Refinement of Helix Boundaries
in -Helical Globular Proteins

I. V. Grigor’ev, A. A. Mironov, and A. B. Rakhmaninova

GosNIIgenetika State Research Center, Moscow, 113545 Russia

Received August 18, 1998

Abstract—A folding model for -helical proteins, with a chain of helices joined by freely moving loops as the
initial state, is considered. Analysis of the local geometry of polypeptide chains in -helical proteins has indi-
cated that solid bodies are 1–4 residues longer for this model as compared with the conventional helices. This
representation not only decreases the conformational space of the globule, but also contributes to formation of
native conformations which are most favorable in terms of energy. The new initial state markedly improves the
results of folding simulations. Another finding is that the native topology of several -helical proteins allows
even longer helices, and that in almost 70% of cases the longest helices correspond to loops with a minimal
energy for the given topology. A hypothesis that the helix length changes during folding is considered.

Key words: -helical proteins, helix length, loops, modeling

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