GRID Maps from Macromolecules

The flexible side chain of the lysine (CH2-CH2-CH2-CH2-NH3 ) is displayed in an all-trans conformation in Fig. 1.5 because it was assigned all-trans coordinates by the X-ray crystallographer. An all-trans structure like this is often reported when the atoms of a side chain are in such vigorous dynamic thermal motion that they cannot be detected by X-ray methods. Arbitrary all-trans coordinates are then assigned by default, because the crystallographer knows that the amino acid is lysine from the DNA sequence although he cannot observe the side chain atoms himself 

This GRID map is therefore misleading, and this figure demonstrates how important it is to use MIF programs with great care because it is very easy to obtain deceptive results by misusing any MIF program. See text. 

One must conclude that hydrophobic interactions may stabilise the multilayer TRP-ARG sandwich of gpl30, in spite of the different character of these two amino acids, and in spite of the entropic penalty mentioned above. However the gpl30 crystals themselves came from a solution which contained glycerol molecules and sulfate ions, and both of these components were trapped in the crystals where they may have helped to stabilise the observed protein structure. It would not be altogether surprising if some alternative conformation or conformations of gpl30 may also occur in vivo, if those somewhat unphysiological substances are not present in the human body in sufficient concentrations to stabilise the structure as observed. 

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