Peptide bond torsion angle

To understand the function of a protein at the molecular level, it is important to know its three-dimensional stmcture. The diversity in protein stmcture, as in many other macromolecules, results from the flexibiUty of rotation about single bonds between atoms. Each peptide unit is planar, ie, oJ = 180°, and has two rotational degrees of freedom, specified by the torsion angles ( ) and /, along the polypeptide backbone. The number of torsion angles associated with the side chains, R, varies from residue to residue. The allowed conformations of a protein are those that avoid atomic coUisions between nonbonded atoms. 

Examination of the backbone torsion angles in a number of crystal stractures of /9-alanine-containing peptides reveals that the conformation around the C(a)-C(/9) bond of /9-alanine residues is essentially gauche or trans (anti) with values close to 60° or 180°, respectively [158]. Populating the gauche conformation of /9-ami-... 

As a consequence of their different turn geometry a 10-membered turn closed by H-bonds between NH and C=0 +i and a 12-membered turn closed by Id-bonds between C=0 and NH +3, antiparallel hairpins formed by y9-peptides 121 and 122 display opposite sheet polarities (see Fig. 2.30A and B). Comparison of backbone torsion angles (X-ray and NMR) for selected y9-amino acids residues within extended strand segments of peptides 117-122 are shown in Tab. 2.7. The observed values are close to ideal values for y9-peptide pleated sheets =-120° (or 120°), 01 = 180°, (/ =120°(or-120°). 

The characteristic properties of peptides result from the presence of a chain of several or many amide bonds. A first problem is that of numbering, and here Fig. 6.1 taken from the IUPAC-IUB rules may help. A second and major aspect of the structure of peptides is their conformational behavior. Three torsion angles exist in the backbone (Fig. 6.2). The dihedral angle co (omega) describes rotation about C-N,

rotation about N-C , and ip (psi) describes rotation about C -C. Fig. 6.2 represents a peptide in a fully extended conformation where these angles have a value of 180°. 

The torsion angle co, which is common to peptides and nonpeptidic amides, always prefers a planar over a nonplanar conformation due to the partial double-bond character of the amide bond (Fig. 6.3, right). Thus, a peptide bond resembles an amide bond in conformational and electronic terms [2] [3], However, peptides differ from amides in that both the carbonyl C-atom and the amido N-atom are nearly always bound to an sp3-hybridized C-atom. As a result, the trans-conformer (a>=180°) is consistently preferred over the cw-conformer, the energy difference usually being ca. 90 kJ mol 1 (Fig. 6.3). The relationship between the partial double-bond character of the amide bond (Fig. 6.3, right) and hydrolysis will be considered in Sect. 6.3. 

The chelation of the Cys(l)-X-Y-Cys(2) fragment induces a distortion from D2d symmetry. We examined the variation of the overlap population of Fe-S bond with various Fe-S(C) torsion angles by extended Hiickel MO calculations (22). Restriction of Fe-S torsion angle in Cys(2) due to the preferable conformation of the chelating peptide leads to a C2 distortion of the Fe(in) active site. This distortion was found to increase the overlap population of the corresponding Fe-S bond and thus to cause the positive shift of the redox potential. 

Perera and Bartlett338 used N-methylacetamide as a model peptide fragment and considered its cis- and -conformations [38] to calculate 3J(HN, Ha) as a function of the torsion angle around the N-Me bond, . 

Figure 1.10 Definitions of the torsional angles fa ip, and w. These are all equal to 180° for a fully extended polypeptide chain (top left). to, defines rotation about the C,—Nl+1 bond. The normal tram planar peptide bond has = i/r = 180°, bottom) left, fa viewed along N —C bond (N >C) right, fa viewed along the C —C(C , — C j).

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