PPII helix

PPII helix is illustrated in Figure 8a. It consists of a left-handed extended helical conformation in which the angles of the constituent residues are restricted to values around —78°, +146° corresponding to a region of the Ramachandran surface adjacent to the /3-region (Fig. 8b). This imparts a perfect threefold rotational symmetry to the structure... 

It has been suggested recently that PPII helix may be the killer conformation in such diseases (Blanch et al., 2000). This was prompted by the observation, described in Section III,B, of a positive band at 1318 cm-1, not present in the ROA spectrum of the native state, that dominates the ROA spectrum of a destabilized intermediate of human lysozyme (produced by heating to 57°C at pH 2.0) that forms prior to amyloid fibril formation. Elimination of water molecules between extended polypeptide chains with fully hydrated 0=0 and N—H groups to form... 

The validity of this model for unfolded proteins rests on elucidation of the physical determinants of the two types of helix and the determination of the energetic favorability of these conformations relative to all other possible conformations in unfolded proteins. The determinants of a-helix formation have received significant attention over the past 15 years, and are thought to be mostly understood (reviewed in part by Aurora et al., 1997). The determinants of PPII helix formation have received far less attention and are only now beginning to be understood. 

The PPII conformation is abundant in known protein structures, although PPII helices are not particularly common. Sreerama and Woody (1994) found that around 10% of all protein residues are in the PPII helical conformation. However, the majority of those are not part of a PPII helix. Stapley and Creamer (1999) and Adzhubei and Sternberg (1993) found that only 2% of the residues in the proteins examined were part of PPII helices four residues or longer in length. Moreover, on average, each protein possesses just one such PPII helix. The PPII helices found tend to be very short. Stapley and Creamer (1999) found that 95% of the PPII helices in their protein data set were only four, five, or six residues long. 

Fig. 2. Plot of %PPII content (Kelly et al., 2001 A. L. Rucker, M. N. Campbell, and T. P. Creamer, unpublished results) against Chou-Fasman frequency to be in a PPII helix, Pppii (Stapley and Creamer, 1999).

If this hypothesis is true, one could expect the solvent-accessible surface area (ASA) of the polypeptide backbone in the PPII conformation to be correlated with measured PPII helix-forming propensities. In order to test this, Monte Carlo computer simulations of short peptides Ac-Ala-Xaa-Ala-NMe (Xaa = Ala, Asn, Gin, Gly, lie, Leu, Met, Pro, Ser, Thr, and Val) were run. These particular residues were examined because their... 

PPII helix-forming propensities have been measured by Kelly et al. (2001) and A. L. Rucker, M. N. Campbell, and T. P. Creamer (unpublished results). In the simulations the peptide backbone was constrained to be in the PPII conformation, defined as (0,VO = ( — 75 25°, +145 25°), using constraint potentials described previously (Yun and Hermans, 1991 Creamer and Rose, 1994). The AMBER/ OPLS potential (Jorgensen and Tirado-Rives, 1988 Jorgensen and Severance, 1990) was employed at a temperature of 298° K, with solvent treated as a dielectric continuum of s = 78. After an initial equilibration period of 1 x 104 cycles, simulations were run for 2 x 106 cycles. Each cycle consisted of a number of attempted rotations about dihedrals equal to the total number of rotatable bonds in the peptide. Conformations were saved for analysis every 100 cycles. Solvent-accessible surface areas were calculated using the method of Richmond (1984) and a probe of 1.40 A radius. 

Estimated PPII Helix-Forming Propensities and Average Sum of Backbone ASAs from Monte Carlo Computer Simulations of Peptides Ac-Ala-Xaa-Ala-NMe Restricted to the PPII Conformation11... 

Other than an effect on backbone solvation, side chains could potentially modulate PPII helix-forming propensities in a number of ways. These include contributions due to side chain conformational entropy and, as discussed previously, side chain-to-backbone hydrogen bonds. Given the extended nature of the PPII conformation, one might expect the side chains to possess significant conformational entropy compared to more compact conformations. The side chain conformational entropy, Y.S ppn (T = 298°K), available to each of the residues simulated in the Ac-Ala-Xaa-Ala-NMe peptides above was estimated using methods outlined in Creamer (2000). In essence, conformational entropy Scan be derived from the distribution of side chain conformations using Boltzmann s equation... 

Once the determinants of PPII helix formation are known in more detail, it will become possible to apply them, along with the known determinants of the cy-helical conformation, to the understanding of protein unfolded states. If, as suggested at the beginning of this article, protein unfolded states are dominated by residues in the PPII and cy-conformal ions, these data will allow for modeling of the unfolded state ensembles of specific proteins with a level of realism that has not been previously anticipated. 

Pi positions) is more twisted than a regular /3-strand to possess the polyproline II (PPII) helix conformation. The PPII conformation is also frequently used in protein-peptide interactions such as those seen in the peptide recognition by SH3 domains (Lim et at, 1994) and class II MHC molecules (Stem et at, 1994). This conformation allows the peptide chain to twist in order to maximize the interaction of its side chains with a protein surface. As a consequence, large proportions of the side chains at the P 2 Po 3.nd Pi positions of the receptor peptides are buried at the TRAF2 interface. Therefore, in the case of TRAF2-receptor interactions, the main chain hydrogen bonds and the PPII conformation maximize both main chain and side chain interactions with the TRAF2 surface. 

Additionally, a recent study on the gas-phase conformations of varying lengths of polyproline ions demonstrated that while PPI conformation is maintained in the gas phase, PPII conformation is not. The authors sustain that as the aqueous phase was removed from the PPII-structured polyproline during an electrospray process, the loss of water destabilized the PPII helix. Although it was not clear what conformations were formed from PPII polyproline in the gas phase, a mixture of cis- and frfliis-proline was evident (Coimterman and Clemmer, 2004). This study also clearly demonstrated the critical importance of water in stabilizing the PPII helix. 

The extended nature of the PPII helix, with the backbone CO and NH groups pointed out from the helical axis into the solvent in a strategic manner, favors interaction with water molecules. Alanine and residues with long, flexible side chains (such as Glu, Lys, Arg, and Gin) seem not to occlude the backbone from water access, or do so to a limited extent, and are therefore favored in this conformation. However, bulky branched or aromatic residues, such as Leu, He, Val, Trp, Phe, Tyr, and Trp, seem to occlude peptide backbone access to solvent (Persikov et al., 2000 Creamer and Campbell, 2002) (Figure 22.4). 

Second, combined evidence from theoretical computer modeling studies of short peptides (too short to form any detectable a-helix or (3-sheet) in aqueous solution and a variety of spectroscopic studies, including ultraviolet CD (Rucker et al., 2002), nuclear magnetic resonance (NMR) (Poon et al., 2000), two-dimensional vibrational spectroscopy (Woutersen and Hamm, 2001), vibrational circular dichroism (VCD) (Keiderling et al., 1999), and vibrational Raman spectroscopy (Blanch et al., 2000), reveal that the PPII helix is the dominant conformation in a variety of these short peptides. 

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