Hydrophobic core, repacking

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. 

Fig. 6. Repacking of the influenza HA2 hydrophobic core. Left. A ribbon trace of HA2 residues 38 to 127, including the helices that make up the core of the stalk in the native HA structure (see Fig. 3). Middle A hypothetical structure obtained by fusing the base of the coiled coil from the native HA structure with the top of the extended coiled coil from the low pH-converted HA structure. This panel helps distinguish the two major components of the HA conformational change on low pH treatment the existence of such an intermediate structure has not been shovm experimentally for influenza and may exist only transiently if at all. This extended structure, known as a prehairpin intermediate, has been detected indirectly in other virus envelope proteins (reviewed in Chan and Kim, 1998). Right Residues 38 to 127 from low pH-converted HA2 (Bullough et al, 1994). Hydrophobic residues that stabilize the jackknifed structure are indicated in one protomer as gray space-filling atoms. The amino (N) and carboxy (C) termini of a protomer within each trimer structure are indicated.

A. Repacking the Hydrophobic Core of a Four Helix Bundle... 

Marsh and co-workers have redesigned an antiparallel 4-helix bundle protein by incorporation of hexafluoroleucines into two, four, or six layers in the core. The free energy of unfolding increased by 0.3 kcal/mol per hexafluoroleucine for repacking of the central two layers and by an additional 0.12kcal/mol for other layers [47, 111]. NMR studies suggested a more structured backbone and a less fluid hydrophobic core in the fluorinated proteins, relative to the hydrocarbon control [111]. 

---