Opening image: The phosphate-binding protein from E. coli. The selectivity of active transport of phosphate into a cell is an excellent example of function achieved through exceedingly high protein-ligand specificity. The is completely dehydrated and buried in the active site; besides van der Waals interactions there are 12 hydrogen bonds to the phosphate and a charge-charge interaction with Arg 135.
The protein-phosphate complex is truly fascinating but we must turn our attention to parallel β-sheets.
A parallel β-sheet from the phosphate-binding protein of E. coli. Only the first 56 out of 321 residues are present in the model.
What difference is there in the connections between the three parallel β-strands in this protein and the connection between the antiparallel strands in the previous models? Explain.
a space-filling model of the sheet without side chains. The green dots show the positions of the β carbons of the side chains.
Complete parallel sheet. The α and β carbons are colored dark gray and green, respectively.
Glycine is exempt from many steric constraints because it lacks a β carbon. Because Gly residues have more conformational freedom than other residues, they are seldom found in the central portions of α helices or β sheets. However, glycines are often found at the ends of these structures. Look for two Gly residues at the ends of the β strands in this parallel sheet.
Now we return to the cartoon depiction of residues 1-56. spacefill. To see which residues in the space-filling model are part of the secondary structural elements in this fragment, between color schemes (color structure; and color cpk;).
alpha-carbons dark gray.
The phosphate-binding protein, with the bound phosphate ion spacefilled.
Loops can be important beyond just serving as connections between α-helices and β-strands. Recall that the phosphate is completely buried and that the binding interactions include 12 hydrogen bonds and one charge-charge interaction, as well as van der Waals contacts. Look carefully at the two loops shown in purple. Is it likely that they make important contributions to the stability of the highly specific complex between phosphate and the protein?