1-start helix

The value of the on-rate constant for a particular growth site will depend on n, the number of growing points on both ends of a tubule. For example, if the tubule is treated as a three-start helix with each helix starting point serving as a distinct growth site, then n will be sbc, and the on-rate constant will be about 3 x 10 M sk. Such a value would be about a factor of 10 below the theoretical limit for diffusion-controlled processes involving macromolecules. 

Each coat subunit in the Ff viruses is coiled into an a-helical rod of 7 nm length. These are arranged in the virus in a right-handed helical pattern with a pitch of 1.5 nm and with 4.4 subunits per turn (Fig. 7-7). The protein rods are inclined to the helix axis and extend inward. This arrangement permits a "knobs-in-holes" hydrophobic bonding between subunits. The helix of pitch 1.5 nm is the primary or one-start helix. However, in every regular helical structure we can also trace a two-start helix, a three-start helix, etc. In this instance the five-start helix is easiest to see. 

It can also be described as a right-handed two-start helix in which two chains of subunits coil around one another with a long pitch (Fig. 7-10). 

Figure 7-10 (A) Model of the F-actin helix composed of eight monomeric subunits. The model was constructed from the known structure of the actin monomer with bound ADP using X-ray data from oriented gels of fibrous actin to deduce the helical arrangement of subunits. The main interactions appear to be along the two-start helix. See also Holmes ef a/.62 (B) Ribbon drawing of an actin monomer with the four domains labeled. Courtesy of Ivan Rayment.

Oncogenic viruses 248 One-start helix 334 Oparin, I. V. 9 Open systems 289 Operator sequence of DNA iH NMR spectrum 269 Operons 240 Opsin(s) 553 Optical rotation 42 Optimum rate for enzymes 469 d Orbitals, participation in covalent bond formation 311 Orcinol 251 Ordered binding 464 Ordered sequential mechanism 475 Organelle(s) 11... 

The hairpin motif is a simple and frequently used way to connect two antiparallel p strands, since the connected ends of the p strands are close together at the same edge of the p sheet. How are parallel p strands connected If two adjacent strands are consecutive in the amino acid sequence, the two ends that must be joined are at opposite edges of the p sheet. The polypeptide chain must cross the p sheet from one edge to the other and connect the next p strand close to the point where the first p strand started. Such CTossover connections are frequently made by a helices. The polypeptide chain must turn twice using loop regions, and the motif that is formed is thus a p strand followed by a loop, an a helix, another loop, and, finally, the second p strand. 

For example, each subunit of the dimeric glycolytic enzyme triosephos-phate isomerase (see Figure 4.1a) consists of one such barrel domain. The polypeptide chain has 248 residues in which the first p strand of the barrel starts at residue 6 and the last a helix of the barrel ends at residue 246. In contrast, the subunit of the glycolytic enzyme pyruvate kinase (Figure 4.5), which was solved at 2.6 A resolution in the laboratory of Ffilary Muirhead, Bristol University, UK, is folded into four different domains. The polypeptide chain of this cat muscle enzyme has 530 residues. In Figure 4.5, residues 1-42... 

They started from the sequence of a domain, Bl, from an IgG-binding protein called Protein G. This domain of 56 amino acid residues folds into a four-stranded p sheet and one a helix (Figure 17.16). Their aim was to convert this structure into an all a-helical structure similar to that of Rop (see Chapter 3). Each subunit of Rop is 63 amino acids long and folds into two a helices connected by a short loop. The last seven residues are unstructured and were not considered in the design procedure. Two subunits of Rop form a four-helix bundle (Figure 17.16). 

Figure 18.11 Electron-density maps at different resolution show more detail at higher resolution, (a) At low resolution (5.0 A) individual groups of atoms are not resolved, and only the rodlike feature of an

Figure 13 shows that the analogous dependence on temperature after longer incubation time at 1 °C becomes nonlinear with higher oligomers. Helix formation starts with n = 6. The ellipticity, depending on the chain lengths at random coil conditions, is shown in Fig. 14. 

Weidner and Engel142 used the relatively short collagen peptide al-CB2 as a model peptide for kinetic measurements. They observed that the rate at the beginning of the helix formation, starting from purely coiled chains, obeys the following equation ... 

In the case of X = Ala, cooperative equilibrium transition curves have been found starting from n = 8 tripeptide units. The reasons for this extraordinary behavior have been discussed concerning the peptide Col 1-3. CD measurements on peptides having chain lengths of 6 and 7 tripeptide units, seem to point out that these peptides are able to form a small amount of triple helix in water near 0 °C. Thus, the sequence (Ala-Gly-... 

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