Circular dichroism of poly‐<scp>L</scp>‐proline in an unordered conformation

Tiffany, M. Lois; Krimm, Samuel

doi:10.1002/bip.1968.360061212

Cited by 193 publications

(151 citation statements)

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“…Interestingly, in the CD spectra of the PAS sequences the absence of a weak positive maximum around 225 nm, which was often seen in other studies for polypeptides in random‐coil conformation having more average amino acid composition,44 is reminiscent of the “unordered poly‐proline structure” described by Tiffany and Krimm40 that is characterized by a strong minimum around 200 nm only (Supporting Information Table S3). Taking into consideration that repetitive amino acid sequences are unlikely to adopt an ideal random conformation without any (at least locally) regular structure,45 it would be plausible that PAS polypeptides show a kind of random‐coil structure influenced by the PPII conformation 46.…”

Section: Resultssupporting

confidence: 58%

“…The measured CD spectra of the pure PAS polypeptides (Figure 4) each revealed a single strong negative band around 200 nm without any positive signal, which is indicative of random coil conformation 40. When correcting the spectra of the PAS‐IL‐1Ra fusion proteins by subtracting the CD spectrum of the isolated IL‐1Ra protein, all recorded under the same conditions, difference spectra with the same characteristics as for the respective free PAS polypeptides were obtained (Figure 4B), similarly as described for other PASylated proteins before 9.…”

Section: Resultsmentioning

confidence: 99%

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The polypeptide biophysics of proline/alanine‐rich sequences (PAS): Recombinant biopolymers with PEG‐like properties

Breibeck

Skerra

2017

Biopolymers

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PAS polypeptides comprise long repetitive sequences of the small L‐amino acids proline, alanine and/or serine that were developed to expand the hydrodynamic volume of conjugated pharmaceuticals and prolong their plasma half‐life by retarding kidney filtration. Here, we have characterized the polymer properties both of the free polypeptides and in fusion with the biopharmaceutical IL‐1Ra. Data from size exclusion chromatography, dynamic light scattering, circular dichroism spectroscopy and quantification of hydrodynamic and polar properties demonstrate that the biosynthetic PAS polypeptides exhibit random coil behavior in aqueous solution astonishingly similar to the chemical polymer poly‐ethylene glycol (PEG). The solvent‐exposed PAS peptide groups, in the absence of secondary structure, account for strong hydrophilicity, with negligible contribution by the Ser side chains. Notably, PAS polypeptides exceed PEG of comparable molecular mass in hydrophilicity and hydrodynamic volume while exhibiting lower viscosity. Their uniform monodisperse composition as genetically encoded polymers and their biological nature, offering biodegradability, render PAS polypeptides a promising PEG mimetic for biopharmaceutical applications.

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Section: Resultssupporting

confidence: 58%

Section: Resultsmentioning

confidence: 99%

The polypeptide biophysics of proline/alanine‐rich sequences (PAS): Recombinant biopolymers with PEG‐like properties

Breibeck

Skerra

2017

Biopolymers

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“…A second line of evidence suggests that unfolded proteins are conformationally biased toward polyproline II (P II ) helical conformations. Both theory (30)(31)(32)(33)(34)(35)(36)(37) and experiment (38)(39)(40)(41)(42) have investigated the preference for P II in unfolded peptide ensembles. If the experimental results are correct and the ensemble is not random, then why is the random-coil model so successful?…”

Section: Discussionmentioning

confidence: 99%

Reassessing random-coil statistics in unfolded proteins

Fitzkee

Rose

2004

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

317

325

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The Gaussian-distributed random coil has been the dominant model for denatured proteins since the 1950s, and it has long been interpreted to mean that proteins are featureless, statistical coils in 6 M guanidinium chloride. Here, we demonstrate that random-coil statistics are not a unique signature of featureless polymers. The random-coil model does predict the experimentally determined coil dimensions of denatured proteins successfully. Yet, other equally convincing experiments have shown that denatured proteins are biased toward specific conformations, in apparent conflict with the random-coil model. We seek to resolve this paradox by introducing a contrived counterexample in which largely native protein ensembles nevertheless exhibit random-coil characteristics. Specifically, proteins of known structure were used to generate disordered conformers by varying backbone torsion angles at random for Ϸ8% of the residues; the remaining Ϸ92% of the residues remained fixed in their native conformation. Ensembles of these disordered structures were generated for 33 proteins by using a torsion-angle Monte Carlo algorithm with hard-sphere sterics; bulk statistics were then calculated for each ensemble. Despite this extreme degree of imposed internal structure, these ensembles have end-to-end distances and mean radii of gyration that agree well with random-coil expectations in all but two cases.T he protein folding reaction, unfolded (U)^native (N), is a reversible disorder^order transition. Typically, proteins are disordered (U) at high temperature, high pressure, extremes of pH, or in the presence of denaturing solvents, but they fold to uniquely ordered, biologically relevant conformers (N) under physiological conditions. With some exceptions (1), the folded state is the biologically relevant form, and it can be characterized to atomic detail by using x-ray crystallography and NMR spectroscopy. In contrast, our understanding of the unfolded state is based primarily on a statistical model, the random-coil model, which was developed largely by Flory (2) and corroborated by Tanford (3) in the 1950s and 1960s.In a random coil, the energy differences among sterically accessible backbone conformers are of order ϷkT (where k is Boltzmann's constant, and T is the absolute temperature). Consequently, there are no strongly preferred conformations, the energy landscape is essentially featureless, and a Boltzmann-weighted ensemble of such polymers would populate this landscape uniformly.Our motivation here is to dispel the belief, which is widespread among protein chemists, that the presence of random-coil statistics for denatured proteins confirms the absence of residual structure in these molecules. Indeed, it is well known to polymer chemists that rods of any stiffness (e.g., steel I-beams) behave as Gaussiandistributed, temperature-dependent random coils if they are long enough. Chains in which the persistence length exceeds one physical link can be treated effectively by rewriting them as polymers of Kuhn segments (ref. 2, pa...

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“…This conformation is known to be adopted by poly(proline) peptides and polymers (16). A cartoon of a poly(proline) peptide in the PPII conformation is shown in Figure 1.…”

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confidence: 96%

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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Circular dichroism of poly‐L‐proline in an unordered conformation

Cited by 193 publications

References 10 publications

The polypeptide biophysics of proline/alanine‐rich sequences (PAS): Recombinant biopolymers with PEG‐like properties

The polypeptide biophysics of proline/alanine‐rich sequences (PAS): Recombinant biopolymers with PEG‐like properties

Reassessing random-coil statistics in unfolded proteins

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

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