Peptide groups

Figure 18.12 The electron-density map is interpreted by fitting into it pieces of a polypeptide chain with known stereochemistry such as peptide groups and phenyl rings. The electron density (blue) is displayed on a graphics screen in combination with a part of the polypeptide chain (red) in an arbitrary orientation (a). The units of the polypeptide chain can then be rotated and translated relative to the electron density until a good fit is obtained (b). Notice that individual atoms are not resolved in such electron densities, there are instead lumps of density corresponding to groups of atoms. [Adapted from A. Jones Methods Enzym. (eds. H.W. Wyckoff, C.H. Hirs, and S.N. Timasheff) 115B 162, New York Academic Press, 1985.]...

Reaction between a peptide group and a lysine side chain... 

FIGURE 6.5 A hydrogen bond between the amide proton and carbonyl oxygen of adjacent peptide groups. 

Avgelj, F., Luo, P., and Baldwin, R. L. (2000). Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities. Proc. Natl. Acad. Sci. USA97, 10786-10791. 

Sugawara, Y., A. Y. Hirakawa, and M. Tsuboi. 1984. In-Plane Force Constants of the Peptide Group Least-Squares Adjustment Starting from Ab Initio Values of N-Methylacetamide. J. Mol. Spectrosc. 108, 206-214. 

Homogeneous Peptide Groups Isolated from Normal Urine. 124... 

Y. Bai, J.S. Milne, L. Mayne and S.W. Englander, Primary structure effects on peptide group hydrogen exchange, Proteins Struct. Function Genet., 17 (1993) 75-86. 

The pH dependence of the trien reaction indicates that no protons are added before the rate-determining step. Hence, this step cannot come after the peptide bond breaks, because the metal-free peptide group must add a proton. Thus, the subsequent displacement reactions of the donors in the first chelate ring occur after the rate-determining step, which agrees with the lack of methyl group effects in this ring. 

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