Peptide planarity

The geometry of the peptide bond is planar and the mam chain is arranged m an anti conformation (Section 27 7)... 

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.

Figure 9.10 Three-dimensional representation of the data volume of a tryptic digest of ovalbumin. Series of planar slices through the data volume produce stacks of disks in order to show peaks. Reprinted from Analytical Chemistry, 67, A. W. Moore Jr and J. W. Jorgenson, Comprehensive three-dimensional separation of peptides using size exclusion chromatogra-phy/reversed phase liquid chromatography/optically gated capillary zone electrophoresis, pp. 3456-3463, copyright 1995, with permission from the American Chemical Society.

Figure 3-4. Dimensions of a fully extended polypeptide chain. The four atoms of the peptide bond (colored blue) are coplanar. The unshaded atoms are the a-carbon atom, the a-hydrogen atom, and the a-R group of the particular amino acid. Free rotation can occur about the bonds that connect the a-carbon with the a-nitrogen and with the a-carbonyl carbon (blue arrows). The extended polypeptide chain is thus a semirigid structure with two-thirds of the atoms of the backbone held in a fixed planar relationship one to another. The distance between adjacent a-carbon atoms is 0.36 nm (3.6 A). The interatomic distances and bond angles, which are not equivalent, are also shown. (Redrawn and reproduced, with permission, from Pauling L, Corey LP, Branson PIR The structure of proteins Two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 1951 37 205.)...

C13-0116. The nitrogen atom of a peptide linkage has trigonal planar geometry. What is the hybridization of the nitrogen atom in a peptide linkage Explain why nitrogen adopts this form of hybridization. 

Sueeessful semipreparative separations of amino aeids and peptides are usually achieved with the use of planar gel eleetrophoresis examples of PLC applieations are presented in Table 9.1. 

Figure 7.5. Peptide array construction by SPOT-synthesis. fl-alanine groups (b-A) interact with the cellulose filter that serves as a planar support. Peptide synthesis then proceeds using Fmoc chemistries using the fl-alanine group as a starting point. The peptide is attached to the filter via its carboxy-terminus. In this case, lysine is added at the second position and various amino acids are present at the amino terminus of the peptide.

Fig. 5. Comparison of ab initio, DFT/BPW91/6-31G -computed IR and VCD spectra over the amide I, II, and III regions for model peptides (of the generic sequence Ac-Alaw-NHCH3). These are designed to reproduce the major structural features of an o -helix (top left, n— 6, in which the center residue is fully H-bonded), a 3i helix (PLP Il-like, top right, n— 4), and an antiparallel /1-sheet (n= 2, 3 strands, central residue fully H-bonded) in planar (bottom left) and twisted (bottom right) conformations. The computations also encompass all the other vibrations in these molecules, but those from the CH3 side chains were shifted by H/D exchange (CH3) to reduce interference with the amide modes.

The peptide bond is characterized by a fixed planar structure, as was discovered by X-ray crystallography of peptides more than 60 years ago. The arrangement of the atoms in the peptide bond is due to resonance stabilisation the lowest-energy state of the system is that in which the four atoms forming the peptide linkage lie in a plane, while the C-N bond has partial double bond character. 

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... 

Peptides and proteins are composed of amino acids polymerized together through the formation of peptide (amide) bonds. The peptide bonded polymer that forms the backbone of polypeptide structure is called the a-chain. The peptide bonds of the a-chain are rigid planar units formed by the reaction of the oc-amino group of one amino acid with the a-carboxyl group of another (Figure 1.1). The peptide bond possesses no rotational freedom due to the partial double bond character of the carbonyl-amino amide bond. The bonds around the oc-carbon atom, however, are true single bonds with considerable freedom of movement. 

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