Extended Peptide Chains

X-ray structural analysis and other physical measurements of a fully extended peptide chain reveal the lengths and angles of bonds (see the ball and stick representation in Fig. 1.15). The peptide bond has partial (40%) double bond character with 71 electrons shared between the C —O and C —N bonds. The resonance energy is about 83.6kJ/mole  

Thus in ribonuclease A, two X-Pro bonds have trans-conformation (Pro-42 and Pro-117), and two have cis-conformation (Pro-93 and Pro-114). The equilibrium between the two isomers is catalyzed by specific enzymes (peptidyl-prolyl-cis/trans-isomerases). This accelerates the folding of a peptide chain (cf. 1.4.2.3.2), which in terms of the biosynthesis occurs initially in all-trans-conformation. 

Six atoms of the peptide bonds, C-, C-, Oi, Ni+i, and Hi+i, lie in one plane (cf. Fig. 1.16). For a trans-peptide bond, coi is 180°. The position of two neighboring planes is determined by the numerical value of the angles (rotational bond between a carbonyl carbon and an a-carbon) and ( )j (rotational bond between an amide-N and an a-carbon). For an extended peptide chain, = 180° and ( )i = 180°. The position of side chains can also be described by a series of angles xl 

The angles are positive when the rotation is clockwise and viewed from the N-terminal side of a bond or (for X) from the atom closer to the main chain respectively. (according to Schulz and Schirmer, 1979) 

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First steps to extended-peptide chain formation... 

Thus, in the non-polar medium, due to the collapse of the otherwise partially extended peptide chain within itself, one can rationalize the steric hindrance in the polar medium, due to the collapse of the otherwise extended polystyrene backbone, some of the peptide chains can be visualized as buried and hence hindered to the approach of reagents and solvents. Thus, based on these models of polystyrene-bound peptides in different environments (Fig. 1), an ideal situation would be that where both the polymer and the peptide chains are extended. This is likely to be attained most easily if the polymer and peptide are of comparable polarities and are placed in a good solvating medium. This is in contrast to the polystyrene case where the macromolecular support is a pure hydrocarbon physicochemically quite dissimilar to the peptide chain being synthesized 44). 

Detailed analyses of the rotational flexibility about this bond in linear fS-Ala peptides revealed that 0 is mostly trans oriented (40, 41). Also, these studies provided almost exclusive evidence for the formation of extended peptide chains, which usually self-aggregate into sheet-like structures. 

Most denatured proteins are insoluble in water as a result of strong interactions between fully extended peptide chains. In the special case of S-sulfochymotrypsinogen and S-sulfotrypsinogen, aggregation may also occur. But, when special precautions are taken, water-clear solutions are obtained which are homogeneous in the ultracentrifuge (52). Under other circumstances (81), however, the S-sulfo derivatives appear to be poorly soluble in the pH range 3-9. Insolubility increases when reduction becomes more complete. 

The jS form of keratin requires still additional models. And, continuing the order of decreasing certainty, these models are again less well corroborated by experimental observations than are the a-helix or a-keratin structures. Pauling and Corey (1598) presented the pleated sheets to explain /3-keratins. These sheets are made up of extended peptide chains H bonded essentially side by side. Two are shown in Fig. 10-7. 

A) Tj ical textbook drawing. The bars represent the extended peptide chains with positions of domain boundaries and chain ends mapped (left side). Locations of some residues of special interest are marked on the right side. (B) A fanciful but more realistic picture of the receptor. See Fabry et al. ... 

How long is an a-helix that contains 74 amino acids Compare the length of this a-helix with the length of a fully extended peptide chain containing the same number of amino acids. (The distance between consecutive amino acids in a fully extended chain is 3.5 A.)... 

For oriented polypeptide chains, IR dichroism provides an informative technique. In a helix, N— 0=C peptide hydrogen bonds are oriented parallel to the long axis of the molecule. Therefore the N—H stretch and amide I bands should preferentially absorb IR radiation when the direction of polarization is parallel to the heUx axis. The amide II band should show the opposite trend. In p sheets, the long axis of the structure is along the extended peptide chains and the hydrogen bonds are perpendicular to this axis. Therefore each IR band in P sheets would have chroism opposite to that observed for the corresponding band in an a helix. 

A transoid arrangement of groups around the relatively rigid amide bond would cause the side-chain R groups to alternate from side to side of a single fully extended peptide chain ... 

However, this structure does not exist in naturally occurring proteins because of the crowding that would exist between R groups. If such a structure did exist, it would have the same repeat distance as the fully extended peptide chain, that is, 7.2 A. 

The conformational landscapes of both peptides are extremely similar. In short, they can adopt open conformations, with a fully extended peptide chain, and folded conformations where the NH groups of the chain are involved in intramolecular H-bonding both types are observed in supersonic expansions of the free molecules [59, 105], The monosaccharides can form complexes with either conformation, although with an apparent preference for the open one, which offers more readily available contact points all H-accepting and H-donating groups are free to interact with the CBH. 

We have seen that X-ray investigations of fibrous proteins indicate that in these substances more or less fully extended peptide chains are bound together by intermolecular interactions, presumably hydrogen ... 

When the dipolar interactions are not included in the calculations, region III loses much of its stability, indicating that the extended peptide chain is mainly stabilized by the electrostatic interactions between the antiparallel amide dipoles. 

The fl-sheet consists of two more fragments of fuUy extended peptide chains which can be arranged in either parallel or anti-parallel direction. The hydrogen bonds are formed by adjacent segments of polypeptides. This structure can be formed by either multiple chains or by a single chain folding onto itself. A typical jS-sheet is shown in Fig. 18. 

Fig. 3 Basic secondary structures a beta strands extended peptide chains held together by hydrogen bonds shown in orange between CO and NH groups in the peptide backbones, and resultant beta-sheets formed by several or more beta strands (actually an example of quaternary structure), b An a-hehx with orange hydrogen bonds along the length of the helix and a coiled coil quaternary structure made of two rdpha-helices. c A proUne helix that goes on to form a collagen helix with other proline helices [36]...

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