Amide–π Interactions in the Structural Stability of Proteins: Role in the Oligomeric Phycocyanins
Abstract
:1. Introduction
2. Materials and Methods
2.1. Dataset
2.2. Amide–π Interaction Analysis in Phycocyanin Interfaces
2.3. Computation of Amide–π Interaction Energy in Phycocyanin Interfaces
2.4. Computation of Hot-Spot Residues
2.5. Computation of Stabilization Centers
2.6. Computation of Conservation of Amino Acid Residues
3. Results and Discussion
3.1. Distribution of Amide–π Interactions
3.2. Interaction Pattern and Energetic Contribution of Amide–π Interactions
3.3. Stabilization Centers and Conservation of Amino Acid Residues
4. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Residue | Amide | π | ||||
---|---|---|---|---|---|---|
Number a | % b | Number a | % b | Nhot-spot c | %hot-spot d | |
Backbone | 2086 | 100 | 0 | 0 | 0 | 0 |
Side-chain | ||||||
His | 0 | 0 | 12 | 0.58 | 0 | 0 |
Phe | 0 | 0 | 885 | 42.42 | 744 | 45.7 |
Trp | 0 | 0 | 9 | 0.43 | 0 | 0 |
Tyr | 0 | 0 | 1180 | 56.57 | 884 | 54.3 |
Total | 2086 | 100 | 2086 | 100 | 1628 | 100 |
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Breberina, L.M.; Zlatović, M.V.; Stojanović, S.Đ.; Nikolić, M.R. Amide–π Interactions in the Structural Stability of Proteins: Role in the Oligomeric Phycocyanins. Computation 2024, 12, 172. https://doi.org/10.3390/computation12090172
Breberina LM, Zlatović MV, Stojanović SĐ, Nikolić MR. Amide–π Interactions in the Structural Stability of Proteins: Role in the Oligomeric Phycocyanins. Computation. 2024; 12(9):172. https://doi.org/10.3390/computation12090172
Chicago/Turabian StyleBreberina, Luka M., Mario V. Zlatović, Srđan Đ. Stojanović, and Milan R. Nikolić. 2024. "Amide–π Interactions in the Structural Stability of Proteins: Role in the Oligomeric Phycocyanins" Computation 12, no. 9: 172. https://doi.org/10.3390/computation12090172