Amino acid side chain protonation

As a basic amino acid side chain removes a proton from the nitrogen of the amino acid, the hydride ion adds to the N-5 position of the flavin ring, and an acidic amino acid side chain protonates N-1. 

Note, however, that the -59In mV change per pH-unit is seldom found for prosthetic groups in proteins because association of protons is usually not directly on the coordination complex (which could result in loss of the metal) but rather on a nearby (or not-so-nearby) amino-acid side chain. So, the change can be anywhere between 0 and -59In mV. This information can be quite valuable for an understanding of the mechanism of action of the metalloprotein, but it does mean that we have to carry out EPR-monitored redox titrations at several different pH-values. 

There are six main decomposition pathways for protonated DKPs and elimination of one of the amino acid side chains or produces an ion which is the origin of five other fragmentation pathways. Owing to the symmetric structure of the DKP ring with regard to R and R, only half of the fragment ions are shown in Figure 3. ... 

Protons are translocated across the membrane by what is described as a proton pnmp . How does the pump operate The change in redox state experienced by the prosthetic gronps of the enzymes in the chain causes conformational changes in the proteins that alter the affinities of some amino acid side-chain gronps for protons. In addition, there is a change in the direction in which these groups face in the membrane. Consequently, oxidation results in an association with a proton on the matrix side of the membrane whereas reduction results in reversal of the direction that the side-chain groups face and an increase in... 

The details obtained fiom the ENDOR work, in addition to past results, allow for the following mechanism for aconitase. In Scheme II the R group on the substrate is CH2COO, -B represents the amino acid side-chain which stereospeci-fically transfers a proton between citrate and isocitrate, and X is either water or a protein ligand. In the presence of c/s-aconitate, bound water can freely exchange... 

The enzyme provides a base (B ) and an acid (A-H) via appropriate amino acid side-chains on the enzyme (see Section 13.4) to facilitate proton removal and supply. A fascinating aspect is that the proton removed from the methylene (steroid position 4) by the base is then donated back to position 6. The base is suitably positioned to serve both sites in the steroid. 

Figure 1 Prototypical polypeptide showing disulfide (SS) linkage, one of many N-Ca bonds, amino acid side chains (wavy lines), protonated amines on side chains (wavy lines), and one of many peptide bonds. Also shown is an anion donor (H3C ) colliding with the peptide.

In the active site of an enzyme, a number of amino acid side chains can similarly act as proton donors and acceptors (Fig. 6-9). These groups can be precisely positioned in an enzyme active site to allow proton transfers, providing rate enhancements of the order of 102 to 105. This type of catalysis occurs on the vast majority of enzymes. In fact, proton transfers are the most common biochemical reactions. 

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