Polyglycine helices

The results of ab initio band-structure calculations of six different polyglycine helices have recently been reported by Otto et As expected, the widths of the conduction and valence bands of these helices depend strongly on their structural (geometrical) parameters, but the gap is in all cases still larger than those given in Table 2.8. For further details we refer to Tables I and II of Otto et al. 

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. 

The Ufson-Roig matrix theory of the helix-coil transition In polyglycine is extended to situations where side-chain interactions (hydrophobic bonds) are present both In the helix and in the random coil. It is shown that the conditional probabilities of the occurrence of any number and size of hydrophobic pockets In the random coil can be adequately described by a 2x2 matrix. This is combined with the Ufson-Roig 3x3 matrix to produce a 4 x 4 matrix which represents all possible combinations of any amount and size sequence of a-helix with random coil containing all possible types of hydrophobic pockets In molecules of any given chain length. The total set of rules is 11) a state h preceded and followed by states h contributes a factor wo to the partition function 12) a state h preceded and followed by states c contributes a factor v to the partition function (3) a state h preceded or followed by one state c contributes a factor v to the partition function 14) a state c contributes a factor u to the partition function IS) a state d preceded by a state other than d contributes a factor s to the partition function 16) a state d preceded by a state d contributes a factor r to the partition function. 

N 042 "Molecular Theory of the Helix-Coil Transition in Polylamino acids). III. Evaluation and Analysis of s and [Pg.431]

In a second form of polyglycine each amino acid residue is rotated 120° from the preceding one about a 3-fold screw axis as is shown in the end view of Fig. 2-23A. The angle / is about 150° while c ) is about -80° for each residue. The distance along the axis is 0.31 nm/residue and the repeat distance is 0.93 iim. The molecules can coil into either a right-handed or a left-handed helix. In this structure, the N-H and C=0 groups protrude perpendicular to the axis of the helix and, as in the (3 structure, can form H-bonds with adjacent chains. 

Figure 2-23 (A) The structure of polyglycine if viewed down the axis of a helix chain. Note the...

A chain of L-amino acids can form either a right-handed or a left-handed helix. From the Ramachandran diagram in Fig. 2-9, can you say anything about the relative stabilities of right and left-handed helices What do you predict for polyglycine ... 

For polypeptide, the B program provides options for building various protein conformations including 3-10 helix, alpha helix, alpha helix (L-H), beta sheet (anti-prl), beta sheet (parallel), various beta turns, extended, gamma turns, omega helix, pi helix, polyglycine, and polyproline. Choose the desired conformation and isomer (l or d) and then add amino acids from N-terminus to construct polypeptide chain. 

Fig. 23. Energy contour diagram for single-stranded helical polyglycine. The units of energy are kcal mole-1. The symbols R and L indicate the location of the standard right-and left-handed a-helical conformations, B that of the B helix of myoglobin, cu that of the to-helix, 3io that of the 3io helix, and II that of the polyglycine II structure (Scott and Scheraga, 1966c).

Crick and Rich (1956). Coordinates are for right-handed polyglycine II helix. 

The development of the two structures may be visualized in two steps, as follows. First, in both structures, the individual polypeptide chains are coiled into a helix with a threefold, left-handed screw axis movement along a single helix from one residue to the next requires a rotation of —120° and a translation of 3.12 A. Thus each complete turn of an individual (or minor) helix requires three residues and a 9.4 A rise along the fiber axis. As pointed out above, this is basically the backbone proposed by Crick and Rich for polyglycine II and for poly-L-proline II by Cowan and McGavin, 1955 (see Section II and below). Two such chains are shown lying side by side in Figs. 10a and 106,... 

Nakano et al) reported a C CP/MAS NMR study on poly(L-Alanine) (PLA)/Polyglycine (PC) blends. The comparison between the C CP/MAS spectra of the blends and those of the parent polymers discloses that upon blending, new conformations of PLA and PC are fonned, which is closely related to the presence of intermolecular hydrogen-bonding interactions. Tip measurements demonstrate that the major parts of PC and PLA in the blends, which are in 3i-helix and a-helix conformation forms respectively, are phase separated. On the other hand, the p-sheet forms of PC and PLA, which are newly formed upon blending, exhibit similar values, demonstrating that these two parts are miscible at the scale of 3-4 nm. 

Abbreviations Ala, L-alanine Leu, L-leucine Glu(OBzl), 7-benzyl L-glutamate NHBu, n-butyl amide OBzl, benzyl ester PG, polyglycine NCA, A-carboxy-a-amino acid anhydride a-helix, right-handed a-helix , 3-sheet, anti-parallel /3-sheet. 

It has been demonstrated that the isotropic chemical shifts of systems, such as (Gly) (polyglycine(PG)), (Ala) , (Leu) (poly(L-leucine)), (Ileu) -(poly(L-isoleucine)), (Val) (poly(L-valine)), (Phe) (poly(L-phenylalanine)), (Glu(OMe)) (poly(y-methyl L-glutamate)), (Asp(OBzl)) (poly()8-benzyl l-aspartate)) and (Pro) in the peptide backbone of polypeptides in the solid state, exhibit a significant conformation-dependent change [5,6]. Both experimental observation and theoretical calculations confirm this. The Sjso for the a-helix form (97.0-99.2 ppm) appears to low frequencies by about 1.2-... 

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