Crystal structures coiled coils

WA Lim, A Hodel, RT Sauer, FM Richards. The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc Natl Acad Sci USA 91 423-427, 1994. PB Harbury, B Tidor, PS Kim. Repacking proteins cores with backbone freedom Structure prediction for coiled coils. Pi oc Natl Acad Sci USA 92 8408-8412, 1995. 

The first structures of this kind were reported in 1993 pectate lyase G from Erwinia chrysanthemi (Yoder et al, 1993) and alkaline protease from Pseudomonas aeruginosa (Baumann et al, 1993). Based on consideration of these crystal structures, the term parallel //-helix was introduced for a fold containing three //-strands per coil, and parallel //-roll for a fold with two //-strands per coil (Baumann etal, 1993 Yoder andjurnak, 1995 Yoder et al., 1993). The epithet parallel was intended to emphasize the distinction between these folds and the previously observed helical structure of the antibiotic gramicidin which contains both l- and D-amino acids and... 

Fig. 2. Ball-and-stick representations of two differently oriented asparagine ladders of (A) W-arcade taken from the crystal structures of pectate lyase C (Lietzke et al., 1996) and (b) ppl-arcade taken from l DP-.V-aretylglucosamine acyltransferase (Raetz and Roderick, 1995). b, l, and so on refer to a one-letter conformational code (Fig. IOC). The ladders are viewed from within the respective /(-solenoids. The arrow shows the orientation (N- to C-terminal) of the solenoid. Oxygen atoms are in red, nitrogen in blue, and carbon in green. Dotted lines designate H-bonds of side chains (red) and inter-coil H-bonds of the polypeptide backbone (black). Except for the ladder-forming asparagines, only the backbones of the coils are shown. Panels are reprinted from Hennetin et al. (2006) with the permission of the publisher.

Fig. 14. Structural prediction and modeling of a fragment of FHA from B. pertussis containing Rl-repeats. (A) Successive stages in the modeling. From top to bottom identification of the consensus sequence repeat, generation of 2D template of the coil, and the modeled 3D structure. In the consensus sequence, letters indicate residues that are conserved at the level of >60% identity, x is any residue and filled circles represent bulky nonpolar residues. Apolar residues are in red glycine in green. In the 2D template, open circles denote any (but mainly polar) residues, while filled circles denote conserved, mainly nonpolar, residues. Circles inside the coil contour indicate side chains located inside the structure and circles outside the contour denote side chains facing the solvent. Arrows indicate /(-strands. (B) A fragment of the crystal structure of FHA (Clantin et al, 2004) (on the top, in green color) and the 3D model (bottom, in brown).

The /(-helix is a well-authenticated fold, having been observed in more than 20 crystal structures, mostly of secreted bacterial proteins (Jenkins and Pickersgill, 2001 Yoder and Jurnak, 1995 see also Kajava and Steven, this volume). In a /(-helix, the polypeptide chain winds around the molecular axis, each coil consisting of three short /(-strands with connecting turns (Fig. 11). Corresponding strands in successive turns are stacked, generating narrow parallel /(-sheets that are aligned with the... 

Fig. 6. Deconvolved amide F region FTIR spectra of apo- and heme-hemopexin. The amide F FTIR spectra of apo- and heme-hemopexin in D2 O were recorded and curve-fitted to resolve the individual bands. The differences between the original and fitted curves are shown in the upper traces in the panels. The estimated helix (15%), beta (54%), turn (19%), and coil (12%) content of the apo-protein are not significantly changed upon heme binding 104). This analysis was required because of the positive 231-nm elhpticity band in hemopexin and is consistent with the derived crystal structure results.

The crystal structure of human HO-1 complexed with heme has been determined to 2.07 A (163). In order to obtain crystals for high-resolution studies 164), it was necessary to use an E. coli expressed version of HO-1 consisting of residues 1-233 (missing residues 234-288, which includes the C-terminal membrane anchor). This shorter version of HO-1 is soluble and retains about 50% wild-type activity (165). As shown in Fig. 16, HO-1 is formed exclusively by helices and connecting segments of random coil. Although the rich helical content is similar to that of... 

Ozbek, S., Muller, J. F., Figgemeier, E., and Stetefeld,J. (2004). Insights into thermostability at atomic level The crystal structure of the right-handed tetrabrachion coiled coil of Staphylothermus marinus at 1.4 A resolution./. Mol. Biol, (in press). 

Stetefeld, J., Jenny, M., Schulthess, T., Landwehr, R., Engel, J., and Kammerer, R. A. (2000). Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer. Nat. Struct. Biol. 7, 772-776. 

Gonzales, L., Jr., Brown, R. A., Richardson, D., and Alber, T. (1996a). Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism. Nat. Struct. Biol. 3, 1002-1010. 

Yang, Z., Kollman, J. M., Pandi, L., and Doolittle, R. F. (2001). Crystal structure of native chicken fibrinogen at 2.7 A resolution. Biochemistry 40, 12515-12523. Yonekura, K., Maki-Yonekura, S., and Namba, K. (2003). Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424, 643-650. Zhang, L., and Hermans, J. (1993). Calculation of the pitch of the a-helical coiled coil An addendum. Proteins 17, 217-218. 

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