Denatured states of low-complexity polypeptide sequences differ dramatically from those of foldable sequences.
How the primary sequence of a protein encodes conformational preferences that operate early in folding to promote efficient formation of the correct native topology is still poorly understood. To address this issue, we have prepared a set of yeast iso-1-cytochrome c variants that contain polyalanine inserts ranging from 6 to 30 residues in length near the N terminus of the protein. We study the thermodynamics and kinetics of His-heme loop formation in the denatured state at 3 and 6 M guanidine-HCl concentration. We find that polyalanine closely approximates a random coil with excluded volume giving scaling exponents, nu(3), for equilibrium loop formation of 2.26 +/- 0.13 and 1.97 +/- 0.04 in 3 and 6 M guanidine-HCl, respectively. The rate of loop breakage initially decreases and then becomes independent of loop size as would be expected for a random coil. Comparison with previously reported data for denatured state His-heme loop formation for iso-1-cytochrome c and Rhodopseudomonas palustris cytochrome c', shows that foldable sequences deviate significantly from random coil behavior and that the deviation is fold-dependent.
Department of Chemistry and Biochemistry, Biochemistry Program and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA.
Franco O
FO
Tzul
Bruce E
BE
Bowler
D045304:Cytochromes c / Q000737:chemistry; D006418:Heme / Q000737:chemistry; D006639:Histidine / Q000737:chemistry; D006657:Histones / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012241:Rhodopseudomonas / Q000378:metabolism; D013816:Thermodynamics
D006657:Histones; D010455:Peptides; D011506:Proteins; C019529:polyalanine; D006418:Heme; D006639:Histidine; D045304:Cytochromes c