Structure of Poly-L-Proline I

Traub, W.; Shmueli, U.

doi:10.1038/1981165a0

Cited by 174 publications

(110 citation statements)

References 10 publications

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“…[16,17] The samples were free from any noticeable cross-contamination, as evidenced by the lack of reflections from the complementary form in both patterns.D espite the high-quality PXRD patterns,s uch data alone were not sufficient for complete structural determinations with atomic precision, and utilization of computational methods was necessary to arrive at detailed solutions.…”

Section: In Memory Of Roberto Orlandomentioning

confidence: 98%

“…[13] Proline is unique amongst naturally occurring amino acids as the only residue able to readily form both cis and trans configurations about its peptide bond linkages, [14] thereby permitting two different helical structures to exist for poly-l-proline. [15] Theall-cis right-handed helix (Form I, PP-I) is tightly wound, [16] while the all-trans left-handed helix (Form II, PP-II) adopts al ess dense geometry (Figure 1). [17] Theavailability of these similar, yet fundamentally different, poly-l-proline helices makes them excellent choices for exploring the connection between molecular structure,l owfrequency vibrational motions,and bulk elastic constants.…”

Section: In Memory Of Roberto Orlandomentioning

confidence: 99%

“…In the case of PP-I, initial crystal structures were constructed using the previously published interatomic distances and angles, [16] but with the solid-state packing arrangements and strand orientations varied (for details,s ee the Supporting Information). After full ss-DFT optimization, the PP-I crystal was found to have monoclinic P2 1 symmetry in agreement with estimates made by Shmueli and Tr aub (Figure 4).…”

Section: In Memory Of Roberto Orlandomentioning

confidence: 99%

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Measuring the Elasticity of Poly‐l‐Proline Helices with Terahertz Spectroscopy

et al. 2016

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The rigidity of poly-l-proline is an important contributor to the stability of many protein secondary structures,w here it has been shown to strongly influence bulk flexibility.T he experimental Youngs moduli of two known poly-l-proline helical forms,right-handed all-cis (Form I) and left-handed all-trans (Form II), were determined in the crystalline state by using an approach that combines terahertz timedomain spectroscopy, X-raydiffraction, and solid-state density functional theory.C ontrary to expectations,t he helices were found to be considerably less rigid than many other natural and synthetic polymers,aswell as differing greatly from each other, with Youngs moduli of 4.9 and 9.6 GPaf or Forms Ia nd II, respectively.

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Section: In Memory Of Roberto Orlandomentioning

confidence: 98%

Section: In Memory Of Roberto Orlandomentioning

confidence: 99%

Section: In Memory Of Roberto Orlandomentioning

confidence: 99%

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Measuring the Elasticity of Poly‐l‐Proline Helices with Terahertz Spectroscopy

et al. 2016

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“…The probability distribution for cis-trans prolyl bonds is affected by neighboring amino acids (2, 3), pH and ionic strength (4), solvent (5-11) and chain length (12). It has been noted experimentally that the PPII structure is favored in water, benzyl alcohol, and most of the other solvents, while the PPI structure is favored in the presence of aliphatic alcohols like propanol (12)(13)(14)(15). The two forms can reversibly interconvert by means of changes in solvent composition (5,7,10,16,17), as analyzed via circular dichronism (CD) spectroscopy experiments (12,(18)(19)(20).…”

Section: Cis-trans Isomerization | Left-handed Helix | Molecular Dynamentioning

confidence: 99%

Conformations and free energy landscapes of polyproline peptides

Moradi

Babin

Roland

et al. 2009

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

146

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The structure of the proline amino acid allows folded polyproline peptides to exist as both left-(PPII) and right-handed (PPI) helices. We have characterized the free energy landscapes of hexamer, nanomer, and tridecamer polyproline peptides in gas phase and implicit water as well as explicit hexane and 1-propanol for the nanomer. To enhance the sampling provided by regular molecular dynamics, we used the recently developed adaptively biased molecular dynamics method, which describes Landau free energy maps in terms of relevant collective variables. These maps, as a function of the collective variables of handedness, radius of gyration, and three others based on the peptide torsion angle ω, were used to determine the relative stability of the different structures, along with an estimate of the transition pathways connecting the different minima. Results show the existence of several metastable isomers and therefore provide a complementary view to experimental conclusions based on photo-induced electron transfer experiments with regard to the existence of stable heterogeneous subpopulations in PPII polyproline.cis-trans isomerization | left-handed helix | molecular dynamics | PPI | PPII T he concept of molecular chirality is used to describe molecular structures that are not superposable on their mirror images. Chiral molecules are quite prevalent in biological systems, which are primarily homochiral systems. For example, most proteins contain only L-amino acids, while DNA is made up primarily of D-deoxyribose. The relationship between chirality and helical polypeptide structure was first mentioned by Pauling (1) in reference to the α-helix. The naturally occurring L-amino acids predominantly form right-handed helices, whereas their stereoisomers D-amino acids favor left-handed helices. Indeed, right-handed helices are prevalent in biology, not only in peptides (with structural motifs such as α-helix , 3 10 helix, and π helix) but also in the double-helical structure of B-and A-DNA. Although much less common, left-handed helices with the same chiral units as right-handed helices also exist, such as those found in PPII and in Z-DNA.In this paper, we investigate the free energy landscape of several short polyproline peptides. Proline is unique among the natural amino acids in that its side chain is cyclized to the backbone, restricting its backbone dihedral angle to φ = −75• , giving proline an exceptional rigidity and a considerably restricted conformational space. Polyproline is known to form helical structures with two well-characterized conformations: a left-handed polyproline helix (PPII) is formed when the sequential residues all adopt backbone dihedral angles (φ, ψ) of (−75• , 146• ), with all prolyl bonds in the trans-isomer conformation (i.e. backbone dihedral angle ω = 180• ) with 3 residues per turn; and a more compact right-handed polyproline helix (PPI) is formed with all sequential residues adopting dihedral angles of roughly (−75• , 160• ) and all prolyl bonds assume a cis-isomer conformation (i.e. b...

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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.

117

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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Structure of Poly-L-Proline I

Cited by 174 publications

References 10 publications

Measuring the Elasticity of Poly‐l‐Proline Helices with Terahertz Spectroscopy

Measuring the Elasticity of Poly‐l‐Proline Helices with Terahertz Spectroscopy

Conformations and free energy landscapes of polyproline peptides

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

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