Peptide carbonyls

B. Channel view showing a channel with a maximal diameter of 4 A. Also seen in this view are three carbonyl oxygens surrounding the channel and directed outward into solution. These are the peptide carbonyls of the Trp15, Trp13 and Trpu residues... 

A. In vacuo lowest energy conformation showing the peptide carbonyls to be slightly librated into the channel by about 10°, Reproduced with permission from Ref.53). 

If all of the peptide carbonyls were optimally librated for conducting then each P, would be one and each K° would be zero, recovering Eq. 9. Since there is a... 

Figure 2-3. Additional polar groups participate in hydrogen bonding. Shown are hydrogen bonds formed between an alcohol and water, between two molecules of ethanol, and between the peptide carbonyl oxygen and the peptide nitrogen hydrogen of an adjacent amino acid.

Fig. 13. The binding sites of calcium in (a) parvalbumin (41a), (b) annexin (41) and (c) calmodulin (42). The drawings show two bidentate carboxylates coordinated to Ca2 in the EF-hand site of parvalbumin, and one bidentate carboxylate coordinated to Ca2 in annexin and calmodulin. All the donor atoms coordinated to the calciums are oxygen donor atoms from carboxylates of asp = aspartate, or glu = glutamate, or else peptide carbonyl oxygens from gly = glycine or met = methionine. Redrawn after Refs. (41-42).

II Exposed and quenched by a hydrated peptide carbonyl group... 

Now that about 70 different disulfides have been seen in proteins and more than 20 of those have been refined at high resolution, it is possible to examine disulfide conformation in more detail, as it occurs in proteins. Many examples resemble the left-handed small-molecule structures extremely closely Fig. 46 shows the Cys-30-Cys-115 disulfide from egg white lysozyme. The x > Xs and x dihedral angles and the Ca-Ca distance can be almost exactly superimposed on Fig. 45 the only major difference is in Xi All of the small-molecule structures have Xi close to 60°. Figure 47 shows the Xi values for halfcystines found in proteins. The preferred value is -60° (which puts S-y trans to the peptide carbonyl), while 60° is quite rare since it produces unfavorable bumps between S-y and the main chain except with a few specific combinations of x value and backbone conformation. 

D-a-hydroxyvaleric add, L-valine, L-lactic acid] 3, having a 36-atom ring with twelve carbonyl oxygen atoms. From i.r. (65) and n.m.r. (66) spectroscopy it was established that the cationic complex has three-fold symmetry with the peptide carbonyl oxygen atoms involved in N—H... O hydrogen bonding. According to optical rotatory dispersion (ORD) and... 

Fig. 11. The valinomycin potassium complex (after (69)). The broken lines represent hydrogen bonds between peptide carbonyl atoms and NH groups shaded, the ester carbonyl atoms are coordinated to potassium in an octahedron...

The importance of oxyanion holes in enzymes was first discovered in chymot-rypsin by David Blow and co-workers and in subtihsin by Jo Kraut and co-workers [39]. In these enzymes, a tetrahedral intermediate is generated after nucleophilic attack of a deprotonated serine side chain on the peptide carbonyl group. It was recognized from the begirming that the geometry of the active site complexes was possibly better complementary to the tetrahedral intermediate than to the planar peptide substrate [40]. 

An analysis of metal binding to peptide carbonyl groups (Chakrabarti, 1990), mainly calcium ions in protein crystal structures, shows that the cations tend to lie in the peptide plane near the C=0 bond direction. Generally, this binding occurs in turns in proteins or in regions with no regular secondary structures. Ca---0 distances range from 2.2 to 2.5 A, and metal ions do not deviate by more than 35° from the peptide plane. Thus, metal ions in proteins do not, Chakrabarti observed, bind in lone-pair directions. 

Interactions of metal ions with peptide carbonyl oxygen atoms have been surveyed by Chakrabarti (1990a). Of the 71 metal—carbonyl oxygen interactions studied, nine were with metals other than Ca. Only refined protein structures were included in the Chakrabarti survey, but structures at both lower and high resolution were accepted. Despite the differences in the proteins sampled, we have obtained values for the geometry... 

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