Steric structure of <scp>L</scp>‐proline oligopeptides. II. Far‐ultraviolet absorption spectra and optical rotations of <scp>L</scp>‐proline oligopeptides

Okabayashi, Hirofumi; Isemura, Toshizo; Sakakibara, Shumpei

doi:10.1002/bip.1968.360060307

Cited by 99 publications

(49 citation statements)

References 4 publications

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“…Previous workers (24,32,33) have shown that the intensities of these positive and negative bands are peptide length dependent. Isemura et al (33,34) have shown that these bands will increase in intensity, on a per residue basis, up to a peptide length of about 15 residues. Petrella et al (32) suggest that this length dependence is due to a combination of electronic effects and flexibility at the ends of proline peptides.…”

Section: Resultsmentioning

confidence: 99%

Host−Guest Study of Left-Handed Polyproline II Helix Formation

et al. 2001

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The importance of the left-handed polyproline II (PPII) helical conformation has recently become apparent. This conformation generally is involved in two important functions: protein-protein interactions and structural integrity. PPII helices play vital roles in a variety of processes including signal transduction, transcription, and cell motility. Proline-rich regions of sequence are often assumed to adopt this structure. Remarkably, little is known about the physical determinants of this secondary structure type. In this study, we have explored the formation of PPII helices by a short poly(proline) peptide. In addition, the results from experiments used to determine the propensities for apolar residues, plus glycine, asparagine, and glutamine, to adopt this structure in a poly(proline)-based host peptide are reported here. Proline possesses the highest intrinsic propensity, with glutamine, alanine, and glycine having surprisingly high propensities.-Branched residues possess the lowest propensities of the residues examined. It is postulated that propensities possessed by apolar residues are due in part to peptide-solvent interactions, and that the remarkably high propensity possessed by glutamine may be due to a side chain to backbone hydrogen bond. These data are the first step toward a molecular understanding of the formation of this important, and yet little studied, secondary structure.In recent years, the left-handed polyproline II (PPII) 1 helical conformation has been elevated from the status of a relatively rare and seemingly uninteresting secondary structure to one that is surprisingly common and of the utmost importance. This structure plays a central role in numerous vital processes including signal transduction, transcription, cell motility, and the immune response. Proline-rich ligands of the cytoskeletal protein profilin (1), as well as those of the SH3, WW, and EVH1 protein interaction domains, are bound in this conformation (2). The peptide ligands of class II MHC molecules are also bound in the PPII conformation (3). PPII helices are major features of collagens (4) and plant cell wall proteins (5). The PPII helix is believed to be the dominant conformation for many proline-rich regions of sequence (PRRs) (6). Sequences not rich in proline also adopt this structure. For example, poly(lysine), poly(glutamate), and poly(aspartate) peptides form PPII helices (7). Around 2% of all residues in known protein structures are found in PPII helices at least four residues long (8, 9). As many as 10% of all residues are found in the PPII conformation, although not necessarily as part of PPII helices (10). PPII helices have also been hypothesized to be a major component of protein denatured states (11-14), giving them a role in a most fundamental process. Recently, Blanch et al. (15) have suggested that the PPII helix might be the precursor conformation in amyloid formation. Given the preceding, it is truly remarkable how little is known about the physical determinants of the PPII helical conformat...

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Section: Resultsmentioning

confidence: 99%

Host−Guest Study of Left-Handed Polyproline II Helix Formation

et al. 2001

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“…Polyprolines have been characterized by various spectroscopic techniques (1,7,8,(13)(14)(15)(16)(17)(18)(19)(20)(21). Two main conformations depending on the isomerization state of the prolyl bond were identified: the polyproline type I helix (PPI) with all peptide bonds in the cis conformation (14); and the polyproline type II helix (PPII) with all peptide bonds being trans isomers (15, 16).…”

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confidence: 99%

Probing polyproline structure and dynamics by photoinduced electron transfer provides evidence for deviations from a regular polyproline type II helix

Doose

Neuweiler

Barsch

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

118

142

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Polyprolines are well known for adopting a regular polyproline type II helix in aqueous solution, rendering them a popular standard as molecular ruler in structural molecular biology. However, single-molecule spectroscopy studies based on Fö rster resonance energy transfer (FRET) have revealed deviations of experimentally observed end-to-end distances of polyprolines from theoretical predictions, and it was proposed that the discrepancy resulted from dynamic flexibility of the polyproline helix. Here, we probe end-to-end distances and conformational dynamics of poly-Lprolines with 1-10 residues using fluorescence quenching by photoinduced-electron transfer (PET). A single fluorophore and a tryptophan residue, introduced at the termini of polyproline peptides, serve as sensitive probes for distance changes on the subnanometer length scale. Using a combination of ensemble fluorescence and fluorescence correlation spectroscopy, we demonstrate that polyproline samples exhibit static structural heterogeneity with subpopulations of distinct end-to-end distances that do not interconvert on time scales from nano-to milliseconds. By observing prolyl isomerization through changes in PET quenching interactions, we provide experimental evidence that the observed heterogeneity can be explained by interspersed cis isomers. Computer simulations elucidate the influence of trans/ cis isomerization on polyproline structures in terms of end-to-end distance and provide a structural justification for the experimentally observed effects. Our results demonstrate that structural heterogeneity inherent in polyprolines, which to date are commonly applied as a molecular ruler, disqualifies them as appropriate tool for an accurate determination of absolute distances at a molecular scale.fluorescence correlation spectroscopy ͉ molecular ruler ͉ prolyl isomerization ͉ biopolymer ͉ Förster resonance energy transfer F luorescence spectroscopy provides a variety of tools to measure distances, monitor dynamics, or observe molecular interactions with sensitivity far beyond that of other biophysical techniques. Distance-dependent interactions between fluorophores and fluorescence-quenching molecular compounds, such as Förster resonance energy transfer (FRET) or photoinduced electron transfer (PET), are capable of reporting on processes on the nanometer length scale, below the diffraction limit generally imposed on optical techniques. Although much information is gained from relative distances or distance changes, the quest for precise determination of absolute distances has been ongoing ever since Stryer and Haugland presented the application of FRET as a spectroscopic ruler (1). FRET is a nonradiative dipole-dipole interaction between two fluorophores (donor D and acceptor A) that can serve as a spectroscopic ruler on length scales between Ϸ2 and Ϸ10 nm (2-6). Structurally well defined model systems (molecular rulers) are needed for validation of spectroscopic rulers as much as the latter are essential for structural investigations. Since the sem...

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“…Agreement with experimental data was satisfactory for the small peptides (127,(217)(218)(219)(220) and form I, but less so for form II (18,210,215,219,221). This is most likely due to solvation effects (213), not taken into account, which may be more important in the case of form II.…”

Section: Physical Properties Of Polyamino Acres Deteitmined Bymentioning

confidence: 48%