Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins

doi:10.1073/pnas.0510549103

Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins

*Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland;
^†Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; and
^‡Facultad de Ciencias Físico Matemáticas y Naturales, Instituto de Matemática Aplicada San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, Ejército de los Andes, Universidad Nacional de San Luis, 950-5700 San Luis, Argentina

Contributed by Harold A. Scheraga, December 9, 2005

Abstract

The alanine-based peptide Ac-XX(A)₇OO-NH₂, referred to as XAO (where X, A, and O denote diaminobutyric acid, alanine, and ornithine, respectively), has recently been proposed to possess a well defined polyproline II (P_II) conformation at low temperatures. Based on the results of extensive NMR and CD investigations combined with theoretical calculations, reported here, we present evidence that, on the contrary, this peptide does not have any significant amount of organized P_II structure but exists in an ensemble of conformations with a distorted bend in the N- and C-terminal regions. The conformational ensemble was obtained by molecular dynamics/simulated annealing calculations using the amber suite of programs with time-averaged distance and dihedral-angle restraints obtained from rotating-frame nuclear Overhauser effect (ROE) volumes and vicinal coupling constants ³J_HNΗα, respectively. The computed ensemble-averaged radius of gyration R_g (7.4 ± 1.0) Å is in excellent agreement with that measured by small-angle x-ray scattering (SAXS) whereas, if the XAO peptide were in the P_II conformation, R_g would be 11.6 Å. Depending on the pH, peptide concentration, and temperature, the CD spectra of XAO do or do not possess the maximum with positive ellipticity in the 217-nm region, which is characteristic of the P_II structure, reflecting a shifting conformational equilibrium rather than an all-or-none transition. The “P_II conformation” should, therefore, be considered as one of the accessible conformational states of individual amino acid residues in peptides and proteins rather than as a structure of most of the chain in the early stage of folding.

Footnotes

§To whom correspondence should be addressed. E-mail: has5{at}cornell.edu
Author contributions: H.A.S. designed research; J.M. performed research; and S.R.-M., K.B., J.A.V., A.L., and L.C. analyzed data.
Conflict of interest statement: No conflicts declared.
Data deposition: The NMR chemical shifts have been deposited in the BioMagResBank, www.bmrb.wisc.edu (accession no. 6941).