Further Evidence for the Absence of Polyproline II Stretch in the XAO Peptide

Abstract

It has been suggested that the alanine-based peptide with sequence Ac-XX-[A](7)-OO-NH(2), termed XAO where X denotes diaminobutyric acid and O denotes ornithine, exists in a predominantly polyproline-helix (P(II)) conformation in aqueous solution. In our recent work, we demonstrated that this "polyproline conformation" should be regarded as a set of local conformational states rather than as the overall conformation of the molecule. In this work, we present further evidence to support this statement. Differential scanning calorimetry measurements showed only a very small peak in the heat capacity of an aqueous solution of XAO at 57 degrees C, whereas the suggested transition to the P(II) structure should occur at approximately 30 degrees C. We also demonstrate that the temperature dependence of the (3)J(HNHalpha) coupling constants of the alanine residues can be explained qualitatively in terms of Boltzmann averaging over all local conformational states; therefore, this temperature dependence proves that a conformational transition does not occur. Canonical MD simulations with the solvent represented by the generalized Born model, and with time-averaged NMR-derived restraints, demonstrate the presence of an ensemble of structures with a substantial amount of local P(II) conformational states but not with an overall P(II) conformation.

Studies on titin PEVK peptides and their interaction

“…Small angle x-ray studies on peptides containing significant polyproline II content (based on CD) showed a much smaller radius of gyration than expected from an extended polyproline structure [32]. Their interpretation was that polyproline II may be a folding conformation of only one or two residues in a continuous flux with other conformations and not lead to an extended semi-rigid rod structure [32]. Ma and Wang [14] also have concluded that the titin PEVK fluctuated between polyproline, beta turn, and unordered structure.…”

“…Recent work [32] has suggested that the polyproline II helix may be only a temporally transient structure. Small angle x-ray studies on peptides containing significant polyproline II content (based on CD) showed a much smaller radius of gyration than expected from an extended polyproline structure [32].…”

Experimental and Computational Studies of Polyproline II Propensity

“…Scheraga and coworkers have presented evidence to challenge the previous claims of Kallenbach and others, reporting that PII is one of many conformations available to alanine in XAO and that PII is not a dominant global conformation of the XAO peptide [49,50] . Supporting this result, small angle X -ray scattering ( SAXS ) also demonstrated that the XAO peptide adopts a much smaller radius of gyration (∼ 7.4 Å ) in solution compared with that expected of an ideal, fully extended PII helix ( ∼ 13 Å ), indicating that PII bias is local and that PII helix is not a global conformation of the peptide [51] .…”

Conformation dependence of the CαDα stretch mode in peptides: Side‐chain influence in dipeptide structures

“…This new tool, because it isolates the determination of structure to an individual C a , could be instrumental in discriminating between current conflicting views of the role of the P conformation in the characterization of ''unfolded'' peptides. 27,28 …”