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Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution.

Yadav MK, Leman LJ, Price DJ, Brooks CL, Stout CD, Ghadiri MR
Biochemistry 45 4463-73 (2006)
Related entries: 1w5h, 1w5j, 1w5k, 1w5l, 2cce, 2ccn

Cited: 47 times
EuropePMC logo PMID: 16584182

Abstract

A detailed understanding of the mechanisms by which particular amino acid sequences can give rise to more than one folded structure, such as for proteins that undergo large conformational changes or misfolding, is a long-standing objective of protein chemistry. Here, we describe the crystal structures of a single coiled-coil peptide in distinct parallel and antiparallel tetrameric configurations and further describe the parallel or antiparallel crystal structures of several related peptide sequences; the antiparallel tetrameric assemblies represent the first crystal structures of GCN4-derived peptides exhibiting such a configuration. Intriguingly, substitution of a single solvent-exposed residue enabled the parallel coiled-coil tetramer GCN4-pLI to populate the antiparallel configuration, suggesting that the two configurations are close enough in energy for subtle sequence changes to have important structural consequences. We present a structural analysis of the small changes to the helix register and side-chain conformations that accommodate the two configurations and have supplemented these results using solution studies and a molecular dynamics energetic analysis using a replica exchange methodology. Considering the previous examples of structural nonspecificity in coiled-coil peptides, the findings reported here not only emphasize the predisposition of the coiled-coil motif to adopt multiple configurations but also call attention to the associated risk that observed crytstal structures may not represent the only (or even the major) species present in solution.

Reviews - 2ccf mentioned but not cited (1)

  1. The Structure and Topology of α-Helical Coiled Coils. Lupas AN, Bassler J, Dunin-Horkawicz S. Subcell Biochem 82 95-129 (2017)

Articles - 2ccf mentioned but not cited (3)

  1. Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Yadav MK, Leman LJ, Price DJ, Brooks CL, Stout CD, Ghadiri MR. Biochemistry 45 4463-4473 (2006)
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Reviews citing this publication (2)

  1. Coiled Coils - A Model System for the 21st Century. Lupas AN, Bassler J. Trends Biochem. Sci. 42 130-140 (2017)
  2. Exploring biomolecular energy landscapes. Joseph JA, Röder K, Chakraborty D, Mantell RG, Wales DJ. Chem. Commun. (Camb.) 53 6974-6988 (2017)

Articles citing this publication (41)

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  14. Measuring the conformational space of square four-helical bundles with the program samCC. Dunin-Horkawicz S, Lupas AN. J. Struct. Biol. 170 226-235 (2010)
  15. Crystal structure of a trimeric form of the K(V)7.1 (KCNQ1) A-domain tail coiled-coil reveals structural plasticity and context dependent changes in a putative coiled-coil trimerization motif. Xu Q, Minor DL. Protein Sci. 18 2100-2114 (2009)
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  17. Unique features of the anti-parallel, heterodimeric coiled-coil interaction between methyl-cytosine binding domain 2 (MBD2) homologues and GATA zinc finger domain containing 2A (GATAD2A/p66α). Walavalkar NM, Gordon N, Williams DC. J. Biol. Chem. 288 3419-3427 (2013)
  18. Coiled-Coil Motifs of RNA-Binding Proteins: Dynamicity in RNA Regulation. Ford LK, Fioriti L. Front Cell Dev Biol 8 607947 (2020)
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