Intrachain diffusion in a protein loop fragment from carp parvalbumin

During protein folding a polypeptide chain has to form specific intrachain interactions starting from an ensemble of unfolded conformation. Thus, intrachain diffusion in unfolded polypeptide chains can be regarded as an elementary step in protein folding, which should determine the dynamics of the early stages in the folding process. We have previously applied exothermic triplet-triplet energy transfer from xanthone to naphthalene to determine rate constants for intrachain end-to-end contact formation in unstructured homo-polypeptide chains. Here we show that the method can be applied to determine absolute rate constants for intrachain diffusion in natural loop sequences, if they are free of methionine, tryptophan and tyrosine. We measured the rate of loop formation in an 18 amino acid polypeptide chain corresponding to a natural loop sequence from carp muscle β-parvalbumin (residues 85-102). Contact formation shows single exponential kinetics with a time constant (τ=1/k) of 53 ± 3 ns at 22.5°C in water. Comparison with the results on homo-polypeptide chains shows that this value agrees well with rates obtained earlier for a polyserine chain of the same length. © 2004 Elsevier B.V. All rights reserved.