Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif
Abstract
:1. Introduction
2. Results
2.1. Identifying Overlap-Based Interactions in -Turns of Proteins
2.2. Analysis of NCIs in -Turns in Terms of Structure and Interaction Energy
2.3. Prevalence of NCIs in -Turns of PDB Structures
2.3.1. Energetics
2.3.2. Geometric Criteria Based on Variations in -Turn Sidechain Structure
- As increases, decreases in strength. A small value of this coordinate is more important than the dihedral in order for the interaction to materialise. From this analysis, it is clear that this interaction exists when 0 Å Å and .
- The strength of the interaction decreases as deviates from , suggesting that this interaction is likely to be present when . Though the lower limit of has emerged from the current analysis of only 22 proteins, it is apparent that the extent of overlap will go to zero as we approach or lower.
- The presents two possible scenarios for its existence. The orbital can overlap with the n orbital either when C=O and are on the same side of the peptide backbone, or on the opposite sides of the backbone because of the cylindrical nature of the orbital. Therefore this interaction is possible when (a) Å Å and , and (b) Å Å and . Though the latter case was not seen in the GB1 variants, the PDB analysis shows that these interactions can occur in more than one orientation. Note that this is in contrast to expecting this interaction to exist simply based on the distance being less than sum of van der Waals radii of and , and an exhaustive NBO analysis was essential to establish the criterion for the existence of even when is large.
2.3.3. Analysis
3. Discussion
4. Methods
4.1. Natural Bond Order Analysis
4.2. Solvent Model
Supplementary Materials
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Interaction | Donor () | Acceptor () | Covalent Bond | ||
---|---|---|---|---|---|
Atom(s) | Orbital | Atom(s) | Orbital | Separation | |
O | n | C=O | 4 | ||
O | n | - | 3 | ||
O | n | - | 3 | ||
C=O | C=O | 3 |
-Variant | (,) | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
d(Å) | () | (Å) | () | () | (Å) | () | ||||||
vT | (−58.8,−46.6) | 2.9 | 97.6 | 0.46 | 2.6 | 51.2 | - | 163.6 | 0.54 | 3.3 | 13.2 | 0.27 |
vA | (−59.7,−42.2) | 3.0 | 102.2 | 0.25 | 2.7 | 44.6 | - | 163.6 | 0.51 | 3.5 | 15.4 | 0.18 |
vS | (−66.3,−28.9) | 3.0 | 112.2 | 0.20 | 2.5 | 43.1 | 0.12 | 162.2 | 0.52 | 3.7 | 21.2 | 0.11 |
vV | (−85.1,−12.4) | 3.3 | 122.8 | - | 2.4 | 24.5 | 0.89 | 150.1 | 0.41 | 4.2 | 15.8 | - |
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Nagesh, J. Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif. Molecules 2021, 26, 1533. https://doi.org/10.3390/molecules26061533
Nagesh J. Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif. Molecules. 2021; 26(6):1533. https://doi.org/10.3390/molecules26061533
Chicago/Turabian StyleNagesh, Jayashree. 2021. "Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif" Molecules 26, no. 6: 1533. https://doi.org/10.3390/molecules26061533