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Elucidating the Folding Problem of Helical Peptides using Empirical Parameters. III>Temperature and pH Dependence
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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“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 [116]
Citations
Cites
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-citationMuñoz, 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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Items 201–233 of 233
Temperature-Induced Transitions in Disordered Proteins Probed by NMR Spectroscopy
Kjærgaard, M., Poulsen, F. M., & Kragelund, B. B. (2012) · Methods in molecular biology · doi:10.1007/978-1-4614-3704-8_15 · Cited by 3
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Observation of unique stable nano-assemblies of a lipidated glucagon-like peptide 1 analogue.
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Schmidler, S. C., Hughes, R. G., Oas, T. G., & Zhao, S. (2023) · bioRxiv · doi:10.1101/2023.09.16.558052 · Cited by 1
“These studies in turn led to numerous refinements and extensions to the Lifson-Roig and Zimm-Bragg models to account for unexplained variances present in the new data sets (7–15).”
BackgroundSwitching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity
Zhao, V. Y., Rodrigues, J., Lozovsky, E. R., Hartl, D., & Shakhnovich, E. (2021) · bioRxiv · doi:10.1101/2021.06.18.448971 · Cited by 1
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Helical Propensity Affects the Conformational Properties of the Denatured State of Cytochrome c'.
Danielson, T., & Bowler, B. (2018) · Biophysical Journal · doi:10.1016/j.bpj.2017.11.3744 · Cited by 1
“es/) (77) was used to evaluate the relative tendency”
MethodCoil-helix transition in poly(L-glutamic acid): Evidence for a 3-state non-cooperative process
Zalczer, G. (2012) · The European Physical Journal E : Soft matter · doi:10.1140/epje/i2012-12100-4 · Cited by 1
Modulation Of Intrinsic Properties By Computational Design
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Diffusion–collision model algorithms for protein folding kinetics
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“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).”
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A basic leucine zipper uses a dimer pathway to locate its targets in DNA mixtures
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What Determines the Activity of Antimicrobial and Cytolytic Peptides in Model Membranes
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“Helical content was predicted using AGADIR [79, 80, 81] at 20°C and ionic strength of 0.”
BackgroundMethodInfluentialPreparation of temperature-sensitive antibody fragments
Kamihira, M., & Iijima, S. (2000) · doi:10.1016/s0921-0423(00)80027-1
- Self-citation
Metadata
- 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)
- 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
- 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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