Protein three-center bonds

Proteins contain, on average, more acceptor than donor sites [596]. Similar proton deficiency in the amino acid zwitterion crystal structures results in the formation of three-center hydrogen bonds rather than in unsatisfied acceptor sites [74] (Part I A, Chap. 2.6). There is less flexibility in the orientation of hydrogen-bond donor and acceptor groups in proteins which would lead to a relatively larger number of unsatisfied acceptor sites. Some of the more unsymmetrical three-center bonds which might have been missed in the survey [596] because of the 3.5 A X - A cut-off limit will also contribute to reduce the number of unsatisfied acceptors in side-chains. 

Internal water molecules tend to form clusters. In general, internal water molecules in protein structures are not found isolated but are assembled in clusters. Their hydrogen-bonding scheme could be derived in actinidin (Fig. 19.13), in lysozyme, and in penicillopepsin, based oh the assumption that water molecules act as double donors and acceptors. In some of the protein structures, which have been analyzed in greater detail, an internal water is associated with three acceptor sites indicating three-center bonding as observed in the amino acid zwitterion crystal structures (see Part IB, Chap. 8). 

The analysis of hydrogen bonds in 15 proteins recognized a number of three-center hydrogen bonds, of which 70 involve main-chain N-H, and 40 are associated with the side-chain N-H of His, Arg, Asn, Gin. Other feasible three-center bonds could be associated with hydroxyl groups of Ser, Thr, iyr but hydrogen atom positions could not be defined in these cases. 

In future high-resolution crystal structure studies of proteins, hydrogen bonding has to be analyzed in terms of two-center and three-center interactions. It should be stressed that three-center bonds may be especially important in protein dynamics because they can be regarded as transition intermediate from one two-center bond to another (see Part IV, Chap. 25). 

Ninety percent of the three-center hydrogen bonds formed by main-chain N-H groups involve at least one protein acceptor atom the other acceptor being either a water molecule (53%) or another protein atom (47%). With side-chain N-H groups, one half interact with water molecules, the other half with one or more protein acceptors. O... 

Water molecules and three-center hydrogen bonds as lubricants in structural transitions. If water participates and contributes to protein helix-to-coil transition as illustrated in Fig. 25.4, then one can also envisage comparable and more general schemes of tertiary- and secondary-structure unfolding and folding for proteins,... 

The hydroxy isomers lack the reactivity of the three-center, two-electron bond characteristic of the [B2oH,8] isomers. As a result, the anion would be expected to be unreactive to intracellular protein moieties and clear from the tissues in biodistribution experiments. The biodistribution of liposomally encapsulated [c -B2oH,70H], with a boron dose of 200 Xg B ( 11 mg/kg body weight), exhibited rapid clearance of the boron concentration from all tissues, consistent with the working hypothesis (Shelly et al 1992). At 48 h, the tumor boron concentration was only 7.3 ig B/g tumor. 

This impressive reaction is catalyzed by stearoyl-CoA desaturase, a 53-kD enzyme containing a nonheme iron center. NADH and oxygen (Og) are required, as are two other proteins cytochrome 65 reductase (a 43-kD flavo-protein) and cytochrome 65 (16.7 kD). All three proteins are associated with the endoplasmic reticulum membrane. Cytochrome reductase transfers a pair of electrons from NADH through FAD to cytochrome (Figure 25.14). Oxidation of reduced cytochrome be, is coupled to reduction of nonheme Fe to Fe in the desaturase. The Fe accepts a pair of electrons (one at a time in a cycle) from cytochrome b and creates a cis double bond at the 9,10-posi-tion of the stearoyl-CoA substrate. Og is the terminal electron acceptor in this fatty acyl desaturation cycle. Note that two water molecules are made, which means that four electrons are transferred overall. Two of these come through the reaction sequence from NADH, and two come from the fatty acyl substrate that is being dehydrogenated. 

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