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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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“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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Items 301–355 of 355
Glaser, M., Bruce, N. J., Han, S. B., & Wade, R. (2021) · Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.1c00902 · Cited by 5
Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity
Zhao, V. Y., Rodrigues, J. V., Lozovsky, E. R., Hartl, D. L., & Shakhnovich, E. I. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.09.032 · Cited by 4
Primary Peptide Folding Dynamics Observed with Ultrafast Temperature Jump
Mohammed, O. F., Jas, G. S., Lin, M. M., & Zewail, A. H. (2009) · Angewandte Chemie · doi:10.1002/ange.200900513 · Cited by 4
Glutamine 53 is a gatekeeper residue in the FK506 binding protein.
Korepanova, A., Douglas, C., & Logan, T. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00943-9 · Cited by 4
Amino Acids: Chemical Properties
Dwyer, D. S. (2008) · Wiley Encyclopedia of Chemical Biology · doi:10.1002/9780470048672.wecb007 · Cited by 4
Yennamalli, R. M. (2019) · Encyclopedia of Bioinformatics and Computational Biology · doi:10.1016/b978-0-12-809633-8.20151-9
Notari, E., Wood, C. W., & Michel, J. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01695 · Cited by 4
Chain Sliding versus β‐Sheet Formation upon Shearing Single α‐Helical Coiled Coils
Tsirigoni, A., Goktas, M., Atris, Z., Valleriani, A., Verde, A. V., & Blank, K. G. (2023) · Macromolecular Bioscience · doi:10.1002/mabi.202200563 · Cited by 3
de Jongh, H. D. (2000) · European Journal of Biochemistry · doi:10.1046/j.1432-1327.2000.01654.x · Cited by 2
Diffusion–collision model algorithms for protein folding kinetics
Vasilkoski, Z., & Weaver, D. L. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20032 · Cited by 1
Design and Stability of Peptide β‐sheets
Searle, M. S. (2005) · doi:10.1002/9783527619498.ch10 · Cited by 3
Effects of residue substitutions on the cellular abundance of proteins
Schulze, T. K., & Lindorff-Larsen, K. (2026) · eLife · doi:10.7554/elife.103721 · Cited by 3
“…scale reports on helix propensities for solvent-exposed, non-capping residues ( Pace and Scholtz, 1998 ), AK/AQ ( Rohl et al., 1996 ) and AGADIR ( Muñoz and Serrano, 1995 ) were constructed from experimental data on peptides in solution, and C. & F. ( Chou and Fasman, 1978 ) and Williams (…”
InfluentialEffects of residue substitutions on the cellular abundance of proteinsPreprint
Schulze, T. K., & Lindorff‐Larsen, K. (2024) · eLife · doi:10.7554/elife.103721.1 · Cited by 3
Condamine, E., Courchay, K., Rego, J. D., Leprince, J., Mayer, C., Davoust, D., Costentin, J., & Vaudry, H. (2010) · Peptides · doi:10.1016/j.peptides.2010.01.012 · Cited by 4
“This algorithm has been shown to provide a consistent quantitative description of the helix stability of peptide in solution compared with CD and NMR data [44,45].”
MethodBera, A., Singh, S. C., D’Souza, J. S., Hosur, R. V., & Mishra, P. (2023) · ChemBioChem · doi:10.1002/cbic.202200682 · Cited by 2
Chimeric dihydrofolate reductases display properties of modularity and biophysical diversity
Rodrigues, J., Ogbunugafor, C. B., Hartl, D. L., & Shakhnovich, E. (2019) · Protein Science · doi:10.1002/pro.3646 · Cited by 2
PESCADOR: The PEptides in Solution ConformAtion Database: Online Resource
Pajon, A., Vranken, W., Jiménez, M., Rico, M., & Wodak, S. (2002) · Journal of Biomolecular NMR · doi:10.1023/a:1016346127093 · Cited by 2
Jensen, K. J. (2009) · Wiley eBooks · doi:10.1002/9780470749708.ch6 · Cited by 2
Sarzedas, C. G., Lima, C. S., Juliano, M., Juliano, L., Valente, A., Poian, A. D. D., & Almeida, F. (2008) · Journal of Peptide Science · doi:10.1002/psc.934 · Cited by 1
Mason, J. (2009) · The FEBS Journal · doi:10.1111/j.1742-4658.2009.07440.x · Cited by 4
Potent In Vitro Peptide Antagonists of the Thrombopoietin Receptor as Potential Myelofibrosis Drugs
Szabó, M., Kowalczyk, W., Tarasova, A., Andrade, J., Be, C. L., Mulder, R. J., White, J., Meyer, A. G., Schwab, K. E., Cartledge, K., et al. (2021) · Advanced Therapeutics · doi:10.1002/adtp.202000241 · Cited by 1
Effects of residue substitutions on the cellular abundance of proteins
Schulze, T. K., & Lindorff-Larsen, K. (2026) · eLife · doi:10.7554/elife.103721.3 · Cited by 1
Wang, J., Chen, J., Li, J., An, L., Wang, Y., Huang, Q., & Yao, L. (2018) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25495 · Cited by 1
“After alanine, charged residues arginine and lysine are also good helix formers.(13,14) A helix stabilization mechanism has been proposed for arginine and lysine that their side chains keep the water away from the backbone C5O and N – H groups, based on peptide molecular dynamics simulation studies.”
