Open Polypeptide Chain

If we consider an open polypeptide chain consisting of N residues, complete hydrolysis will give rise to N amino acids, many of which may... 

Insulin has been studied in rather more detail than most other proteins due to the interest arising from its physiological properties and to the fact that it is one of the few proteins that can be obtained in a reasonably pure form. It possesses a relatively simple structure, being built up of fairly short open polypeptide chains. For the purposes of the following discussion a value of 12,000 (Gutfreund, 1948) will be assumed for the molecular weight. 

These results indicate that insulin is built up of four open polypeptide chains, which seem to be held together by —S—S— bridges of cystine. These are present to the extent of six residues per molecule. By oxidation with performic acid (p. 27) it was possible to split these bridges and thus to liberate the separate peptide chains (Sanger, 1949a). The oxidized insulin was fractionated by precipitation methods and two main fractions were obtained, which appeared to represent the whole of the oxidized insulin. The properties of these two fractions, designated A (acidic) and B (basic), are summarized in Table VIII. The most probable composition of fraction A is,... 

Figure 4.5 The polypeptide chain of the enzyme pyruvate kinase folds into several domains, one of which is an a/p barrel (red). One of the loop regions in this barrel domain is extended and comprises about 100 amino acid residues that fold into a separate domain (blue) built up from antiparallel P strands. The C-terminal region of about 140 residues forms a third domain (green), which is an open twisted a/p structure.

Figure 4.21 The polypeptide chain of the arabinose-binding protein in E. coli contains two open twisted a/P domains of similar structure. A schematic diagram of one of these domains is shown in (a). The two domains are oriented such that the carboxy ends of the parallel P strands face each other on opposite sides of a crevice in which the sugar molecule binds, as illustrated in the topology diagram (b). [(a) Adapted from J. Richardson.)...

The C-terminal transmembrane helix, the inner helix, faces the central pore while the N-terminal helix, the outer helix, faces the lipid membrane. The four inner helices of the molecule are tilted and kinked so that the subunits open like petals of a flower towards the outside of the cell (Figure 12.10). The open petals house the region of the polypeptide chain between the two transmembrane helices. This segment of about 30 residues contains an additional helix, the pore helix, and loop regions which form the outer part of the ion channel. One of these loop regions with its counterparts from the three other subunits forms the narrow selectivity filter that is responsible for ion selectivity. The central and inner parts of the ion channel are lined by residues from the four inner helices. 

Figure 49-9. Possible chain of events leading to opening of the Ca release channel. As indicated in the text, the Ca voltage channel and the Ca release channel have been shown to interact with each other in vitro via specific regions in their polypeptide chains. (DHPR, dihydropyridine receptor RYR1, ryanodine receptor 1.)...

The results of all of these topography studies are summarized in Fig. 1. The open eircles indicate residues of the H -ATPase shown in one way or another to be located on the cytoplasmic side of the membrane and the closed circles indicate residues in membrane-embedded segments. The lines in the sequence indicate minor regions with locations as yet not established. Thus, the topographical locations of nearly all of the 919 residues in the molecule have been established. It should be emphasized that the exact points of entry and exit of the polypeptide chain into and out of the membrane are not implied in the model. 

Figure 5.8 A schematic representation of the N-lobe polypeptide chain fold, showing the conformational change between open and closed forms of human lactoferrin. Reprinted with permission from Nature (Anderson et ah, 1990). Copyright (1990) Macmillan Magazines Limited.

Fig. 3. Comparison of the amino acid sequences predicted from the a- and j3-tubulin mRNA sequences. Open circles indicate homologous, conservative substitutions, and boxed regions indicate areas of high homology. For completeness, the sequence of the first 25 amino acids of chick brain a-tubulin, deduced by the work of Luduena and Woodward (1973), is also included. Note that the asterisks indicate identical amino acids common to both polypeptide chain sequences. [Reproduced from Valenzuela et al. (1981). Nature (London) 289, 650-655.]...

A stretch of DNA that is transcribed as a single continuous RNA strand is called a transcription unit. A unit of transcription may contain one or more sequences encoding different polypeptide chains (translational open reading frames, ORF) or cistrons. The transcription unit is sometimes termed the primary transcript, pre-messenger RNA or heterogeneous nuclear RNA (hnRNA). The primary transcript is further processed to produce mRNA in a form that is relatively stable and readily participates in translation. In order to understand the primary need for processing of this RNA, the biochemical definition of a gene must be discussed. 

The binding change mechanism for the trimeric Fi component resembles the action of a Wankle (or rotary) engine used in some automobiles. Fi s cylinders are made up of three identical polypeptide chains, and each protomeric unit is in a different conformation (designated L for Loose , T for Tight , and O for Open ). ADP and Pi bind to the L-site. Then, an energy-driven step occurs that successively converts L-ADP-Pi to T-ATP and T ATP to O + ATP ... 

There are several types of -class CAs i.e., a-CA I-VII, reported in the literature, out of which the human carbonic anhydrase II (HCA II), the most extensively studied carbonic anhydrase, has an exceptionally high CO2 hydration rate and a wide tissue distribution 107). The HCA II comprises a single polypeptide chain with a molecular mass of 29.3 kDa and contains one catalytic zinc ion, coordinated to three histidine residues, His 94, His 96, and His 119. A tetrahedral coordination geometry around the metal center is completed with a water molecule, which forms a hydroxide ion with a pK value of 7.0 108). Quigley and co-workers 109,110) reported that the inhibition of the synthesis of HCO3 from CO2 and OH- reduces aqueous humor formation and lowers intra-ocular pressure, which is a major risk factor for primary open-angle glaucoma. 

Caseins are highly disordered proteins having rather limited secondary structure. This is mainly due to the unusually high proline content, which is fairly uniformly distributed along the polypeptide chain. This feature leads to an open extended structure of the casein molecules which differentiates them from the globular whey proteins like a-lactalbumin and (3-lactoglobulin. The caseins have been described as rheomorphic ... 

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