Unusual compactness of a polyproline type II structure

Abstract

Polyproline type II (PPII) helix has emerged recently as the dominant paradigm for describing the conformation of unfolded polypeptides. However, most experimental observables used to characterize unfolded proteins typically provide only short-range, sequence-local structural information that is both time-and ensemble-averaged, giving limited detail about the long-range structure of the chain. Here, we report a study of a long-range property: the radius of gyration of an alanine-based peptide, Ace-(diaminobutyric acid) 2-(Ala)7-(ornithine)2-NH2. This molecule has previously been studied as a model for the unfolded state of proteins under folding conditions and is believed to adopt a PPII fold based on short-range techniques such as NMR and CD. By using synchrotron radiation and small-angle x-ray scattering, we have determined the radius of gyration of this peptide to be 7.4 ؎ 0.5 Å, which is significantly less than the value expected from an ideal PPII helix in solution (13.1 Å). To further study this contradiction, we have used molecular dynamics simulations using six variants of the AMBER force field and the GROMOS 53A6 force field. However, in all cases, the simulated ensembles underestimate the PPII content while overestimating the experimental radius of gyration. The conformational model that we propose, based on our small angle x-ray scattering results and what is known about this molecule from before, is that of a very flexible, fluctuating structure that on the level of individual residues explores a wide basin around the ideal PPII geometry but is never, or only rarely, in the ideal extended PPII helical conformation. molecular dynamics ͉ small angle x-ray scattering ͉ unfolded state of proteins T he unfolded and denatured states of proteins have recently received significant attention from experimentalists (1-13) and theoreticians alike (14-21). Because the unfolded state represents one half of the protein-folding free energy diagram, the presence of any residual structure in the unfolded state carries significant implications for both thermodynamics and kinetics of protein folding. With regards to thermodynamics, permanent structure in the unfolded state significantly lowers the entropy of the unfolded state, thereby affecting the free energy change of folding. With regards to kinetics, the presence of preformed native-like contacts potentially speeds up the folding process. When it comes to structure, a consensus has recently begun to emerge about a significant presence of the polyproline type II (PPII) backbone geometry in the unfolded͞denatured state (12,18,(20)(21)(22)(23)(24)(25). The evidence for this view comes predominantly from spectroscopic studies on model peptides (12, 22-28, 61, 62) and computer simulations (18,20,21,(29)(30)(31)(32)62).The unfolded state of proteins, in addition to being intrinsically important in the context of protein folding, presents a fruitful ''laboratory'' for studying the question of the relative importance of local and global structural information in protein s...

The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations

“…4 to calculate the end-to-end distance associated with the considered conformational blend and obtained a value of 19.1 Å. This finding is in excellent agreement with the values derived from the SAXS experiment (29) and underscores the suitability of our analysis.…”

“…4 neglects the C-terminal residue for which we do not have any data. For the two-state model we obtained 30 Å, which far exceeds that of 18.1 Å, derived from the radius of gyration of 7.4 Å, as obtained from SAXS data (29). In a second step, we performed a simulation that considered the entire above-mentioned conformational manifold, containing representatives of all of the local turn structures that emerged from the MD simulations of Makowska et al (30).…”

Structural properties of small semiconductor-binding synthetic peptides

“…In contrast to the Θ collapse transition of polymers between non-structured globular and random-coil conformations, a helix-coil transition is rather a crossover from non-structured conformations to conformations with highly ordered segments (helices). For this reason, the gyration radius is a too rough measure for the order in the helical phase and is therefore of less importance for the understanding of secondary-structure formation and cannot be deduced from the short-range interactions [38,39]. Table II, where the differences between maximal and minimal values of average radius of gyration and mean number of hydrogen bonds are given.…”

Cell-Cell Membrane Fusion Induced by p15 Fusion-associated Small Transmembrane (FAST) Protein Requires a Novel Fusion Peptide Motif Containing a Myristoylated Polyproline Type II Helix

“…In addition, structural plasticity is an inherent, and possibly required, feature of FPs (59,60), including the cystine loop FP of the p10 FAST protein (29). Dynamic structural changes in the PPII helix may also be needed for fusion activity and would be facilitated by the absence of stabilizing backbone hydrogen bonds that allow the PPII helix to fluctuate around an idealized PPII conformation (61). The aliphatic pyrrolidine rings in the PPII helix are interspersed by the polar carbonyl oxygens of the peptide backbone, which are solvent exposed to form hydrogen bonds with water molecules or adjacent polar lipid headgroups (37).…”