BackgroundDesign and Stability of α‐Helices
Doig, A. J., Errington, N., & Iqbalsyah, T. M. (2008) · Protein Science Encyclopedia · doi:10.1002/9783527610754.ed06 · Cited by 1
Design and Stability of Peptide β‐sheets
Searle, M. S. (2008) · Protein Science Encyclopedia · doi:10.1002/9783527610754.ed07 · Cited by 1
Zaccaro, L., Bucci, E., Vitale, R., Perretta, G., Fattorusso, R., Benedetti, E., Saviano, M., & Pedone, C. (2003) · Journal of Peptide Science · doi:10.1002/psc.434 · Cited by 2
“Note that the obtained helical percentages, which showed a higher probability of helical conformation for the HAla peptide, are in agreement with the helical propensities predicted by the AGADIR software [41–43].”
ResultPrediction of Factors Determining Changes in Stability in Protein Mutants
Parthiban, V. (2006) · Kölner Universitäts PublikationsServer (Universität zu Köln) · Cited by 1
Fu, H. (2009) · OakTrust (Texas A&M University Libraries) · Cited by 1
Transition States in Protein Folding Kinetics: The Structural Interpretation of Phi-valuesPreprint
Weikl, T. R., & Dill, K. A. (2006) · arXiv (Cornell University) · doi:10.48550/arxiv.q-bio/0605048 · Cited by 1
“In the case of the CI2 helix, we estimate ∆Gα both with the program AGADIR [54,55,56] and from a helix propensity scale [57], see Table 1.”
MethodProtein Folding and Binding: Effective Potentials, Replica Exchange Simulations, and Network Models
Felts, A. K., Andrec, M., Gallicchio, E., & Levy, R. M. (2009) · Biological and medical physics series · doi:10.1007/978-3-540-88787-4_5 · Cited by 1
Identification of a conserved cluster in the RH domain of GRK critical for activation by GPCRs
Baameur, F. (2009) · Digital Commons-TMC (Texas Medical Center)
SPEKTROSKOPISCHE STRUKTURANALYTIK SYNTHETISCHER POLYPEPTIDE
Petry, R. (2002) · Online Publication Service of Würzburg University (Würzburg University)
Dissecting Key Determinants for Calcium and Calmodulin Regulation of GAP Junction and Viral Protein
Chen, Y. (2022) · Digital Archive @ GSU · doi:10.57709/2791701
Unfolding rates for the diffusion-collision model
Beck, C., & Siemens, X. (2001) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.64.052902
The role of the N-capping box in the x1 helix on the structure and stability of CLIC1
Karatas, F. (2011) · University of the Witwatersrand, Johannesburg Institutional Repository on DSpace (University of the Witwatersrand, Johannesburg)
Modulation Of Intrinsic Properties By Computational Design
Xu, F., Nanda, V., & Hsieh, D. H. (2009) · CRC Press eBooks · doi:10.1201/9781420076592.ch16
Vishwanath, S., Banerjee, S., Jamithireddy, A., Srinivasan, N., Gopal, B., & Chatterjee, J. (2017) · Biochemistry · doi:10.1021/acs.biochem.6b01267
Zhang, K. (2019) · DR-NTU (Nanyang Technological University) · doi:10.32657/10356/137037
Ferdigg, A., Dimmer, K., Rapaport, D., & Vitali, D. G. (2020) · PLoS ONE · doi:10.1371/journal.pone.0237982
Fritz, Z. R., Schloss, R. S., Yarmush, M. L., & Williams, L. J. (2021) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2021.128341
Computational Design of Peptides with Improved Recognition of the Focal Adhesion Kinase FAT Domain
Michael, E., Polydorides, S., & Archontis, G. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1855-4_18
Evans, E. D. (2020) · ChemRxiv · doi:10.26434/chemrxiv.12679226
Evans, E. D. (2020) · ChemRxiv · doi:10.26434/chemrxiv.12679226.v1
Efficient Enumeration and Visualization of Helix-Coil EnsemblesPreprint
Schmidler, S. C., Hughes, R. G., Oas, T. G., & Zhao, S. (2023) · bioRxiv · doi:10.1101/2023.09.16.558052 · Cited by 1
“KDE (KDESYEELLRKTKAELLHWTKELTEEEKKALAEEGKIT) is a 38-residue peptide fragment of the Titin protein (14).”
BackgroundRamya, L., Ragunathan, P. T., & Yennamalli, R. M. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00103-2
Schweitzer‐Stenner, R. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-15964-0.00001-3
Notari, E., Wood, C. W., & Michel, J. (2024) · ChemRxiv · doi:10.26434/chemrxiv-2024-t02df
Transition states and loop-closure principles in protein folding
Weikl, T. R. (2007) · publish.UP (University of Potsdam)
Effects of residue substitutions on the cellular abundance of proteinsPreprint
Schulze, T. K., & Lindorff‐Larsen, K. (2026) · eLife · doi:10.7554/elife.103721.2 · Cited by 1
Do, T., Kraft, E. J., Chappell, G. F., Parnham, S., & Berlow, R. B. (2026) · bioRxiv · doi:10.64898/2026.01.20.700670
Controlled packing of metal–peptide superhelices with β-peptide foldamers
Han, I., Lee, H.-J., & Choi, S. H. (2026) · Organic & Biomolecular Chemistry · doi:10.1039/d6ob00111d
Do, T., Kraft, E. J., Chappell, G. F., Parnham, S., & Berlow, R. B. (2026) · Protein Science · doi:10.1002/pro.70693
“We used AGADIR to predict the helical propensity of the CITED CTADs at our experimental conditions (Figure S8) (Lacroix et al., 1998; Munoz & Serrano, 1994; Munoz & Serrano, 1995a; Munoz & Serrano, 1995b).”
- Self-citation
Metadata
- 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
- Physical Sciences › Chemistry › Organic Chemistry › 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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