Peptide unit planarity

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. 

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.

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... 

The observed lengths in nanometers determined by X-ray diffraction measurements are given in Fig. 2-5 (top). The partial double-bond character of the C-N bond has important consequences. The peptide unit is nearly planar as is indicated by the dashed parallelogram in Fig. 2-5. 

Figure 2-15 A stereoscopic alpha-carbon plot showing the three-dimensional structure of favin, a sugar-binding lectin from the broad bean (Viciafaba). In this plot only the a-carbon atoms are shown at the vertices. The planar peptide units are represented as straight line segments. Side chains are not shown. The protein consists of two identical subunits, each composed of a 20-kDa a chain and a 20-kDa 3 chain. The view is down the twofold rotational axis of the molecule. In the upper subunit the residues involved in the front 3 sheet are connected by double lines, while those in the back sheet are connected by heavy solid lines. In the lower subunit the a chain is emphasized. Notice how the back 3 sheet (not the chain) is continuous between the two subunits. Sites for bound Mn2+ (MN), Ca2+ (CA), and sugar (CHO) are marked by larger circles. From Reeke and Becker.112...

From a structural viewpoint, a polypeptide is composed of planar peptide units as shown in Figure 2.8. The usefulness of considering the peptide unit as opposed to the amino acid is that the peptide unit is almost planar as opposed to the amino acid, which has atoms that are in more than one plane. To illustrate this point, the coordinates of atoms in the peptide unit are given in Table 2.2 and nonbonded atoms cannot be closer than the sum of the minimum atomic distances (Table 2.3). Note that all the atoms from the first alpha carbon (Ca) to the second alpha carbon do not have a z-coordinate. These coordinates come from X-ray diffraction studies on proteins and represent the average coordinates found among many pro-... 

The peptide unit so formed is a planar, rigid structure since there is restricted rotation about the C-N bond. This means that two isomers should be possible—a ds and a trans. 

This planar, trans peptide unit poses serious limitations example, are proteins with catalytic properties. Their on the shapes proteins can adopt. Understanding the catalytic function depends on the shape adopted alter the... 

The polypeptide backbone of a protein consists of a repeated sequence of three atoms—the amide nitrogen (N,), the a-carbon (Ca), and the carbonyl carbon (C,j, where i is the number of the residue starting from the amino end (remember the order of words in amino acids ). The repeat distance between peptide units in an extended trans conformation is approximately 3.8 A. The peptide group has a permanent dipole moment with the negative charge on the carbonyl oxygen atom, and is, as noted first by Pauling in 1933 (7 3), nearly planar and can exist in either the cis or the trans form in practice the trans form is that most commonly found. 

Figure 4 The conformational torsion angles in a protein and the planar peptide units that are hinged together...

A peptide unit is defined as C-CJNi+iC-+i. The bond lengths and bond angles in peptide units do not vary much from unit to unit or in different compounds. Furthermore, the peptide unit is almost always planar, or very nearly so, and the amide bond (C l—N, + i) is generally trans unless constrained to be in the cis conformation in small cyclic peptides. These generalizations are examined in more detail in later sections. 

When molecules are composed of several peptide units, they may adopt the extended conformation, in which the entire backbone is nearly planar and each peptide unit is in the trans form. More often, however, peptides, whether they are linear or cyclic, are folded. The folding is accomplished by rotations about the N—C bonds and the C —C bonds. An international commission has established a convention for the nomenclature (lUPAC-IUB Commission on Biochemical Nomenclature, 1970) for torsional angles (Fig. 1). According to this convention, the torsional angles f, and a>i equal 180° for a fully extended chain. For a planar trans peptide unit, a>i = 180°, whereas... 

Four different types of ring conformations have been observed in the crystal structures of cyclic tetrapeptides and cyclic tetradepsipeptides. They are (1) a cis,trans,cis,trans conformation containing a true or approximate center of symmetry, (2) a cis,trans,cis,trans conformation with a twofold rotation axis perpendicular to the average plane of the ring, (3) an all-trans conformation with a center of symmetry, and (4) an all-trans conformation with an approximate twofold rotation axis (Fig. 4). With the assumption of planar peptide units, it has been shown theoretically that four trans peptide units cannot be closed into a ring (Go and Scheraga, 1970). Crystal structure analyses have demonstrated that some cyclic tetrapeptides do, indeed, exist in the all-trans conformations (Flippen and Karle, 1976 Karimov et al, 1976). In these cases, the peptide units deviate significantly from planarity with co values as low as 156° as compared to 180°. 

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