Helix residue

FIGURE 6.24 (a) The alpha helix consisting of residues 153-166 (red) in flavodoxin from Anahaena is a surface helix and is amphipathic. (b) The two helices (yellow and blue) in the interior of the citrate synthase dimer (residues 260-270 in each monomer) are mostly hydrophobic, (c) The exposed helix (residues 74-87—red) of calmodulin is entirely accessible to solvent and consists mainly of polar and charged residues. 

Less commonly, an a-helix can be completely buried in the protein interior or completely exposed to solvent. Citrate synthase is a dimeric protein in which a-helical segments form part of the subunit-subunit interface. As shown in Figure 6.24, one of these helices (residues 260 to 270) is highly hydrophobic and contains only two polar residues, as would befit a helix in the protein core. On the other hand. Figure 6.24 also shows the solvent-exposed helix (residues 74 to 87) of cahnodulln, which consists of 10 charged residues, 2 polar residues, and only 2 nonpolar residues. 

Each subunit contributes a tower helix (residues 262 to 278) to the sub-unit-subunit contact interface in glycogen phosphorylase. In the phosphorylase dimer, the tower helices extend from their respective subunits and pack against each other in an antiparallel manner. 

Fig. 13. Cluster 1 is a [4Fe-4S] cubane cluster located at the N-terminus of the Fepr molecule and close to the first long helix (residues 24-50 inclusive). The cluster is bound to the protein by four cysteine residues Cys 3, Cys 6, Cys 15, and Cys 21. The distribution of these cysteine residues contrasts mEnkedly with that found in the ferre-doxins.

Superposition of residues 83 to 248 of the family of structures is shown in Figure 9 viewed along the long axis of the catalytic helix. Residues 249 to 255 are disordered and therefore are not shown. In Figure 10 ribbon drawings of two views of the molecule are shown, one from above the (3-sheet and the other from below the Si subsite. The secondary structure of sfSTR consists of a five stranded [. -sheet with four parallel strands and... 

Looking down the axis of an a-helix. Residue sequence is numbered. The angle between residues is 36073.6 residues or 100°. 

Fig. 6. Structure of the T4 short tail fiber. The structure of residues 246-527 is shown it is a composite of two partial structures (Thomassen et al., 2003 van Raaij et al., 2001a). The different domains are indicated the T4-fiber fold consisting of residues 246-286, the triple / -helix (residues 290-329), the collar domain (residues 330-396 and 518-527), and the receptor-binding domain (amino acids 397-517). The zinc ion in the center of the receptor-binding domain is shown as a gray sphere.

Milnes, J.T., Witchel, H.J., Leaney, J., Leishman, D. and Hancox, J.C. (2006) hERG K+ channel blockade by the antipsychotic drug thioridazine an obligatory role for the S6 helix residue F656. Biochemical and Biophysical Research Communications, 351, 273-280. 

Fig. 11. Drawing of a typical a-helix, residues 40-51 of the carp muscle calciumbinding protein. The helical hydrogen bonds are shown as dotted lines and the main chain bonds are solid. The arrow represents the right-handed helical path of the backbone. The direction of view is from the solvent, so that the side groups on the front side of the helix are predominantly hydrophilic and those in the back are predominantly hydrophobic.

Number of skeletal chain atoms contained within the helix residue. 

Figure 28-3 (A) Ribbon view of the dimeric lac repressor bound to a natural operator and to the anti-inducer o-nitro-phenylfucoside (ONPF). The headpiece (residues 2-46) and the hinge helix (residues 50-58) form the DNA-binding domains. The core (residues 62-330), which is divided into N- and C-terminal subdomains, forms the binding site for ONPF. The C-terminal residues 334-360, which form a tetramerization domain, are absent from this MolScript drawing. Notice that the hinge helices bind to and widen the minor groove at the center of the operator. From Lewis et al.5a (B) Model of a 93-bp DNA loop corresponding to residues -82 to +11 of the lac operon (Fig. 28-2) bound to the tetrameric lac repressor. The active sites of the repressor are bound to the major operator O, and to the secondary operator 03. From Lewis et al.5...

The transition state is constructed around an extended, delocalized nucleus (Figure 19.9) consisting of the helix (residues 12-24) and the interactions it makes with hydrophobic residues in the core that are located around position 50, especially from Ala-16. Recall from section B3 that these long-range interactions are precisely those required to stabilize the helix in peptide fragments of CI2. 

Fig. 9. The conformation adopted by a leucine-rich repeat (LRR) is that of a /9-strand followed by an o-helix. In porcine ribonuclease inhibitor, a /9-strand (residues 2-8) is connected to an o-helix (residues 14—27) by a connecting loop (residues 9-13). A horseshoe-shaped structure is formed and is exemplified in the crystal structure of ribonuclease inhibitor (PDB 1A4Y Kobe and Deisenhofer, 1993). This has an inner concave surface formed by curved /9-sheets and an outer convex surface formed by oh el ices. The leucines and other large apolar residues form the hydrophobic core of the structure.

The NMR structures of PYP lacking the N-terminal 25 residues were reported under the dark and illuminated conditions [34]. In the NMR structure of the M intermediate, the three regions at residues 42-58, 63-78, and 96-103 (the amino-acid positions in intact PYP) are highly disordered to bring the exposure of the hydrophobic chromophore to the solvent. Although the structural changes in the a4 helix (residues 55-58) and the loop connecting... 

The second transmembrane helix (residues 69—89) traverses the lipid bilayer from the periplasm back to the cytoplasm along the outside of the TM1 helix bundle, and is consequently responsible for most of the contact with the lipid bilayer. The lipid exposed surface of MscL is composed of approximately 35% TM1 and 65% TM2. The face of TM2 that comes in contact with the lipid bilayer is lined with many hydrophobic residues (Leu-69, Leu-72, Leu-73, Ile-77, Phe-79, Phe-80, Leu-81, Phe-84, and Phe-88) and is more hydrophobic than an average protein core (Rees et al., 1989 Wallin et al., 1997 Spencer and Rees, 2002). The TM2 helix, like the TM1 helix, is tilted about 35° with respect to the membrane normal however, unlike the TM1 helices, the TM2 helices from different subunits are separated by 20 A and do not contact each other. 

In detail The first lobe (residues 1 -39 and 85-129) contains four helices that are close to the Pauling—Corey a-helix type, and one singleturn 310-type helix. There are short stretches (each five to nine residues) of backbone loops and turns connecting the helices. Three a helices (helix A, residues 4—15 helix C, residues 88—99 helix D, residues 108-115) are on the protein surface and are partially exposed to solvent. The a helix (B) consisting of residues 24-36 is totally buried. The 310 helix (residues 119—124) is partially exposed to solvent. The second lobe (residues 40-84) contains a three-stranded antiparallel y3-pleated... 

Table 1. Sequence alignment between the transmembrane helices of bR (Helix 1 -Helix 7) and those reported in various GPCR models based on the bR template . The P2-AR sequence is recorded here for reference even when the authors have modelled other receptors. In each helix, residues in bold are class A sequence motifs or residues involved in ligand binding. A shift if 3 or 4 residues corresponds to a difference of 1 turn and a vertical displacement of about 5 A.

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