Cited by 355Protein Structure and DynamicsChemical Synthesis and AnalysisRNA and protein synthesis mechanisms

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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

Muñoz, Victor, Serrano, Luis·1995·Journal of Molecular Biology

DOI 10.1006/jmbi.1994.0023

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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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Background
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Charron, C., Vitoux, B., & Aubry, A. (2002) · Biopolymers · doi:10.1002/bip.10235 · Cited by 6
A structural study of model peptides derived from HIV-1 integrase central domain.
Maroun, R., Zargarian, L., Stocklin, R., Troalen, F., Jankowski, C., & Fermandjian, S. (2005) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.2093 · Cited by 5
HRMAS NMR observation of β‐sheet secondary structure on a water swollen solid support
Rousselot‐Pailley, P., Boutillon, C., Wieruszeski, J., & Lippens, G. M. (2003) · Journal of Peptide Science · doi:10.1002/psc.431 · Cited by 6
The T850D Phosphomimetic Mutation in the Androgen Receptor Ligand Binding Domain Enhances Recruitment at Activation Function 2
Helsen, C., Nguyen, T. T., Vercruysse, T., Wouters, S. M. L., Daelemans, D., Voet, A. R. D., & Claessens, F. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23031557 · Cited by 5
“These findings confirm the predictions of increased helical content for the T850D modified peptide by AGADIR (Tables S2 and S3) [39].”
Effect of Additional Amino Acid Replacements on the Properties of Multi-point Mutant Bacterial Formate Dehyderogenase PseFDH SM4S
POMETUN, A. A., Parshin, P. D., Galanicheva, N. P., Shaposhnikov, L. A., Atroshenko, D. L., POMETUN, E. V., Бурмакин, В. В., Kleymenov, S. Y., Сергеевич, С. С., & Tishkov, V. I. (2022) · Acta Naturae · doi:10.32607/actanaturae.11665 · Cited by 5
Toxoplasma Gondii Importin α Shows Weak Auto-Inhibition
Bhambid, M., Dey, V., Walunj, S., & Patankar, S. (2023) · The Protein Journal · doi:10.1007/s10930-023-10128-2 · Cited by 5
“The helical content of the predicted structures was determined in the Agadir program (http://agadir.crg.es/protected/academic/calculation.jsp) (Lacroix et al., 1998; Muñoz & Serrano, 1994, 1995a, 1995b, 1997).”
Method
Correlating disordered activation domain ensembles with gene expression levels
Flores, E., Camacho, A. R., Cuevas-Zepeda, E., McCoy, M., Yu, F., Staller, M. V., & Sukenik, S. (2025) · Biophysical Reports · doi:10.1016/j.bpr.2024.100195 · Cited by 6
Design of affinity peptides from natural protein ligands: A study of the cardiac troponin complex
Chandra, D., Sankalia, N., Arcibal, I. G., Banta, S., Cropek, D., & Karande, P. (2014) · Biopolymers · doi:10.1002/bip.22436 · Cited by 5
The effect of point amino acid substitutions in an internal α-helix on thermostability of Aspergillus awamori X100 glucoamylase
Surzhik, M., Churkina, S., Shmidt, A., Shvetsov, A. V., Kozhina, T., Firsov, D., Firsov, L., & Petukhov, M. (2010) · Applied Biochemistry and Microbiology · doi:10.1134/s0003683810020134 · Cited by 6
Transition states in protein folding
Weikl, T. (2009) · Communications in Computational Physics · doi:10.4208/cicp.2009.08.202 · Cited by 12
“The program AGADIR is based on helix/coil transition theory, with parameters fitted to data from Circular Dichroism (CD) spectroscopy.”
MethodInfluential
Structural and mechanistic insights into EchAMP: A antimicrobial protein from the Echidna milk.
Kumar, A., Parveen, S., Sharma, I., Pathak, H., Deshmukh, M., Sharp, J., & Kumar, S. (2019) · Biochimica et Biophysica Acta - Biomembranes · doi:10.1016/j.bbamem.2019.03.020 · Cited by 4
Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification
Yang, C., Kim, J., & Shan, S. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167535 · Cited by 5
“Prediction of helical propensity using the AGADIR algorithm (1) for the first 32 residues of FtsQ variants and first 34 residues of PhoA variants, corresponding to the exposed nascent chain sequence of the respective RNC in Fig.”
Method
Dissection of the basic subdomain of the c-Jun oncoprotein: a structural analysis of two peptide fragments by CD, Fourier-transform infrared and NMR.
Krebs, D., Dahmani, B., Monnot, M., Mauffret, O., Troalen, F., & Fermandjian, S. (1996) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1996.t01-1-00699.x · Cited by 5
Nonadditivity in the alpha‐helix to coil transition
Wood, G. G., Clinkenbeard, D., & Jacobs, D. J. (2010) · Biopolymers · doi:10.1002/bip.21572 · Cited by 5
Highly polar environments catalyze the unfolding of PrPC helix 1
Lingenheil, M., Denschlag, R., & Tavan, P. (2010) · European Biophysics Journal · doi:10.1007/s00249-009-0570-6 · Cited by 5
“We decided to simulate the longer sequence 144–156 identified for H1 in the NMR structure at neutral pH (Calzolai and Zahn 2003) because the positive charge of the C-terminal R156 will, in any case, influence the electrostatics of H1 and, in particular, might contribute to the stability of the helix by favorable inter…”
Background
Genetic algorithms as a tool for helix design – computational and experimental studies on prion protein helix 1
Ziegler, J., & Schwarzinger, S. (2006) · J. Comput. Aided Mol. Des. · doi:10.1007/s10822-006-9035-5 · Cited by 7
Interaction of a designed interleukin‐10 epitope mimic with an antibody studied by isothermal titration microcalorimetry
Welfle, K., Misselwitz, R., Sabat, R., Volk, H., Schneider-Mergener, J., Reineke, U., & Welfle, H. (2001) · Journal of Molecular Recognition · doi:10.1002/jmr.523 · Cited by 4
Efficient enumeration and visualization of helix-coil ensembles
Hughes, R. G., Zhao, S., Oas, T. G., & Schmidler, S. C. (2023) · Biophysical Journal · doi:10.1016/j.bpj.2023.12.021 · Cited by 4
Structural Basis of α-Catenin Recognition by EspB from Enterohaemorrhagic E. coli Based on Hybrid Strategy Using Low-Resolution Structural and Protein Dissection
Hamaguchi, M., Kamikubo, H., Suzuki, K. N., Hagihara, Y., Yanagihara, I., Sakata, I., Kataoka, M., & Hamada, D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071618 · Cited by 4
βαβ Super-Secondary Motifs: Sequence, Structural Overview, and Pursuit of Potential Autonomously Folding βαβ Sequences from (β/α)8/TIM Barrels
Kadumuri, R. V., Irukuvajjula, S. S., & Vadrevu, R. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9161-7_11 · Cited by 4

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)
DOI: 10.1006/jmbi.1994.0023
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
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
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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Elucidating the Folding Problem of Helical Peptides using Empirical Parameters. II†. Helix Macrodipole Effects and Rational Modification of the Helical Content of Natural Peptides

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