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A thermodynamic scale for leucine zipper stability and dimerization specificity: e and g interhelical interactions.
Open accessAbstract
The leucine zipper is a dimeric coiled-coil protein structure composed of two amphipathic alpha-helices with the hydrophobic surfaces interacting to create the dimer interface. This structure has been found to mediate the dimerization of two abundant classes of DNA binding proteins: the bZIP and bHLH-Zip proteins. Several workers have reported that amino acids in the e and g positions of the coiled coil can modulate dimerization stability and specificity. Using the bZIP protein VBP as a host molecule, we report a thermodynamic scale (delta delta G) for 27 interhelical interactions in 35 proteins between amino acids in the g and the following e positions (g<==>e') of a leucine zipper coiled coil. We have examined the four commonly occurring amino acids in the e and g positions of bZIP proteins, lysine (K), arginine (R), glutamine (Q), glutamic acid (E), as well as the only other remaining charged amino acid aspartic acid (D), and finally alanine (A) as a reference amino acid. These results indicate that E<==>R is the most stable interhelical pair, being 0.35 kcal/mol more stable than E<==>K. A thermodynamic cycle analysis shows that the E<==>R pair is 1.33 kcal/mol more stable than A<==>A with -1.14 kcal/mol of coupling energy (delta delta Gint) coming from the interaction of E with R. The E<==>K coupling energy is only -0.14 kcal/mol. E interacts with more specificity than Q. The R<==>R pair is less stable than the K<==>K by 0.24 kcal/mol. R interacts with more specificity than K. Q forms more stable pairs with the basic amino acids K and R rather than with E. Changing amino acids in the e position to A creates bZIP proteins that form tetramers.
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“Thermodynamic cycle analysis of mutant coiled coils showed that charged residues at a g position at residue i can interact favorably or unfavorably with a charged residue at the e' position at i + 5 (Krylov et al., 1994; Zhou et al., 1994a, 1994b; Kohn et al., 1995), consistent with the orientation of ion pairs observed in the crystal structures.”
From Oligomerization properties of GCN4 leucine zipper e and g position mutants (1997) · cites this paper as Krylov et al., 1994
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Metadata
- Authors
- Krylov, D., Mikhailenko, I., & Vinson, C.
- Affiliations
- National Institutes of Health (US)
- Venue
- The EMBO Journal
- Published
- 1994-06-01
- Volume
- 13
- Issue
- 12
- Pages
- 2849-2861
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC395166
- OpenAlex
- W2301031628
- Semantic Scholar
- e223136a6090aa7f84312e0d6991cd8cf28a68c5
- Cited by
- 269
- References
- 68
- Citations by year
- 2026: 2 · 2025: 6 · 2024: 3 · 2023: 1 · 2022: 6 · 2021: 6 · 2020: 6 · 2019: 9 · 2018: 2 · 2017: 4 · 2016: 3 · 2015: 8 · 2014: 12 · 2013: 7 · 2012: 11
- FWCI
- 5.57
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The EMBO Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Center for Research Resources (RR 04328, P41RR004328)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › thermodynamics and calorimetric analyses
- Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
- Keywords
- leucine zipper, coiled coil, interhelical interactions, bZIP transcription factors, thermodynamic cycle analysis, coupling energy, glutamate, L-arginine, lysine, glutamine, tetramer formation, DNA-binding proteins
- MeSH terms
- Amino Acid Sequence, Carrier Proteins, Centrifugation, Isopycnic, Circular Dichroism, DNA-Binding Proteins, Models, Chemical, Molecular Sequence Data, Protein Denaturation, Recombinant Proteins, Thermodynamics, Transcription Factors, Leucine Zippers, Protein Structure, Tertiary, Helix-Loop-Helix Motifs, Avian Proteins, Basic-Leucine Zipper Transcription Factors, G-Box Binding Factors
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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