Peptide unit

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. 

Peptide units are building blocks of protein structures... 

Figure 1.2 shows one way of dividing a polypeptide chain, the biochemist s way. There is, however, a different way to divide the main chain into repeating units that is preferable when we want to describe the structural properties of proteins. For this purpose it is more useful to divide the polypeptide chain into peptide units that go from one Ca atom to the next Ca atom (see Figure 1.5). Each C atom, except the first and the last, thus belongs to two such units. The reason for dividing the chain in this way is that all the atoms in such a unit are fixed in a plane with the bond lengths and bond angles very nearly the same in all units in all proteins. Note that the peptide units of the main chain do not involve the different side chains (Figure 1.5). We will use both of these alternative descriptions of polypeptide chains—the biochemical and the structural—and discuss proteins in terms of the sequence of different amino acids and the sequence of planar peptide units.

Since the peptide units are effectively rigid groups that are linked into a chain by covalent bonds at the Ca atoms, the only degrees of freedom they have are rotations around these bonds. Each unit can rotate around two such bonds the Ca-C and the N-Ca bonds (Figure 1.6). By convention the angle of rotation around the N-Ca bond is called phi (<[)) and the angle around the Ca-C bond from the same C atom is called psi (y). 

Figure 1.6 Diagram showing a polypeptide chain where the main-chain atoms are represented as rigid peptide units, linked through the atoms. Each unit has two degrees of freedom it can rotate around two bonds, its Ca-C bond and its N-Ca bond. The angle of rotation around the N-Ca bond is called phi (cj)) and that around the Co-C bond is called psi (xj/). The conformation of the main-chain atoms is therefore determined by the values of these two angles for each amino acid.

Figure 6.9 (a) Peptide units can adopt two different conformations, trans and cis. In the trans-form the C=0 and the N-H groups point in opposite directions whereas in the c/s-form they point in the same direction. For most peptides the trans-form is about 1000 times more stable than the c/s-form. (b) When the second residue in a peptide is proline the trans-form is only about four times more stable than the c/s-form. C/s-proline peptides are found in many proteins. 

For proteins, the fragment is defined by the peptide unit convention as recommended by the International Union of Pure and Applied Chemistry, although the... 

The sum of the estimated average solvent-accessible surface areas, (ASA), for the peptide units (—CO—NH—) on either side of residue Xaa, plus the Ca of Xaa, in each peptide simulated are given in Table II. Also shown are the estimated PPII helix-forming propensities for each residue measured by Kelly et al. (2001) and A. L. Rucker, M. N. Campbell, and... 

Aida, M. 1993. Theoretical Studies on Hydrogen Bonding Interactions Between Peptide Units. Bull. Chem. Soc. Jpn. 66, 3423-3429. 

Sawaryn, A., and J. S. Yadav. 1982. Ab Initio Studies on the Nonplanarity of a Peptide Unit Calculations on Model Compounds. Int. J. Quantum Chem. 22, 547-556. 

Conformation of a System of Three Linked Peptide Units. Biopol. 6, 1425-1436. von Carlowitz, S., H. Oberhammer, H. Willner, and J. E. Boggs. 1986. Structural Determination of a Recalcitrant Molecule (S2F4). J. Mol. Struct. 100,161-177. von Carlowitz, S., W. Zeil, P. Pulay, and J. E. Boggs. 1982. The Molecular Structure, Vibrational Force Field, Spectral Frequencies, and Infrared Intensities of CH3POF2. J. Mol. Struct. (Theochem) 87, 113-124. 

The dipeptide model implies that the peptide unit is basically rigid and planar which is a good first order approximation, with characteristic deviations (M. W. MacArthur, 1996G). The effectiveness of the model and the significance of the main chain <)> and i / torsions for protein folding was first discovered by Sasisekharan (1962G), but the plots of peptide... 

Fig. 6.1. IUPAC-IUB Commission on Biochemical Nomenclature rules defining residues and peptide units in peptides. In the example shown, residue No. 2 contains the backbone atoms N2, C2, and C2. Peptide unit No. 2 contains the backbone atoms C2, C2, and Nf. Rj, R2, and R3 are the side chains of the amino acid residues (www.chem.qmul.ac.uk/iupac/AminoAcid/).

---