Elucidating the Folding Problem of Helical Peptides using Empirical Parameters. II†. Helix Macrodipole Effects and Rational Modification of the Helical Content of Natural Peptides
Abstract
Explaining the helical behaviour of amino acid sequences in solution could be one of the first steps in solving the protein folding problem in a rational way. The information about the conformational behaviour of helical peptides in solution, as well as the alpha-helix stability in proteins, has been utilised to derive a database with the energy contributions for various interaction taking place in an alpha-helix: intrinsic helical propensities, side-chain to side-chain interactions, main-chain to main-chain hydrogen bonds, and capping effects. This database was implemented in a algorithm based on the helix-coil transition theory (AGADIR). Here, the effects on helix stability due to interactions between charged groups and the helix macrodipole are described, quantified and implemented in AGADIR. The algorithm correctly calculates the average helical behaviour in solution of 423 peptides analysed by circular dichroism and it describes the helicity at a residue level, as found when comparing the prediction for each amino acid residue with the data derived from nuclear magnetic resonance studies. Using AGADIR we have done a rational modification of peptides corresponding to protein secondary structure elements in order to increase their helical content. The circular dichroism analysis of the mutant peptides showed a very good agreement between the experimental and calculated helical content. Moreover, in certain specific cases in which strong tertiary contacts in folded proteins do not exist, the algorithm successfully predicts the length of mutagenised alpha-helices. It is interesting to note that the final values of the parameters used do not significantly differ in absolute terms from those extracted from mutagenesis studies in proteins. This indicates that the same physico-chemical principles stand for both systems.
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Calculations of the percentage of helicity of the CC-Hex*-L24E monomer with Agadir show 13% helicity at pH 2 and 9% helicity at pH 8.5, with intermediate helicities in the pH range 2-8.5.
“indeed, calculations of the percentage of helicity of the CC-Hex*-L24E monomer with Agadir114−118 show 13% helicity at pH 2 and 9% helicity at pH 8.5, with intermediate helicities in the pH range 2–8.5.”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [115]
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Protein folding and stability of human CDK inhibitor p19INK4d
Zeeb, M., Rösner, H. I., Żesławski, W., Canet, D., Holak, T. A., & Balbach, J. (2002) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5242 · Cited by 55 · see citing works
“It is interesting to note that residues of the ®fth ankyrin repeat show the highest helix propensity in an AGADIR investigation of the p19 sequence.(39,40) This ®nding further supports the importance of helices 9 and 10 for the formation of native p19.”
BackgroundSourgen, F., Maroun, R. G., Frère, V., Bouziane, M., Auclair, C., Troalen, F., & Fermandjian, S. (1996) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1996.0765h.x · Cited by 56 · see citing works
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“the presence of both random coil and ~19% of α-helix (Figure 8B) (Greenfield and Fasman, 1969; Morrisett et al., 1973; Schmid, 1997).”
BackgroundMolecular interaction and functional regulation of connexin50 gap junctions by calmodulin
Chen, Y., Zhou, Y.-B., Lin, X.-M., Wong, H., Xu, Q., Jiang, J., Wang, S.-M., Lurtz, M. M., Louis, C., Veenstra, R., et al. (2011) · Biochemical Journal · doi:10.1042/bj20101726 · Cited by 53 · see citing works
Stabilizing nonpolar/polar side‐chain interactions in the α‐helix
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Muñoz, V., Serrano, L., Jiménez, M., & Rico, M. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80145-7 · Cited by 45 · see citing works
Self-citationLi, F., Li, Y., Zhou, Z., Lv, S., Deng, Q., Xu, X., & Yin, L. (2017) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.7b08534 · Cited by 53 · see citing works
Empirical parameterization of a model for predicting peptide helix/coil equilibrium populations
Andersen, N. H., & Tong, H. (1997) · Protein Science · doi:10.1002/pro.5560060913 · Cited by 53 · see citing works
Taddei, N., Chiti, F., Fiaschi, T., Bucciantini, M., Capanni, C., Stefani, M., Serrano, L., Dobson, C. M., & Ramponi, G. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3870 · Cited by 53 · see citing works
Self-citation
- Authors
- Muñoz, V., & Serrano, L.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1995-01
- Volume
- 245
- Issue
- 3
- Pages
- 275-296
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2039104547
- Cited by
- 354
- References
- 0
- Citations by year
- 2026: 5 · 2025: 3 · 2024: 7 · 2023: 6 · 2022: 9 · 2021: 11 · 2020: 9 · 2019: 5 · 2018: 7 · 2017: 7 · 2016: 5 · 2015: 4 · 2014: 11 · 2013: 8 · 2012: 12
- FWCI
- 7.32
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- helical peptides, protein folding, alpha-helix stability, helical propensity, side-chain interactions, hydrogen bonding, peptide modification, circular dichroism
- MeSH terms
- Methyl-Accepting Chemotaxis Proteins, Algorithms, Amino Acid Sequence, Bacterial Proteins, Circular Dichroism, Membrane Proteins, Models, Chemical, Molecular Sequence Data, Peptides, Recombinant Proteins, Spectrin, Protein Structure, Secondary, Protein Folding
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