Hydrogen-bonding wire

Another property relevant to the current discussion is the distribution of water in the active site. Specifically, we characterize the population of various water wires connecting the zinc-bound water/hydroxide and His 64 found in the SCC-DFTB/MM simulations. These wires were identified following a definition of hydrogen-bond in terms of both distance (O—O < 3.5 A) and angle (O—H—O > 140°) and care... 

Figure 2-13 (A) Stereoscopic view of the nucleotide binding domain of glyceraldehyde phosphate dehydrogenase. The enzyme is from Bacillus stearothermophilus but is homologous to the enzyme from animal sources. Residues are numbered 0-148. In this wire model all of the main chain C, O, and N atoms are shown but side chains have been omitted. The large central twisted P sheet, with strands roughly perpendicular to the page, is seen clearly hydrogen bonds are indicated by dashed lines. Helices are visible on both sides of the sheet. The coenzyme NAD+ is bound at the end of the P sheet toward the viewer. Note that the two phosphate groups in the center of the NAD+ are H-bonded to the N terminus of the helix beginning with RIO. From Skarzynski et al.llla (B) Structural formula for NAD+.

Figure 3-22 Stereoscopic view of a section of the structure of cutinase from the fungus Fusarium solani determined to a resolution of 0.10 nm. The three amino acid residues shown are serine 120 (top), histidine 188, and aspartate 175 (lower left). The structure is presented as a contour map with a "wire mesh" drawn at a "cutoff" level of density equal to 1 a above the average, where a is the root mean square density of the entire map. The side chains of these three residues constitute the "catalytic triad" in the active site of this enzyme (see Chapter 12). At this resolution more than one conformation of a group may often be seen. For example, the gamma oxygen (OG) of S120 is seen in two positions, the major one being toward His 188. When the map is drawn with a lower contour level the N-H proton on His 188 that is hydrogen bonded to Asp 175 can also be seen.410 Courtesy of Christian Cambillau.

Linear arrays of protonatable or hydrogen bonded sites may allow the directed long range transfer of protons, thus functioning as proton-conducting channel, i.e., as proton wire. Relevant systems would be linear polyamines or polyphenolic condensed aromatic units [8.218], self-assembled hydrogen bonded heterocyclic ribbons such as 116 (see Section 9.4.4) or polyelectrolyte membranes [8.219] in which collective proton motion may take place and lead to proton conductivity. 

Figure 8.43 (a) Chicken wire and (b) ladder motifs for saturated hydrogen bonded structures. The... 

C. Tanner, C. Manca and S. Leutwyler, Probing the threshold to H atom transfer along a hydrogen-bonded ammonia wire, Science, 302 (2003) 1736-1739. 

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