Conformations of arginine and lysine side chains in association with anions

Abstract

The side chain conformations shown by arginine and lysine in amino-acid and peptide crystal structures and bound to oxyanions in proteins have been analyzed in an attempt to understand the behaviour of these long-chain amino acids in an ionic environment. Except for χ₁, torsions have a preference for the trans conformation. However, for arginine in protein structures, χ₃ and χ₄ appear to be flexible and can be tuned for optimal anion binding. For χ₄, values in the range -80 to 80° are excluded for steric reasons; the remaining region in conformational space is accessible. This orientational variety exhibited by χ₄ has not been hitherto appreciated. Factors that can forbid a χ-angle to be in the trans geometry are the simultaneous binding of the anion by the main- and side-chain atoms, or the sharing of the anion between two different molecules in the crystal structure. Small molecules containing arginine have a distinct tendency to crystallize with two molecules in the asymmetric unit. This may be a general phenomenon for all extended molecules which have hydrogen-bond donors (or acceptors) embedded in a rigid set-up.