The CC+ Database | Documentation | Introduction to Socket The CC+ Database navigation search documentation Recent pages Introduction to Socket An Introduction to SOCKET Coiled coils comprise two or more α-helices wound around each other to give rope-like structures1. Most coiled coils are characterised by a sequence pattern of hydrophobic (H) and polar (P) residues called the heptad repeat, (HPPHPPP)n. Each position within the heptad repeat is typically labelled a to g2. Several coiled-coil prediction algorithms are based on the identification of heptad repeats in the protein sequences3, 4, 5. Some sequence-based algorithms can also predict the oligomerisation state of a coiled coil by scoring the potential of this coiled coil adopting one of two possible states6, 7. Characteristic Packing In addition to the heptad repeat, coiled-coil structures have a particular packing arrangement between the α-helices termed “knobs-into-holes” (KIH) packing, first described by Crick1. In KIH packing, every first (a) and fourth (d) residue of each heptad repeat is a “knob”, which fits into a diamond-shaped “hole” formed by four residues of another α-helix in close proximity. SOCKET is an assignment method that focuses on these knob-into-hole interactions8; i.e. coiled-coil assignments are based on structure and not sequence. SOCKET identifies KIH interactions as follows: all residues within α-helices are represented by their centres of mass; “knob” residues are typically defined as side chains within 7 Å of 4 other residues on a neighbouring helix. This distance is called the packing cutoff, and has been chosen empirically to reduce false-positive assignments; ”hole” residues for a given knob are typically defined as the 4 nearest side chains; 2-stranded coiled coils have pairwise-complementary KIH interactions: when a knob from helix A packs into a hole comprising four side chains of helix B, one or more of these hole residues reciprocate by packing into another hole of side chains on helix A. Higher-order coiled coils have cyclically complementary KIH interactions. In this case, a knob from helix A fits in a hole of helix B, the corresponding knob on B acts into a hole of C, and so on. Detailed information on the SOCKET algorithm can be found in “Socket: a Program For Identifying and Analysing Coiled-coil Motifs Within Protein Structures”8. Visualizing Assignments We have developed a visual means of understanding assignments made with the SOCKET algorithm. Expanding upon SOCKET's existing facility to create RASMOL scripts of assigned coiled coils, we have implemented a similar facility using the PyMOL molecular graphics system9. These new scripts facilitate determining the relative orientation of a coiled coil's α-helices, and the location of heptad/nonheptad repeats, at a glance. This is made possible by identifying each register position using a rainbow colour scheme: Residues at a positions are shown in red. Residues at b positions are shown in orange. Residues at c positions are shown in yellow. Residues at d positions are shown in green. Residues at e positions are shown in cyan. Residues at f positions are shown in blue. Residues at g positions are shown in violet. When rendered using these PyMOL scripts, coiled-coil assignments with antiparallel or mixed configurations of α-helices can be identified by coloured sequences running in different directions. Nonheptad repeats are immediately identifiable by the clustering of similarly coloured residues. Furthermore, the hydrophobic core of coiled-coil assignments can be seen clearly as a stripe of red and green residues, and potential stabilizing interactions flanking this core can sometimes be seen between cyan- and violet-coloured residues. References Crick, F. H. C. Acta Crystallogr., 1953, 6, 689-697. You can view this paper. Lupas, A. Trends Biochem. Sci. 1996, 21, 375-382. You can view this paper. Lupas A, Van Dyke M, Stock J. Science, 1991, 252, 1162-1164. You can view this paper, or visit the site. Delorenzi, M., Speed, T. Bioinformatics 2002, 18, 617-625. You can view this paper, or visit the site. Berger, B., Wilson, D. B., Wolf, E., Tonchev, T., Milla, M., Kim, P. S. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 8259-8263. You can view this paper, or visit the site. Woolfson, D. N., Alber, T. Protein Sci. 1995, 4, 1596-1607. You can view this paper. Wolf, E., Kim, P. S., Berger, B. Protein Sci., 1997, 6, 1179-1189. You can view this paper, or visit the site. Walshaw, J., Woolfson, DN., J. Mol. Biol., 2001, 307, 1427-1450. You can view this paper, or visit the site. DeLano, W. L. 2002. You can visit the site. Badges Last updated 12/12/07 at 1:48 XHTML CSS PHP Firefox
