Peptide unit figure

This unit is called the peptide unit. Figure 13.1 shows the geometry of the peptide backbone. Due to mesomery, the peptide unit is stabilized by a resonance energy of 80-90 kJ mol-i ... 

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. 

The human pancreas secretes about 40—50 units of insulin daily, which represents about 15—20% of the hormone stored in the B cells. Insidin and the C-peptide (see Figure 42—12) are normally secreted in equimolar amounts. Stimuh such as glucose, which provokes insidin secretion, therefore trigger the processing of proinsidin to insidin as an essential part of the secretory response. 

Figure 2-8 Two peptide units in the completely extended (3 conformation. The torsion angles ([>], / , and (0 are defined as 0° when the main chain atoms assume the cis or eclipsed conformation. The angles in the completely extended chain are all 180°. The distance from one a carbon atom (C(I) to the next in a peptide chain is always 0.38 nm, no matter how the chain is folded.

Figure 2-9 Potential energy distribution in the c >—plane for a pair of peptide units with alanyl residues calculated using potential parameters of Scheraga and Flory. Contours are drawn at intervals of 1 kcal (4.184 kj) per mol going down from 0 kcal per mol. The zero contour is dashed.

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...

Figure 1. Drawing illustrating IUPAC terminology describing the conformation of a peptide unit...

Figure 25-12 Ball-and-stick model of a peptide unit showing the coplanarity of the CNCC atoms of the amide linkage, here in the trans configuration, and the possibility of rotation about the C-C and N-C bonds.

Figure 2.2. Diagram of a peptide unit the peptide unit formed by condensation polymerization is enclosed in a box that is within the plane of the paper. All atoms shown are to a first approximation found within the plane of the paper. The unit begins at the first alpha carbon, Ca, and ends at the second alpha carbon, Ca. Two angles (< >, i /) are sites of free rotation along the backbone of the chain and exist between adjacent peptide units. Both ( > and i are defined as positive for counterclockwise rotation looking from the nitrogen and carbonyl carbon positions towards the alpha carbon between these atoms.

In the case of proteins the building blocks that are synthesized into a long polymer chain are amino acids. When amino acids are added together they form peptide units that are more easily visualized because they are contained within a single plane (see Figures 2.5 to 2.7) except for the side chain or R group. The sequence of amino acids is important in dictating the manner in which polymer chains behave because the sequence dictates whether a chain can fold into a specific three-dimensional structure or whether the polymer chain does not fold. Specific examples of these prin-... 

Figure 2.9. Location of the second peptide unit. Dipeptides are constructed by knowing the coordinates of atoms in the first peptide unit (using X-ray diffraction) and then translating along the line between the first and second Ca by a dis-...

Figure 2.10. (Top) Graphical construction of a dipeptide. Once the second peptide unit is located (see Figure 2.12), it is rotated through an angle of 33° clockwise to generate a dipeptide in the standard conformation, with < ) = 180° and / = 180°.

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-... 

What Figure 2.11 tells us is that a conformational map for a dipeptide of glycine (the side chain in glycine is very small, just a hydrogen) has mostly allowed or partially allowed conformations and therefore polyglycine is flexible. One question that you might ask is how do we know that the conformational plot for a polypeptide is the same as for a dipeptide The answer is that because the side chain points away from the backbone for most conformations the atoms in the side chains are separated by more than the sum of the van der Waals radii. However, below we discuss several highly observed conformations of proteins in which the conformational map is an overestimation of the flexibility because of interactions between atoms more than two peptide units apart in space. 

Polypeptides, however, are composed of amino acids with side chains that are longer and therefore the area of allowed conformations is reduced when an alanine (Figure 2.12), aspartic acid (Figure 2.13), or a proline (Figure 2.14) is added to the second peptide unit. Finally, the conformational map for a dipeptide of proline-hydroxyproline is dramatically reduced. Rings in the backbone of any polymer reduce the ability of the polymer backbone to adopt numerous conformations and thereby stiffen the structure. 

Figure 2.17. Hydrogen bonding in antiparallel (3 sheet. Antiparallel hydrogen bonding between carbonyl and amide groups within the peptide unit stabilizes the (3 extended conformation.

Since A has been subtracted from each protein, the mobility becomes a function of the n/K ratio, as seen in the figures of the last column of Table in. n/K values will not correspond to the mobility in proteins not made up from peptide units arising from another site of synthesis, as indicated here by the gamma-globulins, which apparently arise from a different system (Figure 1). 

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