Hydrogen bonding between protein side chains

In conclusion, one important factor that contributes to the strong affinity of TBP proteins to TATA boxes is the large hydrophobic interaction area between them. Major distortions of the B-DNA structure cause the DNA to present a wide and shallow minor groove surface that is sterically complementary to the underside of the saddle structure of the TBP protein. The complementarity of these surfaces, and in addition the six specific hydrogen bonds between four side chains from TBP and four hydrogen bond acceptors from bases in the minor groove, are the main factors responsible for causing TBP to bind to TATA boxes 100,000-fold more readily than to a random DNA sequence. 

Water molecules are small probes. They can hydrogen-bond to protein functional groups with few steric limitations, in contrast to the hydrogen bonds between protein main-chain and side-chain atoms which have been the topic of Part III, Chapter 19. The hydrogen bonds involving water are therefore considered to reflect the intrinsic hydrogen-bonding properties of a protein. 

P. Rastogi, W. Kristof, and G. Zundel, Easily Polarisable Proton Transfer Hydrogen Bonds Between the Side Chains of Histidine and the Carboxylic Acid Groups of Glutamic and Aspartic Acid Residues in Proteins, Int. J. Biol Macromol 3, 154-158 (1981). 

In a consideration of hydrogen bonds between polar side-chain R groups, there are two fundamental questions to be asked. (1) What is the strength of such a bond, and (2) how do such bonds affect protein reactions As examples of protein reactions m which such side-chain hydrogen bonds... 

The cluster is coordinated at the tip of the cluster binding subdomain. Fe" (Fe-2) is close to the surface of the protein with its histidine ligands fully exposed to the solvent, whereas Fe " (Fe-1) is buried within the protein and surrounded by the three loops forming the cluster binding subdomain. However, in NDO the histidine ligands are not solvent accessible, but buried at the interface between the Rieske domain and the catalytic domain both histidine ligands form hydrogen bonds with acidic side chains in the catalytic site close to the catalytic iron. 

Free poiphyrin motions could be considerably altered in the presence of a metal ion, such as the iron, which covalently links the porphyrin to the protein. Linkages between heme and protein involve iron and the porphyrin part of the heme. Iron is linked to an imidazole group of the proximal histidine, His-93. The other heme protein bonds involve, on the heme side, the propionic acid groups, the vinyl groups and the porphyrin as a whole. The two heme propionates help to stabilize the heme by making hydrogen bonds to the side chains of the distal histidine (His-64) and an arginine. 

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