q98NE2 | ||||
F6 | N | W74NE1 | I6 | |||
O | Y157OH | |||||
A7 | O | W148NE1 | V7 | O | W148NE1 | |
T8 | O | W148NE1 K147NZ | W148NE1 | T8 | O | K147NZ |
OG1 | K147NZ | |||||
C9 | N | S78OG | S78OG | F9 | O | N81ND2 Y85OH K147NZ |
O | N81ND2 |
TRP-2 | HLA-A68 | H2-Db | H2-Kb | ||
---|---|---|---|---|---|
Residue | Atom | PDB ID 4HX1 | AF Model | AF Model | AF Model |
S1 | N | Y171OH Y7OH | Y171OH | E164OE | |
O | Y159OH | Y159OH | |||
OG | R62NH N63ND2 | K66NZ | |||
V2 | N | N63OD1 | N63OD1 | ||
O | N66ND2 | ||||
Y3 | N | Y99OH | |||
O | N66ND2 | ||||
OH | Q70OE1 | R97NH | |||
D4 | O | R155NH | |||
F5 | O | Q114NE2 | |||
F6 | O | R155NH | |||
V7 | O | Y116OH | |||
W8 | O | W147NE1 | W147NE1 K146NZ | W147NE1 | |
L9 | N | D77OD | D77OD | D77OD | |
O | T143OG K146NZ | T143OG K146NZ | N81ND2 Y85OH | K146NZ |
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Balasco, N.; Tagliamonte, M.; Buonaguro, L.; Vitagliano, L.; Paladino, A. Structural and Dynamic-Based Characterization of the Recognition Patterns of E7 and TRP-2 Epitopes by MHC Class I Receptors through Computational Approaches. Int. J. Mol. Sci. 2024, 25, 1384. https://doi.org/10.3390/ijms25031384
Balasco N, Tagliamonte M, Buonaguro L, Vitagliano L, Paladino A. Structural and Dynamic-Based Characterization of the Recognition Patterns of E7 and TRP-2 Epitopes by MHC Class I Receptors through Computational Approaches. International Journal of Molecular Sciences. 2024; 25(3):1384. https://doi.org/10.3390/ijms25031384
Chicago/Turabian StyleBalasco, Nicole, Maria Tagliamonte, Luigi Buonaguro, Luigi Vitagliano, and Antonella Paladino. 2024. "Structural and Dynamic-Based Characterization of the Recognition Patterns of E7 and TRP-2 Epitopes by MHC Class I Receptors through Computational Approaches" International Journal of Molecular Sciences 25, no. 3: 1384. https://doi.org/10.3390/ijms25031384