Effects of core-packing on the structure, function, and mechanics of a four-helix-bundle protein ROP

The effects of core-packing on the structure, function and mechanics of the RNA-binding 4-helix-bundle Rop have been studied by molecular dynamics sim ulations. The structural, dynamical and geometrical properties of the Rop h omodimer, (formed by the antiparallel juxtaposition of two helix-turn-helix motifs), have been compared with those of three protein variants described by Munson et al. (Protein Sci, 5:1584-1593, 1996), where the core of the n ative protein has been systematically repacked using a two-amino acid alpha bet: Ala(2)Leu(2)-8, Ala(2)Leu(2)-8-rev, and Leu(2)Ala(2)-8. The results sh owed that it was possible to readily distinguish the inactive protein Leu(2 )Ala(2)-8 from the other functionally active systems based on tertiary and quaternary structure criteria. Structural properties such as native seconda ry structure content did not correlate with biological activity. Biological activity was related in part to the relative arrangement of the residues w ithin the binding site. But, more global aspects, related to the overall to pology of the helical bundle, accounted for the small functional difference s between Ala(2)Leu(2)-8 and Ala(2)Leu(2)-8-rev. Mechanically, the 4-helix- bundle absorbed core mutations by altering the local structure at the seque nce termini and in the turns that join the two helices of each monomer, and by changing the overall orientation and separation of the extremely rigid helices. Proteins 1999;36:436-446. (C) 1999 Wiley-Liss, Inc.