The problem of protein folding and dynamics: time-resolved dynamic nonradiative excitation energy transfer measurements

Abstract

The proteins are molecular machines that are self-assembled infinitely diverse, give rise to complex structures of any size, and have well-controlled vectorial modes of conformational changes, driven by thermal motions. Numerous experiments show that the pathway of folding of globular proteins, from the un-ordered state to the native conformations, and their modes of intramolecular motions, are determined by the sequence of the amino acyl residues (the monomers) in the polypeptide chain (the genetic information) of each protein. Attempts to decipher the mechanism by which the multiple transitions, on a wide range of time and distance scales are directed, depend on development of new methods for determination of distributions of intermolecular distances in flexible molecules and their time dependence. Methods based on time resolved measurements of intramolecular dynamic nonradiative excitation energy transfer, combined with protein engineering and site directed labeling were developed. Global analysis of data sets obtained by these measurements yield distributions of probabilities of segments end-to-end distances (EEDP) (in the range of 8 to 80 W chain). Methods for AMP determination of rates of conformational fluctuations and of the folding transitions, down to picosecond time scale, by means of this approach were also developed. Application of this experimental approach in the study of the denatured state of single-domain globular proteins, show that even in the denatured states, these proteins have compact structures. The bovine pancreatic trypsin inhibitor (BPTI) showed in the denatured state at least two conformational subpopulations, one was native-like and the other was characterized by EEDP distributions corresponding to an unfolded polypeptide chain.