Hydrogen biological function

Most DNA occurs in nature as a right-handed double-helical molecule known as Watson-Crick DNA or B-DNA (Fig I-1-9). The hydrophilic sugar-phosphate backbone of each strand is on the outside of the double helix. The hydrogen-bonded base pairs are stacked in the center of the molecule. There are about 10 base pairs per complete turn of the helix. A rare left-handed double-helical form of DNA that occurs in G-C-rich sequences is known as Z-DNA. The biologic function of Z-DNA is unknown, but may be related to gene regulation. 

Combination of several descriptors believed to be important for oral absorption have been used in various multivariate analysis studies [26]. The general trend is that a combination of size/shape and a hydrogen bond descriptor, sometimes in combination with log D, has good predictive value. At present such models do not account for the biological function of the membrane, such as P-gp-mediated efflux. 

The biological function of Factor-420 is to catalyze the electron transport between hydrogen and pyridine nucleotide in Methanobacteria (anaerob). These Arckaebacteria are obligate anaerobes. In this context some proposals have been put forward with respect to the evolution of biological reactions catalyzed by flavoproteins... 

Catalases are structural relatives of the peroxidases in that they contain a heme tetramer at the active site [241]. Their biological function is to control the cellular concentration of hydrogen peroxide by the following disproportionation reaction ... 

Biomolecular recognition is mediated by water motions, and the dynamics of associated water directly determine local structural fluctuation of interacting partners [4, 9, 91]. The time scales of these interactions reflect their flexibility and adaptability. For water at protein surfaces, the studies of melittin and other proteins [45, 46] show water motions on tens of picoseconds. For trapped water in protein crevices or cavities, the dynamics becomes much slower and could extend to nanoseconds [40, 71, 92], These rigid water molecules are often hydrogen bonded to interior residues and become part of the structural integrity of many enzymes [92]. Here, we study local water motions in various environments, from a buried crevice to an exposed surface using site-selected tryptophan but with different protein conformations, to understand the correlation between hydration dynamics and conformational transitions and then relate them to biological function. 

The a helix is an important component of integral membrane proteins. These are proteins that traverse the hydrophobic plasma and organelle membranes (see Chapter 9) and perform important biologic functions. The portion of the protein that is embedded in the membrane is a-helical because the a helix provides for a maximum number of hydrogen bonds, which serve to reduce the hydrophilic nature of peptide linkages. The side chains of such trans-membrane a helices are also hydrophobic, even though under normal circumstances, such amino acids would prefer to form other secondary structures. 

Noncovalent interactions are weak inter- or intramolecular interactions that result from a combination of electrostatic interactions (ionic), hydrogen bonding, hydrophobic interactions (stacking or intercalation), and van der Waals interactions (dipole-dipole or induced dipole-induced dipole). Complexes formed by these types of interactions are usually fragile. This property is often essential to their biological function, which depends on the equilibria between the associated and free forms of these molecules. 

Table 2.1. Hydrogen bond functional groups in biological molecules...

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