Design and Characterization of a Homodimeric Antiparallel Coiled Coil

Gurnon, Daniel G.; Whitaker, Jennifer A.; Oakley, Martha G.

doi:10.1021/ja0357590

Cited by 69 publications

(91 citation statements)

References 32 publications

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“…Despite the differences between bilayer and aqueous environments, packing motifs identified from racemic crystallization of membrane polypeptides are likely to be useful for the design of soluble heterochiral assemblies. It is possible that the identity of hydrophobic side chains at core positions could be used to control assembly preferences in designed heterochiral coiled coils, as is widely practiced in homochiral systems (60)(61)(62)(63). For instance, placement of Ile residues at interface positions can strongly influence the oligomerization state of homochiral helix-bundles, apparently by favoring assemblies that accommodate the preferred rotameric state of the Ile side chain (60).…”

Section: Discussionmentioning

confidence: 99%

High-resolution structures of a heterochiral coiled coil

Mortenson

Steinkruger

Kreitler

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Interactions between polypeptide chains containing amino acid residues with opposite absolute configurations have long been a source of interest and speculation, but there is very little structural information for such heterochiral associations. The need to address this lacuna has grown in recent years because of increasing interest in the use of peptides generated from D amino acids (D peptides) as specific ligands for natural proteins, e.g., to inhibit deleterious proteinprotein interactions. Coiled-coil interactions, between or among α-helices, represent the most common tertiary and quaternary packing motif in proteins. Heterochiral coiled-coil interactions were predicted over 50 years ago by Crick, and limited experimental data obtained in solution suggest that such interactions can indeed occur. To address the dearth of atomic-level structural characterization of heterochiral helix pairings, we report two independent crystal structures that elucidate coiled-coil packing between L-and D-peptide helices. Both structures resulted from racemic crystallization of a peptide corresponding to the transmembrane segment of the influenza M2 protein. Networks of canonical knobs-into-holes side-chain packing interactions are observed at each helical interface. However, the underlying patterns for these heterochiral coiled coils seem to deviate from the heptad sequence repeat that is characteristic of most homochiral analogs, with an apparent preference for a hendecad repeat pattern.D peptides | transmembrane peptides | racemic crystallization | racemic detergent | coiled coil P olypeptides comprising D-amino acid residues have been sources of growing interest for biological applications, often for functions that depend on recognition by specific natural proteins (1-3). D peptides offer identical versatility in terms of conformation and side-chain functionality relative to conventional peptides (composed of L-amino acid residues), but D peptides are impervious to the action of proteolytic enzymes, which should improve pharmacokinetic properties in vivo relative to those of conventional peptides. The engineering of D peptides to display defined protein-binding preferences is hindered, however, by the dearth of experimental information available for such complexes. Structural principles that are well-known to govern interactions between two L-polypeptide chains are not directly extensible to pairings between peptides of opposite chirality. Favorable heterochiral interactions (between L-and D peptides) that are analogous to homochiral associations between L peptides were postulated decades ago on the basis of geometrical considerations (4, 5). In a 1953 analysis of structural parameters governing coiled-coil formation between right-handed α-helices formed from L peptides, for example, Crick suggested that analogous assemblies should be accessible to pairs of right-and left-handed helices (4). In the same year, Pauling and Corey postulated that heterochiral peptide mixtures could form "rippled" β-sheet assemblies with backbo...

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Section: Discussionmentioning

confidence: 99%

High-resolution structures of a heterochiral coiled coil

Mortenson

Steinkruger

Kreitler

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…In contrast, the antiparallel coiled coils, for which rational design principles have only recently been specified (20)(21)(22)(23)(24)(25)(26), are less structurally scrutinized (15,(27)(28)(29)(30). Both configurations play critical roles in biology, acting for example as oligomerization domains, sites of protein/protein recognition, and nucleic acid binding elements (31-33).…”

