A Periodic Table of Coiled-Coil Protein Structures

Moutevelis, Efrosini; Woolfson, Derek N.

doi:10.1016/j.jmb.2008.11.028

Cited by 190 publications

(177 citation statements)

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“…1A, coiled coils comprise two or more α-helical chains that wrap, or supercoil, around one another to form extended rope-like structures. Although many of these remain as discrete structures (20), others assemble further into supramolecular structures, as seen for example in intermediate filaments (21,22). Well-defined sequence-to-structure relationships for coiled coils are available, which provide a solid basis for rational protein design (23).…”

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confidence: 99%

Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design

Sharp

Bruning

Mantell

et al. 2012

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

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Nature presents various protein fibers that bridge the nanometer to micrometer regimes. These structures provide inspiration for the de novo design of biomimetic assemblies, both to address difficulties in studying and understanding natural systems, and to provide routes to new biomaterials with potential applications in nanotechnology and medicine. We have designed a self-assembling fiber system, the SAFs, in which two small α-helical peptides are programmed to form a dimeric coiled coil and assemble in a controlled manner. The resulting fibers are tens of nm wide and tens of μm long, and, therefore, comprise millions of peptides to give gigadalton supramolecular structures. Here, we describe the structure of the SAFs determined to approximately 8 Å resolution using cryotransmission electron microscopy. Individual micrographs show clear ultrastructure that allowed direct interpretation of the packing of individual α-helices within the fibers, and the construction of a 3D electron density map. Furthermore, a model was derived using the cryotransmission electron microscopy data and side chains taken from a 2.3 Å X-ray crystal structure of a peptide building block incapable of forming fibers. This was validated using singleparticle analysis techniques, and was stable in prolonged molecular-dynamics simulation, confirming its structural viability. The level of self-assembly and self-organization in the SAFs is unprecedented for a designed peptide-based material, particularly for a system of considerably reduced complexity compared with natural proteins. This structural insight is a unique high-resolution description of how α-helical fibrils pack into larger protein fibers, and provides a basis for the design and engineering of future biomaterials.fibrous proteins | protein design | helical reconstruction | X-ray crystallography

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mentioning

confidence: 99%

Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design

Sharp

Bruning

Mantell

et al. 2012

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

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“…Most fibrils of this kind, particularly those having the observed flexibility and resilience, are frequently comprised of successive coiled-coil proteins [11,12] but the greater diameter of these fibrils would also be consistent with other motifs, such as actin or other fibers as are seen composing cellular cytoskeletons. They are unlikely to be formed by a single polypeptide, as that would seem incompatible with a length of 450 nm, nor are they segmented as is seen for the tail fibers in other bacteriophage such as T4 [10].…”

Section: Resultsmentioning

confidence: 82%

Unique Tail Appendages of Marine Bacteriophages

Kuznetsov¹,

Chang²,

Credaroli³

et al. 2013

AiM

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The objective was to visualize a variety of marine bacteriophage and identify unique structural features that set them apart from terrestrial phages. Phages were plaque isolated and characterized using atomic force microscopy. Bacteriophage infecting cyanobacteria synechococcus that exhibits a novel structural feature not previously reported for any other phages were observed. These cyanophages have up to four, 450 nm long, multi-stranded, complex helical fibers that emanate from either the base plate and/or the collar of the phage particle, origins of shorter fibers on well-studied phages such as T4. The flexible fibers terminate at their distal ends in multiple bulbs of diameter 30 nm composed of 20 to 30 closely associated proteins. Bulbs form one of two distinctive patterns, or tassels. Most commonly, the arrangement is a 3 + 1 pattern of three consecutive bulbs at the very end with a forth lying upstream, separated from the terminal three by a gap of 135 nm. In other populations the fibers terminate in 5 consecutive bulbs. It is proposed that the novel appendages may be involved in host cell searching and recognition in a marine environment.

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“…By contrast, the more modular assembly of ␣-helical coiled coils makes their folding generally rapid and efficient on the s-ms time frame (27). However, we note for ␣-helical coil coils that some require particular sequence motifs to trigger folding and assembly (28) and that the more general structure and mechanism of assembly can lead to promiscuity (21,23) as many more coiled-coil architectures are possible in addition to the three-stranded parallel type (3,29).…”

Section: Discussionmentioning

confidence: 99%

Designed Coiled Coils Promote Folding of a Recombinant Bacterial Collagen

Yoshizumi¹,

Fletcher

Yu³

et al. 2011

Journal of Biological Chemistry

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Collagen triple helices fold slowly and inefficiently, often requiring adjacent globular domains to assist this process. In the Streptococcus pyogenes collagen-like protein Scl2, a V domain predicted to be largely ␣-helical, occurs N-terminal to the collagen triple helix (CL). Here, we replace this natural trimerization domain with a de novo designed, hyperstable, parallel, three-stranded, ␣-helical coiled coil (CC), either at the N terminus (CC-CL) or the C terminus (CL-CC) of the collagen domain. CD spectra of the constructs are consistent with additivity of independently and fully folded CC and CL domains, and the proteins retain their distinctive thermal stabilities, CL at ϳ37°C and CC at >90°C. Heating the hybrid proteins to 50°C unfolds CL, leaving CC intact, and upon cooling, the rate of CL refolding is somewhat faster for CL-CC than for CC-CL. A construct with coiled coils on both ends, CC-CL-CC, retains the ϳ37°C thermal stability for CL but shows less triple helix at low temperature and less denaturation at 50°C. Most strikingly however, in CC-CL-CC, the CL refolds slower than in either CC-CL or CL-CC by almost two orders of magnitude. We propose that a single CC promotes folding of the CL domain via nucleation and in-register growth from one end, whereas initiation and growth from both ends in CC-CL-CC results in mismatched registers that frustrate folding. Bioinformatics analysis of natural collagens lends support to this because, where present, there is generally only one coiled-coil domain close to the triple helix, and it is nearly always N-terminal to the collagen repeat.The collagen triple helix and the ␣-helical coiled coil (CC) 4 are well characterized superhelical motifs in proteins (1-3). They form rod-like structures, which are directed by clear amino acid patterns in their sequences. Collagen triple helices require glycine as every third residue and often have a high imino acid (proline and hydroxyproline) content. These features lead to the formation of polyproline II helices, which trimerize via interchain hydrogen bonding and close packing to form the collagen triple helix (see Fig. 1A). By contrast, most coiled coils are low in glycine and proline and have a so-called heptad, or related repeats in which hydrophobic residues alternate three and four residues apart. This pattern promotes the formation of amphipathic ␣-helices that combine via their hydrophobic faces to form rope-like helical bundles (Fig. 1, B and C).These supercoiled collagen and ␣-helical coiled-coil structures were first elucidated as the major elements in fibrous proteins but have since been found in a wide range of proteins, including globular and membrane-spanning structures (2, 3). Some proteins contain both collagen and ␣-helical coiled-coil domains. For instance, three-stranded coiled coils occur immediately C-terminal to collagen triple helices in lung surfactant apoprotein D, lung surfactant apoprotein A, mannose-binding protein, and other collectins (4), whereas the macrophage scavenger receptor has a coiled...

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A Periodic Table of Coiled-Coil Protein Structures

Cited by 190 publications

References 50 publications

Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design

Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design

Unique Tail Appendages of Marine Bacteriophages

Designed Coiled Coils Promote Folding of a Recombinant Bacterial Collagen

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