Cited by 251Protein Structure and DynamicsChemical Synthesis and AnalysisRNA and protein synthesis mechanisms

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Elucidating the Folding Problem of Helical Peptides using Empirical Parameters. III>Temperature and pH Dependence

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

DOI 10.1006/jmbi.1994.0024

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Abstract

Explaining the helical behaviour of amino acid sequences without tertiary interactions, in aqueous solution, could be considered one of the first steps to solve the protein folding problem in a rational way. In the accompanying paper the information about the conformational behaviour of helical peptides in solution, as well as the studies on alpha-helix stability in proteins has been utilised to derive a database of energy interactions. This database, when implemented in an algorithm based on the helix-coil transition theory (AGADIR), correctly calculates the average helical behaviour in solution of 423 peptides analysed by circular dichroism. The majority of these peptides have been studied at low temperatures (0 to 10 degrees C), and neutral pH. However, in vivo, proteins fold at higher temperatures and in some cases low or high pH values. To understand protein folding it is necessary to calculate the helical behaviour of linear peptides under very different temperature and pH experimental conditions. We have included the temperature and pH effects on the helical behaviour of peptides by means of generally accepted assumptions and simplifications. The inclusion of these terms allow us to calculate the helical behaviour of polyalanine-based peptides, as well as of complex natural sequences, under different experimental conditions.

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Elucidating the folding problem of helical peptides using empirical parameters
Muñoz, V., & Serrano, L. (1994) · Nature Structural & Molecular Biology · doi:10.1038/nsb0694-399 · Cited by 721
Self-citation
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, V., & Serrano, L. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.0023 · Cited by 354 · cited 14×
“…is assigned, it is straightforward to introduce this term into our algorithm (equations (8) and (9)), since the term previously described DGHbond (Muñoz & Serrano, 1994, 1995), corresponds mainly to enthalpic interactions arising from hydrogen-bond formation and van der Waals interactions,…”
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Helix-coil transition theories. Are they correct?
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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).”
Triphenylphosphine-Initiated Ring-Opening Polymerization for α-Helical Polypeptides and Application in Constructing Artificial Ion Channels.
Yan, Z., Li, T., Liu, J., Fan, J., Ma, S., Zhao, L., & Bao, C. (2025) · Biomacromolecules · doi:10.1021/acs.biomac.4c01716 · Cited by 5
Residual Structure in the Denatured State of the Fast Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A
Becht, D., Leavens, M. J., Zeng, B.-S., Rothfuss, M. T., Briknarová, K., & Bowler, B. (2022) · Biochemistry · doi:10.1021/acs.biochem.2c00011 · Cited by 5
Simulation of the Positive Inotropic Peptide S100A1ct in Aqueous Environment by Gaussian Accelerated Molecular Dynamics.
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
Analysis of Disordered Proteins by Hydrogen Exchange Mass Spectrometry
Weis, D. D. (2016) · Wiley eBooks · doi:10.1002/9781118703748.ch17 · Cited by 7
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
Absolute Net Charge and the Biological Activity of Oligopeptides
Parthasarathi, L., Devocelle, M., Søndergaard, C. R., Baran, I., O'Dushlaine, C., Davey, N. E., Edwards, R. J., Moran, N., Kenny, D., & Shields, D. (2006) · Journal of Chemical Information and Modeling · doi:10.1021/ci0600760 · Cited by 5
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
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
De novo design of stable α-helices.
Yakimov, A., Rychkov, G., & Petukhov, M. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-1486-9_1 · Cited by 5
Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints
Notari, E., Wood, C. W., & Michel, J. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01695 · Cited by 4
Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations
Champion, C., Hünenberger, P. H., & Riniker, S. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c00370 · Cited by 4
The transition state for coupled folding and binding of a disordered DNA binding domain resembles the unbound state
Kuravsky, M. L., Kelly, C., Redfield, C., & Shammas, S. L. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae794 · Cited by 6
“The helical predictor AGADIR ( 65 ) suggests low levels of helical structure may exist within the DNA binding region of CREB, particularly residues 294–306 ( Supplementary Figure S2 , black lines).”
Background
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
Rational design of a highly reactive dicysteine peptide tag for fluorogenic protein labelling.
Strmiskova, M., Tsao, K. K., & Keillor, J. (2018) · Organic and biomolecular chemistry · doi:10.1039/c8ob01417e · 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
Structural and pharmacological characteristics of chimeric peptides derived from peptide E and beta-endorphin reveal the crucial role of the C-terminal YGGFL and YKKGE motifs in their analgesic properties.
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].”
Method
Electrostatic contacts in the activator protein‐1 coiled coil enhance stability predominantly by decreasing the unfolding rate
Mason, J. (2009) · The FEBS Journal · doi:10.1111/j.1742-4658.2009.07440.x · 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
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
Temperature inducible beta-sheet structure in the transactivation domains of retroviral regulatory proteins of the Rev family.
Thumb, W., Graf, C., Parslow, T., Schneider, R., & Auer, M. (1999) · Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy · doi:10.1016/s1386-1425(99)00162-6 · Cited by 4
ALS mutations disrupt self-association between the ubiquilin STI1 hydrophobic groove and internal placeholder sequences
Onwunma, J., Binsabaan, S., Allen, S. P., Thanthirige, S. R., Gaur, D., Sankaran, B., & Wohlever, M. L. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00745-9 · Cited by 10
“The helical propensity of each TMD was calculated using the Agadir score, which uses helix/coil transition theory to provide an energetic description of a peptide ’ s tendency to fold into an α -helix (Muñoz and Serrano, 1994, 1995).”
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
“To further investigate the structural basis for the observed activity changes, we assessed the helicity of both HIF-1 a and CITED2 mutants using AGADIR and AlphaFold (17,18,29 – 31).”
Effect of an Imposed Contact on Secondary Structure in the Denatured State of Yeast Iso-1-Cytochome c
Danielson, T., Stine, J. M., Dar, T., Briknarová, K., & Bowler, B. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b01002 · Cited by 3
Effects of Temperature and Mobile Phase Condition on Chiral Recognition of Poly(l-phenylalanine) Chiral Stationary Phase
Ohyama, K., Oyamada, K., Kishikawa, N., Wada, M., Ohba, Y., Nakashima, K., & Kuroda, N. (2011) · doi:10.1007/s10337-011-2092-5 · Cited by 3
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)
ORCID: Serrano, Luis
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 1995-01
Volume: 245
Issue: 3
Pages: 297-308
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1006/jmbi.1994.0024
OpenAlex: W2028215008
Cited by: 251
References: 0
Citations by year: 2026: 6 · 2025: 6 · 2024: 5 · 2023: 5 · 2022: 9 · 2021: 8 · 2020: 11 · 2019: 6 · 2018: 8 · 2017: 6 · 2016: 6 · 2015: 2 · 2014: 8 · 2013: 11 · 2012: 6
FWCI: 3.85
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, alpha-helix stability, protein folding, helix-coil transition, temperature dependence, pH dependence, polyalanine peptides, circular dichroism, empirical parameters
MeSH terms: Methyl-Accepting Chemotaxis Proteins, Algorithms, Amino Acid Sequence, Bacterial Proteins, Circular Dichroism, Hydrogen-Ion Concentration, Membrane Proteins, Models, Chemical, Molecular Sequence Data, Muscle Proteins, Myoglobin, Neuropeptide Y, Peptides, Protein Kinases, Temperature, Databases, Factual, Protein Structure, Secondary, Protein Folding, Connectin

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Elucidating the Folding Problem of Helical Peptides using Empirical Parameters. III>Temperature and pH Dependence

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