Hydrogen bonding in polypeptides

Whereas the 3-pleated sheet provides a particularly nice and easily appreciated example of regular hydrogen bonding in polypeptide chains, the most common arrangement found in proteins is actually the a-helix (Figure 13.2). Do not worry about the a or P used in the nomenclature this merely signifies that the helical structure (a) was deduced earlier than that of the pleated sheet (P). 

A comment is in order about the possibility of C—H O=C hydrogen bonds in polypeptide structures. Such a bond was suggested in the structure of polyproline II between a proline CH2 group and the C=O group on an adjacent chain (Sasisekharan, 1959), but the attractive nature of this interaction was subsequently questioned (Arnott and Dover,... 

From such a background, some kinds of polypeptide blend samples have been studied by solid state NMR.27,72 74 Especially, detailed information for four kinds of blend samples such as poly(L-alanine) (PLA)/poly(L-valine) (PLV), PLA/poly(L-isoleucine) (PLIL), poly(D-alanine) (PDA)/PLV and polyglycine (PG)/PLV blends, have been reported. Here, let us describe some reasons why PLA/PLV, PDA/PLV, PLA/PLIL and PG/PLV blends are interesting systems. PLA and PDA in the solid-state can take the a-helix and (3-sheet forms due to intra- and intermolecular HBs, respectively. PG in the solid-state can take the 3j-helix (PG-II) and (3-sheet (PG-I) forms due to intra- and intermolecular HBs, respectively. However, PLIL and PLV in the solid state can predominantly take the (3-sheet form as the stable conformation. For this reason, it is interesting to know whether an isolated a-helix or 3i-helix form polypeptide surrounded by a major polypeptide in the (3-sheet form can take the helical conformation, or not, due to the balance between intramolecular and intermolecular hydrogen bonds. In addition, we would like to know whether a polypeptide in the (3-sheet form surrounded by a major polypeptide in the a-helix or 3 -helix form can take the (3-sheet form. 

Destabilizing. May form hydrogen bonds with polypeptide backbone in unfolded state. Destabilizing because /3-branching allows only the trans conformation in folded state. 

The p pleated sheet structure occurs commonly in insoluble structural proteins and only to a limited extent in soluble proteins. It is characterised by hydrogen-bonding between polypeptide chains lying side by side, as illustrated in Fig. 5.A3b. 

Figure 10.3 shows the number of hydrogen bonds in a peptide, normalized by the length of the polypeptide ni,)/N. We see that with increasing length of a peptide, the coil to helix transition becomes sharper, more cooperative. 

A family of polypeptide helices is stereochemically feasible. The helices are stabilized by intrachain N-H- -0=C hydrogen bonds between different peptide units, depending on type of helix. Tb describe the helices, two numbers are used, X . The X (not necessarily integral) denotes the number of amino acids in one turn n is the number of covalent bonds (including N-H) which are in the main-chain segment and bridged by each of the N-H 0=C hydrogen bonds in the helix. 

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