Polypeptide chain torsional rotation

Note The formal lUPAC-IUB Commission on Biochemical Nomenclature convention for the definition of the torsion angles polypeptide chain (Biochemistry 9 3471-3479, 1970) is different from that used here, where the atom serves as the point of reference for both rotations, but the result is the same. (Irving Gas)... 

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).

The polypeptide chain of a protein has single bonds that permit internal torsional rotation to take place. This is true for the and angles of each... 

Literature contains an important number of papers dealing with proteins fluorescence and espeaally with the origin of the Tryptophan fluorescence. All these studies correlate the origin of the fluorescence to the primary and tertiary structures of the proteins. In peptides and proteins, rotation of the polypeptide chain is observed at the level of the a. carbon atom of each amino acid. This rotation is characterized by two well defined angles of torsion or dihedral < ) and y (Figure 7 ]). 

The atoms that form the backbone of the linear polypeptide chain are usually referred to as the main-chain atoms. By convention the conformational (torsional) angles adopted by the main chain atoms are denoted hycp, /, and 0) as shown in Fig. 3. Of these, co describes the peptide bond and usually adopts a value of 180°. In principle there is free rotation about the other two angles (

peptide bond and presence of a /3-carbon places substantial restrictions on these conformational angles. 

The minima occur when = 60° and 180° and = 0 and 120°. While the data regarding these barriers are uncertain, it is evident that they are much lower than those corresponding to rotations around C—C bonds in hydrocarbons. They play a minor role in the determination of the conformation of a polypeptide chain. Momany and co-workers (1975) have shown that these backbone intrinsic torsional terms are not needed. 

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. 

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