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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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 [116]
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Similar Yet Different–Structural and Functional Diversity among Arabidopsis thaliana LEA_4 Proteins
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“Low-temperature induced folding has, for example, been described for type I fish antifreeze proteins [49,50] and small α-helical peptides [51].”
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- 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
- 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, 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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