Role of water molecules in the crystal structure of gly‐L‐ala‐L‐phe: A possible sequence preference for nucleation of α‐helix?

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Abstract
The synthetic peptide Gly‐L‐Ala‐L‐Phe (C14H19N3O4 · 2H2O; GAF) crystallizes in the monoclinic space group P21, with a = 5.879(1), b = 7.966(1), c = 17.754(2) Å, β = 95.14(2)°, Dx = 1.321 g cm−3, and Z = 2. The crystal structure was solved by direct methods using the program SHELXS‐86 and refined to an R value of 0.031 for 1425 reflections (> 3σ). The tripeptide exists as a zwitterion in the crystal and assumes a near α‐helical backbone conformation with the following torsion angles: ψ1 = −147.8°; ϕ2, ψ2 = −71.2°, −33.4°; ϕ3 ψ3 = −78.3°, −43.3°. In this structure, one water molecule bridges the COO− and NH3+ terminii to complete a turn of an α‐helix and another water molecule participates in head‐to‐tail intermolecular hydrogen bonding, so that the end result is a column of molecules that looks like an α‐helix. Thus, the two water molecules of crystallization play a major role in stabilizing the near α‐helical conformation of each tripeptide molecule and in elongating the helix throughout the crystal. An analysis of all protein sequences around regions containing a GAF fragment by Chou‐Fasman's secondary structure prediction method showed that those regions are likely to assume an α‐helical conformation with twice the probability they are likely to adopt a β‐sheet conformation. It is conceivable that a GAF fragment may be a good part of the nucleation site for forming α‐helical fragments in a polypeptide, with the aqueous medium playing a crucial role in maintaining such transient species.