A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking
Abstract
:1. Introduction
2. Results and Discussion
2.1. ApoB-100 Subunit I Homology Modeling
2.2. Subunit II Modeling
2.3. Subunit III Homology Modeling
2.4. Subunit IV Modeling
2.5. Subunit V Homology Modeling
2.6. Domain Boundaries Prediction and Secondary Structure Determination
2.7. Sequence and Structural Comparison to Lipovitellin
2.8. ApoB-100 Architecture and Dynamics
2.9. β-propeller Folds and Apob-100 Docking Region
3. Methods and Materials
3.1. Sequences and Domain Prediction
3.2. Database Search and Modeling
3.3. Plasma Lipoprotein Separation by Sequential Ultracentrifugation
3.4. Cross-Linking Assay
3.5. Sample Preparation for Mass Spectrometry with Double Trypsin Digestion
3.6. Mass Spectrometry
3.7. Mass Spectrometry Data Analysis
3.8. Protein Painting
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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PDB ID/Chain | Molecule | Classification | Probability | E-Value | p-Value |
---|---|---|---|---|---|
1LSH_A | Lipovitellin | Lipid binding protein | 100.0 | 4 × 10−107 | 5 × 10−112 |
6I7S_G | Microsomal triglyceride transfer protein | Lipid transport | 100.0 | 1 × 10−73 | 1.3 × 10−78 |
4D50_A | Deoxyhypusine hydroxylase | Oxidoreductase | 98.0 | 0.0062 | 8.1 × 10−8 |
5N3U_A | Phycocyanobilin lyase | Lyase | 97.2 | 0.11 | 1.4 × 10−6 |
4XL5_C | bGFP-A | Protein binding | 97.0 | 0.56 | 7.3 × 10−6 |
6QH5_A | AP-2 complex subunit alpha | Protein transport | 97.0 | 0.33 | 4.2 × 10−6 |
4L7M_B | Putative uncharacterized protein | Unknown function | 96.9 | 0.38 | 5 × 10−6 |
5NZR_K | Coatomer subunit gamma-1 | Transport protein | 96.9 | 0.54 | 7 × 10−6 |
5FUR_I | Transcription initiation factor TFIID | Transcription | 96.8 | 0.057 | 7.4 × 10−7 |
6QH5_B | AP-2 complex subunit beta | Protein transport | 96.8 | 0.92 | 1.2 × 10−5 |
2DB0_B | 253aa long hypothetical protein | Protein binding | 96.7 | 0.62 | 8 × 10−6 |
6YAF_B | AP-2 complex subunit beta | Endocytosis | 96.7 | 0.41 | 5.3 × 10−6 |
6GWC_C | IE5 ALPHAREP | Cell cycle | 96.7 | 0.81 | 1 × 10−5 |
1JDH_A | Beta-catenin | Transcription | 96.4 | 0.87 | 1.1 × 10−5 |
5XJG_A | Vacuolar protein 8 | Signaling protein | 96.3 | 0.48 | 6.3 × 10−6 |
5N3U_B | Phycocyanobilin lyase subunit beta | Lyase | 96.3 | 0.27 | 3.6 × 10−6 |
1OYZ_A | Hypothetical protein yibA | Structural genomics | 95.4 | 0.69 | 9 × 10−6 |
1TE4_A | Conserved protein MTH187 | Structural genomics | 95.3 | 0.72 | 9.3 × 10−6 |
PDB ID/Chain | Molecule | Classification | Probability | E-Value | p-Value |
---|---|---|---|---|---|
2L7B_A | Apolipoprotein E | Lipid transport | 96.2 | 1.1 | 2 × 10−5 |
1LS4_A | Apolipophorin III | Lipid transport | 96.0 | 0.98 | 1.7 × 10−5 |
3R2P_A | Apolipoprotein A-I | Lipid transport | 95.9 | 0.91 | 1.6 × 10−5 |
3R2P_A | Apolipoprotein A-I | Lipid transport | 96.8 | 0.37 | 6.4 × 10−6 |
2L7B_A | Apolipoprotein E | Lipid transport | 96.4 | 1.00 | 1.8 × 10−5 |
5VJ4_A | Uncharacterized protein | Lipid binding protein | 96.4 | 0.58 | 1 × 10−5 |
2LEM_A | Apolipoprotein A-I | Lipid transport | 96.2 | 0.99 | 1.7 × 10−5 |
PDB ID/Chain | Molecule | Classification | Probability | E-Value | p-Value |
---|---|---|---|---|---|
1EQ1_A | Apolipophorin III | Lipid binding protein | 93.44 | 4 | 7 × 10−5 |
1KMI_Z | Chemotaxis protein | Signaling protein | 91.98 | 6.7 | 1.2 × 10−4 |
2L7B_A | Apolipoprotein E | Lipid transport | 97.6 | 0.14 | 2.5 × 10−6 |
3S84_A | Apolipoprotein A-IV | Transport protein | 97.3 | 0.27 | 4.7 × 10−6 |
2LEM_A | Apolipoprotein A-I | Lipid transport | 97.1 | 0.24 | 4.1 × 10−6 |
3K2S_B | Apolipoprotein A-I | Lipid binding protein | 96.9 | 0.64 | 1.1 × 10−5 |
3R2P_A | Apolipoprotein A-I | Lipid transport | 96.6 | 0.72 | 1.3 × 10−5 |
Subunit/Domain | Residue Number | α-Helix (Percentage of Total Content) | β-Strand (Percentage of Total Content) | Coil (Percentage of Total Content) |
---|---|---|---|---|
Subunit I | 28–1017 | 7% | 6.5% | ~8% |
Subunit II | 1018–2072 | <0.5% | 12.5% | 10.5% |
Subunit III | 2073–2550 | ~5.0% | 0% | ~5.0% |
Subunit IV | 2551–4057 | ~1% | 22% | 10.5% |
Subunit V | 4058–4563 | ~10.5% | 0% | ~1% |
Total | 28–4563 | ~24% | 41% | 35% |
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Jeiran, K.; Gordon, S.M.; Sviridov, D.O.; Aponte, A.M.; Haymond, A.; Piszczek, G.; Lucero, D.; Neufeld, E.B.; Vaisman, I.I.; Liotta, L.; et al. A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking. Int. J. Mol. Sci. 2022, 23, 11480. https://doi.org/10.3390/ijms231911480
Jeiran K, Gordon SM, Sviridov DO, Aponte AM, Haymond A, Piszczek G, Lucero D, Neufeld EB, Vaisman II, Liotta L, et al. A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking. International Journal of Molecular Sciences. 2022; 23(19):11480. https://doi.org/10.3390/ijms231911480
Chicago/Turabian StyleJeiran, Kianoush, Scott M. Gordon, Denis O. Sviridov, Angel M. Aponte, Amanda Haymond, Grzegorz Piszczek, Diego Lucero, Edward B. Neufeld, Iosif I. Vaisman, Lance Liotta, and et al. 2022. "A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking" International Journal of Molecular Sciences 23, no. 19: 11480. https://doi.org/10.3390/ijms231911480
APA StyleJeiran, K., Gordon, S. M., Sviridov, D. O., Aponte, A. M., Haymond, A., Piszczek, G., Lucero, D., Neufeld, E. B., Vaisman, I. I., Liotta, L., Baranova, A., & Remaley, A. T. (2022). A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking. International Journal of Molecular Sciences, 23(19), 11480. https://doi.org/10.3390/ijms231911480