Section: Nih-pa Author Manuscriptmentioning

confidence: 99%

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^,

et al. 2006

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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 represents 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 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.The diverse functional prowess of proteins derives in large part from their ability to adopt unique tertiary and quaternary structures, and a major goal of protein chemistry is thus to understand in detail how primary amino acid sequences specify three-dimensional structures. Conformational changes and protein misfolding are critical events in biological processes and diseases in which a given polypeptide sequence gives rise to more than one folded structure, but detailed structural analyses of such processes are often difficult because multiple † We thank the Skaggs Institute for Chemical Biology for financial support, and NSF for a predoctoral fellowship (L.J.L.). § Coordinates have been deposited in the RCSB Protein Data Bank: peptide 2, 1W5K; E20C (peptide 3), 2CCN; E20S (peptide 4), 2CCE, 2CCF; ABA-pLI (peptide 5), 1W5I; peptide 6, 1W5J; E20C Y17H (peptide 7), 1W5H; E20C Ak (peptide 8), 1W5G.* Address correspondence to this author. (858) 784-2700 (phone); (858) 784-2798 (fax); ghadiri@scripps.edu (e-mail).. ‡ These authors contributed equally to this study.Supporting Information Available. Additional figures, CD wavelength scans, thermal denaturation curves, crystallization statistics. This material is available free of charge via the Internet at http://pubs.acs.org. 1 Abbreviations: ABA, acetamidobenzoic acid; CD, circular dichroism; Cys, cysteine, Glu, glutamic acid; HPLC, high-performance liquid chromatography; Lys, lysine; MALDI-TOF, matr...

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“…1, red and blue residues). Because charged residues are routinely found at the g and e positions, mutating these residues in a rational manner to add salt bridges to favor formation of hetero-oligomers (10 -12) and charge-charge repulsions to reduce the formation of homo-oligomers (13,14) can change the affinity and specificity of the coiled coil dimer.…”

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confidence: 99%

“…However, although this provides more salt bridges in the hetero-oligomer, these mutations alone are undesirable as they allow the formation of a greater number of salt bridges in the homo-oligomer. To reduce homo-oligomerization in the mutant coiled coil, residues proximal to charged residues on the opposing helix were considered as candidates for mutation to introduce chargecharge repulsion (13,14). Leu-45 and Glu-48 were identified as two such residues (Fig.…”

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confidence: 99%

Disruption of Bcr-Abl Coiled Coil Oligomerization by Design

Dixon

Pendley

Bruno

et al. 2011

Journal of Biological Chemistry

105

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Oligomerization is an important regulatory mechanism for many proteins, including oncoproteins and other pathogenic proteins. The oncoprotein Bcr-Abl relies on oligomerization via its coiled coil domain for its kinase activity, suggesting that a designed coiled coil domain with enhanced binding to Bcr-Abl and reduced self-oligomerization would be therapeutically useful. Key mutations in the coiled coil domain of Bcr-Abl were identified that reduce homo-oligomerization through intermolecular charge-charge repulsion yet increase interaction with the Bcr-Abl coiled coil through additional salt bridges, resulting in an enhanced ability to disrupt the oligomeric state of Bcr-Abl. The mutations were modeled computationally to optimize the design. Assays performed in vitro confirmed the validity and functionality of the optimal mutations, which were found to exhibit reduced homo-oligomerization and increased binding to the Bcr-Abl coiled coil domain. Introduction of the mutant coiled coil into K562 cells resulted in decreased phosphorylation of Bcr-Abl, reduced cell proliferation, and increased caspase-3/7 activity and DNA segmentation. Importantly, the mutant coiled coil domain was more efficacious than the wild type in all experiments performed. The improved inhibition of Bcr-Abl through oligomeric disruption resulting from this modified coiled coil domain represents a viable alternative to small molecule inhibitors for therapeutic intervention.

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Design and Characterization of a Homodimeric Antiparallel Coiled Coil

Cited by 69 publications

References 32 publications

High-resolution structures of a heterochiral coiled coil

High-resolution structures of a heterochiral coiled coil

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^,

Disruption of Bcr-Abl Coiled Coil Oligomerization by Design

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Design and Characterization of a Homodimeric Antiparallel Coiled Coil

Cited by 69 publications

References 32 publications

High-resolution structures of a heterochiral coiled coil

High-resolution structures of a heterochiral coiled coil

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,

Disruption of Bcr-Abl Coiled Coil Oligomerization by Design

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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^,