Knobs into holes packing

Walshaw, J., and Woolfson, D. N. (2003). Extended knobs-into-holes packing in classical and complex coiled-coil assemblies./. Struct. Biol. 144, 349-361. 

The ways in which a-helices pack against one another were initially described by Crick (1953) as knobs into holes side chain packing which could work at either a shallow left-handed crossing angle or a... 

Fig. 9. Coiled-coil spirals. For the phage coat proteins and flagellin, subunits are shown enlarged next to the structures, as well as the cross sections of the coiled-coil sheets they form. The positions of the subunits in the structures are indicated in white. The core packing layers are also shown for the phage coat proteins in order to illustrate the use of knobs-into-holes and ridges-into-grooves layers.

Figure 1. A. Primary structures of the c-Myc and Max LZs. Sequences are taken from Zervo a al. (26) and renumbered. B. Helical wheel diagram of the c-Myc-Max heterodimeric LZ. Potential interhelical electrostatic interactions have been discussed elsewhere (19,20). In the knobs-into-hole model (9), side-chains (knobs) at position <1 in the heptad repeat pack in the holes formed by consecutive g and a residues and two d positions. Accordingly, Max AsnSn is proposed to pack in the hole formed by Valid, Glu4g, GluSa and LeuSd on the c-Myc LZ. Similarly, Max Asnl9a is proposed to pack in the hole formed by LeulSd, ArglSg, Argl9a and Leu22d.

The NOEs from H5 protons of Max Asn 5a and Max Asn 19a connect these side-chains to the residues on the c-Myc LZ that form the holes in which they would pack according to the knobs-into-holes model (see legend of Fig.l). This strongly supports the proposition that both Asn side-chains are buried at the interface of the c-Myc-Max heterodimeric LZ. 

Crick (1953) introduced the first packing scheme for a helices using a graphical construction referred to as the knobs into holes model. He concluded that helices of the same sense can pack together about 20° away from parallel, or about 70° away from parallel in another type of arrangement. In... 

Figure 3.8 Schematic diagram of the dimeric Rop molecule. Each subunit comprises two a helices arranged in a coiled-coil structure with side chains packed into the hydrophobic core according to the "knobs in holes" model. The two subunits are arranged in such a way that a bundle of four a helices is formed.

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