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Hydrophobic packing

The basic structural unit of these two-sheet p helix structures contains 18 amino acids, three in each p strand and six in each loop. A specific amino acid sequence pattern identifies this unit namely a double repeat of a nine-residue consensus sequence Gly-Gly-X-Gly-X-Asp-X-U-X where X is any amino acid and U is large, hydrophobic and frequently leucine. The first six residues form the loop and the last three form a p strand with the side chain of U involved in the hydrophobic packing of the two p sheets. The loops are stabilized by calcium ions which bind to the Asp residue (Figure S.28). This sequence pattern can be used to search for possible two-sheet p structures in databases of amino acid sequences of proteins of unknown structure. [Pg.84]

Karpusas, M., et al. Hydrophobic packing in T4 lysozyme probed by cavity-filling mutants. Proc. Natl. Acad. Sci. USA 86 8237-8241, 1989. [Pg.372]

An alternative possibility is a vertical stacking structure where the p-strands are arranged on top of each other, again satisfying electrostatic and hydrophobic packing considerations (Fig. 20). Whichever is more likely, this is still far from a complete picture because the exact arrangement of the two disulphide-linked peptide chains is not yet known. [Pg.51]

The functional importance of the rigidity of the SCF has been further tested with a Cull mutant, whose NTD and CTD were engineered to be linked by a flexible linker sequence (Figure 7.9) [85]. This mutant was made in two steps. First, the hydrophobic packing interface between the NTD and the CTD was disrupted by mutating two residues on the NTD and three on the CTD to polar amino acids. Second, the two domains were connected with 12- or 18-residue polar linkers. The... [Pg.175]

JCS(P1)1113]. The formation of the trans adduct involves a boatlike endo transition state (110 versus 111), which is enhanced in aqueous solution by some extra charge separation resulting from both secondary orbital interaction and by a hydrophobic packing effect of the substrate (94JOC1358, 94TL595). [Pg.112]

Coiled-coil a-HeUx abcdefg heptad repeat Hydrophobic packing (a d residues) guided by electrostatics (e g residues) Parallel... [Pg.360]

What distinguishes coiled coils from multiple-helix bundles is that coiled coils contain a narrow hydrophobic face on the surface of each a-helix from the 3-4 hydrophobic repeat, whereas in multiple-helix bundles the hydrophobic interface can contain a wider hydro-phobic surface involving hydrophobes additional to the 3-4 repeat (Scheme 1 for a review, see retf22 ). The wider hydrophobic surface will change the hydrophobic packing and relative orientation of the a-helical chains with respect to each other in bundles as opposed to coiled coils.[17 ... [Pg.69]

When Gdn-HCl masks the electrostatic repulsions, the hydrophobic packing in the antiparallel alignment provides a more stable coiled coil. In contrast, in urea, the electro-... [Pg.92]

Initially, we attempted to build a 3-D homology model of the transmembrane regions of the human thrombin receptor from the structure of IBRD, which is available from the Brookhaven Protein Database. Unfortunately, the suboptimal placement of several amino acid side chains resulted in severe deviations from structural standards for membrane-bound receptors with a seven-helix bundle topology (Figure 2). For example, carboxylate and ammonium groups on amino acid side chains at a mid-helix location were directed into the membrane, rather than toward the inside of the helix bundle, and the hydrophobic packing between some helices was either poor or nonexistent. [Pg.250]

The EC interaction model shown in Fig. 14 suggests that these results are due to favorable hydrophobic packing against His227 for the C12 analog (Fig. 14b) while causing steric clash for the C13 methyl (Fig. 14c). The positive impact of the C12 Van der Waals interaction with His227 is extended by its position adjacent... [Pg.172]

Y370F buried, helix 11 1 Perhaps results in more favorable hydrophobic packing. [Pg.248]

A343V buried, helix 10 2 Improves hydrophobic packing between helices 9 and 10. Interacts with loops also affected by L144M, M358V, and H322Y. [Pg.249]

Furthermore, the reverse result is observed when the diene is disubstituted at C-8, i.e., 5c, although the mechanistic rationalization of this result is at present unclear. When R1 = OBn 137,138 and OTBDMS139, only poor asymmetric induction is observed. However, when the reaction is carried out in water137,138 or in water-methanol (6 1) I4°, the d.r. rises to 80 20137,13S, and this result is ascribed to some extra charge separation resulting from both secondary orbital interaction and a hydrophobic packing effect of the substrate14,1. [Pg.1088]


See other pages where Hydrophobic packing is mentioned: [Pg.92]    [Pg.112]    [Pg.270]    [Pg.253]    [Pg.254]    [Pg.206]    [Pg.178]    [Pg.219]    [Pg.138]    [Pg.343]    [Pg.1066]    [Pg.116]    [Pg.600]    [Pg.415]    [Pg.157]    [Pg.375]    [Pg.375]    [Pg.375]    [Pg.486]    [Pg.71]    [Pg.71]    [Pg.59]    [Pg.408]    [Pg.270]    [Pg.258]    [Pg.347]    [Pg.240]    [Pg.77]    [Pg.173]    [Pg.238]    [Pg.253]    [Pg.105]    [Pg.1795]    [Pg.1798]    [Pg.1798]   
See also in sourсe #XX -- [ Pg.159 ]

See also in sourсe #XX -- [ Pg.1066 ]

See also in sourсe #XX -- [ Pg.1066 ]

See also in sourсe #XX -- [ Pg.1066 ]

See also in sourсe #XX -- [ Pg.159 ]




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Molecular packing, hydrophobic tail

Packings hydrophobicity

Packings hydrophobicity

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